From 04a7f49bfb6be78101114489ca3b4426aee3d6e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Fri, 30 Apr 2021 13:12:33 +0200 Subject: [PATCH 001/412] Better comment --- include/bout/region.hxx | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 6fb85a4aee..bfaef335f8 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -643,8 +643,7 @@ public: return *this; // To allow command chaining }; - /// Returns a new region including only indices contained in both - /// this region and the other. + /// Returns a modified region including only indices that are also in the region. Region getIntersection(const Region& otherRegion) { // Get other indices and sort as we're going to be searching through // this vector so if it's sorted we can be more efficient From 804119004e05548fa3ce673197fe20cedcc8fe9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Fri, 30 Apr 2021 13:11:04 +0200 Subject: [PATCH 002/412] Add basic region tracking --- include/bout/mesh.hxx | 8 +- include/bout/region.hxx | 17 +++ include/field2d.hxx | 3 + include/field3d.hxx | 9 ++ include/fieldperp.hxx | 3 + src/field/field3d.cxx | 11 ++ src/field/gen_fieldops.jinja | 20 ++- src/field/generated_fieldops.cxx | 168 +++++++++++++++++++----- src/mesh/mesh.cxx | 51 ++++++- tests/unit/include/bout/test_region.cxx | 33 +++++ 10 files changed, 283 insertions(+), 40 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 0f4bffe86a..20e95f3648 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -1039,6 +1039,10 @@ public: // Switch for communication of corner guard and boundary cells const bool include_corner_cells; + int getCommonRegion(int, int); + int getRegionID(const std::string& region) const; + const Region& getRegion(int RegionID) const { return region3D[RegionID]; } + private: /// Allocates default Coordinates objects @@ -1051,7 +1055,9 @@ private: bool force_interpolate_from_centre=false); //Internal region related information - std::map> regionMap3D; + std::map regionMap3D; + std::vector> region3D; + std::map> region3Dintersect; std::map> regionMap2D; std::map> regionMapPerp; Array indexLookup3Dto2D; diff --git a/include/bout/region.hxx b/include/bout/region.hxx index bfaef335f8..3aaf4530a1 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -546,6 +546,18 @@ public: indices = getRegionIndices(); }; + bool operator==(const Region& other) { + if (this->size() != other.size()) { + return false; + } + for (auto i1 = this->begin(), i2 = other.begin(); i1 != this->end(); ++i1, ++i2) { + if (i1 != i2) { + return false; + } + } + return true; + } + /// Destructor ~Region() = default; @@ -937,4 +949,9 @@ unsigned int size(const Region ®ion){ return region.size(); } +// template +class RegionID { + int value; +}; + #endif /* __REGION_H__ */ diff --git a/include/field2d.hxx b/include/field2d.hxx index dcf89be672..7b2bce2d65 100644 --- a/include/field2d.hxx +++ b/include/field2d.hxx @@ -181,6 +181,9 @@ class Field2D : public Field { /// Return a Region reference to use to iterate over this field const Region& getRegion(REGION region) const; const Region& getRegion(const std::string ®ion_name) const; + const Region& getDefaultRegion(const std::string& region_name) const { + return getRegion(region_name); + } Region::RegionIndices::const_iterator begin() const {return std::begin(getRegion("RGN_ALL"));}; Region::RegionIndices::const_iterator end() const {return std::end(getRegion("RGN_ALL"));}; diff --git a/include/field3d.hxx b/include/field3d.hxx index 82d48f20c0..bba9d58576 100644 --- a/include/field3d.hxx +++ b/include/field3d.hxx @@ -318,6 +318,12 @@ class Field3D : public Field { /// const Region& getRegion(REGION region) const; const Region& getRegion(const std::string ®ion_name) const; + /// Use region provided by the default, and if none is set, use the provided one + const Region& getDefaultRegion(const std::string& region_name) const; + void setRegion(const std::string& region_name); + void resetRegion() { regionID = -1; }; + void setRegion(int id) { regionID = id; }; + int getRegionID() const { return regionID; }; /// Return a Region reference to use to iterate over the x- and /// y-indices of this field @@ -503,6 +509,9 @@ private: /// Fields containing values along Y std::vector yup_fields{}, ydown_fields{}; + + /// RegionID over which the field is valid + int regionID{-1}; }; // Non-member overloaded operators diff --git a/include/fieldperp.hxx b/include/fieldperp.hxx index f6de72e7bb..3fc2ecfcf7 100644 --- a/include/fieldperp.hxx +++ b/include/fieldperp.hxx @@ -98,6 +98,9 @@ class FieldPerp : public Field { /// Return a Region reference to use to iterate over this field const Region& getRegion(REGION region) const; const Region& getRegion(const std::string ®ion_name) const; + const Region& getDefaultRegion(const std::string& region_name) const { + return getRegion(region_name); + } Region::RegionIndices::const_iterator begin() const {return std::begin(getRegion("RGN_ALL"));}; Region::RegionIndices::const_iterator end() const {return std::end(getRegion("RGN_ALL"));}; diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 8b328db338..0109d408cb 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -883,3 +883,14 @@ void swap(Field3D& first, Field3D& second) noexcept { swap(first.yup_fields, second.yup_fields); swap(first.ydown_fields, second.ydown_fields); } + +const Region& Field3D::getDefaultRegion(const std::string& region_name) const { + if (regionID != -1) { + return fieldmesh->getRegion(regionID); + } + return fieldmesh->getRegion(region_name); +} + +void Field3D::setRegion(const std::string& region_name) { + regionID = fieldmesh->getRegionID(region_name); +} diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja index 249245b21c..40a59172a3 100644 --- a/src/field/gen_fieldops.jinja +++ b/src/field/gen_fieldops.jinja @@ -8,6 +8,17 @@ checkData({{lhs.name}}); checkData({{rhs.name}}); + {% if out == "Field3D" %} + {% if lhs == rhs == "Field3D" %} + {{out.name}}.setRegion({{lhs.name}}.getMesh()->getCommonRegion({{lhs.name}}.getRegionID(), + {{rhs.name}}.getRegionID())); + {% elif lhs == "Field3D" %} + {{out.name}}.setRegion({{lhs.name}}.getRegionID()); + {% elif rhs == "Field3D" %} + {{out.name}}.setRegion({{rhs.name}}.getRegionID()); + {% endif %} + {% endif %} + {% if (out == "Field3D") and ((lhs == "Field2D") or (rhs =="Field2D")) %} Mesh *localmesh = {{lhs.name if lhs.field_type != "BoutReal" else rhs.name}}.getMesh(); @@ -41,11 +52,11 @@ } {% elif (operator == "/") and (rhs == "BoutReal") %} const auto tmp = 1.0 / {{rhs.index}}; - {{region_loop}}({{index_var}}, {{out.name}}.getRegion({{region_name}})) { + {{region_loop}}({{index_var}}, {{out.name}}.getDefaultRegion({{region_name}})) { {{out.index}} = {{lhs.index}} * tmp; } {% else %} - {{region_loop}}({{index_var}}, {{out.name}}.getRegion({{region_name}})) { + {{region_loop}}({{index_var}}, {{out.name}}.getDefaultRegion({{region_name}})) { {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}}; } {% endif %} @@ -73,6 +84,11 @@ checkData(*this); checkData({{rhs.name}}); + {% if lhs == rhs == "Field3D" %} + regionID = fieldmesh->getCommonRegion(regionID, {{rhs.name}}.regionID); + {% endif %} + + {% if (lhs == "Field3D") and (rhs =="Field2D") %} {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) { const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}}); diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx index 91fe31f3d1..2d28ae9a32 100644 --- a/src/field/generated_fieldops.cxx +++ b/src/field/generated_fieldops.cxx @@ -14,7 +14,9 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -36,6 +38,8 @@ Field3D& Field3D::operator*=(const Field3D& rhs) { checkData(*this); checkData(rhs); + regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID); + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } checkData(*this); @@ -54,7 +58,9 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -76,6 +82,8 @@ Field3D& Field3D::operator/=(const Field3D& rhs) { checkData(*this); checkData(rhs); + regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID); + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } checkData(*this); @@ -94,7 +102,9 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -116,6 +126,8 @@ Field3D& Field3D::operator+=(const Field3D& rhs) { checkData(*this); checkData(rhs); + regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID); + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } checkData(*this); @@ -134,7 +146,9 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -156,6 +170,8 @@ Field3D& Field3D::operator-=(const Field3D& rhs) { checkData(*this); checkData(rhs); + regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID); + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } checkData(*this); @@ -174,6 +190,8 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(lhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { @@ -224,6 +242,8 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(lhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { @@ -276,6 +296,8 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(lhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { @@ -326,6 +348,8 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(lhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { @@ -455,7 +479,11 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } + result.setRegion(lhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] * rhs; + } checkData(result); return result; @@ -491,8 +519,12 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); + result.setRegion(lhs.getRegionID()); + const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] * tmp; + } checkData(result); return result; @@ -529,7 +561,11 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } + result.setRegion(lhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] + rhs; + } checkData(result); return result; @@ -565,7 +601,11 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } + result.setRegion(lhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] - rhs; + } checkData(result); return result; @@ -602,6 +642,8 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(rhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { @@ -623,6 +665,8 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(rhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { @@ -644,6 +688,8 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(rhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { @@ -665,6 +711,8 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); + result.setRegion(rhs.getRegionID()); + Mesh* localmesh = lhs.getMesh(); BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { @@ -686,7 +734,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -722,7 +770,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -758,7 +806,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -794,7 +842,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -909,7 +957,9 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] * rhs; + } checkData(result); return result; @@ -942,7 +992,9 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] * tmp; + } checkData(result); return result; @@ -975,7 +1027,9 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] + rhs; + } checkData(result); return result; @@ -1007,7 +1061,9 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] - rhs; + } checkData(result); return result; @@ -1408,7 +1464,7 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -1444,7 +1500,7 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -1480,7 +1536,7 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -1516,7 +1572,7 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -1551,7 +1607,9 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] * rhs; + } checkData(result); return result; @@ -1584,7 +1642,9 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] * tmp; + } checkData(result); return result; @@ -1616,7 +1676,9 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] + rhs; + } checkData(result); return result; @@ -1648,7 +1710,9 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs[index] - rhs; + } checkData(result); return result; @@ -1680,7 +1744,11 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } + result.setRegion(rhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs * rhs[index]; + } checkData(result); return result; @@ -1693,7 +1761,11 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } + result.setRegion(rhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs / rhs[index]; + } checkData(result); return result; @@ -1706,7 +1778,11 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } + result.setRegion(rhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs + rhs[index]; + } checkData(result); return result; @@ -1719,7 +1795,11 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } + result.setRegion(rhs.getRegionID()); + + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs - rhs[index]; + } checkData(result); return result; @@ -1732,7 +1812,9 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs * rhs[index]; + } checkData(result); return result; @@ -1745,7 +1827,9 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs / rhs[index]; + } checkData(result); return result; @@ -1758,7 +1842,9 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs + rhs[index]; + } checkData(result); return result; @@ -1771,7 +1857,9 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs - rhs[index]; + } checkData(result); return result; @@ -1784,7 +1872,9 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs * rhs[index]; + } checkData(result); return result; @@ -1797,7 +1887,9 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs / rhs[index]; + } checkData(result); return result; @@ -1810,7 +1902,9 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs + rhs[index]; + } checkData(result); return result; @@ -1823,7 +1917,9 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } + BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + result[index] = lhs - rhs[index]; + } checkData(result); return result; diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 7962e324f1..a809059152 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -444,6 +444,14 @@ std::shared_ptr Mesh::createDefaultCoordinates(const CELL_LOC locat } const Region<>& Mesh::getRegion3D(const std::string& region_name) const { + const auto found = regionMap3D.find(region_name); + if (found == end(regionMap3D)) { + throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name); + } + return region3D[found->second]; +} + +int Mesh::getRegionID(const std::string& region_name) const { const auto found = regionMap3D.find(region_name); if (found == end(regionMap3D)) { throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name); @@ -484,7 +492,21 @@ void Mesh::addRegion3D(const std::string ®ion_name, const Region<> ®ion) { throw BoutException(_("Trying to add an already existing region {:s} to regionMap3D"), region_name); } - regionMap3D[region_name] = region; + + int id = -1; + for (size_t i = 0; i < region3D.size(); ++i) { + if (region3D[i] == region) { + id = i; + break; + } + } + if (id == -1) { + id = region3D.size(); + region3D.push_back(region); + } + + regionMap3D[region_name] = id; + output_verbose.write(_("Registered region 3D {:s}"),region_name); output_verbose << "\n:\t" << region.getStats() << "\n"; } @@ -619,3 +641,30 @@ constexpr decltype(MeshFactory::type_name) MeshFactory::type_name; constexpr decltype(MeshFactory::section_name) MeshFactory::section_name; constexpr decltype(MeshFactory::option_name) MeshFactory::option_name; constexpr decltype(MeshFactory::default_type) MeshFactory::default_type; + +int Mesh::getCommonRegion(int lhs, int rhs) { + if (lhs == rhs) { + return lhs; + } + int low = std::min(lhs, rhs); + int high = std::max(lhs, rhs); + if (low == -1) { + return high; + } + if (not region3Dintersect.count(low)) { + region3Dintersect[low] = {}; + } + if (region3Dintersect[low].count(high)) { + return region3Dintersect[low][high]; + } + auto common = getIntersection(region3D[low], region3D[high]); + for (size_t i = 0; i < region3D.size(); ++i) { + if (common == region3D[i]) { + region3Dintersect[low][high] = i; + return i; + } + } + region3D.push_back(common); + region3Dintersect[low][high] = region3D.size() - 1; + return region3D.size() - 1; +} diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index 6021144956..ddc1b6841e 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -275,6 +275,39 @@ TEST_F(RegionTest, regionLoopAllSection) { EXPECT_EQ(count, nmesh); } +int region_count_helper(Region region) { + int count = 0; + BOUT_OMP(parallel) { + BOUT_FOR_OMP(i, region, for reduction(+:count)) { + ++count; + } + } + return count; +} + +TEST_F(RegionTest, regionIntersection) { + auto& region1 = mesh->getRegion3D("RGN_ALL"); + + auto& region2 = mesh->getRegion3D("RGN_NOBNDRY"); + + int count1 = region_count_helper(region1); + int count2 = region_count_helper(region2); + + const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz; + + EXPECT_EQ(count1, nmesh); + EXPECT_GT(count1, count2); + + const auto& region3 = getIntersection(region1, region2); + int count3 = region_count_helper(region3); + count1 = region_count_helper(region1); + + EXPECT_EQ(count2, count3); + // Ensure this did not change + EXPECT_EQ(count1, nmesh); + EXPECT_EQ(region_count_helper(mesh->getRegion3D("RGN_ALL")), nmesh); +} + TEST_F(RegionTest, regionLoopNoBndrySection) { const auto ®ion = mesh->getRegion3D("RGN_NOBNDRY"); From 07b9606283d12eaa761f85e6ecdad329dd1e30e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Fri, 30 Apr 2021 13:52:03 +0200 Subject: [PATCH 003/412] Ignore test artifacts --- .gitignore | 2 ++ tests/integrated/.gitignore | 12 ++++++++++++ 2 files changed, 14 insertions(+) diff --git a/.gitignore b/.gitignore index fbecac3e22..38a8b321e5 100644 --- a/.gitignore +++ b/.gitignore @@ -55,3 +55,5 @@ src/fmt/format.cxx /include/bout/build_config.hxx /include/bout/revision.hxx /include/bout/version.hxx +/include/bout/build_defines.hxx +/tools/pylib/boutconfig/__init__.py diff --git a/tests/integrated/.gitignore b/tests/integrated/.gitignore index 3eaa8b2d7e..b5e87607c3 100644 --- a/tests/integrated/.gitignore +++ b/tests/integrated/.gitignore @@ -40,3 +40,15 @@ BOUT.settings /test-snb/test_snb /test-twistshift-staggered/test-twistshift /test-twistshift/test-twistshift +/test-communications/test-communications +/test-interpolate-z/test_interpolate +/test-options-netcdf/fields.nc +/test-options-netcdf/fields2.nc +/test-options-netcdf/settings.ini +/test-options-netcdf/settings.nc +/test-options-netcdf/test-options-netcdf +/test-options-netcdf/test-out.ini +/test-options-netcdf/test-out.nc +/test-options-netcdf/test.nc +/test-options-netcdf/time.nc +/test-yupdown-weights/test_yupdown_weights From 413da69b81edf079a2698672205c4bfe57652eb9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Tue, 4 May 2021 15:11:16 +0200 Subject: [PATCH 004/412] Add region ypar --- src/mesh/parallel/fci.cxx | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 7c16dd27fb..f06ef74c2d 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -239,6 +239,16 @@ FCIMap::FCIMap(Mesh& mesh, const Field2D& dy, Options& options, int offset_, } interp->setMask(boundary_mask); + + const auto region = fmt::format("RGN_YPAR_{:+d}", offset); + if (not map_mesh.hasRegion3D(region)) { + // The valid region for this slice + map_mesh.addRegion3D(region, + Region(map_mesh.xstart, map_mesh.xend, + map_mesh.ystart+offset, map_mesh.yend+offset, + 0, map_mesh.LocalNz-1, + map_mesh.LocalNy, map_mesh.LocalNz)); + } } Field3D FCIMap::integrate(Field3D &f) const { From e392deaf169352001edba413f9bbac0eae8ab83f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Tue, 4 May 2021 16:14:17 +0200 Subject: [PATCH 005/412] Set region for parallel slices --- src/mesh/parallel/fci.cxx | 1 + 1 file changed, 1 insertion(+) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index f06ef74c2d..272a0d31ba 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -336,6 +336,7 @@ void FCITransform::calcParallelSlices(Field3D& f) { // Interpolate f onto yup and ydown fields for (const auto& map : field_line_maps) { f.ynext(map.offset) = map.interpolate(f); + f.ynext(map.offset).setRegion(fmt::format("RGN_YPAR_{:+d}", map.offset)); } } From a57146588715e0f23ff167d065821cf4bcdb4362 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Tue, 4 May 2021 17:51:48 +0200 Subject: [PATCH 006/412] Check within valid region, if set --- src/field/field3d.cxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 0109d408cb..ae77a6c7cd 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -187,7 +187,7 @@ const Field3D& Field3D::ynext(int dir) const { if (dir > 0) { return yup(dir - 1); } else if (dir < 0) { - return ydown(std::abs(dir) - 1); + return ydown(- dir - 1); } else { return *this; } @@ -807,7 +807,7 @@ namespace { #if CHECK > 2 void checkDataIsFiniteOnRegion(const Field3D& f, const std::string& region) { // Do full checks - BOUT_FOR_SERIAL(i, f.getRegion(region)) { + BOUT_FOR_SERIAL(i, f.getDefaultRegion(region)) { if (!finite(f[i])) { throw BoutException("Field3D: Operation on non-finite data at [{:d}][{:d}][{:d}]\n", i.x(), i.y(), i.z()); From 7b248a71dc2c84938ceccd88d6ee3493b56a793e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Tue, 18 May 2021 19:37:46 +0200 Subject: [PATCH 007/412] Avoid maps in fieldops Direct indexing should be faster --- include/bout/mesh.hxx | 2 +- src/mesh/mesh.cxx | 27 ++++++++++++++++++++------- 2 files changed, 21 insertions(+), 8 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 20e95f3648..ba6557c29f 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -1057,7 +1057,7 @@ private: //Internal region related information std::map regionMap3D; std::vector> region3D; - std::map> region3Dintersect; + std::vector region3Dintersect; std::map> regionMap2D; std::map> regionMapPerp; Array indexLookup3Dto2D; diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index a809059152..7f59de3009 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -651,20 +651,33 @@ int Mesh::getCommonRegion(int lhs, int rhs) { if (low == -1) { return high; } - if (not region3Dintersect.count(low)) { - region3Dintersect[low] = {}; - } - if (region3Dintersect[low].count(high)) { - return region3Dintersect[low][high]; + /* Memory layout of indices + * left is lower index, bottom is higher index + * 0 1 2 3 + * 0 + * 1 0 + * 2 1 2 + * 3 3 4 5 + * 4 6 7 8 9 + * + * As we only need half of the square, the indices do not depend on + * the total number of elements. + */ + const size_t pos = (high * (high - 1)) /2 + low; + if (region3Dintersect.size() <= pos) { + region3Dintersect.resize(pos+1, -1); + } + if (region3Dintersect[pos] != -1){ + return region3Dintersect[pos]; } auto common = getIntersection(region3D[low], region3D[high]); for (size_t i = 0; i < region3D.size(); ++i) { if (common == region3D[i]) { - region3Dintersect[low][high] = i; + region3Dintersect[pos] = i; return i; } } region3D.push_back(common); - region3Dintersect[low][high] = region3D.size() - 1; + region3Dintersect[pos] = region3D.size() - 1; return region3D.size() - 1; } From 68c2d0160955f36393ec7669e737c73062b76a95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Tue, 18 May 2021 20:01:33 +0200 Subject: [PATCH 008/412] Add nicer formatting to output Format output as mardown table and print time in micro seconds. --- .../performance/arithmetic/arithmetic.cxx | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/examples/performance/arithmetic/arithmetic.cxx b/examples/performance/arithmetic/arithmetic.cxx index 30d2a72893..9d78e4e039 100644 --- a/examples/performance/arithmetic/arithmetic.cxx +++ b/examples/performance/arithmetic/arithmetic.cxx @@ -13,17 +13,16 @@ using SteadyClock = std::chrono::time_point; using Duration = std::chrono::duration; using namespace std::chrono; -#define TIMEIT(elapsed, ...) \ - { \ - SteadyClock start = steady_clock::now(); \ - { \ - __VA_ARGS__ ; \ - } \ - Duration diff = steady_clock::now() - start; \ - elapsed.min = diff > elapsed.min ? elapsed.min : diff; \ - elapsed.max = diff < elapsed.max ? elapsed.max : diff; \ - elapsed.count++; \ - elapsed.avg = elapsed.avg * (1 - 1. / elapsed.count) + diff / elapsed.count; \ +#define TIMEIT(elapsed, ...) \ + { \ + SteadyClock start = steady_clock::now(); \ + { __VA_ARGS__; } \ + Duration diff = steady_clock::now() - start; \ + diff *= 1000 * 1000; \ + elapsed.min = diff > elapsed.min ? elapsed.min : diff; \ + elapsed.max = diff < elapsed.max ? elapsed.max : diff; \ + elapsed.count++; \ + elapsed.avg = elapsed.avg * (1 - 1. / elapsed.count) + diff / elapsed.count; \ } struct Durations { @@ -40,6 +39,8 @@ class Arithmetic : public PhysicsModel { Field3D a = 1.0; Field3D b = 2.0; Field3D c = 3.0; + a.setRegion("RGN_ALL"); + b.setRegion("RGN_NOBNDRY"); Field3D result1, result2, result3, result4; @@ -50,7 +51,7 @@ class Arithmetic : public PhysicsModel { Durations elapsed1 = dur_init, elapsed2 = dur_init, elapsed3 = dur_init, elapsed4 = dur_init; - for (int ik = 0; ik < 1e2; ++ik) { + for (int ik = 0; ik < 1e3; ++ik) { TIMEIT(elapsed1, result1 = 2. * a + b * c;); // Using C loops @@ -78,12 +79,13 @@ class Arithmetic : public PhysicsModel { } output.enable(); - output << "TIMING\n======\n"; + output << "TIMING | minimum | mean | maximum\n" + << "----------- | ---------- | ---------- | ----------\n"; //#define PRINT(str,elapsed) output << str << elapsed.min.count()<< //elapsed.avg.count()<< elapsed.max.count() << endl; -#define PRINT(str, elapsed) \ - output.write("{:s} {:8.3g} {:8.3g} {:8.3g}\n", str, elapsed.min.count(), elapsed.avg.count(), \ - elapsed.max.count()) +#define PRINT(str, elapsed) \ + output.write("{:s} | {:7.3f} us | {:7.3f} us | {:7.3f} us\n", str, \ + elapsed.min.count(), elapsed.avg.count(), elapsed.max.count()) PRINT("Fields: ", elapsed1); PRINT("C loop: ", elapsed2); PRINT("Templates: ", elapsed3); From 21c64595c1e394ac4f3bb8088fb0c66894fe5e97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Wed, 22 Sep 2021 11:28:45 +0200 Subject: [PATCH 009/412] Switch toward regions --- include/bout/region.hxx | 5 -- include/interpolation_xz.hxx | 53 +++++++++++++++---- include/mask.hxx | 10 ++++ src/mesh/interpolation/bilinear_xz.cxx | 12 ++--- src/mesh/interpolation/hermite_spline_xz.cxx | 12 ++--- src/mesh/interpolation/lagrange_4pt_xz.cxx | 15 ++---- .../monotonic_hermite_spline_xz.cxx | 7 +-- 7 files changed, 65 insertions(+), 49 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 3aaf4530a1..050d836a3e 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -949,9 +949,4 @@ unsigned int size(const Region ®ion){ return region.size(); } -// template -class RegionID { - int value; -}; - #endif /* __REGION_H__ */ diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx index d8d7b3f73b..c4f869ef3d 100644 --- a/include/interpolation_xz.hxx +++ b/include/interpolation_xz.hxx @@ -35,24 +35,56 @@ const Field3D interpolate(const Field2D &f, const Field3D &delta_x, const Field3D interpolate(const Field2D &f, const Field3D &delta_x); class XZInterpolation { +public: + int y_offset; + protected: Mesh* localmesh{nullptr}; - // 3D vector of points to skip (true -> skip this point) - BoutMask skip_mask; + std::string region_name{""}; + std::shared_ptr> region{nullptr}; public: XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr) - : localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), - skip_mask(*localmesh, false), y_offset(y_offset) {} + : y_offset(y_offset), + localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), + region_name("RGN_ALL") {} XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) : XZInterpolation(y_offset, mesh) { - skip_mask = mask; + region = regionFromMask(mask, localmesh); } + XZInterpolation(const std::string& region_name, int y_offset = 0, Mesh* mesh = nullptr) + : y_offset(y_offset), localmesh(mesh), region_name(region_name) {} + XZInterpolation(std::shared_ptr> region, int y_offset = 0, + Mesh* mesh = nullptr) + : y_offset(y_offset), localmesh(mesh), region(region) {} virtual ~XZInterpolation() = default; - - void setMask(const BoutMask &mask) { skip_mask = mask; } + void setMask(const BoutMask& mask) { + region = regionFromMask(mask, localmesh); + region_name = ""; + } + void setRegion(const std::string& region_name) { + this->region_name = region_name; + this->region = nullptr; + } + void setRegion(const std::shared_ptr>& region) { + this->region_name = ""; + this->region = region; + } + Region getRegion() const { + if (region_name != "") { + return localmesh->getRegion(region_name); + } + ASSERT1(region != nullptr); + return *region; + } + Region getRegion(const std::string& region) const { + if (region != "" and region != "RGN_ALL") { + return getIntersection(localmesh->getRegion(region), getRegion()); + } + return getRegion(); + } virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region = "RGN_NOBNDRY") = 0; virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z, @@ -69,7 +101,6 @@ public: const std::string& region = "RGN_NOBNDRY") = 0; // Interpolate using the field at (x,y+y_offset,z), rather than (x,y,z) - int y_offset; void setYOffset(int offset) { y_offset = offset; } virtual std::vector @@ -117,7 +148,7 @@ public: XZHermiteSpline(int y_offset = 0, Mesh *mesh = nullptr); XZHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) : XZHermiteSpline(y_offset, mesh) { - skip_mask = mask; + region = regionFromMask(mask, localmesh); } void calcWeights(const Field3D& delta_x, const Field3D& delta_z, @@ -175,7 +206,7 @@ public: XZLagrange4pt(int y_offset = 0, Mesh *mesh = nullptr); XZLagrange4pt(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) : XZLagrange4pt(y_offset, mesh) { - skip_mask = mask; + region = regionFromMask(mask, localmesh); } void calcWeights(const Field3D& delta_x, const Field3D& delta_z, @@ -208,7 +239,7 @@ public: XZBilinear(int y_offset = 0, Mesh *mesh = nullptr); XZBilinear(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) : XZBilinear(y_offset, mesh) { - skip_mask = mask; + region = regionFromMask(mask, localmesh); } void calcWeights(const Field3D& delta_x, const Field3D& delta_z, diff --git a/include/mask.hxx b/include/mask.hxx index 8940edbb16..c26bf31d61 100644 --- a/include/mask.hxx +++ b/include/mask.hxx @@ -72,4 +72,14 @@ public: } }; +inline std::unique_ptr> regionFromMask(const BoutMask& mask, + const Mesh* mesh) { + std::vector indices; + for (auto i : mesh->getRegion("RGN_ALL")) { + if (not mask(i.x(), i.y(), i.z())) { + indices.push_back(i); + } + } + return std::make_unique>(indices); +} #endif //__MASK_H__ diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx index 7819fafe6f..1869df3218 100644 --- a/src/mesh/interpolation/bilinear_xz.cxx +++ b/src/mesh/interpolation/bilinear_xz.cxx @@ -45,14 +45,11 @@ XZBilinear::XZBilinear(int y_offset, Mesh *mesh) void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, delta_x.getRegion(region)) { + BOUT_FOR(i, getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - // The integer part of xt_prime, zt_prime are the indices of the cell // containing the field line end-point i_corner(x, y, z) = static_cast(floor(delta_x(x, y, z))); @@ -87,7 +84,7 @@ void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z, void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const BoutMask& mask, const std::string& region) { - skip_mask = mask; + setMask(mask); calcWeights(delta_x, delta_z, region); } @@ -95,14 +92,11 @@ Field3D XZBilinear::interpolate(const Field3D& f, const std::string& region) con ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR(i, this->getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - const int y_next = y + y_offset; // Due to lack of guard cells in z-direction, we need to ensure z-index // wraps around diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx index 8f6bf0d419..b3c5b3c70f 100644 --- a/src/mesh/interpolation/hermite_spline_xz.cxx +++ b/src/mesh/interpolation/hermite_spline_xz.cxx @@ -55,14 +55,11 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh) void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, delta_x.getRegion(region)) { + BOUT_FOR(i, getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - // The integer part of xt_prime, zt_prime are the indices of the cell // containing the field line end-point i_corner(x, y, z) = static_cast(floor(delta_x(x, y, z))); @@ -112,7 +109,7 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const BoutMask& mask, const std::string& region) { - skip_mask = mask; + setMask(mask); calcWeights(delta_x, delta_z, region); } @@ -175,14 +172,11 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region localmesh->wait(h); } - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR(i, getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - // Due to lack of guard cells in z-direction, we need to ensure z-index // wraps around const int ncz = localmesh->LocalNz; diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx index 3a5de28e59..7c79a3f713 100644 --- a/src/mesh/interpolation/lagrange_4pt_xz.cxx +++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx @@ -39,15 +39,12 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh *mesh) void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - - BOUT_FOR(i, delta_x.getRegion(region)) { + const auto curregion = getRegion(region); + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - // The integer part of xt_prime, zt_prime are the indices of the cell // containing the field line end-point i_corner(x, y, z) = static_cast(floor(delta_x(x, y, z))); @@ -80,7 +77,7 @@ void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z, void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const BoutMask& mask, const std::string& region) { - skip_mask = mask; + setMask(mask); calcWeights(delta_x, delta_z, region); } @@ -89,14 +86,12 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const std::string& region) ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR(i, f.getRegion(region)) { + const auto curregion{getRegion(region)}; + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - const int jx = i_corner(x, y, z); const int jx2mnew = (jx == 0) ? 0 : (jx - 1); const int jxpnew = jx + 1; diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx index c393c94667..c74ea0ce50 100644 --- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx +++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx @@ -22,7 +22,7 @@ #include "globals.hxx" #include "interpolation_xz.hxx" -#include "output.hxx" +//#include "output.hxx" #include "bout/index_derivs_interface.hxx" #include "bout/mesh.hxx" @@ -58,14 +58,11 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f, localmesh->wait(h); } - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR(i, getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) - continue; - // Due to lack of guard cells in z-direction, we need to ensure z-index // wraps around const int ncz = localmesh->LocalNz; From 4a1259e8d5f267c5501f5ab8a8d7bfa36669ac49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Thu, 23 Sep 2021 17:57:17 +0200 Subject: [PATCH 010/412] Simplify expression --- src/mesh/parallel/fci.cxx | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index a8e06b52fa..691a5a95fc 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -280,10 +280,7 @@ Field3D FCIMap::integrate(Field3D &f) const { if (boundary_mask(x,y,z)) continue; - int zm = z - 1; - if (z == 0) { - zm = nz-1; - } + const int zm = z == 0 ? nz - 1 : z - 1; BoutReal f_c = centre(x,ynext,z); From 99fe484ba243d1680b0ad2e81a2fd205eb0c301c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Thu, 23 Sep 2021 17:57:55 +0200 Subject: [PATCH 011/412] Assume periodicity in z --- src/mesh/parallel/fci.cxx | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 691a5a95fc..845d69ca07 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -208,20 +208,8 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, const BoutReal dR_dx = 0.5 * (R[i_xp] - R[i_xm]); const BoutReal dZ_dx = 0.5 * (Z[i_xp] - Z[i_xm]); - BoutReal dR_dz, dZ_dz; - // Handle the edge cases in Z - if (z == 0) { - dR_dz = R[i_zp] - R[i]; - dZ_dz = Z[i_zp] - Z[i]; - - } else if (z == map_mesh.LocalNz - 1) { - dR_dz = R[i] - R[i_zm]; - dZ_dz = Z[i] - Z[i_zm]; - - } else { - dR_dz = 0.5 * (R[i_zp] - R[i_zm]); - dZ_dz = 0.5 * (Z[i_zp] - Z[i_zm]); - } + const BoutReal dR_dz = 0.5 * (R[i_zp] - R[i_zm]); + const BoutReal dZ_dz = 0.5 * (Z[i_zp] - Z[i_zm]); const BoutReal det = dR_dx * dZ_dz - dR_dz * dZ_dx; // Determinant of 2x2 matrix From a61a000b9940937c8037ec47eba4549ba859c38c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Fri, 24 Sep 2021 11:19:50 +0200 Subject: [PATCH 012/412] Switch to regions for FCI regions --- include/bout/region.hxx | 23 ++++++ include/interpolation_xz.hxx | 14 +++- include/mask.hxx | 1 + include/utils.hxx | 13 +++- src/mesh/interpolation/bilinear_xz.cxx | 6 +- src/mesh/interpolation/hermite_spline_xz.cxx | 6 +- src/mesh/interpolation/lagrange_4pt_xz.cxx | 2 +- .../monotonic_hermite_spline_xz.cxx | 3 +- src/mesh/parallel/fci.cxx | 76 +++++++++---------- src/mesh/parallel/fci.hxx | 7 +- 10 files changed, 95 insertions(+), 56 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 050d836a3e..68a2b7c62d 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -51,6 +51,7 @@ #include "bout_types.hxx" #include "bout/assert.hxx" #include "bout/openmpwrap.hxx" +class BoutMask; /// The MAXREGIONBLOCKSIZE value can be tuned to try to optimise /// performance on specific hardware. It determines what the largest @@ -655,6 +656,28 @@ public: return *this; // To allow command chaining }; + /// Return a new region equivalent to *this but with indices contained + /// in mask Region removed + Region mask(const BoutMask& mask) { + // Get the current set of indices that we're going to mask and then + // use to create the result region. + auto currentIndices = getIndices(); + + // Lambda that returns true/false depending if the passed value is in maskIndices + // With C++14 T can be auto instead + auto isInVector = [&](T val) { return mask[val]; }; + + // Erase elements of currentIndices that are in maskIndices + currentIndices.erase( + std::remove_if(std::begin(currentIndices), std::end(currentIndices), isInVector), + std::end(currentIndices)); + + // Update indices + setIndices(currentIndices); + + return *this; // To allow command chaining + }; + /// Returns a modified region including only indices that are also in the region. Region getIntersection(const Region& otherRegion) { // Get other indices and sort as we're going to be searching through diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx index c4f869ef3d..703e3973f5 100644 --- a/include/interpolation_xz.hxx +++ b/include/interpolation_xz.hxx @@ -47,8 +47,7 @@ protected: public: XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr) : y_offset(y_offset), - localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), - region_name("RGN_ALL") {} + localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn) {} XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) : XZInterpolation(y_offset, mesh) { region = regionFromMask(mask, localmesh); @@ -72,6 +71,10 @@ public: this->region_name = ""; this->region = region; } + void setRegion(const Region& region) { + this->region_name = ""; + this->region = std::make_shared>(region); + } Region getRegion() const { if (region_name != "") { return localmesh->getRegion(region_name); @@ -80,9 +83,14 @@ public: return *region; } Region getRegion(const std::string& region) const { + const bool has_region = region_name != "" or this->region != nullptr; if (region != "" and region != "RGN_ALL") { - return getIntersection(localmesh->getRegion(region), getRegion()); + if (has_region) { + return getIntersection(localmesh->getRegion(region), getRegion()); + } + return localmesh->getRegion(region); } + ASSERT1(has_region); return getRegion(); } virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z, diff --git a/include/mask.hxx b/include/mask.hxx index c26bf31d61..6113e94d63 100644 --- a/include/mask.hxx +++ b/include/mask.hxx @@ -70,6 +70,7 @@ public: inline const bool& operator()(int jx, int jy, int jz) const { return mask(jx, jy, jz); } + inline const bool& operator[](const Ind3D& i) const { return mask[i]; } }; inline std::unique_ptr> regionFromMask(const BoutMask& mask, diff --git a/include/utils.hxx b/include/utils.hxx index 5e6eb9b8c1..53d1614e5b 100644 --- a/include/utils.hxx +++ b/include/utils.hxx @@ -33,10 +33,11 @@ #include "dcomplex.hxx" #include "boutexception.hxx" -#include "bout/array.hxx" -#include "bout/assert.hxx" #include "msg_stack.hxx" #include "unused.hxx" +#include "bout/array.hxx" +#include "bout/assert.hxx" +#include "bout/region.hxx" #include #include @@ -347,6 +348,14 @@ public: return data[(i1*n2+i2)*n3 + i3]; } + const T& operator[](Ind3D i) const { + // ny and nz are private :-( + // ASSERT2(i.nz == n3); + // ASSERT2(i.ny == n2); + ASSERT2(0 <= i.ind && i.ind < n1 * n2 * n3); + return data[i.ind]; + } + Tensor& operator=(const T&val){ for(auto &i: data){ i = val; diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx index 1869df3218..e36527e765 100644 --- a/src/mesh/interpolation/bilinear_xz.cxx +++ b/src/mesh/interpolation/bilinear_xz.cxx @@ -45,7 +45,8 @@ XZBilinear::XZBilinear(int y_offset, Mesh *mesh) void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, getRegion(region)) { + const auto curregion{getRegion(region)}; + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -92,7 +93,8 @@ Field3D XZBilinear::interpolate(const Field3D& f, const std::string& region) con ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR(i, this->getRegion(region)) { + const auto curregion{getRegion(region)}; + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx index b3c5b3c70f..cd85d6241b 100644 --- a/src/mesh/interpolation/hermite_spline_xz.cxx +++ b/src/mesh/interpolation/hermite_spline_xz.cxx @@ -55,7 +55,8 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh) void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, getRegion(region)) { + const auto curregion{getRegion(region)}; + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -172,7 +173,8 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region localmesh->wait(h); } - BOUT_FOR(i, getRegion(region)) { + const auto curregion{getRegion(region)}; + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx index 7c79a3f713..caf4ce45eb 100644 --- a/src/mesh/interpolation/lagrange_4pt_xz.cxx +++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx @@ -39,7 +39,7 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh *mesh) void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - const auto curregion = getRegion(region); + const auto curregion{getRegion(region)}; BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx index c74ea0ce50..8477e5fe72 100644 --- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx +++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx @@ -58,7 +58,8 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f, localmesh->wait(h); } - BOUT_FOR(i, getRegion(region)) { + const auto curregion{getRegion(region)}; + BOUT_FOR(i, curregion) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 845d69ca07..9aa4286f38 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -50,7 +50,8 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, int offset_, BoundaryRegionPar* inner_boundary, BoundaryRegionPar* outer_boundary, bool zperiodic) - : map_mesh(mesh), offset(offset_), boundary_mask(map_mesh), + : map_mesh(mesh), offset(offset_), + region_no_boundary(map_mesh.getRegion("RGN_NOBNDRY")), corner_boundary_mask(map_mesh) { TRACE("Creating FCIMAP for direction {:d}", offset); @@ -156,6 +157,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, const int ncz = map_mesh.LocalNz; + BoutMask to_remove(map_mesh); // Serial loop because call to BoundaryRegionPar::addPoint // (probably?) can't be done in parallel BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) { @@ -185,7 +187,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, // indices (forward/backward_xt_prime and forward/backward_zt_prime) // are set to -1 - boundary_mask(x, y, z) = true; + to_remove(x, y, z) = true; // Need to specify the index of the boundary intersection, but // this may not be defined in general. @@ -200,13 +202,11 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, // and the gradients dR/dx etc. are evaluated at (x,y,z) // Cache the offsets - const auto i_xp = i.xp(); - const auto i_xm = i.xm(); const auto i_zp = i.zp(); const auto i_zm = i.zm(); - const BoutReal dR_dx = 0.5 * (R[i_xp] - R[i_xm]); - const BoutReal dZ_dx = 0.5 * (Z[i_xp] - Z[i_xm]); + const BoutReal dR_dx = 0.5 * (R[i.xp()] - R[i.xm()]); + const BoutReal dZ_dx = 0.5 * (Z[i.xp()] - Z[i.xm()]); const BoutReal dR_dz = 0.5 * (R[i_zp] - R[i_zm]); const BoutReal dZ_dz = 0.5 * (Z[i_zp] - Z[i_zm]); @@ -229,8 +229,9 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, PI // Right-angle intersection ); } + region_no_boundary = region_no_boundary.mask(to_remove); - interp->setMask(boundary_mask); + interp->setRegion(region_no_boundary); const auto region = fmt::format("RGN_YPAR_{:+d}", offset); if (not map_mesh.hasRegion3D(region)) { @@ -259,42 +260,33 @@ Field3D FCIMap::integrate(Field3D &f) const { int nz = map_mesh.LocalNz; - for(int x = map_mesh.xstart; x <= map_mesh.xend; x++) { - for(int y = map_mesh.ystart; y <= map_mesh.yend; y++) { - - int ynext = y+offset; - - for(int z = 0; z < nz; z++) { - if (boundary_mask(x,y,z)) - continue; - - const int zm = z == 0 ? nz - 1 : z - 1; - - BoutReal f_c = centre(x,ynext,z); - - if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z) || - corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm) || - (x == map_mesh.xstart)) { - // One of the corners leaves the domain. - // Use the cell centre value, since boundary conditions are not - // currently applied to corners. - result(x, ynext, z) = f_c; - - } else { - BoutReal f_pp = corner(x, ynext, z); // (x+1/2, z+1/2) - BoutReal f_mp = corner(x - 1, ynext, z); // (x-1/2, z+1/2) - BoutReal f_pm = corner(x, ynext, zm); // (x+1/2, z-1/2) - BoutReal f_mm = corner(x - 1, ynext, zm); // (x-1/2, z-1/2) - - // This uses a simple weighted average of centre and corners - // A more sophisticated approach might be to use e.g. Gauss-Lobatto points - // which would include cell edges and corners - result(x, ynext, z) = 0.5 * (f_c + 0.25 * (f_pp + f_mp + f_pm + f_mm)); - - ASSERT2(finite(result(x,ynext,z))); - } - } + BOUT_FOR(i, region_no_boundary) { + const auto inext = i.yp(offset); + BoutReal f_c = centre[inext]; + const auto izm = i.zm(); + const int x = i.x(); + const int y = i.y(); + const int z = i.z(); + const int zm = izm.z(); + if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z) + || corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm) + || (x == map_mesh.xstart)) { + // One of the corners leaves the domain. + // Use the cell centre value, since boundary conditions are not + // currently applied to corners. + result[inext] = f_c; + } else { + BoutReal f_pp = corner[inext]; // (x+1/2, z+1/2) + BoutReal f_mp = corner[inext.xm()]; // (x-1/2, z+1/2) + BoutReal f_pm = corner[inext.zm()]; // (x+1/2, z-1/2) + BoutReal f_mm = corner[inext.xm().zm()]; // (x-1/2, z-1/2) + + // This uses a simple weighted average of centre and corners + // A more sophisticated approach might be to use e.g. Gauss-Lobatto points + // which would include cell edges and corners + result[inext] = 0.5 * (f_c + 0.25 * (f_pp + f_mp + f_pm + f_mm)); } + ASSERT2(finite(result[inext])); } return result; } diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 3ecd964bfa..ef7c98693e 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -54,11 +54,12 @@ public: /// Direction of map const int offset; - /// boundary mask - has the field line left the domain - BoutMask boundary_mask; + /// region containing all points where the field line has not left the + /// domain + Region region_no_boundary; /// If any of the integration area has left the domain BoutMask corner_boundary_mask; - + Field3D interpolate(Field3D& f) const { ASSERT1(&map_mesh == f.getMesh()); return interp->interpolate(f); From cd4a1d2758c13892fb7f7218cc4d784d5d5786be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Fri, 1 Oct 2021 16:49:20 +0200 Subject: [PATCH 013/412] Recommendations from clang-tidy --- include/interpolation_xz.hxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx index 703e3973f5..67a0f0973c 100644 --- a/include/interpolation_xz.hxx +++ b/include/interpolation_xz.hxx @@ -56,7 +56,7 @@ public: : y_offset(y_offset), localmesh(mesh), region_name(region_name) {} XZInterpolation(std::shared_ptr> region, int y_offset = 0, Mesh* mesh = nullptr) - : y_offset(y_offset), localmesh(mesh), region(region) {} + : y_offset(y_offset), localmesh(mesh), region(std::move(region)) {} virtual ~XZInterpolation() = default; void setMask(const BoutMask& mask) { @@ -76,15 +76,15 @@ public: this->region = std::make_shared>(region); } Region getRegion() const { - if (region_name != "") { + if (!region_name.empty()) { return localmesh->getRegion(region_name); } ASSERT1(region != nullptr); return *region; } Region getRegion(const std::string& region) const { - const bool has_region = region_name != "" or this->region != nullptr; - if (region != "" and region != "RGN_ALL") { + const bool has_region = !region_name.empty() or this->region != nullptr; + if (!region.empty() and region != "RGN_ALL") { if (has_region) { return getIntersection(localmesh->getRegion(region), getRegion()); } From 23e1fc5a53b352699e497ceef86f5eed4d6b827f Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 25 Feb 2022 16:26:36 +0100 Subject: [PATCH 014/412] Remove unsed variable --- src/mesh/parallel/fci.cxx | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 453dbcc07b..bc54a905f9 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -262,8 +262,6 @@ Field3D FCIMap::integrate(Field3D &f) const { result = BoutNaN; #endif - int nz = map_mesh.LocalNz; - BOUT_FOR(i, region_no_boundary) { const auto inext = i.yp(offset); BoutReal f_c = centre[inext]; From b5e9eca7366007a99d3bc2870cf701f772f20d88 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 12:31:31 +0100 Subject: [PATCH 015/412] BugFix: Fix separation of inner and outer boundary --- src/mesh/parallel/fci.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index bc54a905f9..1b81066115 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -222,7 +222,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, // Negative xt_prime means we've hit the inner boundary, otherwise // the outer boundary - auto* boundary = (xt_prime[i] < 0.0) ? inner_boundary : outer_boundary; + auto* boundary = (xt_prime[i] < map_mesh.xstart) ? inner_boundary : outer_boundary; boundary->add_point(x, y, z, x + dx, y + 0.5 * offset, z + dz, // Intersection point in local index space 0.5 * dy[i], // Distance to intersection From a88796890f5b7b68039f2334505c5dd0013fce45 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 23 Feb 2022 09:59:26 +0100 Subject: [PATCH 016/412] ensure getCommonRegion is thread safe --- src/mesh/mesh.cxx | 34 +++++++++++++++++++++++++--------- 1 file changed, 25 insertions(+), 9 deletions(-) diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index a9aa8b4487..7f91258dfb 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -679,19 +679,35 @@ int Mesh::getCommonRegion(int lhs, int rhs) { */ const size_t pos = (high * (high - 1)) /2 + low; if (region3Dintersect.size() <= pos) { - region3Dintersect.resize(pos+1, -1); + BOUT_OMP(critical(mesh_getIntersection_realloc)) +#if BOUT_USE_OPENMP + if (region3Dintersect.size() <= pos) +#endif + { + region3Dintersect.resize(pos+1, -1); + } } if (region3Dintersect[pos] != -1){ return region3Dintersect[pos]; } - auto common = getIntersection(region3D[low], region3D[high]); - for (size_t i = 0; i < region3D.size(); ++i) { - if (common == region3D[i]) { - region3Dintersect[pos] = i; - return i; + { + BOUT_OMP(critical(mesh_getIntersection)) +#if BOUT_USE_OPENMP + if (region3Dintersect[pos] == -1) +#endif + { + auto common = getIntersection(region3D[low], region3D[high]); + for (size_t i = 0; i < region3D.size(); ++i) { + if (common == region3D[i]) { + region3Dintersect[pos] = i; + break; + } + } + if (region3Dintersect[pos] == -1) { + region3D.push_back(common); + region3Dintersect[pos] = region3D.size() - 1; + } } } - region3D.push_back(common); - region3Dintersect[pos] = region3D.size() - 1; - return region3D.size() - 1; + return region3Dintersect[pos]; } From 6b3e4c1a2b56ec4eda2b19abd3770353109f66ce Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 9 Mar 2022 16:03:14 +0000 Subject: [PATCH 017/412] [skip ci] Apply black changes --- bin/bout-v5-physics-model-upgrader.py | 8 +++--- tests/MMS/GBS/circle.py | 2 +- tests/MMS/GBS/mms-slab2d.py | 20 ++++++------- tests/MMS/GBS/mms-slab3d.py | 28 +++++++++---------- tests/MMS/GBS/runtest-slab2d | 2 +- tests/MMS/GBS/runtest-slab3d | 2 +- tests/MMS/advection/mms.py | 4 +-- tests/MMS/advection/runtest | 2 +- tests/MMS/bracket/runtest | 2 +- tests/MMS/diffusion2/mms.py | 2 +- tests/MMS/diffusion2/runtest | 2 +- tests/MMS/elm-pb/makegrids.py | 2 +- tests/MMS/elm-pb/mms.py | 8 +++--- tests/MMS/elm-pb/runtest.broken | 4 +-- tests/MMS/fieldalign/runtest.broken | 2 +- tests/MMS/hw/mms.py | 6 ++-- tests/MMS/hw/runtest | 2 +- tests/MMS/laplace/runtest | 2 +- tests/MMS/spatial/advection/mms.py | 4 +-- tests/MMS/spatial/d2dx2/runtest | 2 +- tests/MMS/spatial/d2dz2/runtest | 2 +- tests/MMS/spatial/diffusion/mms.py | 2 +- tests/MMS/spatial/diffusion/runtest | 2 +- tests/MMS/spatial/fci/mms.py | 2 +- tests/MMS/time/runtest | 2 +- tests/MMS/tokamak/mms.py | 8 +++--- tests/MMS/tokamak/runtest.broken | 2 +- tests/MMS/wave-1d-y/mms.py | 2 +- tests/MMS/wave-1d-y/runtest | 2 +- tests/MMS/wave-1d/mms.py | 4 +-- tests/MMS/wave-1d/runtest | 2 +- .../integrated/test-drift-instability/runtest | 2 +- tests/integrated/test-initial/runtest | 2 +- tests/integrated/test-interpolate-z/runtest | 2 +- tests/integrated/test-interpolate/runtest | 2 +- tests/integrated/test_suite | 8 +++--- tools/pylib/post_bout/pb_corral.py | 6 ++-- tools/pylib/post_bout/pb_draw.py | 2 +- tools/pylib/zoidberg/field.py | 15 +++++----- tools/pylib/zoidberg/fieldtracer.py | 2 +- tools/pylib/zoidberg/plot.py | 2 +- tools/pylib/zoidberg/poloidal_grid.py | 18 ++++++------ tools/pylib/zoidberg/progress.py | 10 +++---- tools/pylib/zoidberg/zoidberg.py | 4 +-- tools/tokamak_grids/cyclone/cyclone.py | 4 +-- tools/tokamak_grids/gato/gato2nc | 2 +- 46 files changed, 108 insertions(+), 109 deletions(-) diff --git a/bin/bout-v5-physics-model-upgrader.py b/bin/bout-v5-physics-model-upgrader.py index 7c7a4e484a..26fb8ef6e0 100755 --- a/bin/bout-v5-physics-model-upgrader.py +++ b/bin/bout-v5-physics-model-upgrader.py @@ -52,7 +52,7 @@ def create_function_signature_re(function_name, argument_types): ] ) - return fr"int\s+{function_name}\s*\({arguments}\)" + return rf"int\s+{function_name}\s*\({arguments}\)" LEGACY_MODEL_INCLUDE_RE = re.compile( @@ -158,7 +158,7 @@ def fix_model_operator( arguments = ", ".join(arg_names) # Modify the definition: it's out-of-line so we need the qualified name - modified = operator_re.sub(fr"int {model_name}::{new_name}({arguments})", source) + modified = operator_re.sub(rf"int {model_name}::{new_name}({arguments})", source) # Create the declaration return ( @@ -264,7 +264,7 @@ def convert_old_solver_api(source, name): if decl: method_decls.append(decl) # Almost a straight replacement, but it's now a member-function pointer - source = PRECON_RE.sub(fr"setPrecon(&{name}::\1)", source) + source = PRECON_RE.sub(rf"setPrecon(&{name}::\1)", source) # Fix uses of solver->setJacobian, basically the same as for setPrecon jacobians = JACOBIAN_RE.findall(source) @@ -274,7 +274,7 @@ def convert_old_solver_api(source, name): ) if decl: method_decls.append(decl) - source = JACOBIAN_RE.sub(fr"setJacobian(&{name}::\1)", source) + source = JACOBIAN_RE.sub(rf"setJacobian(&{name}::\1)", source) # If we didn't find any free functions that need to be made into # methods, we're done diff --git a/tests/MMS/GBS/circle.py b/tests/MMS/GBS/circle.py index 4fa77105ed..b2553f47c3 100644 --- a/tests/MMS/GBS/circle.py +++ b/tests/MMS/GBS/circle.py @@ -76,7 +76,7 @@ def generate( Bpxy[:, :] = Bt Bxy = ndarray([nx, ny]) - Bxy[:, :] = sqrt(Bt ** 2 + Bp ** 2) + Bxy[:, :] = sqrt(Bt**2 + Bp**2) hthe = ndarray([nx, ny]) hthe[:, :] = R diff --git a/tests/MMS/GBS/mms-slab2d.py b/tests/MMS/GBS/mms-slab2d.py index 061474edd5..215e711a53 100644 --- a/tests/MMS/GBS/mms-slab2d.py +++ b/tests/MMS/GBS/mms-slab2d.py @@ -50,7 +50,7 @@ def C(f): # mi_me = AA * 1.67262158e-27 / 9.109e-31 -beta_e = qe * Tnorm * Nnorm / (old_div(Bnorm ** 2, mu0)) +beta_e = qe * Tnorm * Nnorm / (old_div(Bnorm**2, mu0)) # Normalisation parameters Cs0 = sqrt(qe * Tnorm / (AA * Mp)) @@ -86,9 +86,9 @@ def C(f): Bxy /= Bnorm hthe /= rho_s0 -dx /= rho_s0 ** 2 * Bnorm +dx /= rho_s0**2 * Bnorm -bxcvz *= rho_s0 ** 2 +bxcvz *= rho_s0**2 # Define a metric metric = Metric() # Identity @@ -96,8 +96,8 @@ def C(f): Lx = dx * (nx - 2.0 * MXG) # Size of the X domain metric.g11 = (Rxy * Bpxy) ** 2 -metric.g22 = old_div(1.0, (hthe ** 2)) -metric.g33 = (sinty ** 2) * metric.g11 + old_div((Bxy ** 2), metric.g11) +metric.g22 = old_div(1.0, (hthe**2)) +metric.g33 = (sinty**2) * metric.g11 + old_div((Bxy**2), metric.g11) metric.g12 = 0.0 metric.g13 = -sinty * metric.g11 metric.g23 = -sbp * Btxy / (hthe * Bpxy * Rxy) @@ -115,15 +115,15 @@ def C(f): # Define the manufactured solution in terms of input x,y and z -Ne = 0.9 + 0.9 * x + 0.2 * cos(t) * sin(5.0 * x ** 2 - 5.0 * z) -Te = 1 + 0.5 * cos(t) * cos(3 * x ** 2 - 4 * z) +Ne = 0.9 + 0.9 * x + 0.2 * cos(t) * sin(5.0 * x**2 - 5.0 * z) +Te = 1 + 0.5 * cos(t) * cos(3 * x**2 - 4 * z) Vort = sin(2 * t) * cos(x - z) -VePsi = 0.5 * cos(7 * t) * cos(3 * x ** 2 - 3 * z) -Vi = -0.1 * cos(7 * t) * cos(3 * x ** 2 - 3 * z) +VePsi = 0.5 * cos(7 * t) * cos(3 * x**2 - 3 * z) +Vi = -0.1 * cos(7 * t) * cos(3 * x**2 - 3 * z) phi = sin(z - x + t) * sin(2.0 * pi * x) # Must satisfy Dirichlet BCs for now psi = sin(pi * x) * ( - 0.5 * x - cos(7 * t) * sin(3.0 * x ** 2 - 3 * z) + 0.5 * x - cos(7 * t) * sin(3.0 * x**2 - 3 * z) ) # Must satisfy Dirichlet BCs for now # Substitute to get in terms of actual x,y,z coordinates diff --git a/tests/MMS/GBS/mms-slab3d.py b/tests/MMS/GBS/mms-slab3d.py index 5e050d84ec..f88a897c98 100644 --- a/tests/MMS/GBS/mms-slab3d.py +++ b/tests/MMS/GBS/mms-slab3d.py @@ -43,7 +43,7 @@ def C(f): # mi_me = AA * 1.67262158e-27 / 9.109e-31 -beta_e = qe * Tnorm * Nnorm / (old_div(Bnorm ** 2, mu0)) +beta_e = qe * Tnorm * Nnorm / (old_div(Bnorm**2, mu0)) # Normalisation parameters Cs0 = sqrt(qe * Tnorm / (AA * Mp)) @@ -87,9 +87,9 @@ def C(f): Bxy /= Bnorm hthe /= rho_s0 -dx /= rho_s0 ** 2 * Bnorm +dx /= rho_s0**2 * Bnorm -bxcvz *= rho_s0 ** 2 +bxcvz *= rho_s0**2 # Define a metric metric = Metric() # Identity @@ -98,8 +98,8 @@ def C(f): Ly = dy * ny # Size of the Y domain metric.g11 = (Rxy * Bpxy) ** 2 -metric.g22 = old_div(1.0, (hthe ** 2)) -metric.g33 = (sinty ** 2) * metric.g11 + old_div((Bxy ** 2), metric.g11) +metric.g22 = old_div(1.0, (hthe**2)) +metric.g33 = (sinty**2) * metric.g11 + old_div((Bxy**2), metric.g11) metric.g12 = 0.0 metric.g13 = -sinty * metric.g11 metric.g23 = -sbp * Btxy / (hthe * Bpxy * Rxy) @@ -123,18 +123,18 @@ def C(f): # Define the manufactured solution in terms of input x,y and z -Ne = 0.9 + 0.9 * x + 0.5 * cos(t) * sin(5.0 * x ** 2 - z) + 0.01 * sin(y - z) -Te = 1 + 0.5 * cos(t) * cos(3 * x ** 2 - 2 * z) + 0.005 * sin(y - z) * sin(t) +Ne = 0.9 + 0.9 * x + 0.5 * cos(t) * sin(5.0 * x**2 - z) + 0.01 * sin(y - z) +Te = 1 + 0.5 * cos(t) * cos(3 * x**2 - 2 * z) + 0.005 * sin(y - z) * sin(t) Vort = 2.0 * sin(2 * t) * cos(x - z + 4 * y) -VePsi = cos(1.5 * t) * (2.0 * sin((x - 0.5) ** 2 + z) + 0.05 * cos(3 * x ** 2 + y - z)) -Vi = -0.01 * cos(7 * t) * cos(3 * x ** 2 + 2 * y - 2 * z) +VePsi = cos(1.5 * t) * (2.0 * sin((x - 0.5) ** 2 + z) + 0.05 * cos(3 * x**2 + y - z)) +Vi = -0.01 * cos(7 * t) * cos(3 * x**2 + 2 * y - 2 * z) # phi = sin(z - x + t)*sin(2.*pi*x) phi = (sin(z - x + t) + 0.001 * cos(y - z)) * sin( 2.0 * pi * x ) # Must satisfy Dirichlet BCs for now psi = sin(pi * x) * ( - 0.5 * x - 0.1 * cos(7 * t) * sin(3.0 * x ** 2 + y - z) + 0.5 * x - 0.1 * cos(7 * t) * sin(3.0 * x**2 + y - z) ) # Must satisfy Dirichlet BCs for now # Substitute to get in terms of actual x,y,z coordinates @@ -168,7 +168,7 @@ def C(f): Gi = 0.0 Ge = 0.0 -tau_e = Omega_ci * tau_e0 * (Te ** 1.5) / Ne +tau_e = Omega_ci * tau_e0 * (Te**1.5) / Ne # Normalised collision time nu = old_div(1.0, (1.96 * Ne * tau_e * mi_me)) @@ -203,7 +203,7 @@ def C(f): dVortdt = -bracket(phi, Vort, metric) + 2.0 * B * C(Pe) / Ne + B * C(Gi) / (3.0 * Ne) if parallel: - dVortdt += -Vpar_Grad_par(Vi, Vort, metric) + B ** 2 * ( + dVortdt += -Vpar_Grad_par(Vi, Vort, metric) + B**2 * ( Grad_par(Vi - Ve, metric) + (Vi - Ve) * Grad_par(Ne, metric) / Ne ) @@ -355,10 +355,10 @@ def exprmag(expr): print(" C(Pe) : ", exprmag(2.0 * B * C(Pe) / Ne), "\n") print(" C(Gi) : ", exprmag(B * C(Gi) / (3.0 * Ne)), "\n") print(" Vpar_Grad_par(Vi, Vort) : ", exprmag(-Vpar_Grad_par(Vi, Vort, metric)), "\n") -print(" B**2*Grad_par(Vi - Ve) :", exprmag(B ** 2 * Grad_par(Vi - Ve, metric)), "\n") +print(" B**2*Grad_par(Vi - Ve) :", exprmag(B**2 * Grad_par(Vi - Ve, metric)), "\n") print( " B**2*(Vi - Ve)*Grad_par(log(Ne)) :", - exprmag(B ** 2 * (Vi - Ve) * Grad_par(log(Ne), metric)), + exprmag(B**2 * (Vi - Ve) * Grad_par(log(Ne), metric)), "\n", ) diff --git a/tests/MMS/GBS/runtest-slab2d b/tests/MMS/GBS/runtest-slab2d index 282bbd0520..97c7e11459 100755 --- a/tests/MMS/GBS/runtest-slab2d +++ b/tests/MMS/GBS/runtest-slab2d @@ -66,7 +66,7 @@ for nx in nxlist: E = collect("E_" + var, tind=[1, 1], path=path) E = E[0, 1:-1, 0, :] - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2[var].append(l2) diff --git a/tests/MMS/GBS/runtest-slab3d b/tests/MMS/GBS/runtest-slab3d index e072c93733..cdcde3e1b3 100755 --- a/tests/MMS/GBS/runtest-slab3d +++ b/tests/MMS/GBS/runtest-slab3d @@ -74,7 +74,7 @@ for nx in nxlist: E = collect("E_" + var, tind=[1, 1], path=path, info=False) E = E[0, 2:-2, :, :] - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2[var].append(l2) diff --git a/tests/MMS/advection/mms.py b/tests/MMS/advection/mms.py index 646b78da9a..0c82f74508 100644 --- a/tests/MMS/advection/mms.py +++ b/tests/MMS/advection/mms.py @@ -14,9 +14,9 @@ # Define solution in terms of input x,y,z -g = sin(6 * x ** 2 - z) # Constant drive for advection +g = sin(6 * x**2 - z) # Constant drive for advection -f = cos(4 * x ** 2 + z) + sin(t) * sin(3 * x + 2 * z) +f = cos(4 * x**2 + z) + sin(t) * sin(3 * x + 2 * z) # Turn solution into real x and z coordinates replace = [(x, metric.x / Lx), (z, metric.z / ZMAX)] diff --git a/tests/MMS/advection/runtest b/tests/MMS/advection/runtest index 1f6822777d..1290a4c247 100755 --- a/tests/MMS/advection/runtest +++ b/tests/MMS/advection/runtest @@ -73,7 +73,7 @@ def run_mms(options, exit=True): E_f = collect("E_f", xguards=False, tind=[1, 1], info=False, path="data") # Average error over domain - l2 = sqrt(mean(E_f ** 2)) + l2 = sqrt(mean(E_f**2)) linf = max(abs(E_f)) error_2.append(l2) diff --git a/tests/MMS/bracket/runtest b/tests/MMS/bracket/runtest index b816f634a6..113498d3d8 100755 --- a/tests/MMS/bracket/runtest +++ b/tests/MMS/bracket/runtest @@ -65,7 +65,7 @@ for in1, in2, outfunc in funcs: err = inf - outf slize = [slice(2, -2), 0, slice(None)] err = err[slize] - err = np.sqrt(np.mean(err ** 2)) + err = np.sqrt(np.mean(err**2)) errors.append(err) errc = np.log(errors[-2] / errors[-1]) difc = np.log(nlist[-1] / nlist[-2]) diff --git a/tests/MMS/diffusion2/mms.py b/tests/MMS/diffusion2/mms.py index d849e88657..934b7fccb2 100644 --- a/tests/MMS/diffusion2/mms.py +++ b/tests/MMS/diffusion2/mms.py @@ -88,7 +88,7 @@ def exprToStr(expr): n = ( 0.9 + 0.9 * x - + 0.2 * sin(5.0 * x ** 2 - 2 * z) + + 0.2 * sin(5.0 * x**2 - 2 * z) + cos(10 * z) * cos(y) * sin(y * 7 + 1.234) ) diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest index 954af9f52d..d915018d8d 100755 --- a/tests/MMS/diffusion2/runtest +++ b/tests/MMS/diffusion2/runtest @@ -73,7 +73,7 @@ for dir, sizes in inputs: E_N = collect("E_N", tind=[nout, nout], path=dir, info=False) # Average error over domain, not including guard cells - l2 = sqrt(mean(E_N ** 2)) + l2 = sqrt(mean(E_N**2)) linf = max(abs(E_N)) error_2.append(l2) diff --git a/tests/MMS/elm-pb/makegrids.py b/tests/MMS/elm-pb/makegrids.py index 939b66795c..b627977469 100644 --- a/tests/MMS/elm-pb/makegrids.py +++ b/tests/MMS/elm-pb/makegrids.py @@ -34,7 +34,7 @@ Lbar = 1.0 Bbar = 1.0 J0 = -J0 * shape.Bxy / (MU0 * Lbar) # Turn into A/m^2 -P0 = P0 * Bbar ** 2 / (2.0 * MU0) # Pascals +P0 = P0 * Bbar**2 / (2.0 * MU0) # Pascals shape.add(P0, "pressure") shape.add(J0, "Jpar0") diff --git a/tests/MMS/elm-pb/mms.py b/tests/MMS/elm-pb/mms.py index d55fc295a8..308bce8b6b 100644 --- a/tests/MMS/elm-pb/mms.py +++ b/tests/MMS/elm-pb/mms.py @@ -21,11 +21,11 @@ 2.0 * pi * x ) # Must satisfy Dirichlet BCs for now -Psi = 1e-2 * cos(4 * x ** 2 + z - y) # + sin(t)*sin(3*x + 2*z - y)) +Psi = 1e-2 * cos(4 * x**2 + z - y) # + sin(t)*sin(3*x + 2*z - y)) U = 2.0 * cos(2 * t) * cos(x - z + 4 * y) -P = 1 + 0.5 * cos(t) * cos(3 * x ** 2 - z + y) + 0.005 * sin(y - z) * sin(t) +P = 1 + 0.5 * cos(t) * cos(3 * x**2 - z + y) + 0.005 * sin(y - z) * sin(t) P0 = 2 + cos(x * pi) # Pressure pedestal J0 = 1 - x - sin(x * pi) ** 2 * cos(y) # Parallel current @@ -97,9 +97,9 @@ def Grad_parP(f): # Vorticity dUdt = ( - B0 ** 2 * b0xGrad_dot_Grad(Psi, J0, metric) + B0**2 * b0xGrad_dot_Grad(Psi, J0, metric) + bxcvz * diff(P, metric.z) - - (B0 ** 2) * Grad_parP(Jpar) + - (B0**2) * Grad_parP(Jpar) ) if nonlinear: # Bracket method '0' (STD) goes to b0xGrad_dot_Grad diff --git a/tests/MMS/elm-pb/runtest.broken b/tests/MMS/elm-pb/runtest.broken index 672e7e7031..a31f8b9868 100755 --- a/tests/MMS/elm-pb/runtest.broken +++ b/tests/MMS/elm-pb/runtest.broken @@ -46,7 +46,7 @@ bxcvz = -((1.0 / shape.Rxy) ** 2) * cos(y) # Curvature Lbar = 1.0 Bbar = 1.0 J0 = -J0 * shape.Bxy / (MU0 * Lbar) # Turn into A/m^2 -P0 = P0 * Bbar ** 2 / (2.0 * MU0) # Pascals +P0 = P0 * Bbar**2 / (2.0 * MU0) # Pascals shape.add(P0, "pressure") shape.add(J0, "Jpar0") @@ -119,7 +119,7 @@ for nx, nproc in zip(nxlist, nprocs): E = E[:, 2:-2, :, :] # Average error over domain - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2[var].append(l2) diff --git a/tests/MMS/fieldalign/runtest.broken b/tests/MMS/fieldalign/runtest.broken index bf59f95588..e09fbeccd5 100755 --- a/tests/MMS/fieldalign/runtest.broken +++ b/tests/MMS/fieldalign/runtest.broken @@ -105,7 +105,7 @@ for dir in inputs: E_f = collect("E_f", tind=[nout, nout], path=directory, info=False) # Average error over domain, not including guard cells - l2 = sqrt(mean(E_f ** 2)) + l2 = sqrt(mean(E_f**2)) linf = max(abs(E_f)) error_2.append(l2) diff --git a/tests/MMS/hw/mms.py b/tests/MMS/hw/mms.py index 11962de15a..a03d7cbfc8 100644 --- a/tests/MMS/hw/mms.py +++ b/tests/MMS/hw/mms.py @@ -71,10 +71,10 @@ def exprToStr(expr): # Define the manufactured solution -n = 0.9 + 0.9 * x + 0.2 * cos(10 * t) * sin(5.0 * x ** 2 - 2 * z) -vort = 0.9 + 0.7 * x + 0.2 * cos(7 * t) * sin(2.0 * x ** 2 - 3 * z) +n = 0.9 + 0.9 * x + 0.2 * cos(10 * t) * sin(5.0 * x**2 - 2 * z) +vort = 0.9 + 0.7 * x + 0.2 * cos(7 * t) * sin(2.0 * x**2 - 3 * z) phi = sin(pi * x) * ( - 0.5 * x - cos(7 * t) * sin(3.0 * x ** 2 - 3 * z) + 0.5 * x - cos(7 * t) * sin(3.0 * x**2 - 3 * z) ) # Must satisfy Dirichlet BCs for now # Calculate gradients in x for boundaries diff --git a/tests/MMS/hw/runtest b/tests/MMS/hw/runtest index 03ea7d585e..b6abadc3b9 100755 --- a/tests/MMS/hw/runtest +++ b/tests/MMS/hw/runtest @@ -68,7 +68,7 @@ for nx in nxlist: # Average error over domain, not including guard cells E = concatenate([E_n[1:-1, :], E_vort[2:-1, :]]) - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2.append(l2) diff --git a/tests/MMS/laplace/runtest b/tests/MMS/laplace/runtest index 00bddbc57e..98eb62da87 100755 --- a/tests/MMS/laplace/runtest +++ b/tests/MMS/laplace/runtest @@ -50,7 +50,7 @@ for nx in nxlist: E = collect("error", tind=[nout, nout], path="data") E = E[1:-1, 0, :] - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2.append(l2) diff --git a/tests/MMS/spatial/advection/mms.py b/tests/MMS/spatial/advection/mms.py index 48c9c8a8ea..bc574f8b0e 100644 --- a/tests/MMS/spatial/advection/mms.py +++ b/tests/MMS/spatial/advection/mms.py @@ -14,9 +14,9 @@ # Define solution in terms of input x,y,z -g = sin(6 * x ** 2 - z) # Constant drive for advection +g = sin(6 * x**2 - z) # Constant drive for advection -f = cos(4 * x ** 2 + z) +f = cos(4 * x**2 + z) # Turn solution into real x and z coordinates replace = [(x, metric.x / Lx), (z, metric.z / ZMAX)] diff --git a/tests/MMS/spatial/d2dx2/runtest b/tests/MMS/spatial/d2dx2/runtest index afd293d5d9..ba1611a653 100755 --- a/tests/MMS/spatial/d2dx2/runtest +++ b/tests/MMS/spatial/d2dx2/runtest @@ -62,7 +62,7 @@ for nx in nxlist: err = result[1:-1, 0, 0] - solution[1:-1, 0, 0] # Average error - l2 = sqrt(mean(err ** 2)) + l2 = sqrt(mean(err**2)) linf = max(abs(err)) error_2.append(l2) diff --git a/tests/MMS/spatial/d2dz2/runtest b/tests/MMS/spatial/d2dz2/runtest index 081f13dc96..1afbd4416d 100755 --- a/tests/MMS/spatial/d2dz2/runtest +++ b/tests/MMS/spatial/d2dz2/runtest @@ -51,7 +51,7 @@ for mz in mzlist: err = result - solution # Average error - l2 = sqrt(mean(err ** 2)) + l2 = sqrt(mean(err**2)) linf = max(abs(err)) error_2.append(l2) diff --git a/tests/MMS/spatial/diffusion/mms.py b/tests/MMS/spatial/diffusion/mms.py index 6a54b2948e..847c09c76a 100644 --- a/tests/MMS/spatial/diffusion/mms.py +++ b/tests/MMS/spatial/diffusion/mms.py @@ -82,7 +82,7 @@ def exprToStr(expr): # Define the manufactured solution # n = 0.9 + 0.9*x + 0.2*sin(5.*x**2 - 2*z) + cos(y) -n = 0.9 + 0.9 * x + 0.2 * sin(5.0 * x ** 2) +n = 0.9 + 0.9 * x + 0.2 * sin(5.0 * x**2) # Calculate gradients for boundaries diff --git a/tests/MMS/spatial/diffusion/runtest b/tests/MMS/spatial/diffusion/runtest index 5f4c31f6aa..000cf8f09b 100755 --- a/tests/MMS/spatial/diffusion/runtest +++ b/tests/MMS/spatial/diffusion/runtest @@ -75,7 +75,7 @@ for dir, sizes in inputs: E_N = E_N[:, 1:-1, :, :] # Average error over domain - l2 = sqrt(mean(E_N ** 2)) + l2 = sqrt(mean(E_N**2)) linf = max(abs(E_N)) error_2.append(l2) diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py index ba13724d7e..806441b330 100755 --- a/tests/MMS/spatial/fci/mms.py +++ b/tests/MMS/spatial/fci/mms.py @@ -23,7 +23,7 @@ Bpprime = 0.1 Bpx = Bp + (x - 0.5) * Lx * Bpprime # Note: x in range [0,1] -B = sqrt(Bpx ** 2 + Bt ** 2) +B = sqrt(Bpx**2 + Bt**2) def FCI_ddy(f): diff --git a/tests/MMS/time/runtest b/tests/MMS/time/runtest index 003f401e00..8c539e9635 100755 --- a/tests/MMS/time/runtest +++ b/tests/MMS/time/runtest @@ -81,7 +81,7 @@ for opts, label, sym, expected_order in options: # Collect data E_f = collect("E_f", tind=[1, 1], info=False, path="data") # Average error over domain - l2 = sqrt(mean(E_f ** 2)) + l2 = sqrt(mean(E_f**2)) linf = max(abs(E_f)) error_2.append(l2) diff --git a/tests/MMS/tokamak/mms.py b/tests/MMS/tokamak/mms.py index 6c31538947..9b8ed5c85d 100644 --- a/tests/MMS/tokamak/mms.py +++ b/tests/MMS/tokamak/mms.py @@ -16,11 +16,11 @@ # NOTE: These are orthogonal tokamak coordinates # so y is poloidal angle, not parallel coordinate -drive = sin(6 * x ** 2 - z + y) # Constant drive for advection +drive = sin(6 * x**2 - z + y) # Constant drive for advection -advect = cos(4 * x ** 2 + z - y) + sin(t) * sin(3 * x + 2 * z - y) -delp2 = cos(4 * x ** 2 + z - y) + sin(t) * sin(3 * x + 2 * z - y) -laplacepar = cos(4 * x ** 2 + z - y) + sin(t) * sin(3 * x + 2 * z - y) +advect = cos(4 * x**2 + z - y) + sin(t) * sin(3 * x + 2 * z - y) +delp2 = cos(4 * x**2 + z - y) + sin(t) * sin(3 * x + 2 * z - y) +laplacepar = cos(4 * x**2 + z - y) + sin(t) * sin(3 * x + 2 * z - y) ZMAX = 1 diff --git a/tests/MMS/tokamak/runtest.broken b/tests/MMS/tokamak/runtest.broken index e833126016..b949b6e0e4 100755 --- a/tests/MMS/tokamak/runtest.broken +++ b/tests/MMS/tokamak/runtest.broken @@ -86,7 +86,7 @@ for nx, nproc in zip(nxlist, nprocs): E = E[:, 2:-2, :, :] # Average error over domain - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2[var].append(l2) diff --git a/tests/MMS/wave-1d-y/mms.py b/tests/MMS/wave-1d-y/mms.py index e5306d954b..98fb12035e 100644 --- a/tests/MMS/wave-1d-y/mms.py +++ b/tests/MMS/wave-1d-y/mms.py @@ -17,7 +17,7 @@ # Define the manufactured solution f = y + cos(y) - sin(t) * cos(0.5 * y) -g = y ** 2 + sin(y) + cos(t) * cos(0.1 * y * y) +g = y**2 + sin(y) + cos(t) * cos(0.1 * y * y) # Calculate gradients in x for boundaries diff --git a/tests/MMS/wave-1d-y/runtest b/tests/MMS/wave-1d-y/runtest index e398b940cf..9a4de5a3bb 100755 --- a/tests/MMS/wave-1d-y/runtest +++ b/tests/MMS/wave-1d-y/runtest @@ -75,7 +75,7 @@ for ny in nylist: # Average error over domain - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2[var].append(l2) diff --git a/tests/MMS/wave-1d/mms.py b/tests/MMS/wave-1d/mms.py index 2cc0e20b57..cd6d0425e8 100644 --- a/tests/MMS/wave-1d/mms.py +++ b/tests/MMS/wave-1d/mms.py @@ -20,8 +20,8 @@ # Define the manufactured solution -f = 0.9 + 0.9 * x + 0.2 * cos(10 * t) * sin(5.0 * x ** 2) -g = 0.9 + 0.7 * x + 0.2 * cos(7 * t) * sin(2.0 * x ** 2) +f = 0.9 + 0.9 * x + 0.2 * cos(10 * t) * sin(5.0 * x**2) +g = 0.9 + 0.7 * x + 0.2 * cos(7 * t) * sin(2.0 * x**2) # Calculate gradients in x for boundaries diff --git a/tests/MMS/wave-1d/runtest b/tests/MMS/wave-1d/runtest index 44ab4aa0e3..f13fb7bd11 100755 --- a/tests/MMS/wave-1d/runtest +++ b/tests/MMS/wave-1d/runtest @@ -57,7 +57,7 @@ for nx in nxlist: # Average error over domain, not including guard cells E = concatenate([E_f[1:-1], E_g[2:-1]]) - l2 = sqrt(mean(E ** 2)) + l2 = sqrt(mean(E**2)) linf = max(abs(E)) error_2.append(l2) diff --git a/tests/integrated/test-drift-instability/runtest b/tests/integrated/test-drift-instability/runtest index 02eb2621e8..16b35d69d9 100755 --- a/tests/integrated/test-drift-instability/runtest +++ b/tests/integrated/test-drift-instability/runtest @@ -171,7 +171,7 @@ def run_zeff_case(zeff): gamma = gamma / wstar # Calculate analytic result - t = 0.5 * (np.sqrt(sparn ** 4 + 16 * sparn ** 2) - sparn ** 2) + t = 0.5 * (np.sqrt(sparn**4 + 16 * sparn**2) - sparn**2) wr = 0.5 * np.sqrt(t) wi = sparn / np.sqrt(t) - 0.5 * sparn diff --git a/tests/integrated/test-initial/runtest b/tests/integrated/test-initial/runtest index 37aa02d162..25ad7d09f1 100755 --- a/tests/integrated/test-initial/runtest +++ b/tests/integrated/test-initial/runtest @@ -63,7 +63,7 @@ def gauss(x, width=1.0): """ Normalised gaussian """ - return np.exp(-(x ** 2) / (2 * width ** 2)) / np.sqrt(2 * np.pi) + return np.exp(-(x**2) / (2 * width**2)) / np.sqrt(2 * np.pi) def mixmode(x, seed=0.5): diff --git a/tests/integrated/test-interpolate-z/runtest b/tests/integrated/test-interpolate-z/runtest index 6596536497..1b461d8d4f 100755 --- a/tests/integrated/test-interpolate-z/runtest +++ b/tests/integrated/test-interpolate-z/runtest @@ -69,7 +69,7 @@ for method in methods: E = interp - solution - l2 = float(sqrt(mean(E ** 2))) + l2 = float(sqrt(mean(E**2))) linf = float(max(abs(E))) error_2[var].append(l2) diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/runtest index 900c95cbf0..08975cfd33 100755 --- a/tests/integrated/test-interpolate/runtest +++ b/tests/integrated/test-interpolate/runtest @@ -71,7 +71,7 @@ for method in methods: E = interp - solution - l2 = float(sqrt(mean(E ** 2))) + l2 = float(sqrt(mean(E**2))) linf = float(max(abs(E))) error_2[var].append(l2) diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite index d44cb7de56..e6012e3869 100755 --- a/tests/integrated/test_suite +++ b/tests/integrated/test_suite @@ -181,14 +181,14 @@ class Test(threading.Thread): print("{:{width}}".format(self.name, width=self.width), end="") if self.status == 0: # ✓ Passed - print(u"\u2713", end="") # No newline + print("\u2713", end="") # No newline elif self.status == 124: # 💤 timeout - print(u"\U0001f4a4", end="") # No newline + print("\U0001f4a4", end="") # No newline self.output += "\n(It is likely that a timeout occured)" else: # ❌ Failed - print(u"\u274C", end="") # No newline + print("\u274C", end="") # No newline print(" %7.3f s" % (time.time() - self.local.start_time), flush=True) def _cost(self): @@ -351,7 +351,7 @@ if failed: print("======= FAILURES ========") for test, output in failed: # Note: need Unicode string in case output contains unicode - print(u"\n----- {0} -----\n{1}".format(test, output)) + print("\n----- {0} -----\n{1}".format(test, output)) print( "======= {0} failed in {1:.2f} seconds ========".format( diff --git a/tools/pylib/post_bout/pb_corral.py b/tools/pylib/post_bout/pb_corral.py index 70c9acf51f..412a677921 100644 --- a/tools/pylib/post_bout/pb_corral.py +++ b/tools/pylib/post_bout/pb_corral.py @@ -372,13 +372,13 @@ def __init__(self, input_obj, name="haswak", haswak=True): if haswak: omega = old_div(-omega_star, (1 + (k) ** 2)) - gamma = old_div(((k ** 2) * omega_star ** 2), (nu * (1 + k ** 2) ** 3)) + gamma = old_div(((k**2) * omega_star**2), (nu * (1 + k**2) ** 3)) else: # omega = -np.sqrt(nu*omega_star)/(np.sqrt(2)*k) + nu**(3/2)/(8*np.sqrt(2*omega_star)*k**3) # gamma = np.sqrt(nu*omega_star)/(np.sqrt(2)*k) - nu/(2* k**2) + nu**(3/2)/(8*np.sqrt(2*omega_star)*k**3) - omega = -omega_star + old_div((2 * k ** 4 * omega_star ** 3), nu ** 2) + omega = -omega_star + old_div((2 * k**4 * omega_star**3), nu**2) gamma = old_div((k * omega_star) ** 2, nu) - ( - 5 * (k ** 6 * omega_star * 4 / nu ** 3) + 5 * (k**6 * omega_star * 4 / nu**3) ) self.gamma.append(gamma) self.omega.append(omega) diff --git a/tools/pylib/post_bout/pb_draw.py b/tools/pylib/post_bout/pb_draw.py index 57ea8835fb..75bca03a15 100644 --- a/tools/pylib/post_bout/pb_draw.py +++ b/tools/pylib/post_bout/pb_draw.py @@ -972,7 +972,7 @@ def plotvsK( Ln_drive_scale = s.meta["w_Ln"][0] ** -1 # Ln_drive_scale = 2.1e3 # clonex.set_ylim(Ln_drive_scale*ymin, Ln_drive_scale*ymax) - clonex.set_ylim(ynorm ** -1 * ymin, ynorm ** -1 * ymax) + clonex.set_ylim(ynorm**-1 * ymin, ynorm**-1 * ymax) try: if trans: diff --git a/tools/pylib/zoidberg/field.py b/tools/pylib/zoidberg/field.py index 7935413d4c..1c11e53f76 100644 --- a/tools/pylib/zoidberg/field.py +++ b/tools/pylib/zoidberg/field.py @@ -414,7 +414,7 @@ def __init__( self.z = Symbol("z") self.y = Symbol("y") self.r = Symbol("r") - self.r = (self.x ** 2 + self.z ** 2) ** (0.5) + self.r = (self.x**2 + self.z**2) ** (0.5) self.phi = Symbol("phi") self.xcentre = xcentre @@ -440,7 +440,7 @@ def __init__( for c in self.coil_list: xc, zc, Ic = c - rc = (xc ** 2 + zc ** 2) ** (0.5) + rc = (xc**2 + zc**2) ** (0.5) r2 = (self.x - xc) ** 2 + (self.z - zc) ** 2 theta = atan2(self.z - zc, self.x - xc) # Angle relative to coil @@ -520,7 +520,7 @@ def __init__( self.z = Symbol("z") self.y = Symbol("y") self.r = Symbol("r") - self.r = (self.x ** 2 + self.z ** 2) ** (0.5) + self.r = (self.x**2 + self.z**2) ** (0.5) self.phi = Symbol("phi") self.xcentre = xcentre @@ -546,7 +546,7 @@ def __init__( for c in self.coil_list: xc, zc, Ic = c - rc = (xc ** 2 + zc ** 2) ** (0.5) + rc = (xc**2 + zc**2) ** (0.5) r2 = (self.x - xc) ** 2 + (self.z - zc) ** 2 theta = atan2(self.z - zc, self.x - xc) # Angle relative to coil @@ -943,7 +943,7 @@ def __init__( alpha = shear self.theta = atan2(self.z - zcentre, self.x - xcentre) - A = alpha * self.r ** 2 + A = alpha * self.r**2 Bx = -alpha * self.r * self.r * sin(self.theta) Bz = alpha * self.r * self.r * cos(self.theta) By = Btor / self.x @@ -956,7 +956,6 @@ def __init__( def Rfunc(self, x, z, phi): return np.full(x.shape, x) - except ImportError: class StraightStellarator(MagneticField): @@ -1746,11 +1745,11 @@ def magnetic_axis(self, phi_axis=0, configuration=0): ) # (m) -- REAL SPACE from an arbitrary start point magnetic_axis_z = np.asarray(res.axis.vertices.x3) # (m) magnetic_axis_rmaj = np.sqrt( - magnetic_axis_x ** 2 + magnetic_axis_y ** 2 + magnetic_axis_z ** 2 + magnetic_axis_x**2 + magnetic_axis_y**2 + magnetic_axis_z**2 ) magnetic_axis_r = np.sqrt( - np.asarray(magnetic_axis_x) ** 2 + np.asarray(magnetic_axis_y ** 2) + np.asarray(magnetic_axis_x) ** 2 + np.asarray(magnetic_axis_y**2) ) magnetic_axis_phi = np.arctan(magnetic_axis_y / magnetic_axis_x) diff --git a/tools/pylib/zoidberg/fieldtracer.py b/tools/pylib/zoidberg/fieldtracer.py index e6dc1ce741..28e2c5f21a 100644 --- a/tools/pylib/zoidberg/fieldtracer.py +++ b/tools/pylib/zoidberg/fieldtracer.py @@ -298,7 +298,7 @@ def follow_field_lines( x_pos -= dx z_pos -= dz # Check for convergence within tolerance - if np.amax(dx ** 2 + dz ** 2) < rtol: + if np.amax(dx**2 + dz**2) < rtol: break # Finished Newton iteration, taken step to (x_pos,y_pos,z_pos) # Finished sub-steps, reached y_pos = y_next diff --git a/tools/pylib/zoidberg/plot.py b/tools/pylib/zoidberg/plot.py index 58b0c24a60..0ce26c1b20 100644 --- a/tools/pylib/zoidberg/plot.py +++ b/tools/pylib/zoidberg/plot.py @@ -231,7 +231,7 @@ def plot_streamlines(grid, magnetic_field, y_slice=0, width=None, **kwargs): if width is not None: # Get the B field magnitude in the poloidal plane - bxz_mag = np.sqrt(magnetic_field.b_mag ** 2 - magnetic_field.by ** 2) + bxz_mag = np.sqrt(magnetic_field.b_mag**2 - magnetic_field.by**2) linewidth = width * (bxz_mag[full_slice] / bxz_mag.max()).T else: linewidth = 1 diff --git a/tools/pylib/zoidberg/poloidal_grid.py b/tools/pylib/zoidberg/poloidal_grid.py index 5616cc86cd..00365832fa 100644 --- a/tools/pylib/zoidberg/poloidal_grid.py +++ b/tools/pylib/zoidberg/poloidal_grid.py @@ -411,7 +411,7 @@ def findIndex(self, R, Z, tol=1e-10, show=False): # Check if close enough # Note: only check the points which are not in the boundary - val = np.amax(mask * (dR ** 2 + dZ ** 2)) + val = np.amax(mask * (dR**2 + dZ**2)) if val < tol: break cnt += 1 @@ -487,15 +487,15 @@ def metric(self): dRdz /= dz dZdz /= dz - g_xx = dRdx ** 2 + dZdx ** 2 + g_xx = dRdx**2 + dZdx**2 g_xz = dRdx * dRdz + dZdx * dZdz - g_zz = dRdz ** 2 + dZdz ** 2 + g_zz = dRdz**2 + dZdz**2 # Calculate metric by inverting # ( gxx gxz ) = ( g_xx g_xz )^-1 # ( gxz gzz ) ( g_xz g_zz ) - determinant = g_xx * g_zz - g_xz ** 2 + determinant = g_xx * g_zz - g_xz**2 gxx = g_zz / determinant gzz = g_xx / determinant gxz = -g_xz / determinant @@ -794,17 +794,17 @@ def grid_elliptic( dZdz = (Z_zp - Z_zm) / (2.0 * dz) dZdx = (Z_xp - Z_xm) / (2.0 * dx) - a = dRdz ** 2 + dZdz ** 2 + a = dRdz**2 + dZdz**2 b = dRdz * dRdx + dZdx * dZdz - c = dRdx ** 2 + dZdx ** 2 + c = dRdx**2 + dZdx**2 # Now solve a*R_xx - 2*b*R_xz + c*R_zz = 0 # For now using Jacobi update - a_dx2 = a / dx ** 2 + a_dx2 = a / dx**2 b_dxdz = b / (2.0 * dx * dz) - c_dz2 = c / dz ** 2 - inv_diag = 1.0 / (2 * a / dx ** 2 + 2 * c / dz ** 2) + c_dz2 = c / dz**2 + inv_diag = 1.0 / (2 * a / dx**2 + 2 * c / dz**2) Rold = R.copy() Zold = Z.copy() diff --git a/tools/pylib/zoidberg/progress.py b/tools/pylib/zoidberg/progress.py index 93927ec16b..141aee7a6f 100644 --- a/tools/pylib/zoidberg/progress.py +++ b/tools/pylib/zoidberg/progress.py @@ -27,7 +27,7 @@ def update_progress(progress, barLength=10, ascii=False, **kwargs): if ascii: cursor = "#" else: - cursor = u"█" + cursor = "█" status = "" if isinstance(progress, int): @@ -42,7 +42,7 @@ def update_progress(progress, barLength=10, ascii=False, **kwargs): progress = 1 status = "Done...\r\n" block = int(round(barLength * progress)) - text = u"\rPercent: [{prog:-<{len}}] {perc:6.2f}% {stat}".format( + text = "\rPercent: [{prog:-<{len}}] {perc:6.2f}% {stat}".format( len=barLength, prog=cursor * block, perc=progress * 100, stat=status ) @@ -55,8 +55,8 @@ def update_progress(progress, barLength=10, ascii=False, **kwargs): face = " (;,,,;) " ink = "#" else: - face = u" (°,,,°) " - ink = u"█" + face = " (°,,,°) " + ink = "█" open_claw = "(\/)" closed_claw = "(|)" @@ -71,7 +71,7 @@ def update_progress(progress, barLength=10, ascii=False, **kwargs): zb = left_claw + face + right_claw zb_middle = int(len(zb) / 2) start = int(round((barLength - zb_middle) * progress)) - text = u"\rProgress: [{start}{zb}{rest}] {perc:6.2f}% {stat}".format( + text = "\rProgress: [{start}{zb}{rest}] {perc:6.2f}% {stat}".format( start=ink * start, zb=zb, perc=progress * 100, diff --git a/tools/pylib/zoidberg/zoidberg.py b/tools/pylib/zoidberg/zoidberg.py index 21dcae8696..873a9b0e19 100644 --- a/tools/pylib/zoidberg/zoidberg.py +++ b/tools/pylib/zoidberg/zoidberg.py @@ -216,8 +216,8 @@ def write_maps( for yindex in range(grid.numberOfPoloidalGrids()): pol_grid, ypos = grid.getPoloidalGrid(yindex) Rmaj[:, yindex, :] = magnetic_field.Rfunc(pol_grid.R, pol_grid.Z, ypos) - metric["gyy"] = 1.0 / Rmaj ** 2 - metric["g_yy"] = Rmaj ** 2 + metric["gyy"] = 1.0 / Rmaj**2 + metric["g_yy"] = Rmaj**2 # Get magnetic field and pressure Bmag = np.zeros(grid.shape) diff --git a/tools/tokamak_grids/cyclone/cyclone.py b/tools/tokamak_grids/cyclone/cyclone.py index b6496d9bc6..00b4307d6e 100755 --- a/tools/tokamak_grids/cyclone/cyclone.py +++ b/tools/tokamak_grids/cyclone/cyclone.py @@ -94,7 +94,7 @@ def eps_integral(eps, theta=None): dx = Bp * (dr / float(nx - 1)) * Rxy -Bxy = sqrt(Btxy ** 2 + Bpxy ** 2) +Bxy = sqrt(Btxy**2 + Bpxy**2) zShift = zeros([nx, ny]) qint = eps_integral(epsilon) @@ -137,7 +137,7 @@ def eps_integral(eps, theta=None): rpos = (float(x) / float(nx - 1) - 0.5) * dr R = Rmaj - (rminor + rpos) * cos(theta[y]) Bt = Bt0 * Rmaj / R - logB[x, y] = log(sqrt(Bt ** 2 + Bp ** 2)) + logB[x, y] = log(sqrt(Bt**2 + Bp**2)) ###################################################### # Topology: Just in the core diff --git a/tools/tokamak_grids/gato/gato2nc b/tools/tokamak_grids/gato/gato2nc index 81af8ccc3d..ba4cdc6e69 100755 --- a/tools/tokamak_grids/gato/gato2nc +++ b/tools/tokamak_grids/gato/gato2nc @@ -209,7 +209,7 @@ if (Br == None) or (Bz == None): # Use dpsi = 2*PI*R*Bp dx (for now) Bpol = None else: - Bpol = np.sqrt(Br ** 2 + Bz ** 2) + Bpol = np.sqrt(Br**2 + Bz**2) # Calculate toroidal field Btor = old_div(fnorm, xnorm) From d3150d0fff429c91aa01a0a668ae45741337fa25 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Fri, 4 Nov 2022 23:05:52 +0000 Subject: [PATCH 018/412] Apply clang-format changes --- include/field2d.hxx | 2 +- include/interpolation_xz.hxx | 2 +- include/utils.hxx | 2 +- src/field/field3d.cxx | 2 +- src/mesh/mesh.cxx | 16 ++++++++-------- src/mesh/parallel/fci.cxx | 9 ++++----- 6 files changed, 16 insertions(+), 17 deletions(-) diff --git a/include/field2d.hxx b/include/field2d.hxx index 49fe07fbcf..bf5b6516a7 100644 --- a/include/field2d.hxx +++ b/include/field2d.hxx @@ -172,7 +172,7 @@ public: // Data access /// Return a Region reference to use to iterate over this field - const Region& getRegion(REGION region) const; + const Region& getRegion(REGION region) const; const Region& getRegion(const std::string& region_name) const; const Region& getDefaultRegion(const std::string& region_name) const { return getRegion(region_name); diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx index df7badcc7e..d9bf7c1894 100644 --- a/include/interpolation_xz.hxx +++ b/include/interpolation_xz.hxx @@ -58,7 +58,7 @@ public: : y_offset(y_offset), localmesh(mesh), region_name(region_name) {} XZInterpolation(std::shared_ptr> region, int y_offset = 0, Mesh* mesh = nullptr) - : y_offset(y_offset), localmesh(mesh), region(std::move(region)) {} + : y_offset(y_offset), localmesh(mesh), region(std::move(region)) {} virtual ~XZInterpolation() = default; void setMask(const BoutMask& mask) { diff --git a/include/utils.hxx b/include/utils.hxx index 7175cc937e..ea293f7bf8 100644 --- a/include/utils.hxx +++ b/include/utils.hxx @@ -37,8 +37,8 @@ #include "unused.hxx" #include "bout/array.hxx" #include "bout/assert.hxx" -#include "bout/region.hxx" #include "bout/build_config.hxx" +#include "bout/region.hxx" #include #include diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 0e22313e79..e959c2bc47 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -173,7 +173,7 @@ const Field3D& Field3D::ynext(int dir) const { if (dir > 0) { return yup(dir - 1); } else if (dir < 0) { - return ydown(- dir - 1); + return ydown(-dir - 1); } else { return *this; } diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 33a44b3a9e..024f6dd57c 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -776,17 +776,17 @@ int Mesh::getCommonRegion(int lhs, int rhs) { * As we only need half of the square, the indices do not depend on * the total number of elements. */ - const size_t pos = (high * (high - 1)) /2 + low; + const size_t pos = (high * (high - 1)) / 2 + low; if (region3Dintersect.size() <= pos) { BOUT_OMP(critical(mesh_getIntersection_realloc)) #if BOUT_USE_OPENMP if (region3Dintersect.size() <= pos) #endif { - region3Dintersect.resize(pos+1, -1); + region3Dintersect.resize(pos + 1, -1); } } - if (region3Dintersect[pos] != -1){ + if (region3Dintersect[pos] != -1) { return region3Dintersect[pos]; } { @@ -797,13 +797,13 @@ int Mesh::getCommonRegion(int lhs, int rhs) { { auto common = getIntersection(region3D[low], region3D[high]); for (size_t i = 0; i < region3D.size(); ++i) { - if (common == region3D[i]) { - region3Dintersect[pos] = i; - break; - } + if (common == region3D[i]) { + region3Dintersect[pos] = i; + break; + } } if (region3Dintersect[pos] == -1) { - region3D.push_back(common); + region3D.push_back(common); region3Dintersect[pos] = region3D.size() - 1; } } diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 1b81066115..c40fab4677 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -236,11 +236,10 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, const auto region = fmt::format("RGN_YPAR_{:+d}", offset); if (not map_mesh.hasRegion3D(region)) { // The valid region for this slice - map_mesh.addRegion3D(region, - Region(map_mesh.xstart, map_mesh.xend, - map_mesh.ystart+offset, map_mesh.yend+offset, - 0, map_mesh.LocalNz-1, - map_mesh.LocalNy, map_mesh.LocalNz)); + map_mesh.addRegion3D( + region, Region(map_mesh.xstart, map_mesh.xend, map_mesh.ystart + offset, + map_mesh.yend + offset, 0, map_mesh.LocalNz - 1, + map_mesh.LocalNy, map_mesh.LocalNz)); } } From 9541fd555b014cbccef8d339ed6920e81838097e Mon Sep 17 00:00:00 2001 From: David Bold Date: Sat, 5 Nov 2022 06:31:21 +0100 Subject: [PATCH 019/412] ensure types are the same for iteration --- include/bout/region.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 9bb7e35804..16ea1f3dc7 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -552,7 +552,7 @@ public: if (this->size() != other.size()) { return false; } - for (auto i1 = this->begin(), i2 = other.begin(); i1 != this->end(); ++i1, ++i2) { + for (auto i1 = const_cast*>(this)->begin(), i2 = other.begin(); i1 != this->end(); ++i1, ++i2) { if (i1 != i2) { return false; } From 896ac341e81e4c356e220aea7abffe15000a6d82 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Sat, 5 Nov 2022 05:36:49 +0000 Subject: [PATCH 020/412] Apply clang-format changes --- include/bout/region.hxx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 16ea1f3dc7..c612846191 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -552,7 +552,8 @@ public: if (this->size() != other.size()) { return false; } - for (auto i1 = const_cast*>(this)->begin(), i2 = other.begin(); i1 != this->end(); ++i1, ++i2) { + for (auto i1 = const_cast*>(this)->begin(), i2 = other.begin(); + i1 != this->end(); ++i1, ++i2) { if (i1 != i2) { return false; } From e066d7bf10c937a653fb85082f9fe46423daf85b Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 15 Nov 2022 11:34:33 +0100 Subject: [PATCH 021/412] Do not use redundant initialisation Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- include/interpolation_xz.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx index d9bf7c1894..52885e67eb 100644 --- a/include/interpolation_xz.hxx +++ b/include/interpolation_xz.hxx @@ -43,7 +43,7 @@ public: protected: Mesh* localmesh{nullptr}; - std::string region_name{""}; + std::string region_name; std::shared_ptr> region{nullptr}; public: From 6d3d0222daedea4449443556f45857b5e17e706e Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 9 Jan 2023 08:38:10 +0100 Subject: [PATCH 022/412] Use the actuall position of the boundary --- src/mesh/parallel_boundary_op.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index 4e46687369..971374877d 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -233,7 +233,7 @@ void BoundaryOpPar_neumann::apply(Field3D &f, BoutReal t) { int x = bndry->x; int y = bndry->y; int z = bndry->z; // Generate the boundary value - BoutReal value = getValue(x, y, z, t); + BoutReal value = getValue(*bndry, t); BoutReal dy = coord.dy(x, y, z); f_next(x, y+bndry->dir, z) = f(x, y, z) + bndry->dir*value*dy; From 8526a697c028bfd4dc3142ad2670effd98a972d0 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 9 Jan 2023 08:42:47 +0100 Subject: [PATCH 023/412] Remove broken getValue --- include/parallel_boundary_op.hxx | 1 - src/mesh/parallel_boundary_op.cxx | 23 ----------------------- 2 files changed, 24 deletions(-) diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx index 08e157e9d5..ad8ff8d327 100644 --- a/include/parallel_boundary_op.hxx +++ b/include/parallel_boundary_op.hxx @@ -59,7 +59,6 @@ protected: enum class ValueType {GEN, FIELD, REAL}; const ValueType value_type{ValueType::REAL}; - BoutReal getValue(int x, int y, int z, BoutReal t); BoutReal getValue(const BoundaryRegionPar &bndry, BoutReal t); }; diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index 971374877d..f73f88e294 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -7,29 +7,6 @@ using bout::generator::Context; -BoutReal BoundaryOpPar::getValue(int x, int y, int z, BoutReal t) { - - Mesh* mesh = bndry->localmesh; - - BoutReal value; - - switch (value_type) { - case ValueType::GEN: - // This works but doesn't quite do the right thing... should - // generate value on the boundary, but that gives wrong - // answer. This instead generates the value at the gridpoint - return gen_values->generate(Context(x, y, z, CELL_CENTRE, mesh, t)); - case ValueType::FIELD: - value = (*field_values)(x,y,z); - return value; - case ValueType::REAL: - return real_value; - default: - throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue"); - } - -} - BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar &bndry, BoutReal t) { Mesh* mesh = bndry.localmesh; From 223d0918cc78e3d46e117b6af78f34980b217ecf Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 9 Jan 2023 11:09:52 +0100 Subject: [PATCH 024/412] Simplify parallel boundary ops Avoid some of the code duplication --- include/parallel_boundary_op.hxx | 167 +++++++++++++----------------- src/mesh/parallel_boundary_op.cxx | 145 +++++++------------------- 2 files changed, 111 insertions(+), 201 deletions(-) diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx index ad8ff8d327..2c474465f8 100644 --- a/include/parallel_boundary_op.hxx +++ b/include/parallel_boundary_op.hxx @@ -3,9 +3,10 @@ #include "boundary_op.hxx" #include "bout_types.hxx" +#include "field_factory.hxx" #include "parallel_boundary_region.hxx" -#include "utils.hxx" #include "unused.hxx" +#include "utils.hxx" #include @@ -15,22 +16,20 @@ class BoundaryOpPar : public BoundaryOpBase { public: BoundaryOpPar() = default; - BoundaryOpPar(BoundaryRegionPar *region, std::shared_ptr value) + BoundaryOpPar(BoundaryRegionPar* region, std::shared_ptr value) : bndry(region), gen_values(std::move(value)), value_type(ValueType::GEN) {} - BoundaryOpPar(BoundaryRegionPar *region, Field3D* value) : - bndry(region), - field_values(value), - value_type(ValueType::FIELD) {} - BoundaryOpPar(BoundaryRegionPar *region, BoutReal value) : - bndry(region), - real_value(value), - value_type(ValueType::REAL) {} + BoundaryOpPar(BoundaryRegionPar* region, Field3D* value) + : bndry(region), field_values(value), value_type(ValueType::FIELD) {} + BoundaryOpPar(BoundaryRegionPar* region, BoutReal value) + : bndry(region), real_value(value), value_type(ValueType::REAL) {} + BoundaryOpPar(BoundaryRegionPar* region) + : bndry(region), real_value(0.), value_type(ValueType::REAL) {} ~BoundaryOpPar() override = default; // Note: All methods must implement clone, except for modifiers (see below) - virtual BoundaryOpPar* clone(BoundaryRegionPar *UNUSED(region), const std::list &UNUSED(args)) {return nullptr; } - virtual BoundaryOpPar* clone(BoundaryRegionPar *UNUSED(region), Field3D *UNUSED(f)) {return nullptr; } - + virtual BoundaryOpPar* clone(BoundaryRegionPar* region, + const std::list& args) = 0; + virtual BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) = 0; virtual BoundaryOpPar* clone(BoundaryRegionPar* region, const std::list& args, const std::map& UNUSED(keywords)) { @@ -38,120 +37,100 @@ public: return clone(region, args); } - using BoundaryOpBase::apply; - void apply(Field2D &UNUSED(f)) override { - throw BoutException("Can't apply parallel boundary conditions to Field2D!"); - } - void apply(Field2D &UNUSED(f), BoutReal UNUSED(t)) override { - throw BoutException("Can't apply parallel boundary conditions to Field2D!"); - } - BoundaryRegionPar* bndry{nullptr}; protected: - /// Possible ways to get boundary values - std::shared_ptr gen_values; + std::shared_ptr gen_values; Field3D* field_values; BoutReal real_value{0.}; /// Where to take boundary values from - the generator, field or BoutReal - enum class ValueType {GEN, FIELD, REAL}; + enum class ValueType { GEN, FIELD, REAL }; const ValueType value_type{ValueType::REAL}; - BoutReal getValue(const BoundaryRegionPar &bndry, BoutReal t); - + BoutReal getValue(const BoundaryRegionPar& bndry, BoutReal t); }; -////////////////////////////////////////////////// -// Implementations - -class BoundaryOpPar_dirichlet : public BoundaryOpPar { +template +class BoundaryOpParTemp : public BoundaryOpPar { public: - BoundaryOpPar_dirichlet() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + using BoundaryOpPar::BoundaryOpPar; using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; - using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; + // Note: All methods must implement clone, except for modifiers (see below) + BoundaryOpPar* clone(BoundaryRegionPar* region, const std::list& args) { + if (!args.empty()) { + try { + real_value = stringToReal(args.front()); + return new T(region, real_value); + } catch (const BoutException&) { + std::shared_ptr newgen = nullptr; + // First argument should be an expression + newgen = FieldFactory::get()->parse(args.front()); + return new T(region, newgen); + } + } + + return new T(region); + } -}; + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) { return new T(region, f); } -class BoundaryOpPar_dirichlet_O3 : public BoundaryOpPar { -public: - BoundaryOpPar_dirichlet_O3() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + using BoundaryOpBase::apply; + void apply(Field2D& UNUSED(f)) final { + throw BoutException("Can't apply parallel boundary conditions to Field2D!"); + } + void apply(Field2D& UNUSED(f), BoutReal UNUSED(t)) final { + throw BoutException("Can't apply parallel boundary conditions to Field2D!"); + } + void apply(Field3D& f) override { return apply(f, 0); } +}; - using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; +////////////////////////////////////////////////// +// Implementations - using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; +class BoundaryOpPar_dirichlet : public BoundaryOpParTemp { +public: + using BoundaryOpParTemp::BoundaryOpParTemp; + using BoundaryOpParTemp::apply; + void apply(Field3D& f, BoutReal t) override; }; -class BoundaryOpPar_dirichlet_interp : public BoundaryOpPar { +class BoundaryOpPar_dirichlet_O3 : public BoundaryOpParTemp { public: - BoundaryOpPar_dirichlet_interp() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + using BoundaryOpParTemp::BoundaryOpParTemp; - using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; + using BoundaryOpParTemp::apply; + void apply(Field3D& f, BoutReal t) override; +}; - using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; +class BoundaryOpPar_dirichlet_interp + : public BoundaryOpParTemp { +public: + using BoundaryOpParTemp::BoundaryOpParTemp; + using BoundaryOpParTemp::apply; + void apply(Field3D& f, BoutReal t) override; }; -class BoundaryOpPar_neumann : public BoundaryOpPar { +class BoundaryOpPar_neumann : public BoundaryOpParTemp { public: - BoundaryOpPar_neumann() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + using BoundaryOpParTemp::BoundaryOpParTemp; - using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; + using BoundaryOpParTemp::apply; + void apply(Field3D& f, BoutReal t) override; +}; - using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; +class BoundaryOpPar_neumann_c2_simple + : public BoundaryOpParTemp { +public: + using BoundaryOpParTemp::BoundaryOpParTemp; + using BoundaryOpParTemp::apply; + void apply(Field3D& f, BoutReal t) override; }; #endif // __PAR_BNDRY_OP_H__ diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index f73f88e294..30fd2cdde9 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -1,13 +1,13 @@ -#include "bout/constants.hxx" -#include "bout/mesh.hxx" +#include "parallel_boundary_op.hxx" #include "field_factory.hxx" #include "globals.hxx" #include "output.hxx" -#include "parallel_boundary_op.hxx" +#include "bout/constants.hxx" +#include "bout/mesh.hxx" using bout::generator::Context; -BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar &bndry, BoutReal t) { +BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { Mesh* mesh = bndry.localmesh; @@ -15,42 +15,23 @@ BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar &bndry, BoutReal t) { switch (value_type) { case ValueType::GEN: - return gen_values->generate(Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); + return gen_values->generate( + Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); case ValueType::FIELD: // FIXME: Interpolate to s_x, s_y, s_z... - value = (*field_values)(bndry.x,bndry.y,bndry.z); + value = (*field_values)(bndry.x, bndry.y, bndry.z); return value; case ValueType::REAL: return real_value; default: throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue"); } - } ////////////////////////////////////////// // Dirichlet boundary -BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { - try { - real_value = stringToReal(args.front()); - return new BoundaryOpPar_dirichlet(region, real_value); - } catch (const BoutException&) { - std::shared_ptr newgen = nullptr; - // First argument should be an expression - newgen = FieldFactory::get()->parse(args.front()); - return new BoundaryOpPar_dirichlet(region, newgen); - } - } - return new BoundaryOpPar_dirichlet(region); -} - -BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar *region, Field3D *f) { - return new BoundaryOpPar_dirichlet(region, f); -} - -void BoundaryOpPar_dirichlet::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_dirichlet::apply(Field3D& f, BoutReal t) { Field3D& f_next = f.ynext(bndry->dir); Coordinates& coord = *(f.getCoordinates()); @@ -59,7 +40,9 @@ void BoundaryOpPar_dirichlet::apply(Field3D &f, BoutReal t) { // f_next such that the field would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convenience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal value = getValue(*bndry, t); @@ -68,33 +51,14 @@ void BoundaryOpPar_dirichlet::apply(Field3D &f, BoutReal t) { BoutReal y_prime = bndry->length; BoutReal f2 = (f(x, y, z) - value) * (coord.dy(x, y, z) - y_prime) / y_prime; - f_next(x, y+bndry->dir, z) = value - f2; + f_next(x, y + bndry->dir, z) = value - f2; } } ////////////////////////////////////////// // Dirichlet boundary - Third order -BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { - try { - real_value = stringToReal(args.front()); - return new BoundaryOpPar_dirichlet_O3(region, real_value); - } catch (const BoutException&) { - std::shared_ptr newgen = nullptr; - // First argument should be an expression - newgen = FieldFactory::get()->parse(args.front()); - return new BoundaryOpPar_dirichlet_O3(region, newgen); - } - } - return new BoundaryOpPar_dirichlet_O3(region); -} - -BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar *region, Field3D *f) { - return new BoundaryOpPar_dirichlet_O3(region, f); -} - -void BoundaryOpPar_dirichlet_O3::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_dirichlet_O3::apply(Field3D& f, BoutReal t) { Field3D& f_next = f.ynext(bndry->dir); Field3D& f_prev = f.ynext(-bndry->dir); @@ -105,48 +69,31 @@ void BoundaryOpPar_dirichlet_O3::apply(Field3D &f, BoutReal t) { // f_next such that the field would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convenience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal fb = getValue(*bndry, t); - BoutReal f1 = f_prev(x, y-bndry->dir, z); - BoutReal f2 = f(x,y,z); + BoutReal f1 = f_prev(x, y - bndry->dir, z); + BoutReal f2 = f(x, y, z); BoutReal l1 = coord.dy(x, y, z); BoutReal l2 = bndry->length; BoutReal l3 = coord.dy(x, y, z) - l2; - BoutReal denom = (l1*l1*l2 + l1*l2*l2); - BoutReal term1 = (l2*l2*l3 + l2*l3*l3); - BoutReal term2 = l1*(l1+l2+l3)*(l2+l3); - BoutReal term3 = l3*((l1+l2)*l3 + (l1+l2)*(l1+l2)); + BoutReal denom = (l1 * l1 * l2 + l1 * l2 * l2); + BoutReal term1 = (l2 * l2 * l3 + l2 * l3 * l3); + BoutReal term2 = l1 * (l1 + l2 + l3) * (l2 + l3); + BoutReal term3 = l3 * ((l1 + l2) * l3 + (l1 + l2) * (l1 + l2)); - f_next(x, y+bndry->dir, z) = (term1*f1 + term2*fb - term3*f2)/denom; + f_next(x, y + bndry->dir, z) = (term1 * f1 + term2 * fb - term3 * f2) / denom; } } ////////////////////////////////////////// // Dirichlet with interpolation -BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { - try { - real_value = stringToReal(args.front()); - return new BoundaryOpPar_dirichlet_interp(region, real_value); - } catch (const BoutException&) { - std::shared_ptr newgen = nullptr; - // First argument should be an expression - newgen = FieldFactory::get()->parse(args.front()); - return new BoundaryOpPar_dirichlet_interp(region, newgen); - } - } - return new BoundaryOpPar_dirichlet_interp(region); -} - -BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar *region, Field3D *f) { - return new BoundaryOpPar_dirichlet_interp(region, f); -} - -void BoundaryOpPar_dirichlet_interp::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_dirichlet_interp::apply(Field3D& f, BoutReal t) { Field3D& f_next = f.ynext(bndry->dir); Field3D& f_prev = f.ynext(-bndry->dir); @@ -157,63 +104,47 @@ void BoundaryOpPar_dirichlet_interp::apply(Field3D &f, BoutReal t) { // f_next such that the field would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convenience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal fs = getValue(*bndry, t); // Scale the field and normalise to the desired value BoutReal dy = coord.dy(x, y, z); - BoutReal s = bndry->length*dy; + BoutReal s = bndry->length * dy; - f_next(x, y+bndry->dir, z) = f_prev(x, y-bndry->dir, z)*(1.-(2.*s/(dy+s))) - + 2.*f(x, y, z)*((s-dy)/s) - + fs*(dy/s - (2./s + 1.)); + f_next(x, y + bndry->dir, z) = + f_prev(x, y - bndry->dir, z) * (1. - (2. * s / (dy + s))) + + 2. * f(x, y, z) * ((s - dy) / s) + fs * (dy / s - (2. / s + 1.)); } - } ////////////////////////////////////////// // Neumann boundary -BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { - try { - real_value = stringToReal(args.front()); - return new BoundaryOpPar_neumann(region, real_value); - } catch (const BoutException&) { - std::shared_ptr newgen = nullptr; - // First argument should be an expression - newgen = FieldFactory::get()->parse(args.front()); - return new BoundaryOpPar_neumann(region, newgen); - } - } - return new BoundaryOpPar_neumann(region); -} - -BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar *region, Field3D *f) { - return new BoundaryOpPar_neumann(region, f); -} - -void BoundaryOpPar_neumann::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_neumann::apply(Field3D& f, BoutReal t) { TRACE("BoundaryOpPar_neumann::apply"); - + Field3D& f_next = f.ynext(bndry->dir); f_next.allocate(); // Ensure unique before modifying - + Coordinates& coord = *(f.getCoordinates()); // If point is in boundary, then fill in f_next such that the derivative // would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal value = getValue(*bndry, t); BoutReal dy = coord.dy(x, y, z); - f_next(x, y+bndry->dir, z) = f(x, y, z) + bndry->dir*value*dy; + f_next(x, y + bndry->dir, z) = f(x, y, z) + bndry->dir * value * dy; } } From 78b96dd4af12165bdd38ad850dfd144df14167ac Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 10 Jan 2023 11:49:42 +0100 Subject: [PATCH 025/412] Add Context constructor taking real values --- include/bout/sys/generator_context.hxx | 3 +++ src/sys/generator_context.cxx | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx index 6be5c8df96..4809c73181 100644 --- a/include/bout/sys/generator_context.hxx +++ b/include/bout/sys/generator_context.hxx @@ -27,6 +27,9 @@ public: /// Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t); + /// Specify the values directly + Context(BoutReal x, BoutReal y, BoutReal z, Mesh* msh, BoutReal t); + /// If constructed without parameters, contains no values (null). /// Requesting x,y,z or t should throw an exception /// diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx index 4bb05f1e4e..c7223354e6 100644 --- a/src/sys/generator_context.cxx +++ b/src/sys/generator_context.cxx @@ -45,5 +45,9 @@ Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, parameters["t"] = t; } +Context::Context(BoutReal x, BoutReal y, BoutReal z, Mesh* msh, BoutReal t) + : localmesh(msh), parameters{{"x", x}, {"y", y}, {"z", z}, {"t", t}} +{} + } // namespace generator } // namespace bout From ee43a561223aeeccf3028f88a15f742fcd63180f Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 10 Jan 2023 12:07:07 +0100 Subject: [PATCH 026/412] Initialise values --- include/parallel_boundary_op.hxx | 6 +++--- src/mesh/parallel_boundary_op.cxx | 4 +--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx index 2c474465f8..69d914e270 100644 --- a/include/parallel_boundary_op.hxx +++ b/include/parallel_boundary_op.hxx @@ -42,7 +42,7 @@ public: protected: /// Possible ways to get boundary values std::shared_ptr gen_values; - Field3D* field_values; + Field3D* field_values{nullptr}; BoutReal real_value{0.}; /// Where to take boundary values from - the generator, field or BoutReal @@ -60,7 +60,7 @@ public: using BoundaryOpPar::clone; // Note: All methods must implement clone, except for modifiers (see below) - BoundaryOpPar* clone(BoundaryRegionPar* region, const std::list& args) { + BoundaryOpPar* clone(BoundaryRegionPar* region, const std::list& args) override { if (!args.empty()) { try { real_value = stringToReal(args.front()); @@ -76,7 +76,7 @@ public: return new T(region); } - BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) { return new T(region, f); } + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override { return new T(region, f); } using BoundaryOpBase::apply; void apply(Field2D& UNUSED(f)) final { diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index 30fd2cdde9..ad254598d0 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -5,7 +5,6 @@ #include "bout/constants.hxx" #include "bout/mesh.hxx" -using bout::generator::Context; BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { @@ -16,7 +15,7 @@ BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { switch (value_type) { case ValueType::GEN: return gen_values->generate( - Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); + bout::generator::Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); case ValueType::FIELD: // FIXME: Interpolate to s_x, s_y, s_z... value = (*field_values)(bndry.x, bndry.y, bndry.z); @@ -146,5 +145,4 @@ void BoundaryOpPar_neumann::apply(Field3D& f, BoutReal t) { f_next(x, y + bndry->dir, z) = f(x, y, z) + bndry->dir * value * dy; } - } From cb600b08a0aa3bfa92f2106b39818a669bd2e9b7 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Tue, 10 Jan 2023 11:07:54 +0000 Subject: [PATCH 027/412] Apply clang-format changes --- include/parallel_boundary_op.hxx | 7 +++++-- src/mesh/parallel_boundary_op.cxx | 1 - src/sys/generator_context.cxx | 3 +-- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx index 69d914e270..35415914b5 100644 --- a/include/parallel_boundary_op.hxx +++ b/include/parallel_boundary_op.hxx @@ -60,7 +60,8 @@ public: using BoundaryOpPar::clone; // Note: All methods must implement clone, except for modifiers (see below) - BoundaryOpPar* clone(BoundaryRegionPar* region, const std::list& args) override { + BoundaryOpPar* clone(BoundaryRegionPar* region, + const std::list& args) override { if (!args.empty()) { try { real_value = stringToReal(args.front()); @@ -76,7 +77,9 @@ public: return new T(region); } - BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override { return new T(region, f); } + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override { + return new T(region, f); + } using BoundaryOpBase::apply; void apply(Field2D& UNUSED(f)) final { diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index ad254598d0..d391e8ff2e 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -5,7 +5,6 @@ #include "bout/constants.hxx" #include "bout/mesh.hxx" - BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { Mesh* mesh = bndry.localmesh; diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx index c7223354e6..ad713d4e1a 100644 --- a/src/sys/generator_context.cxx +++ b/src/sys/generator_context.cxx @@ -46,8 +46,7 @@ Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, } Context::Context(BoutReal x, BoutReal y, BoutReal z, Mesh* msh, BoutReal t) - : localmesh(msh), parameters{{"x", x}, {"y", y}, {"z", z}, {"t", t}} -{} + : localmesh(msh), parameters{{"x", x}, {"y", y}, {"z", z}, {"t", t}} {} } // namespace generator } // namespace bout From b92b240020cb6857106c216ce9ea80b72f890ab5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Thu, 25 Nov 2021 10:32:38 +0100 Subject: [PATCH 028/412] Make function const Needed for intel --- include/bout/region.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index c612846191..194e1b869a 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -548,7 +548,7 @@ public: indices = getRegionIndices(); }; - bool operator==(const Region& other) { + bool operator==(const Region& other) const { if (this->size() != other.size()) { return false; } From b73bd03cca84cf1d3ef8fbf04cd769dacbb01ed8 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 25 Feb 2022 16:26:11 +0100 Subject: [PATCH 029/412] Allow to iterate over only spefic parallel boundaries For example: get all regions: mesh->getBoundariesPar(Mesh::BoundaryParType::all) get only xout: mesh->getBoundariesPar(Mesh::BoundaryParType::xout) --- include/bout/mesh.hxx | 5 ++-- src/mesh/impls/bout/boutmesh.cxx | 34 +++++++++++++++++++---- src/mesh/impls/bout/boutmesh.hxx | 6 ++-- src/mesh/parallel/fci.hxx | 8 +++--- src/mesh/parallel/shiftedmetricinterp.cxx | 8 +++--- 5 files changed, 43 insertions(+), 18 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 128163c9d1..359cc78cf4 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -480,11 +480,12 @@ class Mesh { /// Add a boundary region to this processor virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {} + enum class BoundaryParType {all, xin, xout, fwd, bwd, xin_fwd, xout_fwd, xin_bwd, xout_bwd, SIZE}; /// Get all the parallel (Y) boundaries on this processor - virtual std::vector getBoundariesPar() = 0; + virtual std::vector getBoundariesPar(BoundaryParType type=BoundaryParType::all) = 0; /// Add a parallel(Y) boundary to this processor - virtual void addBoundaryPar(BoundaryRegionPar* UNUSED(bndry)) {} + virtual void addBoundaryPar(BoundaryRegionPar* UNUSED(bndry), BoundaryParType UNUSED(type)) {} /// Branch-cut special handling (experimental) virtual Field3D smoothSeparatrix(const Field3D &f) {return f;} diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 3bc5d0d506..f2116849cf 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -70,6 +70,7 @@ If you want the old setting, you have to specify mesh:symmetricGlobalY=false in comm_outer = MPI_COMM_NULL; mpi = bout::globals::mpi; + par_boundary.resize(static_cast(BoundaryParType::SIZE)); } BoutMesh::~BoutMesh() { @@ -80,8 +81,10 @@ BoutMesh::~BoutMesh() { for (const auto& bndry : boundary) { delete bndry; } - for (const auto& bndry : par_boundary) { - delete bndry; + for (const auto& type : par_boundary) { + for (const auto& bndry : type) { + delete bndry; + } } if (comm_x != MPI_COMM_NULL) { @@ -2955,11 +2958,32 @@ RangeIterator BoutMesh::iterateBndryUpperY() const { std::vector BoutMesh::getBoundaries() { return boundary; } -std::vector BoutMesh::getBoundariesPar() { return par_boundary; } +//std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { return par_boundary[type] ; } -void BoutMesh::addBoundaryPar(BoundaryRegionPar *bndry) { +void BoutMesh::addBoundaryPar(BoundaryRegionPar *bndry, BoundaryParType type) { output_info << "Adding new parallel boundary: " << bndry->label << endl; - par_boundary.push_back(bndry); + switch (type) { + case BoundaryParType::xin_fwd: + par_boundary[static_cast(BoundaryParType::xin)].push_back(bndry); + par_boundary[static_cast(BoundaryParType::fwd)].push_back(bndry); + break; + case BoundaryParType::xin_bwd: + par_boundary[static_cast(BoundaryParType::xin)].push_back(bndry); + par_boundary[static_cast(BoundaryParType::bwd)].push_back(bndry); + break; + case BoundaryParType::xout_fwd: + par_boundary[static_cast(BoundaryParType::xout)].push_back(bndry); + par_boundary[static_cast(BoundaryParType::fwd)].push_back(bndry); + break; + case BoundaryParType::xout_bwd: + par_boundary[static_cast(BoundaryParType::xout)].push_back(bndry); + par_boundary[static_cast(BoundaryParType::bwd)].push_back(bndry); + break; + default: + throw BoutException("Unexpected type of boundary {}", type); + } + par_boundary[static_cast(type)].push_back(bndry); + par_boundary[static_cast(BoundaryParType::all)].push_back(bndry); } Field3D BoutMesh::smoothSeparatrix(const Field3D& f) { diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx index 603bd501f0..565f15ce34 100644 --- a/src/mesh/impls/bout/boutmesh.hxx +++ b/src/mesh/impls/bout/boutmesh.hxx @@ -155,8 +155,8 @@ class BoutMesh : public Mesh { // Boundary regions std::vector getBoundaries() override; - std::vector getBoundariesPar() override; - void addBoundaryPar(BoundaryRegionPar* bndry) override; + std::vector getBoundariesPar(BoundaryParType type) override final; + void addBoundaryPar(BoundaryRegionPar* bndry, BoundaryParType type) override final; std::set getPossibleBoundaries() const override; Field3D smoothSeparatrix(const Field3D& f) override; @@ -391,7 +391,7 @@ protected: private: std::vector boundary; // Vector of boundary regions - std::vector par_boundary; // Vector of parallel boundary regions + std::vector> par_boundary; // Vector of parallel boundary regions ////////////////////////////////////////////////// // Communications diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 3ecd964bfa..37195c5a6d 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -89,10 +89,10 @@ public: new BoundaryRegionPar("FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh); // Add the boundary region to the mesh's vector of parallel boundaries - mesh.addBoundaryPar(forward_boundary_xin); - mesh.addBoundaryPar(backward_boundary_xin); - mesh.addBoundaryPar(forward_boundary_xout); - mesh.addBoundaryPar(backward_boundary_xout); + mesh.addBoundaryPar(forward_boundary_xin, Mesh::BoundaryParType::xin_fwd); + mesh.addBoundaryPar(backward_boundary_xin, Mesh::BoundaryParType::xin_bwd); + mesh.addBoundaryPar(forward_boundary_xout, Mesh::BoundaryParType::xout_fwd); + mesh.addBoundaryPar(backward_boundary_xout, Mesh::BoundaryParType::xout_bwd); field_line_maps.reserve(mesh.ystart * 2); for (int offset = 1; offset < mesh.ystart + 1; ++offset) { diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 0e8a9afaa8..38201e3a7e 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -186,10 +186,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, } // Add the boundary region to the mesh's vector of parallel boundaries - mesh.addBoundaryPar(forward_boundary_xin); - mesh.addBoundaryPar(backward_boundary_xin); - mesh.addBoundaryPar(forward_boundary_xout); - mesh.addBoundaryPar(backward_boundary_xout); + mesh.addBoundaryPar(forward_boundary_xin, Mesh::BoundaryParType::xin_fwd); + mesh.addBoundaryPar(backward_boundary_xin, Mesh::BoundaryParType::xin_bwd); + mesh.addBoundaryPar(forward_boundary_xout, Mesh::BoundaryParType::xout_fwd); + mesh.addBoundaryPar(backward_boundary_xout, Mesh::BoundaryParType::xin_bwd); } void ShiftedMetricInterp::checkInputGrid() { From f556862b6aa7d0c57ff60dff62d980fd43b2e338 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 28 Feb 2022 13:44:13 +0100 Subject: [PATCH 030/412] Fix issues par_boundary * Cleanup was broken due to double free. Just cleaning [all] is sufficient. * Include commented out code --- src/mesh/impls/bout/boutmesh.cxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index f2116849cf..010621bb9d 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -81,8 +81,8 @@ BoutMesh::~BoutMesh() { for (const auto& bndry : boundary) { delete bndry; } - for (const auto& type : par_boundary) { - for (const auto& bndry : type) { + if (par_boundary.size() > 0) { + for (const auto& bndry : par_boundary[0]) { delete bndry; } } @@ -2958,7 +2958,7 @@ RangeIterator BoutMesh::iterateBndryUpperY() const { std::vector BoutMesh::getBoundaries() { return boundary; } -//std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { return par_boundary[type] ; } +std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { return par_boundary[static_cast(type)] ; } void BoutMesh::addBoundaryPar(BoundaryRegionPar *bndry, BoundaryParType type) { output_info << "Adding new parallel boundary: " << bndry->label << endl; From f12271ec50c0dc5039ea7eb3c3a5a9edc428e7ed Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 28 Feb 2022 14:25:40 +0100 Subject: [PATCH 031/412] Update unit tests for new signature --- tests/unit/test_extras.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index edd096b0a0..2a7b405c30 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -233,7 +233,7 @@ public: RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); } void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); } std::vector getBoundaries() override { return boundaries; } - std::vector getBoundariesPar() override { + std::vector getBoundariesPar(Mesh::BoundaryParType) override { return std::vector(); } BoutReal GlobalX(int jx) const override { return jx; } From 4027285446d4ed03da1c2e31666d3ecfb318c22b Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 12:30:58 +0100 Subject: [PATCH 032/412] switch to bout_enum_class Allows to use toString --- include/bout/mesh.hxx | 5 ++++- src/mesh/parallel/fci.hxx | 8 ++++---- src/mesh/parallel/shiftedmetricinterp.cxx | 8 ++++---- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 359cc78cf4..0163299e04 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -71,6 +71,8 @@ class Mesh; #include #include "bout/generic_factory.hxx" +#include + #include #include #include @@ -89,6 +91,8 @@ public: ReturnType create(Options* options = nullptr, GridDataSource* source = nullptr) const; }; +BOUT_ENUM_CLASS(BoundaryParType, all, xin, xout, fwd, bwd, xin_fwd, xout_fwd, xin_bwd, xout_bwd, SIZE); + template using RegisterMesh = MeshFactory::RegisterInFactory; @@ -480,7 +484,6 @@ class Mesh { /// Add a boundary region to this processor virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {} - enum class BoundaryParType {all, xin, xout, fwd, bwd, xin_fwd, xout_fwd, xin_bwd, xout_bwd, SIZE}; /// Get all the parallel (Y) boundaries on this processor virtual std::vector getBoundariesPar(BoundaryParType type=BoundaryParType::all) = 0; diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 37195c5a6d..663e20c635 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -89,10 +89,10 @@ public: new BoundaryRegionPar("FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh); // Add the boundary region to the mesh's vector of parallel boundaries - mesh.addBoundaryPar(forward_boundary_xin, Mesh::BoundaryParType::xin_fwd); - mesh.addBoundaryPar(backward_boundary_xin, Mesh::BoundaryParType::xin_bwd); - mesh.addBoundaryPar(forward_boundary_xout, Mesh::BoundaryParType::xout_fwd); - mesh.addBoundaryPar(backward_boundary_xout, Mesh::BoundaryParType::xout_bwd); + mesh.addBoundaryPar(forward_boundary_xin, BoundaryParType::xin_fwd); + mesh.addBoundaryPar(backward_boundary_xin, BoundaryParType::xin_bwd); + mesh.addBoundaryPar(forward_boundary_xout, BoundaryParType::xout_fwd); + mesh.addBoundaryPar(backward_boundary_xout, BoundaryParType::xout_bwd); field_line_maps.reserve(mesh.ystart * 2); for (int offset = 1; offset < mesh.ystart + 1; ++offset) { diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 38201e3a7e..694c34f084 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -186,10 +186,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, } // Add the boundary region to the mesh's vector of parallel boundaries - mesh.addBoundaryPar(forward_boundary_xin, Mesh::BoundaryParType::xin_fwd); - mesh.addBoundaryPar(backward_boundary_xin, Mesh::BoundaryParType::xin_bwd); - mesh.addBoundaryPar(forward_boundary_xout, Mesh::BoundaryParType::xout_fwd); - mesh.addBoundaryPar(backward_boundary_xout, Mesh::BoundaryParType::xin_bwd); + mesh.addBoundaryPar(forward_boundary_xin, BoundaryParType::xin_fwd); + mesh.addBoundaryPar(backward_boundary_xin, BoundaryParType::xin_bwd); + mesh.addBoundaryPar(forward_boundary_xout, BoundaryParType::xout_fwd); + mesh.addBoundaryPar(backward_boundary_xout, BoundaryParType::xin_bwd); } void ShiftedMetricInterp::checkInputGrid() { From f53d8ca39817db162f60dd47826a7f3d40dc04f4 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 13:53:29 +0100 Subject: [PATCH 033/412] Add test for parallel boundary --- tests/integrated/CMakeLists.txt | 2 +- .../test-fci-boundary/CMakeLists.txt | 19 ++++++ .../test-fci-boundary/data/BOUT.inp | 20 ++++++ .../test-fci-boundary/get_par_bndry.cxx | 29 ++++++++ tests/integrated/test-fci-boundary/grid.py | 55 +++++++++++++++ tests/integrated/test-fci-boundary/makefile | 6 ++ tests/integrated/test-fci-boundary/runtest | 68 +++++++++++++++++++ 7 files changed, 198 insertions(+), 1 deletion(-) create mode 100644 tests/integrated/test-fci-boundary/CMakeLists.txt create mode 100644 tests/integrated/test-fci-boundary/data/BOUT.inp create mode 100644 tests/integrated/test-fci-boundary/get_par_bndry.cxx create mode 100644 tests/integrated/test-fci-boundary/grid.py create mode 100644 tests/integrated/test-fci-boundary/makefile create mode 100755 tests/integrated/test-fci-boundary/runtest diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt index 2fe72dfe2d..b6cd886438 100644 --- a/tests/integrated/CMakeLists.txt +++ b/tests/integrated/CMakeLists.txt @@ -9,7 +9,7 @@ add_subdirectory(test-cyclic) add_subdirectory(test-delp2) add_subdirectory(test-drift-instability) add_subdirectory(test-drift-instability-staggered) -add_subdirectory(test-fieldgroupComm) +add_subdirectory(test-fci-boundary) add_subdirectory(test-griddata) add_subdirectory(test-griddata-yboundary-guards) add_subdirectory(test-gyro) diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt new file mode 100644 index 0000000000..9e89898aa4 --- /dev/null +++ b/tests/integrated/test-fci-boundary/CMakeLists.txt @@ -0,0 +1,19 @@ +bout_add_mms_test(test-fci-boundary + SOURCES get_par_bndry.cxx + USE_RUNTEST + USE_DATA_BOUT_INP + PROCESSORS 1 + ) + + +set(gridfile ${CMAKE_CURRENT_BINARY_DIR}/grid.fci.nc) +add_custom_command(OUTPUT ${gridfile} + COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py + DEPENDS grid.py + COMMENT "Creating test-fci-boundary grid file" + ) +add_custom_target(test-fci-boundary-grid DEPENDS ${gridfile}) +add_dependencies(test-fci-boundary + test-fci-boundary-grid) diff --git a/tests/integrated/test-fci-boundary/data/BOUT.inp b/tests/integrated/test-fci-boundary/data/BOUT.inp new file mode 100644 index 0000000000..b631f16295 --- /dev/null +++ b/tests/integrated/test-fci-boundary/data/BOUT.inp @@ -0,0 +1,20 @@ +grid = grid.fci.nc + +MXG = 1 +NXPE = 1 +MYG = 1 + +[mesh] +symmetricglobalx = true + +[mesh:ddy] +first = C2 +second = C2 + +[mesh:paralleltransform] +type = fci +y_periodic = true +z_periodic = true + +[mesh:paralleltransform:xzinterpolation] +type = lagrange4pt diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx new file mode 100644 index 0000000000..0ad49c3cbb --- /dev/null +++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx @@ -0,0 +1,29 @@ +#include "bout.hxx" +#include "derivs.hxx" +#include "field_factory.hxx" + +int main(int argc, char** argv) { + BoutInitialise(argc, argv); + + using bout::globals::mesh; + + std::vector fields; + fields.resize(static_cast(BoundaryParType::SIZE)); + for (int i=0; i< fields.size(); i++){ + fields[i] = Field3D{0.0}; + mesh->communicate(fields[i]); + for (const auto &bndry_par : mesh->getBoundariesPar(static_cast(i))) { + output.write("{:s} region\n", toString(static_cast(i))); + for (bndry_par->first(); !bndry_par->isDone(); bndry_par->next()) { + fields[i](bndry_par->x, bndry_par->y, bndry_par->z) += 1; + output.write("{:s} increment\n", toString(static_cast(i))); + } + } + output.write("{:s} done\n", toString(static_cast(i))); + bout::globals::dump.addOnce(fields[i], fmt::format("field_{:s}", toString(static_cast(i)))); + } + + bout::globals::dump.write(); + + BoutFinalise(); +} diff --git a/tests/integrated/test-fci-boundary/grid.py b/tests/integrated/test-fci-boundary/grid.py new file mode 100644 index 0000000000..d544f0cdf7 --- /dev/null +++ b/tests/integrated/test-fci-boundary/grid.py @@ -0,0 +1,55 @@ +import zoidberg as zb +import numpy as np +import sys +import boutconfig as bc + + +def rotating_ellipse( + nx=68, + ny=16, + nz=128, + npoints=421, + xcentre=5.5, + I_coil=0.01, + curvilinear=True, + rectangular=False, + fname="rotating-ellipse.fci.nc", + a=0.4, + Btor=2.5, +): + yperiod = 2 * np.pi / 5.0 + field = zb.field.RotatingEllipse( + xcentre=xcentre, + I_coil=I_coil, + radius=2 * a, + yperiod=yperiod, + Btor=Btor, + ) + # Define the y locations + ycoords = np.linspace(0.0, yperiod, ny, endpoint=False) + + if rectangular: + print("Making rectangular poloidal grid") + poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid( + nx, nz, 1.0, 1.0, Rcentre=xcentre + ) + elif curvilinear: + print("Making curvilinear poloidal grid") + inner = zb.rzline.shaped_line( + R0=xcentre, a=a / 2.0, elong=0, triang=0.0, indent=0, n=npoints + ) + outer = zb.rzline.shaped_line( + R0=xcentre, a=a, elong=0, triang=0.0, indent=0, n=npoints + ) + + print("creating grid...") + poloidal_grid = zb.poloidal_grid.grid_elliptic(inner, outer, nx, nz) + + # Create the 3D grid by putting together 2D poloidal grids + grid = zb.grid.Grid(poloidal_grid, ycoords, yperiod, yperiodic=True) + maps = zb.make_maps(grid, field, quiet=True) + zb.write_maps(grid, field, maps, str(fname), metric2d=bc.isMetric2D()) + + +if __name__ == "__main__": + rotating_ellipse(fname=sys.argv[1]) diff --git a/tests/integrated/test-fci-boundary/makefile b/tests/integrated/test-fci-boundary/makefile new file mode 100644 index 0000000000..c1c6c6f8b8 --- /dev/null +++ b/tests/integrated/test-fci-boundary/makefile @@ -0,0 +1,6 @@ + +BOUT_TOP ?= ../../.. + +SOURCEC = get_par_bndry.cxx + +include $(BOUT_TOP)/make.config diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest new file mode 100755 index 0000000000..668bca0708 --- /dev/null +++ b/tests/integrated/test-fci-boundary/runtest @@ -0,0 +1,68 @@ +#!/usr/bin/env python3 +# +# Python script to run and analyse MMS test +# + +# Cores: 2 +from boututils.run_wrapper import launch_safe +from boututils.datafile import DataFile +from boutdata.collect import collect as _collect + +import numpy as np + + +def collect(var): + return _collect( + var, + info=False, + path=directory, + xguards=False, + yguards=False, + ) + + +nprocs = [1] # , 2, 4] +mthread = 2 + +directory = "data" + +with DataFile("grid.fci.nc") as grid: + xfwd = grid.read("forward_xt_prime")[1:-1] + xbwd = grid.read("backward_xt_prime")[1:-1] + +nx = xfwd.shape[0] + +regions = { + "xin_fwd": xfwd < 1, + "xout_fwd": xfwd > nx, + "xin_bwd": xbwd < 1, + "xout_bwd": xbwd > nx, +} +regions = {k: v.astype(int) for k, v in regions.items()} + +# for x in "xout", "xin": +# regions[x] = np.logical_or(regions[f"{x}_fwd"], regions[f"{x}_bwd"]) +# for x in "fwd", "bwd": +# regions[x] = np.logical_or(regions[f"xin_{x}"], regions[f"xout_{x}"]) +# regions["all"] = np.logical_or(regions["xin"], regions["xout"]) +for x in "xout", "xin": + regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"] +for x in "fwd", "bwd": + regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"] +regions["all"] = regions["xin"] + regions["xout"] + +for nproc in nprocs: + cmd = "./get_par_bndry" + + # Launch using MPI + _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True) + + for k, v in regions.items(): + # Collect data + data = collect(f"field_{k}") + assert np.allclose(data, v), ( + k + " does not match", + np.sum(data), + np.sum(v), + np.max(data), + ) From 3c7f8589911820bc4e9d490810cda8b61bd104e9 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 7 Feb 2023 15:46:27 +0100 Subject: [PATCH 034/412] Re-add accidentially removed test --- tests/integrated/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt index b6cd886438..62a11bbec7 100644 --- a/tests/integrated/CMakeLists.txt +++ b/tests/integrated/CMakeLists.txt @@ -9,6 +9,7 @@ add_subdirectory(test-cyclic) add_subdirectory(test-delp2) add_subdirectory(test-drift-instability) add_subdirectory(test-drift-instability-staggered) +add_subdirectory(test-fieldgroupComm) add_subdirectory(test-fci-boundary) add_subdirectory(test-griddata) add_subdirectory(test-griddata-yboundary-guards) From 0180e1a96dfae32494eb471947ebc34a54c74ce5 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 14:36:42 +0100 Subject: [PATCH 035/412] Don't run before directory exists --- tests/integrated/test-fci-boundary/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt index 9e89898aa4..187d79f80a 100644 --- a/tests/integrated/test-fci-boundary/CMakeLists.txt +++ b/tests/integrated/test-fci-boundary/CMakeLists.txt @@ -12,6 +12,7 @@ add_custom_command(OUTPUT ${gridfile} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py DEPENDS grid.py + IMPLICIT_DEPENDS ${CMAKE_CURRENT_BINARY_DIR} COMMENT "Creating test-fci-boundary grid file" ) add_custom_target(test-fci-boundary-grid DEPENDS ${gridfile}) From 9aec092c8fc7162aa735abacf8a9412526247cc0 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 15:20:06 +0100 Subject: [PATCH 036/412] Use nicer message Broken with recent fmt changes. Explicitly casting to int would be an alternative. --- src/mesh/impls/bout/boutmesh.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 010621bb9d..5abc3664bd 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -2980,7 +2980,7 @@ void BoutMesh::addBoundaryPar(BoundaryRegionPar *bndry, BoundaryParType type) { par_boundary[static_cast(BoundaryParType::bwd)].push_back(bndry); break; default: - throw BoutException("Unexpected type of boundary {}", type); + throw BoutException("Unexpected type of boundary {}", toString(type)); } par_boundary[static_cast(type)].push_back(bndry); par_boundary[static_cast(BoundaryParType::all)].push_back(bndry); From 2dba93689c49d6532fe575d4fe722e2fc7783fc0 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 15:29:48 +0100 Subject: [PATCH 037/412] use python3 interpreter for test --- tests/integrated/test-fci-boundary/CMakeLists.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt index 187d79f80a..3349d88994 100644 --- a/tests/integrated/test-fci-boundary/CMakeLists.txt +++ b/tests/integrated/test-fci-boundary/CMakeLists.txt @@ -5,10 +5,9 @@ bout_add_mms_test(test-fci-boundary PROCESSORS 1 ) - set(gridfile ${CMAKE_CURRENT_BINARY_DIR}/grid.fci.nc) add_custom_command(OUTPUT ${gridfile} - COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile} + COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py DEPENDS grid.py From ec265e7aea5b352b41065987f2321861db45e54a Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 15:51:50 +0100 Subject: [PATCH 038/412] Always use python3 --- cmake/FindCython.cmake | 2 +- cmake/FindNumpy.cmake | 10 +++++----- manual/sphinx/conf.py | 2 +- tools/pylib/_boutpp_build/CMakeLists.txt | 12 ++++++------ 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/cmake/FindCython.cmake b/cmake/FindCython.cmake index 76f43480d9..3b98cde89e 100644 --- a/cmake/FindCython.cmake +++ b/cmake/FindCython.cmake @@ -10,7 +10,7 @@ # CYTHON_FOUND - true if Cython was found # CYTHON_VERSION - Cython version -execute_process(COMMAND ${Python_EXECUTABLE} -c "import cython ; print(cython.__version__)" +execute_process(COMMAND ${Python3_EXECUTABLE} -c "import cython ; print(cython.__version__)" RESULT_VARIABLE _cython_runs OUTPUT_VARIABLE CYTHON_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE diff --git a/cmake/FindNumpy.cmake b/cmake/FindNumpy.cmake index 5ab59c948f..cb204d7a2c 100644 --- a/cmake/FindNumpy.cmake +++ b/cmake/FindNumpy.cmake @@ -12,26 +12,26 @@ # Numpy_INCLUDE_DIR - Required libraries -find_package(Python 3.6 REQUIRED COMPONENTS Interpreter Development) +find_package(Python3 3.6 REQUIRED COMPONENTS Interpreter Development) if (NOT Numpy_FOUND) - execute_process(COMMAND ${Python_EXECUTABLE} -c "import numpy ; print(numpy.__version__)" + execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.__version__)" OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE Numpy_VERSION ) - execute_process(COMMAND ${Python_EXECUTABLE} -c "import numpy ; print(numpy.get_include())" + execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.get_include())" OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE _numpy_include_dirs ) endif() if (Numpy_DEBUG) - message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${PYTHON_INCLUDE_DIR}") + message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${Python3_INCLUDE_DIRS}") endif() find_path(Numpy_INCLUDE_DIR numpy/arrayobject.h - PATHS "${_numpy_include_dirs}" "${PYTHON_INCLUDE_DIR}" + PATHS "${_numpy_include_dirs}" "${Python3_INCLUDE_DIRS}" PATH_SUFFIXES numpy/core/include ) diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py index ad84e17cbc..587de6880d 100755 --- a/manual/sphinx/conf.py +++ b/manual/sphinx/conf.py @@ -86,7 +86,7 @@ def __getattr__(cls, name): + " -DBOUT_ENABLE_PYTHON=ON" + " -DBOUT_UPDATE_GIT_SUBMODULE=OFF" + " -DBOUT_TESTS=OFF" - + f" -DPython_ROOT_DIR={pydir}" + + f" -DPython3_ROOT_DIR={pydir}" + f" -Dmpark_variant_DIR={pwd}/externalpackages/mpark.variant/" + f" -Dfmt_DIR={pwd}/externalpackages/fmt/" ) diff --git a/tools/pylib/_boutpp_build/CMakeLists.txt b/tools/pylib/_boutpp_build/CMakeLists.txt index 7ceae04f0e..6391c7d0ab 100644 --- a/tools/pylib/_boutpp_build/CMakeLists.txt +++ b/tools/pylib/_boutpp_build/CMakeLists.txt @@ -25,7 +25,7 @@ bout_python_maybe_error(${Cython_FOUND} Cython) find_package(Bash) bout_python_maybe_error(${Bash_FOUND} Bash) -execute_process(COMMAND ${Python_EXECUTABLE} -c "import jinja2" +execute_process(COMMAND ${Python3_EXECUTABLE} -c "import jinja2" RESULT_VARIABLE jinja2_FOUND) if (jinja2_FOUND EQUAL 0) # We have jinja2 - all good @@ -33,7 +33,7 @@ else() bout_python_maybe_error(OFF jinja2) endif() -execute_process(COMMAND ${Python_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX')[:-3])" +execute_process(COMMAND ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX')[:-3])" RESULT_VARIABLE PYTHON_WORKING OUTPUT_VARIABLE PYTHON_EXT_SUFFIX OUTPUT_STRIP_TRAILING_WHITESPACE @@ -73,7 +73,7 @@ foreach(file IN LISTS files) #message(FATAL_ERROR "${gen} ${src}/${file}.jinja") add_custom_command(OUTPUT ${gen} COMMAND ${CMAKE_COMMAND} -E make_directory ${tar} - COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${tar}/..:\${PYTHONPATH} ${Python_EXECUTABLE} generate.py ${file}.jinja ${gen} + COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${tar}/..:\${PYTHONPATH} ${Python3_EXECUTABLE} generate.py ${file}.jinja ${gen} DEPENDS ${src}/${file}.jinja DEPENDS ${src}/helper.py DEPENDS ${src}/resolve_enum_inv.pyx.jinja @@ -93,8 +93,7 @@ endforeach() add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libboutpp.cpp COMMAND ${CMAKE_COMMAND} -E copy boutpp.pyx libboutpp.pyx - COMMAND ${Python_EXECUTABLE} -m cython libboutpp.pyx --cplus -3 -X binding=True -X embedsignature=True - COMMENT "Cythonizing python interface" + COMMAND ${Python3_EXECUTABLE} -m cython libboutpp.pyx --cplus -3 -X binding=True -X embedsignature=True WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${boutpp_depends} ) @@ -120,5 +119,6 @@ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/boutpp.py DESTINATION ${CMAKE_INSTALL_PYTHON_SITEARCH}/boutpp/ RENAME __init__.py ) + target_link_libraries(boutpp${PYTHON_EXT_SUFFIX} bout++) -target_include_directories(boutpp${PYTHON_EXT_SUFFIX} PRIVATE $ ${Numpy_INCLUDE_DIRS} ${Python_INCLUDE_DIRS}) +target_include_directories(boutpp${PYTHON_EXT_SUFFIX} PRIVATE $ ${Numpy_INCLUDE_DIRS} ${Python3_INCLUDE_DIRS}) From fce158f9f45f870570a7b3d00c9748e7be761bf0 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 3 Mar 2022 15:56:22 +0100 Subject: [PATCH 039/412] fixup: change boundaryParType to bout enum class --- tests/unit/test_extras.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 2a7b405c30..26e9fac10d 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -233,7 +233,7 @@ public: RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); } void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); } std::vector getBoundaries() override { return boundaries; } - std::vector getBoundariesPar(Mesh::BoundaryParType) override { + std::vector getBoundariesPar(BoundaryParType) override { return std::vector(); } BoutReal GlobalX(int jx) const override { return jx; } From 89b52a7fe6a9fb57c72d6422418cd33035e3efdd Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 18 Jan 2023 10:53:04 +0100 Subject: [PATCH 040/412] Avoid unneeded includes includes should be done in the cxx files, and if possible only forward declared in the header files --- include/boundary_factory.hxx | 11 +++++++---- include/bout/mesh.hxx | 4 ++-- include/field_data.hxx | 7 +++---- src/field/field3d.cxx | 2 ++ src/field/field_data.cxx | 2 ++ src/mesh/boundary_factory.cxx | 2 ++ 6 files changed, 18 insertions(+), 10 deletions(-) diff --git a/include/boundary_factory.hxx b/include/boundary_factory.hxx index 5bdb11b20e..bc5ff496b4 100644 --- a/include/boundary_factory.hxx +++ b/include/boundary_factory.hxx @@ -4,10 +4,13 @@ class BoundaryFactory; #ifndef __BNDRY_FACTORY_H__ #define __BNDRY_FACTORY_H__ -#include "boundary_op.hxx" -#include "boundary_region.hxx" -#include "parallel_boundary_op.hxx" -#include "parallel_boundary_region.hxx" +class BoundaryOpBase; +class BoundaryOpPar; +class BoundaryOp; +class BoundaryRegionBase; +class BoundaryRegionPar; +class BoundaryRegion; +class BoundaryModifier; #include #include diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 0163299e04..66ea61ac82 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -57,8 +57,8 @@ class Mesh; #include "fieldgroup.hxx" -#include "boundary_region.hxx" -#include "parallel_boundary_region.hxx" +class BoundaryRegion; +class BoundaryRegionPar; #include "sys/range.hxx" // RangeIterator diff --git a/include/field_data.hxx b/include/field_data.hxx index f0408b0c91..8d98709c6c 100644 --- a/include/field_data.hxx +++ b/include/field_data.hxx @@ -38,15 +38,14 @@ class FieldData; #include #include -// Including the next line leads to compiler errors -//#include "boundary_op.hxx" class BoundaryOp; class BoundaryOpPar; class Coordinates; class Mesh; -#include "boundary_region.hxx" -#include "parallel_boundary_region.hxx" +class BoundaryRegion; +class BoundaryRegionPar; +enum class BndryLoc; #include "bout/sys/expressionparser.hxx" diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 9068b9c1a3..8ad531ef74 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -39,6 +39,8 @@ #include #include #include +#include "parallel_boundary_region.hxx" +#include "parallel_boundary_op.hxx" #include #include #include diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx index 7a7157ce13..2b46d0bf50 100644 --- a/src/field/field_data.cxx +++ b/src/field/field_data.cxx @@ -3,6 +3,8 @@ #include #include #include +#include "parallel_boundary_region.hxx" +#include "parallel_boundary_op.hxx" #include #include #include "unused.hxx" diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx index 3d259d30c3..0e06ac71cb 100644 --- a/src/mesh/boundary_factory.cxx +++ b/src/mesh/boundary_factory.cxx @@ -1,6 +1,8 @@ #include #include #include +#include "parallel_boundary_region.hxx" +#include "parallel_boundary_op.hxx" #include #include From cdc164409a18ca2de0baf710a796490011884289 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 17 Jan 2023 11:13:09 +0100 Subject: [PATCH 041/412] Copy stencil code from nonuniform boundary branch --- src/mesh/stencils.md | 29 +++++++++++++++ src/mesh/stencils_sympy.py | 73 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 src/mesh/stencils.md create mode 100644 src/mesh/stencils_sympy.py diff --git a/src/mesh/stencils.md b/src/mesh/stencils.md new file mode 100644 index 0000000000..0c7d181481 --- /dev/null +++ b/src/mesh/stencils.md @@ -0,0 +1,29 @@ +Notes concerning the generation of stencils +================ + +We want to create a Taylor function +$f(x-x_0)=\sum_i=0^n \frac{1}{i!}f_i(x-x_0)^i$ where $n$ +is the order of the function, $x_0$ is the point in the boundary +where we want to calculate the function. $f_i$ are some coefficients +that we need to determine. To be precise, only $f_0$ needs to be +determined. +We know that the function has at some points certain values. If the +value at some distance `spacing.f0` is a given value `val` then we +can build a linear system of equations using the above formula. +If rather the derivative is given, the above equations needs to be +differentiated once. + +stencils_sympy.py calculates the coefficients of the above matrix +which represents our system of equations. The derivative is simply +one the factor of the next smaller term (or zero if the there is no +smaller one). This is what is calculated by `taylor`, `dirichlet` +and `neumann`, the respective matrix coefficients. + +sympy does all the heavy lifting on analytically inverting the +matrix. + +With the analytic inversion we can put in the numerical offsets +`spacing.f?` in C++ and get a fast expression for the respective +coefficients. As mentioned before, we do not need the full inverse, +just the first row, as we only care about the value, not about it's +derivative. diff --git a/src/mesh/stencils_sympy.py b/src/mesh/stencils_sympy.py new file mode 100644 index 0000000000..130d70996d --- /dev/null +++ b/src/mesh/stencils_sympy.py @@ -0,0 +1,73 @@ +#!/usr/bin/env python3 + +from sympy import Symbol, Eq +from sympy.matrices import Matrix +from sympy.printing import ccode +from sympy.simplify import combsimp as simp +from sympy.utilities.codegen import codegen + + +def pow(a, b): + if b == 0: + return "1" + if b == 1: + return a + else: + return "%s**%d" % (a, b) + + +def factorial(a): + if a == 0 or a == 1: + return 1 + else: + assert a > 0 + return a * factorial(a - 1) + + +def gen_code(order, matrix_type): + x = [Symbol("spacing.f%d" % i) for i in range(order)] + matrix = matrix_type(x) + A = Matrix(order, order, matrix) + + try: + iA = A.inv() + except: + import sys + + print(A, matrix, file=sys.stderr) + raise + ret = "" + for i in range(order): + ret += ccode(simp(iA[0, i]), assign_to="facs.f%d" % i) + ret += "\n" + return ret + + +def taylor(x, i, j): + if j >= 0: + return x[i] ** j / factorial(j) + else: + return 0 + + +class dirichlet: + def __init__(self, x): + self.x = x + + def __call__(self, i, j): + return taylor(self.x, i, j) + + +class neumann: + def __init__(self, x): + self.x = x + + def __call__(self, i, j): + if i == 0: + return taylor(self.x, i, j - 1) + else: + return taylor(self.x, i, j) + + +if __name__ == "__main__": + print(gen_code(3, dirichlet)) From d6bc5784f0ce33cac2ae81852f513e4cef32ca47 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 17 Jan 2023 11:28:19 +0100 Subject: [PATCH 042/412] Add code to generate stencils for parallel boundaries --- src/mesh/parallel_boundary_stencil.cxx.py | 62 +++++++++++++++++++++++ src/mesh/stencils_sympy.py | 4 ++ 2 files changed, 66 insertions(+) create mode 100644 src/mesh/parallel_boundary_stencil.cxx.py diff --git a/src/mesh/parallel_boundary_stencil.cxx.py b/src/mesh/parallel_boundary_stencil.cxx.py new file mode 100644 index 0000000000..d0988ee099 --- /dev/null +++ b/src/mesh/parallel_boundary_stencil.cxx.py @@ -0,0 +1,62 @@ +import os +from tempfile import NamedTemporaryFile as tmpf +from stencils_sympy import dirichlet, neumann, simp, Symbol, Matrix, ccode + + +def gen_code(order, matrix_type): + x = [Symbol("spacing%d" % i) for i in range(order)] + matrix = matrix_type(x) + A = Matrix(order, order, matrix) + + try: + iA = A.inv() + except: + import sys + + print(A, matrix, file=sys.stderr) + raise + return ccode(simp(sum([iA[0, i] * Symbol("value%d" % i) for i in range(order)]))) + + +def run(cmd): + print(cmd) + out = os.system(cmd) + assert out == 0 + + +if __name__ == "__main__": + with tmpf("w", dir=".", delete=False) as f: + f.write("namespace {\n") + f.write( + """ +inline BoutReal pow(BoutReal val, int exp) { + //constexpr int expval = exp; + //static_assert(expval == 2 or expval == 3, "This pow is only for exponent 2 or 3"); + if (exp == 2) { + return val * val; + } + ASSERT3(exp == 3); + return val * val * val; +} +""" + ) + + for order in range(1, 4): + for matrix in dirichlet, neumann: + if order == 1 and matrix == neumann: + continue + print(f"generating {matrix.name}_o{order}") + args = ", ".join( + [ + "BoutReal spacing%d, BoutReal value%d" % (i, i) + for i in range(order) + ] + ) + f.write( + f"inline BoutReal stencil_{matrix.name}_o{order}({args}) {{\n return " + ) + f.write(gen_code(order, matrix)) + f.write(";\n}\n") + f.write("}\n") + run("clang-format -i " + f.name) + run(f"mv {f.name} {__file__[:-3]}") diff --git a/src/mesh/stencils_sympy.py b/src/mesh/stencils_sympy.py index 130d70996d..64677f1985 100644 --- a/src/mesh/stencils_sympy.py +++ b/src/mesh/stencils_sympy.py @@ -51,6 +51,8 @@ def taylor(x, i, j): class dirichlet: + name = "dirichlet" + def __init__(self, x): self.x = x @@ -59,6 +61,8 @@ def __call__(self, i, j): class neumann: + name = "neumann" + def __init__(self, x): self.x = x From 1126d77408fee7ac1566986e9659d26491aeea4c Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 17 Jan 2023 11:31:34 +0100 Subject: [PATCH 043/412] Use forward declaration for parallel boundary --- include/bout/mesh.hxx | 2 +- include/field_data.hxx | 3 +-- src/mesh/impls/bout/boutmesh.cxx | 3 +++ src/mesh/parallel/shiftedmetric.cxx | 1 + src/mesh/parallel/shiftedmetricinterp.cxx | 1 + 5 files changed, 7 insertions(+), 3 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 128163c9d1..b141a42430 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -58,7 +58,7 @@ class Mesh; #include "fieldgroup.hxx" #include "boundary_region.hxx" -#include "parallel_boundary_region.hxx" +class BoundaryRegionPar; #include "sys/range.hxx" // RangeIterator diff --git a/include/field_data.hxx b/include/field_data.hxx index f0408b0c91..c6c8f6a32f 100644 --- a/include/field_data.hxx +++ b/include/field_data.hxx @@ -39,14 +39,13 @@ class FieldData; #include // Including the next line leads to compiler errors -//#include "boundary_op.hxx" class BoundaryOp; class BoundaryOpPar; class Coordinates; class Mesh; #include "boundary_region.hxx" -#include "parallel_boundary_region.hxx" +class BoundaryRegionPar; #include "bout/sys/expressionparser.hxx" diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 3bc5d0d506..0de257d8ba 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -47,6 +47,9 @@ #include #include +#include "parallel_boundary_region.hxx" +#include "boundary_region.hxx" + #include #include #include diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index f5ed3a7987..f7c64ed28e 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -12,6 +12,7 @@ #include #include #include +#include "parallel_boundary_region.hxx" #include diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 0e8a9afaa8..75cad5efb4 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -30,6 +30,7 @@ #include "shiftedmetricinterp.hxx" #include "mask.hxx" #include "bout/constants.hxx" +#include "parallel_boundary_region.hxx" ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, Field2D zShift_in, BoutReal zlength_in, From f2f134a7b19acb8ca0256d9c2942d66b6009234c Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 17 Jan 2023 11:36:59 +0100 Subject: [PATCH 044/412] Add new ParallelBoundary code * Consistent naming of parallel boundaries * Consistent treatment of the meaning of the parallel length * Fall back to lower order code if for the given point is on a short field line --- include/parallel_boundary_op.hxx | 68 ++++++--- include/parallel_boundary_region.hxx | 173 ++++++++++++++++++---- src/mesh/boundary_factory.cxx | 10 +- src/mesh/parallel/shiftedmetricinterp.cxx | 33 +++-- src/mesh/parallel_boundary_op.cxx | 129 +--------------- src/mesh/parallel_boundary_region.cxx | 40 ----- 6 files changed, 219 insertions(+), 234 deletions(-) diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx index 35415914b5..6a578b2a32 100644 --- a/include/parallel_boundary_op.hxx +++ b/include/parallel_boundary_op.hxx @@ -52,7 +52,7 @@ protected: BoutReal getValue(const BoundaryRegionPar& bndry, BoutReal t); }; -template +template class BoundaryOpParTemp : public BoundaryOpPar { public: using BoundaryOpPar::BoundaryOpPar; @@ -89,51 +89,73 @@ public: throw BoutException("Can't apply parallel boundary conditions to Field2D!"); } void apply(Field3D& f) override { return apply(f, 0); } + + void apply(Field3D& f, BoutReal t) override { + f.ynext(bndry->dir).allocate(); // Ensure unique before modifying + + auto dy = f.getCoordinates()->dy; + + for (bndry->first(); !bndry->isDone(); bndry->next()) { + BoutReal value = getValue(*bndry, t); + if (isNeumann) { + value *= dy[bndry->ind()]; + } + static_cast(this)->apply_stencil(f, bndry, value); + } + } }; ////////////////////////////////////////////////// // Implementations -class BoundaryOpPar_dirichlet : public BoundaryOpParTemp { +class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - - using BoundaryOpParTemp::apply; - void apply(Field3D& f, BoutReal t) override; + void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + bndry->dirichlet_o1(f, value); + } }; -class BoundaryOpPar_dirichlet_O3 : public BoundaryOpParTemp { +class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - - using BoundaryOpParTemp::apply; - void apply(Field3D& f, BoutReal t) override; + void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + bndry->dirichlet_o2(f, value); + } }; -class BoundaryOpPar_dirichlet_interp - : public BoundaryOpParTemp { +class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - - using BoundaryOpParTemp::apply; - void apply(Field3D& f, BoutReal t) override; + void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + bndry->dirichlet_o3(f, value); + } }; -class BoundaryOpPar_neumann : public BoundaryOpParTemp { +class BoundaryOpPar_neumann_o1 + : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - - using BoundaryOpParTemp::apply; - void apply(Field3D& f, BoutReal t) override; + void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + bndry->neumann_o1(f, value); + } }; -class BoundaryOpPar_neumann_c2_simple - : public BoundaryOpParTemp { +class BoundaryOpPar_neumann_o2 + : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - - using BoundaryOpParTemp::apply; - void apply(Field3D& f, BoutReal t) override; + void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + bndry->neumann_o2(f, value); + } }; +class BoundaryOpPar_neumann_o3 + : public BoundaryOpParTemp { +public: + using BoundaryOpParTemp::BoundaryOpParTemp; + void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + bndry->neumann_o3(f, value); + } +}; #endif // __PAR_BNDRY_OP_H__ diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx index d9ea22814d..823d989139 100644 --- a/include/parallel_boundary_region.hxx +++ b/include/parallel_boundary_region.hxx @@ -5,18 +5,53 @@ #include "bout_types.hxx" #include +#include + /** * Boundary region for parallel direction. This contains a vector of points that are * inside the boundary. * */ -class BoundaryRegionPar : public BoundaryRegionBase { - struct IndexPoint { - int jx; - int jy; - int jz; - }; +namespace parallel_stencil { +// generated by src/mesh/parallel_boundary_stencil.cxx.py +inline BoutReal pow(BoutReal val, int exp) { + // constexpr int expval = exp; + // static_assert(expval == 2 or expval == 3, "This pow is only for exponent 2 or 3"); + if (exp == 2) { + return val * val; + } + ASSERT3(exp == 3); + return val * val * val; +} +inline BoutReal dirichlet_o1(BoutReal UNUSED(spacing0), BoutReal value0) { + return value0; +} +inline BoutReal dirichlet_o2(BoutReal spacing0, BoutReal value0, BoutReal spacing1, + BoutReal value1) { + return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1); +} +inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1, + BoutReal value1) { + return -spacing1 * value0 + value1; +} +inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1, + BoutReal value1, BoutReal spacing2, BoutReal value2) { + return (pow(spacing0, 2) * spacing1 * value2 - pow(spacing0, 2) * spacing2 * value1 + - spacing0 * pow(spacing1, 2) * value2 + spacing0 * pow(spacing2, 2) * value1 + + pow(spacing1, 2) * spacing2 * value0 - spacing1 * pow(spacing2, 2) * value0) + / ((spacing0 - spacing1) * (spacing0 - spacing2) * (spacing1 - spacing2)); +} +inline BoutReal neumann_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1, + BoutReal value1, BoutReal spacing2, BoutReal value2) { + return (2 * spacing0 * spacing1 * value2 - 2 * spacing0 * spacing2 * value1 + + pow(spacing1, 2) * spacing2 * value0 - pow(spacing1, 2) * value2 + - spacing1 * pow(spacing2, 2) * value0 + pow(spacing2, 2) * value1) + / ((spacing1 - spacing2) * (2 * spacing0 - spacing1 - spacing2)); +} +} // namespace parallel_stencil + +class BoundaryRegionPar : public BoundaryRegionBase { struct RealPoint { BoutReal s_x; @@ -26,13 +61,15 @@ class BoundaryRegionPar : public BoundaryRegionBase { struct Indices { // Indices of the boundary point - IndexPoint index; + Ind3D index; // Intersection with boundary in index space RealPoint intersection; // Distance to intersection BoutReal length; // Angle between field line and boundary - BoutReal angle; + // BoutReal angle; + // How many points we can go in the opposite direction + signed char valid; }; using IndicesVec = std::vector; @@ -44,29 +81,115 @@ class BoundaryRegionPar : public BoundaryRegionBase { IndicesIter bndry_position; public: - BoundaryRegionPar(const std::string &name, int dir, Mesh* passmesh) : - BoundaryRegionBase(name, passmesh), dir(dir) { - BoundaryRegionBase::isParallel = true;} - BoundaryRegionPar(const std::string &name, BndryLoc loc,int dir, Mesh* passmesh) : - BoundaryRegionBase(name, loc, passmesh), dir(dir) { - BoundaryRegionBase::isParallel = true;} + BoundaryRegionPar(const std::string& name, int dir, Mesh* passmesh) + : BoundaryRegionBase(name, passmesh), dir(dir) { + ASSERT0(std::abs(dir) == 1); + BoundaryRegionBase::isParallel = true; + } + BoundaryRegionPar(const std::string& name, BndryLoc loc, int dir, Mesh* passmesh) + : BoundaryRegionBase(name, loc, passmesh), dir(dir) { + BoundaryRegionBase::isParallel = true; + ASSERT0(std::abs(dir) == 1); + } /// Add a point to the boundary - void add_point(int jx,int jy,int jz, - BoutReal x,BoutReal y,BoutReal z, - BoutReal length,BoutReal angle); + void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length, + char valid) { + bndry_points.push_back({ind, {x, y, z}, length, valid}); + } + void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z, + BoutReal length, char valid) { + bndry_points.push_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid}); + } + + // final, so they can be inlined + void first() final { bndry_position = begin(bndry_points); } + void next() final { ++bndry_position; } + bool isDone() final { return (bndry_position == end(bndry_points)); } + + // getter + Ind3D ind() const { return bndry_position->index; } + BoutReal s_x() const { return bndry_position->intersection.s_x; } + BoutReal s_y() const { return bndry_position->intersection.s_y; } + BoutReal s_z() const { return bndry_position->intersection.s_z; } + BoutReal length() const { return bndry_position->length; } + char valid() const { return bndry_position->valid; } - void first() override; - void next() override; - bool isDone() override; + // extrapolate a given point to the boundary + BoutReal extrapolate_o1(const Field3D& f) const { return f[ind()]; } + BoutReal extrapolate_o2(const Field3D& f) const { + ASSERT3(valid() >= 0); + if (valid() < 1) { + return extrapolate_o1(f); + } + return f[ind()] * (1 + length()) - f.ynext(-dir)[ind().yp(-dir)] * length(); + } - /// Index of the point in the boundary - int x, y, z; - BoutReal s_x, s_y, s_z; - BoutReal length; - BoutReal angle; + // dirichlet boundary code + void dirichlet_o1(Field3D& f, BoutReal value) const { + f.ynext(dir)[ind().yp(dir)] = value; + } + + void dirichlet_o2(Field3D& f, BoutReal value) const { + if (length() < small_value) { + return dirichlet_o1(f, value); + } + ynext(f) = parallel_stencil::dirichlet_o2(1, f[ind()], 1 - length(), value); + // ynext(f) = f[ind()] * (1 + 1/length()) + value / length(); + } + + void dirichlet_o3(Field3D& f, BoutReal value) const { + ASSERT3(valid() >= 0); + if (valid() < 1) { + return dirichlet_o2(f, value); + } + if (length() < small_value) { + ynext(f) = parallel_stencil::dirichlet_o2(2, yprev(f), 1 - length(), value); + } else { + ynext(f) = + parallel_stencil::dirichlet_o3(2, yprev(f), 1, f[ind()], 1 - length(), value); + } + } + + // NB: value needs to be scaled by dy + // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil. + // But in general we do not, and thus for normal C2 stencils, this is 1st order. + void neumann_o1(Field3D& f, BoutReal value) const { ynext(f) = f[ind()] + value; } + + // NB: value needs to be scaled by dy + void neumann_o2(Field3D& f, BoutReal value) const { + ASSERT3(valid() >= 0); + if (valid() < 1) { + return neumann_o1(f, value); + } + ynext(f) = yprev(f) + 2 * value; + } + + // NB: value needs to be scaled by dy + void neumann_o3(Field3D& f, BoutReal value) const { + ASSERT3(valid() >= 0); + if (valid() < 1) { + return neumann_o1(f, value); + } + ynext(f) = + parallel_stencil::neumann_o3(1 - length(), value, 1, f[ind()], 2, yprev(f)); + } const int dir; + +private: + const BoutReal small_value = 1e-2; + + // BoutReal get(const Field3D& f, int off) + const BoutReal& ynext(const Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; } + BoutReal& ynext(Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; } + const BoutReal& yprev(const Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; } + BoutReal& yprev(Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; } + Ind3D xyz2ind(int x, int y, int z, Mesh* mesh) const { + const int ny = mesh->LocalNy; + const int nz = mesh->LocalNz; + return Ind3D{(x * ny + y) * nz + z, ny, nz}; + } }; #endif // __PAR_BNDRY_H__ diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx index 3d259d30c3..dcbab38284 100644 --- a/src/mesh/boundary_factory.cxx +++ b/src/mesh/boundary_factory.cxx @@ -41,10 +41,12 @@ BoundaryFactory::BoundaryFactory() { addMod(new BoundaryFromFieldAligned(), "fromFieldAligned"); // Parallel boundaries - add(new BoundaryOpPar_dirichlet(), "parallel_dirichlet"); - add(new BoundaryOpPar_dirichlet_O3(), "parallel_dirichlet_O3"); - add(new BoundaryOpPar_dirichlet_interp(), "parallel_dirichlet_interp"); - add(new BoundaryOpPar_neumann(), "parallel_neumann"); + add(new BoundaryOpPar_dirichlet_o1(), "parallel_dirichlet_o1"); + add(new BoundaryOpPar_dirichlet_o2(), "parallel_dirichlet_o2"); + add(new BoundaryOpPar_dirichlet_o3(), "parallel_dirichlet_o3"); + add(new BoundaryOpPar_neumann_o1(), "parallel_neumann_o1"); + add(new BoundaryOpPar_neumann_o2(), "parallel_neumann_o2"); + add(new BoundaryOpPar_neumann_o3(), "parallel_neumann_o3"); } BoundaryFactory::~BoundaryFactory() { diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 75cad5efb4..a8690629d8 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -113,6 +113,11 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, interp_from_aligned->calcWeights(zt_prime_from); + int yvalid = mesh.LocalNy - 2 * mesh.ystart; + // avoid overflow - no stencil need more than 5 points + if (yvalid > 20) { + yvalid = 20; + } // Create regions for parallel boundary conditions Field2D dy; mesh.get(dy, "dy", 1.); @@ -127,10 +132,9 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z + 0.5 * (zShift(it.ind, mesh.yend + 1) - zShift(it.ind, mesh.yend)), 0.25 - * (dy(it.ind, mesh.yend) // dy/2 - + dy(it.ind, mesh.yend + 1)), - 0. // angle? - ); + * (1 // dy/2 + + dy(it.ind, mesh.yend + 1) / dy(it.ind, mesh.yend)), // length + yvalid); } } auto backward_boundary_xin = @@ -144,10 +148,9 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z + 0.5 * (zShift(it.ind, mesh.ystart) - zShift(it.ind, mesh.ystart - 1)), 0.25 - * (dy(it.ind, mesh.ystart - 1) // dy/2 - + dy(it.ind, mesh.ystart)), - 0. // angle? - ); + * (1 // dy/2 + + dy(it.ind, mesh.ystart - 1) / dy(it.ind, mesh.ystart)), + yvalid); } } // Create regions for parallel boundary conditions @@ -162,10 +165,9 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z + 0.5 * (zShift(it.ind, mesh.yend + 1) - zShift(it.ind, mesh.yend)), 0.25 - * (dy(it.ind, mesh.yend) // dy/2 - + dy(it.ind, mesh.yend + 1)), - 0. // angle? - ); + * (1 // dy/2 + + dy(it.ind, mesh.yend + 1) / dy(it.ind, mesh.yend)), + yvalid); } } auto backward_boundary_xout = @@ -179,10 +181,9 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z + 0.5 * (zShift(it.ind, mesh.ystart) - zShift(it.ind, mesh.ystart - 1)), 0.25 - * (dy(it.ind, mesh.ystart - 1) // dy/2 - + dy(it.ind, mesh.ystart)), - 0. // angle? - ); + * (dy(it.ind, mesh.ystart - 1) / dy(it.ind, mesh.ystart) // dy/2 + + 1), + yvalid); } } diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index d391e8ff2e..8997fb6564 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -6,18 +6,15 @@ #include "bout/mesh.hxx" BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { - - Mesh* mesh = bndry.localmesh; - BoutReal value; switch (value_type) { case ValueType::GEN: - return gen_values->generate( - bout::generator::Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); + return gen_values->generate(bout::generator::Context( + bndry.s_x(), bndry.s_y(), bndry.s_z(), CELL_CENTRE, bndry.localmesh, t)); case ValueType::FIELD: // FIXME: Interpolate to s_x, s_y, s_z... - value = (*field_values)(bndry.x, bndry.y, bndry.z); + value = (*field_values)[bndry.ind()]; return value; case ValueType::REAL: return real_value; @@ -25,123 +22,3 @@ BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue"); } } - -////////////////////////////////////////// -// Dirichlet boundary - -void BoundaryOpPar_dirichlet::apply(Field3D& f, BoutReal t) { - Field3D& f_next = f.ynext(bndry->dir); - - Coordinates& coord = *(f.getCoordinates()); - - // Loop over grid points If point is in boundary, then fill in - // f_next such that the field would be VALUE on the boundary - for (bndry->first(); !bndry->isDone(); bndry->next()) { - // temp variables for convenience - int x = bndry->x; - int y = bndry->y; - int z = bndry->z; - - // Generate the boundary value - BoutReal value = getValue(*bndry, t); - - // Scale the field and normalise to the desired value - BoutReal y_prime = bndry->length; - BoutReal f2 = (f(x, y, z) - value) * (coord.dy(x, y, z) - y_prime) / y_prime; - - f_next(x, y + bndry->dir, z) = value - f2; - } -} - -////////////////////////////////////////// -// Dirichlet boundary - Third order - -void BoundaryOpPar_dirichlet_O3::apply(Field3D& f, BoutReal t) { - - Field3D& f_next = f.ynext(bndry->dir); - Field3D& f_prev = f.ynext(-bndry->dir); - - Coordinates& coord = *(f.getCoordinates()); - - // Loop over grid points If point is in boundary, then fill in - // f_next such that the field would be VALUE on the boundary - for (bndry->first(); !bndry->isDone(); bndry->next()) { - // temp variables for convenience - int x = bndry->x; - int y = bndry->y; - int z = bndry->z; - - // Generate the boundary value - BoutReal fb = getValue(*bndry, t); - BoutReal f1 = f_prev(x, y - bndry->dir, z); - BoutReal f2 = f(x, y, z); - BoutReal l1 = coord.dy(x, y, z); - BoutReal l2 = bndry->length; - BoutReal l3 = coord.dy(x, y, z) - l2; - - BoutReal denom = (l1 * l1 * l2 + l1 * l2 * l2); - BoutReal term1 = (l2 * l2 * l3 + l2 * l3 * l3); - BoutReal term2 = l1 * (l1 + l2 + l3) * (l2 + l3); - BoutReal term3 = l3 * ((l1 + l2) * l3 + (l1 + l2) * (l1 + l2)); - - f_next(x, y + bndry->dir, z) = (term1 * f1 + term2 * fb - term3 * f2) / denom; - } -} - -////////////////////////////////////////// -// Dirichlet with interpolation - -void BoundaryOpPar_dirichlet_interp::apply(Field3D& f, BoutReal t) { - - Field3D& f_next = f.ynext(bndry->dir); - Field3D& f_prev = f.ynext(-bndry->dir); - - Coordinates& coord = *(f.getCoordinates()); - - // Loop over grid points If point is in boundary, then fill in - // f_next such that the field would be VALUE on the boundary - for (bndry->first(); !bndry->isDone(); bndry->next()) { - // temp variables for convenience - int x = bndry->x; - int y = bndry->y; - int z = bndry->z; - - // Generate the boundary value - BoutReal fs = getValue(*bndry, t); - - // Scale the field and normalise to the desired value - BoutReal dy = coord.dy(x, y, z); - BoutReal s = bndry->length * dy; - - f_next(x, y + bndry->dir, z) = - f_prev(x, y - bndry->dir, z) * (1. - (2. * s / (dy + s))) - + 2. * f(x, y, z) * ((s - dy) / s) + fs * (dy / s - (2. / s + 1.)); - } -} - -////////////////////////////////////////// -// Neumann boundary - -void BoundaryOpPar_neumann::apply(Field3D& f, BoutReal t) { - TRACE("BoundaryOpPar_neumann::apply"); - - Field3D& f_next = f.ynext(bndry->dir); - f_next.allocate(); // Ensure unique before modifying - - Coordinates& coord = *(f.getCoordinates()); - - // If point is in boundary, then fill in f_next such that the derivative - // would be VALUE on the boundary - for (bndry->first(); !bndry->isDone(); bndry->next()) { - // temp variables for convience - int x = bndry->x; - int y = bndry->y; - int z = bndry->z; - - // Generate the boundary value - BoutReal value = getValue(*bndry, t); - BoutReal dy = coord.dy(x, y, z); - - f_next(x, y + bndry->dir, z) = f(x, y, z) + bndry->dir * value * dy; - } -} diff --git a/src/mesh/parallel_boundary_region.cxx b/src/mesh/parallel_boundary_region.cxx index 510286e27a..e69de29bb2 100644 --- a/src/mesh/parallel_boundary_region.cxx +++ b/src/mesh/parallel_boundary_region.cxx @@ -1,40 +0,0 @@ -#include "parallel_boundary_region.hxx" - -void BoundaryRegionPar::add_point(const int jx, const int jy, const int jz, - const BoutReal x, const BoutReal y, const BoutReal z, - const BoutReal length, const BoutReal angle) { - bndry_points.push_back({{jx, jy, jz}, {x, y, z}, length, angle}); -} - -void BoundaryRegionPar::first() { - bndry_position = begin(bndry_points); - if (!isDone()) { - x = bndry_position->index.jx; - y = bndry_position->index.jy; - z = bndry_position->index.jz; - s_x = bndry_position->intersection.s_x; - s_y = bndry_position->intersection.s_y; - s_z = bndry_position->intersection.s_z; - length = bndry_position->length; - angle = bndry_position->angle; - } -} - -void BoundaryRegionPar::next() { - ++bndry_position; - if (!isDone()) { - x = bndry_position->index.jx; - y = bndry_position->index.jy; - z = bndry_position->index.jz; - s_x = bndry_position->intersection.s_x; - s_y = bndry_position->intersection.s_y; - s_z = bndry_position->intersection.s_z; - length = bndry_position->length; - angle = bndry_position->angle; - } -} - -bool BoundaryRegionPar::isDone() { - return (bndry_position == end(bndry_points)); -} - From b28ef7ebbae07394690cf59e7d8bc6e325fcb626 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 17 Jan 2023 12:09:10 +0100 Subject: [PATCH 045/412] set valid number of points for FCI boundaries --- include/parallel_boundary_region.hxx | 12 ++++++++++++ src/mesh/parallel/fci.cxx | 6 +++--- src/mesh/parallel/fci.hxx | 15 +++++++++++++++ 3 files changed, 30 insertions(+), 3 deletions(-) diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx index 823d989139..035fe8bbc6 100644 --- a/include/parallel_boundary_region.hxx +++ b/include/parallel_boundary_region.hxx @@ -115,6 +115,18 @@ public: BoutReal length() const { return bndry_position->length; } char valid() const { return bndry_position->valid; } + // setter + void setValid(char val) { bndry_position->valid = val; } + + bool contains(const Ind3D ind) const { + for (auto it = begin(bndry_points); end(bndry_points) != it; ++it) { + if (it->index == ind) { + return true; + } + } + return false; + } + // extrapolate a given point to the boundary BoutReal extrapolate_o1(const Field3D& f) const { return f[ind()]; } BoutReal extrapolate_o2(const Field3D& f) const { diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index c25765852e..a8cd1947c2 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -236,9 +236,9 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, // the outer boundary auto* boundary = (xt_prime[i] < 0.0) ? inner_boundary : outer_boundary; boundary->add_point(x, y, z, x + dx, y + 0.5 * offset, - z + dz, // Intersection point in local index space - 0.5 * dy[i], // Distance to intersection - PI // Right-angle intersection + z + dz, // Intersection point in local index space + 0.5, // Distance to intersection + 1 // Default to that there is a point in the other direction ); } diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 3ecd964bfa..512d0e2833 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -101,6 +101,21 @@ public: field_line_maps.emplace_back(mesh, dy, options, -offset, backward_boundary_xin, backward_boundary_xout, zperiodic); } + ASSERT0(mesh.ystart == 1); + BoundaryRegionPar* bndries[]{forward_boundary_xin, forward_boundary_xout, + backward_boundary_xin, backward_boundary_xout}; + for (auto bndry : bndries) { + for (auto bndry2 : bndries) { + if (bndry->dir == bndry2->dir) { + continue; + } + for (bndry->first(); !bndry->isDone(); bndry->next()) { + if (bndry2->contains(bndry->ind().yp(-2 * bndry->dir))) { + bndry->setValid(0); + } + } + } + } } void calcParallelSlices(Field3D &f) override; From 5589da721e213fdd28a8a2c59857a5108652352a Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 18 Jan 2023 10:53:56 +0100 Subject: [PATCH 046/412] Use binary_search for contains Should be much faster --- include/parallel_boundary_region.hxx | 9 ++------- src/mesh/parallel/fci.hxx | 2 +- 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx index 035fe8bbc6..9ac4b9bbf9 100644 --- a/include/parallel_boundary_region.hxx +++ b/include/parallel_boundary_region.hxx @@ -118,13 +118,8 @@ public: // setter void setValid(char val) { bndry_position->valid = val; } - bool contains(const Ind3D ind) const { - for (auto it = begin(bndry_points); end(bndry_points) != it; ++it) { - if (it->index == ind) { - return true; - } - } - return false; + bool contains(const BoundaryRegionPar& bndry) const { + return std::binary_search(begin(bndry_points), end(bndry_points), *bndry.bndry_position, [](const Indices& i1, const Indices& i2) { return i1.index < i2.index; }); } // extrapolate a given point to the boundary diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 512d0e2833..b2f25d5fa3 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -110,7 +110,7 @@ public: continue; } for (bndry->first(); !bndry->isDone(); bndry->next()) { - if (bndry2->contains(bndry->ind().yp(-2 * bndry->dir))) { + if (bndry2->contains(*bndry)) { bndry->setValid(0); } } From 8f56cd46d9a417935758a672832d32a657e62c33 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 18 Jan 2023 08:14:09 +0100 Subject: [PATCH 047/412] Use parallel_neumann_o2 Previous parallel_neumann was dropped, thus use the new one --- examples/fci-wave-logn/boundary/BOUT.inp | 10 +++++----- examples/fci-wave-logn/div-integrate/BOUT.inp | 10 +++++----- examples/fci-wave-logn/expanded/BOUT.inp | 10 +++++----- examples/fci-wave-logn/fci-wave.cxx | 2 +- examples/fci-wave/div-integrate/BOUT.inp | 10 +++++----- examples/fci-wave/div/BOUT.inp | 10 +++++----- examples/fci-wave/fci-wave.cxx | 2 +- examples/fci-wave/logn/BOUT.inp | 10 +++++----- examples/laplace-petsc3d/data/BOUT.inp | 6 +++--- src/mesh/coordinates.cxx | 4 +++- .../data_circular_core-sol/BOUT.inp | 4 ++-- .../test-laplace-hypre3d/data_circular_core/BOUT.inp | 2 +- .../data_circular_core-sol/BOUT.inp | 2 +- .../test-laplace-petsc3d/data_circular_core/BOUT.inp | 2 +- 14 files changed, 43 insertions(+), 41 deletions(-) diff --git a/examples/fci-wave-logn/boundary/BOUT.inp b/examples/fci-wave-logn/boundary/BOUT.inp index 11e57ec47d..0632aa949b 100644 --- a/examples/fci-wave-logn/boundary/BOUT.inp +++ b/examples/fci-wave-logn/boundary/BOUT.inp @@ -20,7 +20,7 @@ expand_divergence = false background = 1e-06 # Background density [all] -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 bndry_all = neumann [n] @@ -28,15 +28,15 @@ bndry_all = neumann zl = z / (2*pi) function = fciwave:background + 1e-3*exp(-((x-0.7)/0.1)^2 - ((zl-0.3)/0.1)^2) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [logn] function = log(n:function) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [v] diff --git a/examples/fci-wave-logn/div-integrate/BOUT.inp b/examples/fci-wave-logn/div-integrate/BOUT.inp index a37bf3e2a5..66bdbce5f2 100644 --- a/examples/fci-wave-logn/div-integrate/BOUT.inp +++ b/examples/fci-wave-logn/div-integrate/BOUT.inp @@ -20,7 +20,7 @@ expand_divergence = false background = 1e-06 # Background density [all] -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 bndry_all = neumann [n] @@ -28,15 +28,15 @@ bndry_all = neumann zl = z / (2*pi) function = fciwave:background + 1e-3*exp(-((x-0.7)/0.1)^2 - ((zl-0.3)/0.1)^2) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [logn] function = log(n:function) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [v] diff --git a/examples/fci-wave-logn/expanded/BOUT.inp b/examples/fci-wave-logn/expanded/BOUT.inp index 3a2935c6e8..e084511d24 100644 --- a/examples/fci-wave-logn/expanded/BOUT.inp +++ b/examples/fci-wave-logn/expanded/BOUT.inp @@ -20,7 +20,7 @@ expand_divergence = true background = 1e-06 # Background density [all] -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 bndry_all = neumann [n] @@ -28,15 +28,15 @@ bndry_all = neumann zl = z / (2*pi) function = fciwave:background + 1e-3*exp(-((x-0.7)/0.1)^2 - ((zl-0.3)/0.1)^2) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [logn] function = log(n:function) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [v] diff --git a/examples/fci-wave-logn/fci-wave.cxx b/examples/fci-wave-logn/fci-wave.cxx index 8c801dfefa..5fd4deef9d 100644 --- a/examples/fci-wave-logn/fci-wave.cxx +++ b/examples/fci-wave-logn/fci-wave.cxx @@ -65,7 +65,7 @@ class FCIwave : public PhysicsModel { // Neumann boundaries simplifies parallel derivatives Bxyz.applyBoundary("neumann"); - Bxyz.applyParallelBoundary("parallel_neumann"); + Bxyz.applyParallelBoundary("parallel_neumann_o2"); SAVE_ONCE(Bxyz); Options::getRoot()->getSection("fciwave")->get("expand_divergence", expand_divergence, true); diff --git a/examples/fci-wave/div-integrate/BOUT.inp b/examples/fci-wave/div-integrate/BOUT.inp index eb41d5f228..68f2326f52 100644 --- a/examples/fci-wave/div-integrate/BOUT.inp +++ b/examples/fci-wave/div-integrate/BOUT.inp @@ -21,7 +21,7 @@ log_density = false # Evolve log(n)? background = 1e-06 # Background density [all] -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 bndry_all = neumann [n] @@ -29,15 +29,15 @@ bndry_all = neumann zl = z / (2*pi) function = fciwave:background + 1e-3*exp(-((x-0.7)/0.1)^2 - ((zl-0.3)/0.1)^2) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [logn] function = log(n:function) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [v] diff --git a/examples/fci-wave/div/BOUT.inp b/examples/fci-wave/div/BOUT.inp index 70b60757eb..3f497df6c7 100644 --- a/examples/fci-wave/div/BOUT.inp +++ b/examples/fci-wave/div/BOUT.inp @@ -21,7 +21,7 @@ log_density = false # Evolve log(n)? background = 1e-06 # Background density [all] -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 bndry_all = neumann [n] @@ -29,15 +29,15 @@ bndry_all = neumann zl = z / (2*pi) function = fciwave:background + 1e-3*exp(-((x-0.7)/0.1)^2 - ((zl-0.3)/0.1)^2) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [logn] function = log(n:function) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [v] diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx index 62cfd4d3d9..2c96ce7ffa 100644 --- a/examples/fci-wave/fci-wave.cxx +++ b/examples/fci-wave/fci-wave.cxx @@ -69,7 +69,7 @@ class FCIwave : public PhysicsModel { // Neumann boundaries simplifies parallel derivatives Bxyz.applyBoundary("neumann"); - Bxyz.applyParallelBoundary("parallel_neumann"); + Bxyz.applyParallelBoundary("parallel_neumann_o2"); SAVE_ONCE(Bxyz); SOLVE_FOR(nv); diff --git a/examples/fci-wave/logn/BOUT.inp b/examples/fci-wave/logn/BOUT.inp index f97d8cc891..26f8a99d63 100644 --- a/examples/fci-wave/logn/BOUT.inp +++ b/examples/fci-wave/logn/BOUT.inp @@ -21,7 +21,7 @@ log_density = true # Evolve log(n)? background = 1e-06 # Background density [all] -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 bndry_all = neumann [n] @@ -29,15 +29,15 @@ bndry_all = neumann zl = z / (2*pi) function = fciwave:background + 1e-3*exp(-((x-0.7)/0.1)^2 - ((zl-0.3)/0.1)^2) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [logn] function = log(n:function) -bndry_par_yup = parallel_neumann -bndry_par_ydown = parallel_neumann +bndry_par_yup = parallel_neumann_o2 +bndry_par_ydown = parallel_neumann_o2 [nv] diff --git a/examples/laplace-petsc3d/data/BOUT.inp b/examples/laplace-petsc3d/data/BOUT.inp index 86a52c69f2..7e81d992a2 100644 --- a/examples/laplace-petsc3d/data/BOUT.inp +++ b/examples/laplace-petsc3d/data/BOUT.inp @@ -6,7 +6,7 @@ mz = 128 function = mixmode(x, 1.)*mixmode(y, 2.)*mixmode(z, 3.) bndry_xin = none bndry_xout = none -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [rhs] function = mixmode(x, 4.)*mixmode(y, 5.)*mixmode(z, 6.) @@ -22,7 +22,7 @@ function = 1. + .1*mixmode(x, 10.)*mixmode(y, 11.)*mixmode(z, 12.) [C2] #function = 0. function = .1*mixmode(x, 13.)*mixmode(y, 14.)*mixmode(z, 15.) -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [A] function = 0.0 @@ -46,7 +46,7 @@ transform_from_field_aligned = false [initial] bndry_xin = neumann bndry_xout = neumann -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [input1] function = mixmode(x, 1.)*mixmode(z, 2.) diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx index ad1ed6fb6d..d9adf5abd0 100644 --- a/src/mesh/coordinates.cxx +++ b/src/mesh/coordinates.cxx @@ -1574,7 +1574,7 @@ Field3D Coordinates::DDY(const Field3D& f, CELL_LOC outloc, const std::string& m if (! f.hasParallelSlices() and ! transform->canToFromFieldAligned()) { Field3D f_parallel = f; transform->calcParallelSlices(f_parallel); - f_parallel.applyParallelBoundary("parallel_neumann"); + f_parallel.applyParallelBoundary("parallel_neumann_o2"); return bout::derivatives::index::DDY(f_parallel, outloc, method, region); } #endif @@ -1686,6 +1686,7 @@ Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outl auto invSg = 1.0 / sqrt(g_22); // Communicate to get parallel slices localmesh->communicate(invSg); + invSg.applyParallelBoundary("parallel_neumann_o2"); auto result = DDY(invSg, outloc, method) * DDY(f, outloc, method) * invSg + D2DY2(f, outloc, method) / g_22; @@ -1703,6 +1704,7 @@ Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc, auto invSg = 1.0 / sqrt(g_22); // Communicate to get parallel slices localmesh->communicate(invSg); + invSg.applyParallelBoundary("parallel_neumann_o2"); auto sg = DDY(invSg, outloc, method) * invSg; Field3D result = ::DDY(f, outloc, method); diff --git a/tests/integrated/test-laplace-hypre3d/data_circular_core-sol/BOUT.inp b/tests/integrated/test-laplace-hypre3d/data_circular_core-sol/BOUT.inp index 9a6ac24fa1..46d3cb55ba 100644 --- a/tests/integrated/test-laplace-hypre3d/data_circular_core-sol/BOUT.inp +++ b/tests/integrated/test-laplace-hypre3d/data_circular_core-sol/BOUT.inp @@ -1,7 +1,7 @@ [f] #function = 0. function = mixmode(x, 1.)*mixmode(y, 2.)*mixmode(z, 3.) -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [rhs] function = mixmode(x, 4.)*mixmode(y, 5.)*mixmode(z, 6.) @@ -17,7 +17,7 @@ function = 1. + .1*mixmode(x, 10.)*mixmode(y, 11.)*mixmode(z, 12.) [C2] #function = 0. function = .1*mixmode(x, 13.)*mixmode(y, 14.)*mixmode(z, 15.) -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [A] function = 0. diff --git a/tests/integrated/test-laplace-hypre3d/data_circular_core/BOUT.inp b/tests/integrated/test-laplace-hypre3d/data_circular_core/BOUT.inp index eb78644f0f..be0c697d80 100644 --- a/tests/integrated/test-laplace-hypre3d/data_circular_core/BOUT.inp +++ b/tests/integrated/test-laplace-hypre3d/data_circular_core/BOUT.inp @@ -16,7 +16,7 @@ function = 1. + .1*mixmode(x, 10.)*mixmode(y, 11.)*mixmode(z, 12.) [C2] #function = 0. function = .1*mixmode(x, 13.)*mixmode(y, 14.)*mixmode(z, 15.) -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [A] function = 0. diff --git a/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp b/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp index d69cb51166..1453e99b77 100644 --- a/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp +++ b/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp @@ -17,7 +17,7 @@ function = 1. + .1*mixmode(x, 10.)*mixmode(y, 11.)*mixmode(z, 12.) [C2] #function = 0. function = .1*mixmode(x, 13.)*mixmode(y, 14.)*mixmode(z, 15.) -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [A] function = 0.0 diff --git a/tests/integrated/test-laplace-petsc3d/data_circular_core/BOUT.inp b/tests/integrated/test-laplace-petsc3d/data_circular_core/BOUT.inp index ae7cfaa5b4..059b99e91c 100644 --- a/tests/integrated/test-laplace-petsc3d/data_circular_core/BOUT.inp +++ b/tests/integrated/test-laplace-petsc3d/data_circular_core/BOUT.inp @@ -17,7 +17,7 @@ function = 1. + .1*mixmode(x, 10.)*mixmode(y, 11.)*mixmode(z, 12.) [C2] #function = 0. function = .1*mixmode(x, 13.)*mixmode(y, 14.)*mixmode(z, 15.) -bndry_par_all = parallel_neumann +bndry_par_all = parallel_neumann_o2 [A] function = 0.0 From f8354ddfc03bf938a778ba8b53d78a1778892bed Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 18 Jan 2023 10:54:44 +0100 Subject: [PATCH 048/412] dy is currently not used keep it in the interface for the case we ever support higher order parallel derivatives, including non-uniform dy. --- src/mesh/parallel/fci.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index a8cd1947c2..075463323b 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -47,7 +47,7 @@ #include -FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, +FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options& options, int offset_, BoundaryRegionPar* inner_boundary, BoundaryRegionPar* outer_boundary, bool zperiodic) : map_mesh(mesh), offset(offset_), boundary_mask(map_mesh), From 4e5fd789ab56cd7f19ac878f980e8d6431072a4c Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 2 Feb 2023 11:58:58 +0100 Subject: [PATCH 049/412] Add missing headers --- tests/unit/fake_parallel_mesh.hxx | 3 +++ tests/unit/mesh/test_boundary_factory.cxx | 1 + tests/unit/test_extras.hxx | 1 + 3 files changed, 5 insertions(+) diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx index 0228042955..e03d181b36 100644 --- a/tests/unit/fake_parallel_mesh.hxx +++ b/tests/unit/fake_parallel_mesh.hxx @@ -17,6 +17,9 @@ #include "bout/fieldgroup.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" +#include "boundary_region.hxx" +#include "boundary_op.hxx" + class Options; diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx index fced8be432..19dc8d07ca 100644 --- a/tests/unit/mesh/test_boundary_factory.cxx +++ b/tests/unit/mesh/test_boundary_factory.cxx @@ -2,6 +2,7 @@ #include "boundary_factory.hxx" #include "boundary_region.hxx" +#include "boundary_op.hxx" #include "test_extras.hxx" diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index edd096b0a0..31a20b9a53 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -15,6 +15,7 @@ #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" #include "bout/operatorstencil.hxx" +#include "boundary_region.hxx" static constexpr BoutReal BoutRealTolerance{1e-15}; // FFTs have a slightly looser tolerance than other functions From 5b2030edbf92f506208c8496c444523fab82a29b Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 8 Feb 2023 09:29:11 +0000 Subject: [PATCH 050/412] Apply black changes --- bin/bout-v5-xzinterpolation-upgrader.py | 3 --- bin/bout_3to4.py | 1 - src/field/gen_fieldops.py | 2 -- tests/MMS/GBS/circle.py | 1 - tests/MMS/GBS/mms-slab3d.py | 1 - tests/MMS/GBS/runtest-slab3d | 1 - tests/integrated/test-drift-instability/runtest | 1 - tests/integrated/test-multigrid_laplace/runtest | 1 - .../test-multigrid_laplace/runtest_multiple_grids | 1 - tests/integrated/test-multigrid_laplace/runtest_unsheared | 1 - tests/integrated/test-naulin-laplace/runtest | 1 - .../integrated/test-naulin-laplace/runtest_multiple_grids | 1 - tests/integrated/test-naulin-laplace/runtest_unsheared | 1 - tests/integrated/test-petsc_laplace_MAST-grid/runtest | 1 - tests/integrated/test-twistshift-staggered/runtest | 1 + tests/integrated/test-twistshift/runtest | 2 ++ tests/integrated/test-yupdown-weights/runtest | 1 - tests/integrated/test-yupdown/runtest | 1 - tests/integrated/test_suite | 1 + tools/pylib/post_bout/__init__.py | 1 - tools/pylib/post_bout/basic_info.py | 3 --- tools/pylib/post_bout/grate2.py | 2 -- tools/pylib/post_bout/pb_corral.py | 4 ---- tools/pylib/post_bout/pb_draw.py | 7 ------- tools/pylib/post_bout/pb_nonlinear.py | 1 - tools/pylib/post_bout/pb_present.py | 1 - tools/pylib/post_bout/read_cxx.py | 1 - tools/pylib/post_bout/read_inp.py | 3 --- tools/pylib/post_bout/rms.py | 1 - tools/tokamak_grids/elite/elite2nc | 1 + tools/tokamak_grids/gato/gato2nc | 1 + 31 files changed, 6 insertions(+), 43 deletions(-) diff --git a/bin/bout-v5-xzinterpolation-upgrader.py b/bin/bout-v5-xzinterpolation-upgrader.py index 1e19c6a034..37c79e0de8 100755 --- a/bin/bout-v5-xzinterpolation-upgrader.py +++ b/bin/bout-v5-xzinterpolation-upgrader.py @@ -64,7 +64,6 @@ def fix_header_includes(old_header, new_header, source): def fix_interpolations(old_interpolation, new_interpolation, source): - return re.sub( r""" \b{}\b @@ -118,7 +117,6 @@ def clang_fix_interpolation(old_interpolation, new_interpolation, node, source): def fix_factories(old_factory, new_factory, source): - return re.sub( r""" \b{}\b @@ -186,7 +184,6 @@ def apply_fixes(headers, interpolations, factories, source): def clang_apply_fixes(headers, interpolations, factories, filename, source): - # translation unit tu = clang_parse(filename, source) diff --git a/bin/bout_3to4.py b/bin/bout_3to4.py index 02481fcf6e..d41db36fbb 100755 --- a/bin/bout_3to4.py +++ b/bin/bout_3to4.py @@ -195,7 +195,6 @@ def throw_warnings(line_text, filename, line_num): if __name__ == "__main__": - epilog = """ Currently bout_3to4 can detect the following transformations are needed: - Triple square brackets instead of round brackets for subscripts diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py index 646580559f..68a3a1b059 100755 --- a/src/field/gen_fieldops.py +++ b/src/field/gen_fieldops.py @@ -189,7 +189,6 @@ def returnType(f1, f2): if __name__ == "__main__": - parser = argparse.ArgumentParser( description="Generate code for the Field arithmetic operators" ) @@ -274,7 +273,6 @@ def returnType(f1, f2): rhs.name = "rhs" for operator, operator_name in operators.items(): - template_args = { "operator": operator, "operator_name": operator_name, diff --git a/tests/MMS/GBS/circle.py b/tests/MMS/GBS/circle.py index b2553f47c3..b33cc77d8c 100644 --- a/tests/MMS/GBS/circle.py +++ b/tests/MMS/GBS/circle.py @@ -30,7 +30,6 @@ def generate( mxg=2, file="circle.nc", ): - # q = rBt / RBp Bp = r * Bt / (R * q) diff --git a/tests/MMS/GBS/mms-slab3d.py b/tests/MMS/GBS/mms-slab3d.py index f88a897c98..2f958cfa69 100644 --- a/tests/MMS/GBS/mms-slab3d.py +++ b/tests/MMS/GBS/mms-slab3d.py @@ -277,7 +277,6 @@ def C(f): # print "\n\nDelp2 phi = ", Delp2(phi, metric).subs(replace) if not estatic: - Spsi = Delp2(psi, metric) - 0.5 * Ne * mi_me * beta_e * psi - Ne * (Vi - VePsi) print("\n[psi]") print("\nsolution = " + exprToStr(psi.subs(replace))) diff --git a/tests/MMS/GBS/runtest-slab3d b/tests/MMS/GBS/runtest-slab3d index cdcde3e1b3..f193583e47 100755 --- a/tests/MMS/GBS/runtest-slab3d +++ b/tests/MMS/GBS/runtest-slab3d @@ -95,7 +95,6 @@ with open("mms-slab3d.pkl", "wb") as output: # plot errors for var, mark in zip(varlist, markers): - order = log(error_2[var][-1] / error_2[var][-2]) / log(dx[-1] / dx[-2]) print("%s Convergence order = %f" % (var, order)) if 1.9 < order < 2.1: diff --git a/tests/integrated/test-drift-instability/runtest b/tests/integrated/test-drift-instability/runtest index 16b35d69d9..e8ddddc11d 100755 --- a/tests/integrated/test-drift-instability/runtest +++ b/tests/integrated/test-drift-instability/runtest @@ -197,7 +197,6 @@ def run_zeff_case(zeff): if __name__ == "__main__": - parser = argparse.ArgumentParser("Run drift-instability test") parser.add_argument( "-Z", diff --git a/tests/integrated/test-multigrid_laplace/runtest b/tests/integrated/test-multigrid_laplace/runtest index 76914d19e4..4a7455f80b 100755 --- a/tests/integrated/test-multigrid_laplace/runtest +++ b/tests/integrated/test-multigrid_laplace/runtest @@ -29,7 +29,6 @@ print("Running multigrid Laplacian inversion test") success = True for nproc in [1, 3]: - # Make sure we don't use too many cores: # Reduce number of OpenMP threads when using multiple MPI processes mthread = 2 diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids index 26cdd96ff6..6817120b13 100755 --- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids +++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids @@ -26,7 +26,6 @@ success = True for nproc in [1, 2, 4]: for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]: - # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver) cmd = "./test_multigrid_laplace -f " + inputfile + " NXPE=" + str(nproc) diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared index fd0e11fbbf..cda68f2167 100755 --- a/tests/integrated/test-multigrid_laplace/runtest_unsheared +++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared @@ -25,7 +25,6 @@ print("Running multigrid Laplacian inversion test") success = True for nproc in [1, 3]: - # Make sure we don't use too many cores: # Reduce number of OpenMP threads when using multiple MPI processes mthread = 2 diff --git a/tests/integrated/test-naulin-laplace/runtest b/tests/integrated/test-naulin-laplace/runtest index 82dd22776e..f972eab6cc 100755 --- a/tests/integrated/test-naulin-laplace/runtest +++ b/tests/integrated/test-naulin-laplace/runtest @@ -29,7 +29,6 @@ print("Running LaplaceNaulin inversion test") success = True for nproc in [1, 3]: - # Make sure we don't use too many cores: # Reduce number of OpenMP threads when using multiple MPI processes mthread = 2 diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids index 2d583fd1b8..c0281c3a4e 100755 --- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids +++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids @@ -26,7 +26,6 @@ success = True for nproc in [1, 2, 4]: for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]: - # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver) cmd = "./test_naulin_laplace -f " + inputfile + " NXPE=" + str(nproc) diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared index ec956686ef..8f47f33026 100755 --- a/tests/integrated/test-naulin-laplace/runtest_unsheared +++ b/tests/integrated/test-naulin-laplace/runtest_unsheared @@ -25,7 +25,6 @@ print("Running LaplaceNaulin inversion test") success = True for nproc in [1, 3]: - # Make sure we don't use too many cores: # Reduce number of OpenMP threads when using multiple MPI processes mthread = 2 diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/runtest b/tests/integrated/test-petsc_laplace_MAST-grid/runtest index c1c973e3b2..bf6656fbf2 100755 --- a/tests/integrated/test-petsc_laplace_MAST-grid/runtest +++ b/tests/integrated/test-petsc_laplace_MAST-grid/runtest @@ -43,7 +43,6 @@ for nproc in [1, 2, 4]: # if nproc > 2: # nxpe = 2 for jy in [2, 34, 65, 81, 113]: - cmd = ( "./test_petsc_laplace_MAST_grid grid=grids/grid_MAST_SOL_jyis{}.nc".format( jy diff --git a/tests/integrated/test-twistshift-staggered/runtest b/tests/integrated/test-twistshift-staggered/runtest index 2976a80ecd..5bb9963db7 100755 --- a/tests/integrated/test-twistshift-staggered/runtest +++ b/tests/integrated/test-twistshift-staggered/runtest @@ -24,6 +24,7 @@ check = collect("check", path=datapath, yguards=True, info=False) success = True + # Check test_aligned is *not* periodic in y def test1(ylower, yupper): global success diff --git a/tests/integrated/test-twistshift/runtest b/tests/integrated/test-twistshift/runtest index 26b5c2b135..c4858970c4 100755 --- a/tests/integrated/test-twistshift/runtest +++ b/tests/integrated/test-twistshift/runtest @@ -24,6 +24,7 @@ result = collect("result", path=datapath, yguards=True, info=False) success = True + # Check test_aligned is *not* periodic in y def test1(ylower, yupper): global success @@ -49,6 +50,7 @@ if numpy.any(numpy.abs(result - test) > tol): print("Fail - result has not been communicated correctly - is different from input") success = False + # Check result is periodic in y def test2(ylower, yupper): global success diff --git a/tests/integrated/test-yupdown-weights/runtest b/tests/integrated/test-yupdown-weights/runtest index e40b81368f..4b59d08cb0 100755 --- a/tests/integrated/test-yupdown-weights/runtest +++ b/tests/integrated/test-yupdown-weights/runtest @@ -10,7 +10,6 @@ build_and_log("parallel slices and weights test") failed = False for shifttype in ["shiftedinterp"]: - s, out = launch_safe( "./test_yupdown_weights mesh:paralleltransform:type=" + shifttype, nproc=1, diff --git a/tests/integrated/test-yupdown/runtest b/tests/integrated/test-yupdown/runtest index 1b24f86327..34fcd36496 100755 --- a/tests/integrated/test-yupdown/runtest +++ b/tests/integrated/test-yupdown/runtest @@ -12,7 +12,6 @@ build_and_log("parallel slices test") failed = False for shifttype in ["shifted", "shiftedinterp"]: - s, out = launch_safe( "./test_yupdown mesh:paralleltransform:type=" + shifttype, nproc=1, diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite index e6012e3869..307a8d84b3 100755 --- a/tests/integrated/test_suite +++ b/tests/integrated/test_suite @@ -241,6 +241,7 @@ if args.get_list: print(test) sys.exit(0) + # A function to get more threads from the job server def get_threads(): global js_read diff --git a/tools/pylib/post_bout/__init__.py b/tools/pylib/post_bout/__init__.py index a06792ed41..069ae3e85b 100644 --- a/tools/pylib/post_bout/__init__.py +++ b/tools/pylib/post_bout/__init__.py @@ -15,7 +15,6 @@ import os try: - boutpath = os.environ["BOUT_TOP"] pylibpath = boutpath + "/tools/pylib" boutdatapath = pylibpath + "/boutdata" diff --git a/tools/pylib/post_bout/basic_info.py b/tools/pylib/post_bout/basic_info.py index 28660c39bc..563bfe6e98 100644 --- a/tools/pylib/post_bout/basic_info.py +++ b/tools/pylib/post_bout/basic_info.py @@ -10,7 +10,6 @@ def basic_info(data, meta, rescale=True, rotate=False, user_peak=0, nonlinear=None): - print("in basic_info") # from . import read_grid,parse_inp,read_inp,show @@ -227,7 +226,6 @@ def fft_info( jumps = np.where(abs(phase_r) > old_div(np.pi, 32)) # print jumps if len(jumps[0]) != 0: - all_pts = np.array(list(range(0, nt))) good_pts = (np.where(abs(phase_r) < old_div(np.pi, 3)))[0] # print good_pts,good_pts @@ -363,7 +361,6 @@ def fft_info( # return a 2d array fof boolean values, a very simple boolian filter def local_maxima(array2d, user_peak, index=False, count=4, floor=0, bug=False): - from operator import itemgetter, attrgetter if user_peak == 0: diff --git a/tools/pylib/post_bout/grate2.py b/tools/pylib/post_bout/grate2.py index 58f5a47e2b..5157863cc2 100644 --- a/tools/pylib/post_bout/grate2.py +++ b/tools/pylib/post_bout/grate2.py @@ -13,7 +13,6 @@ def avgrate(p, y=None, tind=None): - if tind is None: tind = 0 @@ -25,7 +24,6 @@ def avgrate(p, y=None, tind=None): growth = np.zeros((ni, nj)) with np.errstate(divide="ignore"): - for i in range(ni): for j in range(nj): growth[i, j] = np.gradient(np.log(rmsp_f[tind::, i, j]))[-1] diff --git a/tools/pylib/post_bout/pb_corral.py b/tools/pylib/post_bout/pb_corral.py index 412a677921..df9a9b00b6 100644 --- a/tools/pylib/post_bout/pb_corral.py +++ b/tools/pylib/post_bout/pb_corral.py @@ -40,7 +40,6 @@ def corral( cached=True, refresh=False, debug=False, IConly=1, logname="status.log", skew=False ): - print("in corral") log = read_log(logname=logname) # done = log['done'] @@ -53,7 +52,6 @@ def corral( print("current:", current) if refresh == True: - for i, path in enumerate(runs): print(i, path) a = post_bout.save(path=path, IConly=IConly) # re post-process a run @@ -61,7 +59,6 @@ def corral( elif ( cached == False ): # if all the ind. simulation pkl files are in place skip this part - a = post_bout.save(path=current) # save to current dir # here is really where you shoudl write to status.log # write_log('status.log', @@ -111,7 +108,6 @@ def islist(input): class LinRes(object): def __init__(self, all_modes): - self.mode_db = all_modes self.db = all_modes # self.ave_db = all_ave diff --git a/tools/pylib/post_bout/pb_draw.py b/tools/pylib/post_bout/pb_draw.py index 75bca03a15..272aab9c35 100644 --- a/tools/pylib/post_bout/pb_draw.py +++ b/tools/pylib/post_bout/pb_draw.py @@ -140,7 +140,6 @@ def plottheory( fig1.savefig(pp, format="pdf") plt.close(fig1) else: # if not plot its probably plotted iwth sim data, print chi somewhere - for i, m in enumerate(s.models): textstr = r"$\chi^2$" + "$=%.2f$" % (m.chi[comp].sum()) print(textstr) @@ -173,7 +172,6 @@ def plotomega( trans=False, infobox=True, ): - colors = [ "b.", "r.", @@ -1064,7 +1062,6 @@ def plotmodes( linestyle="-", summary=True, ): - Nplots = self.nrun colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] @@ -1265,7 +1262,6 @@ def plotmodes( def plotradeigen( self, pp, field="Ni", comp="amp", yscale="linear", xscale="linear" ): - Nplots = self.nrun colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] fig1 = plt.figure() @@ -1368,7 +1364,6 @@ def plotmodes2( xrange=1, debug=False, ): - Nplots = self.nrun Modes = subset(self.db, "field", [field]) # pick field colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] @@ -1464,7 +1459,6 @@ def plotMacroDep( def savemovie( self, field="Ni", yscale="log", xscale="log", moviename="spectrum.avi" ): - print("Making movie animation.mpg - this make take a while") files = [] @@ -1504,7 +1498,6 @@ def savemovie( os.system("rm *png") def printmeta(self, pp, filename="output2.pdf", debug=False): - import os from pyPdf import PdfFileWriter, PdfFileReader diff --git a/tools/pylib/post_bout/pb_nonlinear.py b/tools/pylib/post_bout/pb_nonlinear.py index c14072cff5..3fb726d4f8 100644 --- a/tools/pylib/post_bout/pb_nonlinear.py +++ b/tools/pylib/post_bout/pb_nonlinear.py @@ -46,7 +46,6 @@ def plotnlrhs( xscale="linear", xrange=1, ): - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] Modes = subset(self.db, "field", [field]) # pick field diff --git a/tools/pylib/post_bout/pb_present.py b/tools/pylib/post_bout/pb_present.py index e1fc92ea6d..64fcaf1ec6 100644 --- a/tools/pylib/post_bout/pb_present.py +++ b/tools/pylib/post_bout/pb_present.py @@ -96,7 +96,6 @@ def show( for j in list( set(s.dz).union() ): # looping over runs, over unique 'dz' key values - ss = subset(s.db, "dz", [j]) # subset where dz = j plt.scatter(ss.MN[:, 1], ss.MN[:, 0], c=colors[i]) plt.annotate(str(j), (ss.MN[0, 1], ss.MN[0, 0])) diff --git a/tools/pylib/post_bout/read_cxx.py b/tools/pylib/post_bout/read_cxx.py index 907edc48a7..eda88aac5b 100644 --- a/tools/pylib/post_bout/read_cxx.py +++ b/tools/pylib/post_bout/read_cxx.py @@ -98,7 +98,6 @@ def get_evolved_cxx(cxxfile=None): def read_cxx(path=".", boutcxx="physics_code.cxx.ref", evolved=""): - # print path, boutcxx boutcxx = path + "/" + boutcxx # boutcxx = open(boutcxx,'r').readlines() diff --git a/tools/pylib/post_bout/read_inp.py b/tools/pylib/post_bout/read_inp.py index 40a60774af..87de7ddf3a 100644 --- a/tools/pylib/post_bout/read_inp.py +++ b/tools/pylib/post_bout/read_inp.py @@ -12,7 +12,6 @@ def read_inp(path="", boutinp="BOUT.inp"): - boutfile = path + "/" + boutinp boutinp = open(boutfile, "r").readlines() @@ -29,7 +28,6 @@ def read_inp(path="", boutinp="BOUT.inp"): def parse_inp(boutlist): - import re from ordereddict import OrderedDict @@ -67,7 +65,6 @@ def parse_inp(boutlist): def read_log(path=".", logname="status.log"): - print("in read_log") import re from ordereddict import OrderedDict diff --git a/tools/pylib/post_bout/rms.py b/tools/pylib/post_bout/rms.py index 9ec23d9f90..6a9bdb1929 100644 --- a/tools/pylib/post_bout/rms.py +++ b/tools/pylib/post_bout/rms.py @@ -14,7 +14,6 @@ def rms(f): - nt = f.shape[0] ns = f.shape[1] diff --git a/tools/tokamak_grids/elite/elite2nc b/tools/tokamak_grids/elite/elite2nc index eb17c13bd9..669c36aef9 100755 --- a/tools/tokamak_grids/elite/elite2nc +++ b/tools/tokamak_grids/elite/elite2nc @@ -57,6 +57,7 @@ if not desc: print("Description: " + desc) + # Define a generator to get the next token from the file def file_tokens(fp): toklist = [] diff --git a/tools/tokamak_grids/gato/gato2nc b/tools/tokamak_grids/gato/gato2nc index ba4cdc6e69..4ed2b2d632 100755 --- a/tools/tokamak_grids/gato/gato2nc +++ b/tools/tokamak_grids/gato/gato2nc @@ -68,6 +68,7 @@ print("Date: " + date) desc = f.readline() print("Description: " + desc) + # Define a generator to get the next token from the file def file_tokens(fp): """Generator to get numbers from a text file""" From 71c04f2d6b6f1d3ea6c5f6ecfa769c91973c8d1a Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 8 Feb 2023 10:09:47 +0000 Subject: [PATCH 051/412] Apply clang-format changes --- include/bout/mesh.hxx | 15 ++++++++----- src/field/field3d.cxx | 22 +++++++++---------- src/field/field_data.cxx | 12 +++++----- src/mesh/boundary_factory.cxx | 6 ++--- src/mesh/difops.cxx | 3 ++- src/mesh/impls/bout/boutmesh.cxx | 6 +++-- src/mesh/impls/bout/boutmesh.hxx | 3 ++- .../test-fci-boundary/get_par_bndry.cxx | 14 +++++++----- 8 files changed, 45 insertions(+), 36 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 66ea61ac82..c3126f8ce0 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -91,7 +91,8 @@ public: ReturnType create(Options* options = nullptr, GridDataSource* source = nullptr) const; }; -BOUT_ENUM_CLASS(BoundaryParType, all, xin, xout, fwd, bwd, xin_fwd, xout_fwd, xin_bwd, xout_bwd, SIZE); +BOUT_ENUM_CLASS(BoundaryParType, all, xin, xout, fwd, bwd, xin_fwd, xout_fwd, xin_bwd, + xout_bwd, SIZE); template using RegisterMesh = MeshFactory::RegisterInFactory; @@ -484,12 +485,14 @@ class Mesh { /// Add a boundary region to this processor virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {} - /// Get all the parallel (Y) boundaries on this processor - virtual std::vector getBoundariesPar(BoundaryParType type=BoundaryParType::all) = 0; + /// Get all the parallel (Y) boundaries on this processor + virtual std::vector + getBoundariesPar(BoundaryParType type = BoundaryParType::all) = 0; + + /// Add a parallel(Y) boundary to this processor + virtual void addBoundaryPar(BoundaryRegionPar* UNUSED(bndry), + BoundaryParType UNUSED(type)) {} - /// Add a parallel(Y) boundary to this processor - virtual void addBoundaryPar(BoundaryRegionPar* UNUSED(bndry), BoundaryParType UNUSED(type)) {} - /// Branch-cut special handling (experimental) virtual Field3D smoothSeparatrix(const Field3D &f) {return f;} diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 8ad531ef74..7d48b3914d 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -32,20 +32,20 @@ #include -#include -#include -#include -#include -#include -#include -#include -#include "parallel_boundary_region.hxx" #include "parallel_boundary_op.hxx" +#include "parallel_boundary_region.hxx" +#include +#include +#include +#include #include -#include +#include +#include +#include +#include #include -#include -#include +#include +#include /// Constructor Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx index 2b46d0bf50..2c7ba6b1fb 100644 --- a/src/field/field_data.cxx +++ b/src/field/field_data.cxx @@ -1,13 +1,13 @@ +#include "parallel_boundary_op.hxx" +#include "parallel_boundary_region.hxx" +#include "unused.hxx" #include -#include -#include #include -#include "parallel_boundary_region.hxx" -#include "parallel_boundary_op.hxx" -#include +#include #include -#include "unused.hxx" +#include +#include namespace bout { /// Make sure \p location is a sensible value for \p mesh diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx index 0e06ac71cb..87f7835796 100644 --- a/src/mesh/boundary_factory.cxx +++ b/src/mesh/boundary_factory.cxx @@ -1,8 +1,8 @@ -#include +#include "parallel_boundary_op.hxx" +#include "parallel_boundary_region.hxx" #include #include -#include "parallel_boundary_region.hxx" -#include "parallel_boundary_op.hxx" +#include #include #include diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx index 2fa2e36a81..17cf135e4f 100644 --- a/src/mesh/difops.cxx +++ b/src/mesh/difops.cxx @@ -348,7 +348,8 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f, CELL_LOC outloc) } Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc) { - if (outloc == CELL_DEFAULT) outloc = f.getLocation(); + if (outloc == CELL_DEFAULT) + outloc = f.getLocation(); return interp_to(kY, outloc)*Grad2_par2(f, outloc) + Div_par(kY, outloc)*Grad_par(f, outloc); } diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 5abc3664bd..f836e2370d 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -2958,9 +2958,11 @@ RangeIterator BoutMesh::iterateBndryUpperY() const { std::vector BoutMesh::getBoundaries() { return boundary; } -std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { return par_boundary[static_cast(type)] ; } +std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { + return par_boundary[static_cast(type)]; +} -void BoutMesh::addBoundaryPar(BoundaryRegionPar *bndry, BoundaryParType type) { +void BoutMesh::addBoundaryPar(BoundaryRegionPar* bndry, BoundaryParType type) { output_info << "Adding new parallel boundary: " << bndry->label << endl; switch (type) { case BoundaryParType::xin_fwd: diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx index 565f15ce34..98fb1548bd 100644 --- a/src/mesh/impls/bout/boutmesh.hxx +++ b/src/mesh/impls/bout/boutmesh.hxx @@ -391,7 +391,8 @@ protected: private: std::vector boundary; // Vector of boundary regions - std::vector> par_boundary; // Vector of parallel boundary regions + std::vector> + par_boundary; // Vector of parallel boundary regions ////////////////////////////////////////////////// // Communications diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx index 0ad49c3cbb..0d58a4b082 100644 --- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx +++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx @@ -9,20 +9,22 @@ int main(int argc, char** argv) { std::vector fields; fields.resize(static_cast(BoundaryParType::SIZE)); - for (int i=0; i< fields.size(); i++){ + for (int i = 0; i < fields.size(); i++) { fields[i] = Field3D{0.0}; mesh->communicate(fields[i]); - for (const auto &bndry_par : mesh->getBoundariesPar(static_cast(i))) { + for (const auto& bndry_par : + mesh->getBoundariesPar(static_cast(i))) { output.write("{:s} region\n", toString(static_cast(i))); for (bndry_par->first(); !bndry_par->isDone(); bndry_par->next()) { - fields[i](bndry_par->x, bndry_par->y, bndry_par->z) += 1; - output.write("{:s} increment\n", toString(static_cast(i))); + fields[i](bndry_par->x, bndry_par->y, bndry_par->z) += 1; + output.write("{:s} increment\n", toString(static_cast(i))); } } output.write("{:s} done\n", toString(static_cast(i))); - bout::globals::dump.addOnce(fields[i], fmt::format("field_{:s}", toString(static_cast(i)))); + bout::globals::dump.addOnce( + fields[i], fmt::format("field_{:s}", toString(static_cast(i)))); } - + bout::globals::dump.write(); BoutFinalise(); From 6ce73052e6e122276a9f090135f479768dfd4f0a Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 8 Feb 2023 13:33:21 +0100 Subject: [PATCH 052/412] Fix missing includes --- src/mesh/impls/bout/boutmesh.cxx | 2 ++ src/mesh/parallel/shiftedmetric.cxx | 1 + src/mesh/parallel/shiftedmetricinterp.cxx | 3 +++ tests/integrated/test-fci-boundary/get_par_bndry.cxx | 8 +++++--- tests/unit/fake_parallel_mesh.hxx | 1 + tests/unit/mesh/test_boundary_factory.cxx | 1 + tests/unit/test_extras.hxx | 1 + 7 files changed, 14 insertions(+), 3 deletions(-) diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index f836e2370d..b82d58a429 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -39,6 +39,8 @@ #include #include #include +#include +#include #include #include #include diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index f5ed3a7987..9c686b801f 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -10,6 +10,7 @@ #include #include #include +#include #include #include diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 694c34f084..facb9d6ac1 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -30,6 +30,9 @@ #include "shiftedmetricinterp.hxx" #include "mask.hxx" #include "bout/constants.hxx" +#include +#include + ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, Field2D zShift_in, BoutReal zlength_in, diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx index 0d58a4b082..d656b736bf 100644 --- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx +++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx @@ -1,6 +1,7 @@ #include "bout.hxx" #include "derivs.hxx" #include "field_factory.hxx" +#include "parallel_boundary_region.hxx" int main(int argc, char** argv) { BoutInitialise(argc, argv); @@ -9,6 +10,7 @@ int main(int argc, char** argv) { std::vector fields; fields.resize(static_cast(BoundaryParType::SIZE)); + Options dump; for (int i = 0; i < fields.size(); i++) { fields[i] = Field3D{0.0}; mesh->communicate(fields[i]); @@ -21,11 +23,11 @@ int main(int argc, char** argv) { } } output.write("{:s} done\n", toString(static_cast(i))); - bout::globals::dump.addOnce( - fields[i], fmt::format("field_{:s}", toString(static_cast(i)))); + + dump[fmt::format("field_{:s}", toString(static_cast(i)))] = fields[i]; } - bout::globals::dump.write(); + bout::writeDefaultOutputFile(dump); BoutFinalise(); } diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx index 0228042955..d0c9f90233 100644 --- a/tests/unit/fake_parallel_mesh.hxx +++ b/tests/unit/fake_parallel_mesh.hxx @@ -17,6 +17,7 @@ #include "bout/fieldgroup.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" +#include "boundary_region.hxx" class Options; diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx index fced8be432..19dc8d07ca 100644 --- a/tests/unit/mesh/test_boundary_factory.cxx +++ b/tests/unit/mesh/test_boundary_factory.cxx @@ -2,6 +2,7 @@ #include "boundary_factory.hxx" #include "boundary_region.hxx" +#include "boundary_op.hxx" #include "test_extras.hxx" diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 26e9fac10d..b0ed45c12e 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -15,6 +15,7 @@ #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" #include "bout/operatorstencil.hxx" +#include "boundary_region.hxx" static constexpr BoutReal BoutRealTolerance{1e-15}; // FFTs have a slightly looser tolerance than other functions From c29da789812c4a61c2a2849d1682dcb98e0c111d Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 8 Feb 2023 12:34:50 +0000 Subject: [PATCH 053/412] Apply clang-format changes --- src/mesh/impls/bout/boutmesh.cxx | 4 ++-- src/mesh/parallel/shiftedmetricinterp.cxx | 1 - tests/integrated/test-fci-boundary/get_par_bndry.cxx | 5 +++-- tests/unit/fake_parallel_mesh.hxx | 2 +- tests/unit/mesh/test_boundary_factory.cxx | 2 +- tests/unit/test_extras.hxx | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index b82d58a429..98e30cb646 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -37,16 +37,16 @@ #include #include +#include #include #include -#include -#include #include #include #include #include #include #include +#include #include #include diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index facb9d6ac1..58e2a59191 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -33,7 +33,6 @@ #include #include - ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, Field2D zShift_in, BoutReal zlength_in, Options* opt) diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx index d656b736bf..438effbd9d 100644 --- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx +++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx @@ -23,8 +23,9 @@ int main(int argc, char** argv) { } } output.write("{:s} done\n", toString(static_cast(i))); - - dump[fmt::format("field_{:s}", toString(static_cast(i)))] = fields[i]; + + dump[fmt::format("field_{:s}", toString(static_cast(i)))] = + fields[i]; } bout::writeDefaultOutputFile(dump); diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx index d0c9f90233..fc1a0670fb 100644 --- a/tests/unit/fake_parallel_mesh.hxx +++ b/tests/unit/fake_parallel_mesh.hxx @@ -8,6 +8,7 @@ #include #include "../../src/mesh/impls/bout/boutmesh.hxx" +#include "boundary_region.hxx" #include "boutcomm.hxx" #include "field2d.hxx" #include "field3d.hxx" @@ -17,7 +18,6 @@ #include "bout/fieldgroup.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" -#include "boundary_region.hxx" class Options; diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx index 19dc8d07ca..589ef971b1 100644 --- a/tests/unit/mesh/test_boundary_factory.cxx +++ b/tests/unit/mesh/test_boundary_factory.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" #include "boundary_factory.hxx" -#include "boundary_region.hxx" #include "boundary_op.hxx" +#include "boundary_region.hxx" #include "test_extras.hxx" diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index b0ed45c12e..1ad94ddc0e 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -8,6 +8,7 @@ #include #include +#include "boundary_region.hxx" #include "boutcomm.hxx" #include "field3d.hxx" #include "unused.hxx" @@ -15,7 +16,6 @@ #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" #include "bout/operatorstencil.hxx" -#include "boundary_region.hxx" static constexpr BoutReal BoutRealTolerance{1e-15}; // FFTs have a slightly looser tolerance than other functions From 1f193d83c2d671572ea06ec430b5176aa03dadc4 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 8 Feb 2023 14:02:21 +0100 Subject: [PATCH 054/412] Improve readability Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- src/mesh/impls/bout/boutmesh.cxx | 2 +- src/mesh/impls/bout/boutmesh.hxx | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 98e30cb646..a052c304f8 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -83,7 +83,7 @@ BoutMesh::~BoutMesh() { for (const auto& bndry : boundary) { delete bndry; } - if (par_boundary.size() > 0) { + if (!par_boundary.empty()) { for (const auto& bndry : par_boundary[0]) { delete bndry; } diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx index 98fb1548bd..384f40e076 100644 --- a/src/mesh/impls/bout/boutmesh.hxx +++ b/src/mesh/impls/bout/boutmesh.hxx @@ -155,8 +155,8 @@ class BoutMesh : public Mesh { // Boundary regions std::vector getBoundaries() override; - std::vector getBoundariesPar(BoundaryParType type) override final; - void addBoundaryPar(BoundaryRegionPar* bndry, BoundaryParType type) override final; + std::vector getBoundariesPar(BoundaryParType type) final; + void addBoundaryPar(BoundaryRegionPar* bndry, BoundaryParType type) final; std::set getPossibleBoundaries() const override; Field3D smoothSeparatrix(const Field3D& f) override; From 7b435b0537735334abd0f084054edc2736685393 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 9 Feb 2023 13:30:06 +0100 Subject: [PATCH 055/412] Skip test-fci-boundary with legacy configure --- tests/integrated/test-fci-boundary/runtest | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest index 668bca0708..16cb4ee443 100755 --- a/tests/integrated/test-fci-boundary/runtest +++ b/tests/integrated/test-fci-boundary/runtest @@ -4,6 +4,8 @@ # # Cores: 2 +# only working with cmake +# requires: False from boututils.run_wrapper import launch_safe from boututils.datafile import DataFile from boutdata.collect import collect as _collect From 1c0a7a71e6362882f9c1258b382ba33dc0fcb708 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 11:44:41 +0100 Subject: [PATCH 056/412] get script from next --- .clang-format | 9 +- bin/bout-v5-header-upgrader.py | 217 +++++++++++++++++++++++++++++++++ 2 files changed, 223 insertions(+), 3 deletions(-) create mode 100755 bin/bout-v5-header-upgrader.py diff --git a/.clang-format b/.clang-format index f8a08001e3..f51c5bde87 100644 --- a/.clang-format +++ b/.clang-format @@ -76,6 +76,8 @@ IndentCaseLabels: false # IndentPPDirectives: None IndentWidth: 2 IndentWrappedFunctionNames: false +# requires clang-format 15+ +# InsertBraces: true KeepEmptyLinesAtTheStartOfBlocks: true MacroBlockBegin: '' MacroBlockEnd: '' @@ -91,7 +93,7 @@ PenaltyBreakString: 1000 PenaltyExcessCharacter: 1000000 PenaltyReturnTypeOnItsOwnLine: 60 PointerAlignment: Left -ReflowComments: true +ReflowComments: false SortIncludes: true # SortUsingDeclarations: true SpaceAfterCStyleCast: false @@ -105,7 +107,8 @@ SpacesInContainerLiterals: true SpacesInCStyleCastParentheses: false SpacesInParentheses: false SpacesInSquareBrackets: false -Standard: Cpp11 +StatementMacros: + - BOUT_OMP +Standard: c++14 TabWidth: 8 UseTab: Never -... diff --git a/bin/bout-v5-header-upgrader.py b/bin/bout-v5-header-upgrader.py new file mode 100755 index 0000000000..49a8fbcbe4 --- /dev/null +++ b/bin/bout-v5-header-upgrader.py @@ -0,0 +1,217 @@ +#!/usr/bin/env python3 + +import argparse +import copy +import difflib +import re +import textwrap +from pathlib import Path +from typing import List +from subprocess import run + + +header_shim_sentinel = "// BOUT++ header shim" + +header_warning = f"""\ +#pragma once +{header_shim_sentinel} +#warning Header "{{0}}" has moved to "bout/{{0}}". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/{{0}}" +""" + + +def header_needs_moving(header: Path) -> bool: + """Check if `header` has not yet been moved""" + with open(header, "r") as f: + return header_shim_sentinel not in f.read() + + +def deprecated_header_list(include_path: Path = Path("./include")): + """List of deprecated header paths (that is, those in bare + ``include`` directory) + + """ + return include_path.glob("*.hxx") + + +def write_header_shim(header: Path): + """Write 'shim' for header, that ``include``s new location""" + with open(header, "w") as f: + f.write(header_warning.format(header.name)) + + +def fix_library_header_locations( + include_path: Path = Path("./include"), quiet: bool = False +): + unmoved_headers = list( + filter(header_needs_moving, deprecated_header_list(include_path)) + ) + include_bout_path = include_path / "bout" + + if unmoved_headers == []: + print("No headers to move!") + return + + out = run("git diff-index --cached HEAD --quiet", shell=True) + if out.returncode: + raise RuntimeError( + "git index not clean! Please commit or discard any changes before continuing" + ) + + # First we move any existing headers and commit this change, so + # that history is preserved + for header in unmoved_headers: + new_path = include_bout_path / header.name + if not quiet: + print(f"Moving '{header}' to '{new_path}'") + run(f"git mv {header} {new_path}", shell=True, check=True) + + run(r"git commit -m 'Move headers to `include/bout`'", shell=True, check=True) + + # Now we can write the compatibility shim + for header in unmoved_headers: + write_header_shim(header) + + run(f"git add {' '.join(map(str, unmoved_headers))}", shell=True, check=True) + run( + r"git commit -m 'Add compatibility shims for old header locations'", + shell=True, + check=True, + ) + + +def make_header_regex(deprecated_headers: List[str]) -> re.Pattern: + """Create a regular expression to match deprecated header locations""" + deprecated_header_joined = "|".join((header.name for header in deprecated_headers)) + return re.compile(rf'(#include\s+<|")(?:\.\./)?({deprecated_header_joined})(>|")') + + +def apply_fixes(header_regex, source): + """Apply all fixes in this module""" + modified = copy.deepcopy(source) + + return header_regex.sub(r"\1bout/\2\3", modified) + + +def yes_or_no(question): + """Convert user input from yes/no variations to True/False""" + while True: + reply = input(question + " [y/N] ").lower().strip() + if not reply or reply[0] == "n": + return False + if reply[0] == "y": + return True + + +def create_patch(filename, original, modified): + """Create a unified diff between original and modified""" + + patch = "\n".join( + difflib.unified_diff( + original.splitlines(), + modified.splitlines(), + fromfile=filename, + tofile=filename, + lineterm="", + ) + ) + + return patch + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, + description=textwrap.dedent( + """\ + Fix deprecated header locations for BOUT++ v4 -> v5 + + All BOUT++ headers are now under ``include/bout`` and + should be included as ``#include ``. This + tool will fix such includes. + + For developers: the option ``--move-deprecated-headers`` + will move the headers from ``include`` to + ``include/bout``, and add a compatibility shim in the old + location. This option is mutually exclusive with + ``--files``, and should be used after running this tool + over the library files. + + WARNING: If any files do need moving, this will create a + git commit in order to preserve history across file moves. + If you have staged changes, this tool will not work, so to + avoid committing undesired or unrelated changes. + + """ + ), + ) + + parser.add_argument( + "--force", "-f", action="store_true", help="Make changes without asking" + ) + parser.add_argument( + "--quiet", "-q", action="store_true", help="Don't print patches" + ) + parser.add_argument( + "--patch-only", "-p", action="store_true", help="Print the patches and exit" + ) + parser.add_argument( + "--include-path", + "-i", + help="Path to `include` directory", + default="./include", + type=Path, + ) + + group = parser.add_mutually_exclusive_group(required=True) + group.add_argument("--files", nargs="*", action="store", help="Input files") + group.add_argument( + "--move-deprecated-headers", + action="store_true", + help="Move the deprecated headers", + ) + + args = parser.parse_args() + + if args.force and args.patch_only: + raise ValueError("Incompatible options: --force and --patch") + + deprecated_headers = deprecated_header_list(args.include_path) + + if args.move_deprecated_headers: + fix_library_header_locations(args.include_path, args.quiet) + exit(0) + + header_regex = make_header_regex(deprecated_headers) + + for filename in args.files: + with open(filename, "r") as f: + contents = f.read() + original = copy.deepcopy(contents) + + modified = apply_fixes(header_regex, contents) + patch = create_patch(filename, original, modified) + + if args.patch_only: + print(patch) + continue + + if not patch: + if not args.quiet: + print(f"No changes to make to {filename}") + continue + + if not args.quiet: + print("\n******************************************") + print(f"Changes to {filename}\n") + print(patch) + print("\n******************************************") + + if args.force: + make_change = True + else: + make_change = yes_or_no(f"Make changes to {filename}?") + + if make_change: + with open(filename, "w") as f: + f.write(modified) From cb822d759a1d30f68a15257bd0e40786797d8739 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 11:44:42 +0100 Subject: [PATCH 057/412] Move headers to `include/bout` --- include/{ => bout}/boundary_factory.hxx | 0 include/{ => bout}/boundary_op.hxx | 0 include/{ => bout}/boundary_region.hxx | 0 include/{ => bout}/boundary_standard.hxx | 0 include/{ => bout}/bout.hxx | 0 include/{ => bout}/bout_types.hxx | 0 include/{ => bout}/boutcomm.hxx | 0 include/{ => bout}/boutexception.hxx | 0 include/{ => bout}/cyclic_reduction.hxx | 0 include/{ => bout}/dcomplex.hxx | 0 include/{ => bout}/derivs.hxx | 0 include/{ => bout}/difops.hxx | 0 include/{ => bout}/fft.hxx | 0 include/{ => bout}/field.hxx | 0 include/{ => bout}/field2d.hxx | 0 include/{ => bout}/field3d.hxx | 0 include/{ => bout}/field_data.hxx | 0 include/{ => bout}/field_factory.hxx | 0 include/{ => bout}/fieldperp.hxx | 0 include/{ => bout}/globals.hxx | 0 include/{ => bout}/gyro_average.hxx | 0 include/{ => bout}/initialprofiles.hxx | 0 include/{ => bout}/interpolation.hxx | 0 include/{ => bout}/interpolation_xz.hxx | 0 include/{ => bout}/interpolation_z.hxx | 0 include/{ => bout}/invert_laplace.hxx | 0 include/{ => bout}/invert_parderiv.hxx | 0 include/{ => bout}/lapack_routines.hxx | 0 include/{ => bout}/mask.hxx | 0 include/{ => bout}/msg_stack.hxx | 0 include/{ => bout}/multiostream.hxx | 0 include/{ => bout}/options.hxx | 0 include/{ => bout}/options_netcdf.hxx | 0 include/{ => bout}/optionsreader.hxx | 0 include/{ => bout}/output.hxx | 0 include/{ => bout}/parallel_boundary_op.hxx | 0 include/{ => bout}/parallel_boundary_region.hxx | 0 include/{ => bout}/smoothing.hxx | 0 include/{ => bout}/sourcex.hxx | 0 include/{ => bout}/stencils.hxx | 0 include/{ => bout}/unused.hxx | 0 include/{ => bout}/utils.hxx | 0 include/{ => bout}/vecops.hxx | 0 include/{ => bout}/vector2d.hxx | 0 include/{ => bout}/vector3d.hxx | 0 include/{ => bout}/where.hxx | 0 46 files changed, 0 insertions(+), 0 deletions(-) rename include/{ => bout}/boundary_factory.hxx (100%) rename include/{ => bout}/boundary_op.hxx (100%) rename include/{ => bout}/boundary_region.hxx (100%) rename include/{ => bout}/boundary_standard.hxx (100%) rename include/{ => bout}/bout.hxx (100%) rename include/{ => bout}/bout_types.hxx (100%) rename include/{ => bout}/boutcomm.hxx (100%) rename include/{ => bout}/boutexception.hxx (100%) rename include/{ => bout}/cyclic_reduction.hxx (100%) rename include/{ => bout}/dcomplex.hxx (100%) rename include/{ => bout}/derivs.hxx (100%) rename include/{ => bout}/difops.hxx (100%) rename include/{ => bout}/fft.hxx (100%) rename include/{ => bout}/field.hxx (100%) rename include/{ => bout}/field2d.hxx (100%) rename include/{ => bout}/field3d.hxx (100%) rename include/{ => bout}/field_data.hxx (100%) rename include/{ => bout}/field_factory.hxx (100%) rename include/{ => bout}/fieldperp.hxx (100%) rename include/{ => bout}/globals.hxx (100%) rename include/{ => bout}/gyro_average.hxx (100%) rename include/{ => bout}/initialprofiles.hxx (100%) rename include/{ => bout}/interpolation.hxx (100%) rename include/{ => bout}/interpolation_xz.hxx (100%) rename include/{ => bout}/interpolation_z.hxx (100%) rename include/{ => bout}/invert_laplace.hxx (100%) rename include/{ => bout}/invert_parderiv.hxx (100%) rename include/{ => bout}/lapack_routines.hxx (100%) rename include/{ => bout}/mask.hxx (100%) rename include/{ => bout}/msg_stack.hxx (100%) rename include/{ => bout}/multiostream.hxx (100%) rename include/{ => bout}/options.hxx (100%) rename include/{ => bout}/options_netcdf.hxx (100%) rename include/{ => bout}/optionsreader.hxx (100%) rename include/{ => bout}/output.hxx (100%) rename include/{ => bout}/parallel_boundary_op.hxx (100%) rename include/{ => bout}/parallel_boundary_region.hxx (100%) rename include/{ => bout}/smoothing.hxx (100%) rename include/{ => bout}/sourcex.hxx (100%) rename include/{ => bout}/stencils.hxx (100%) rename include/{ => bout}/unused.hxx (100%) rename include/{ => bout}/utils.hxx (100%) rename include/{ => bout}/vecops.hxx (100%) rename include/{ => bout}/vector2d.hxx (100%) rename include/{ => bout}/vector3d.hxx (100%) rename include/{ => bout}/where.hxx (100%) diff --git a/include/boundary_factory.hxx b/include/bout/boundary_factory.hxx similarity index 100% rename from include/boundary_factory.hxx rename to include/bout/boundary_factory.hxx diff --git a/include/boundary_op.hxx b/include/bout/boundary_op.hxx similarity index 100% rename from include/boundary_op.hxx rename to include/bout/boundary_op.hxx diff --git a/include/boundary_region.hxx b/include/bout/boundary_region.hxx similarity index 100% rename from include/boundary_region.hxx rename to include/bout/boundary_region.hxx diff --git a/include/boundary_standard.hxx b/include/bout/boundary_standard.hxx similarity index 100% rename from include/boundary_standard.hxx rename to include/bout/boundary_standard.hxx diff --git a/include/bout.hxx b/include/bout/bout.hxx similarity index 100% rename from include/bout.hxx rename to include/bout/bout.hxx diff --git a/include/bout_types.hxx b/include/bout/bout_types.hxx similarity index 100% rename from include/bout_types.hxx rename to include/bout/bout_types.hxx diff --git a/include/boutcomm.hxx b/include/bout/boutcomm.hxx similarity index 100% rename from include/boutcomm.hxx rename to include/bout/boutcomm.hxx diff --git a/include/boutexception.hxx b/include/bout/boutexception.hxx similarity index 100% rename from include/boutexception.hxx rename to include/bout/boutexception.hxx diff --git a/include/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx similarity index 100% rename from include/cyclic_reduction.hxx rename to include/bout/cyclic_reduction.hxx diff --git a/include/dcomplex.hxx b/include/bout/dcomplex.hxx similarity index 100% rename from include/dcomplex.hxx rename to include/bout/dcomplex.hxx diff --git a/include/derivs.hxx b/include/bout/derivs.hxx similarity index 100% rename from include/derivs.hxx rename to include/bout/derivs.hxx diff --git a/include/difops.hxx b/include/bout/difops.hxx similarity index 100% rename from include/difops.hxx rename to include/bout/difops.hxx diff --git a/include/fft.hxx b/include/bout/fft.hxx similarity index 100% rename from include/fft.hxx rename to include/bout/fft.hxx diff --git a/include/field.hxx b/include/bout/field.hxx similarity index 100% rename from include/field.hxx rename to include/bout/field.hxx diff --git a/include/field2d.hxx b/include/bout/field2d.hxx similarity index 100% rename from include/field2d.hxx rename to include/bout/field2d.hxx diff --git a/include/field3d.hxx b/include/bout/field3d.hxx similarity index 100% rename from include/field3d.hxx rename to include/bout/field3d.hxx diff --git a/include/field_data.hxx b/include/bout/field_data.hxx similarity index 100% rename from include/field_data.hxx rename to include/bout/field_data.hxx diff --git a/include/field_factory.hxx b/include/bout/field_factory.hxx similarity index 100% rename from include/field_factory.hxx rename to include/bout/field_factory.hxx diff --git a/include/fieldperp.hxx b/include/bout/fieldperp.hxx similarity index 100% rename from include/fieldperp.hxx rename to include/bout/fieldperp.hxx diff --git a/include/globals.hxx b/include/bout/globals.hxx similarity index 100% rename from include/globals.hxx rename to include/bout/globals.hxx diff --git a/include/gyro_average.hxx b/include/bout/gyro_average.hxx similarity index 100% rename from include/gyro_average.hxx rename to include/bout/gyro_average.hxx diff --git a/include/initialprofiles.hxx b/include/bout/initialprofiles.hxx similarity index 100% rename from include/initialprofiles.hxx rename to include/bout/initialprofiles.hxx diff --git a/include/interpolation.hxx b/include/bout/interpolation.hxx similarity index 100% rename from include/interpolation.hxx rename to include/bout/interpolation.hxx diff --git a/include/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx similarity index 100% rename from include/interpolation_xz.hxx rename to include/bout/interpolation_xz.hxx diff --git a/include/interpolation_z.hxx b/include/bout/interpolation_z.hxx similarity index 100% rename from include/interpolation_z.hxx rename to include/bout/interpolation_z.hxx diff --git a/include/invert_laplace.hxx b/include/bout/invert_laplace.hxx similarity index 100% rename from include/invert_laplace.hxx rename to include/bout/invert_laplace.hxx diff --git a/include/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx similarity index 100% rename from include/invert_parderiv.hxx rename to include/bout/invert_parderiv.hxx diff --git a/include/lapack_routines.hxx b/include/bout/lapack_routines.hxx similarity index 100% rename from include/lapack_routines.hxx rename to include/bout/lapack_routines.hxx diff --git a/include/mask.hxx b/include/bout/mask.hxx similarity index 100% rename from include/mask.hxx rename to include/bout/mask.hxx diff --git a/include/msg_stack.hxx b/include/bout/msg_stack.hxx similarity index 100% rename from include/msg_stack.hxx rename to include/bout/msg_stack.hxx diff --git a/include/multiostream.hxx b/include/bout/multiostream.hxx similarity index 100% rename from include/multiostream.hxx rename to include/bout/multiostream.hxx diff --git a/include/options.hxx b/include/bout/options.hxx similarity index 100% rename from include/options.hxx rename to include/bout/options.hxx diff --git a/include/options_netcdf.hxx b/include/bout/options_netcdf.hxx similarity index 100% rename from include/options_netcdf.hxx rename to include/bout/options_netcdf.hxx diff --git a/include/optionsreader.hxx b/include/bout/optionsreader.hxx similarity index 100% rename from include/optionsreader.hxx rename to include/bout/optionsreader.hxx diff --git a/include/output.hxx b/include/bout/output.hxx similarity index 100% rename from include/output.hxx rename to include/bout/output.hxx diff --git a/include/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx similarity index 100% rename from include/parallel_boundary_op.hxx rename to include/bout/parallel_boundary_op.hxx diff --git a/include/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx similarity index 100% rename from include/parallel_boundary_region.hxx rename to include/bout/parallel_boundary_region.hxx diff --git a/include/smoothing.hxx b/include/bout/smoothing.hxx similarity index 100% rename from include/smoothing.hxx rename to include/bout/smoothing.hxx diff --git a/include/sourcex.hxx b/include/bout/sourcex.hxx similarity index 100% rename from include/sourcex.hxx rename to include/bout/sourcex.hxx diff --git a/include/stencils.hxx b/include/bout/stencils.hxx similarity index 100% rename from include/stencils.hxx rename to include/bout/stencils.hxx diff --git a/include/unused.hxx b/include/bout/unused.hxx similarity index 100% rename from include/unused.hxx rename to include/bout/unused.hxx diff --git a/include/utils.hxx b/include/bout/utils.hxx similarity index 100% rename from include/utils.hxx rename to include/bout/utils.hxx diff --git a/include/vecops.hxx b/include/bout/vecops.hxx similarity index 100% rename from include/vecops.hxx rename to include/bout/vecops.hxx diff --git a/include/vector2d.hxx b/include/bout/vector2d.hxx similarity index 100% rename from include/vector2d.hxx rename to include/bout/vector2d.hxx diff --git a/include/vector3d.hxx b/include/bout/vector3d.hxx similarity index 100% rename from include/vector3d.hxx rename to include/bout/vector3d.hxx diff --git a/include/where.hxx b/include/bout/where.hxx similarity index 100% rename from include/where.hxx rename to include/bout/where.hxx From 6b26c20a856c04df657246ce6da9df3ece58c314 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 11:44:42 +0100 Subject: [PATCH 058/412] Add compatibility shims for old header locations --- include/boundary_factory.hxx | 4 ++++ include/boundary_op.hxx | 4 ++++ include/boundary_region.hxx | 4 ++++ include/boundary_standard.hxx | 4 ++++ include/bout.hxx | 4 ++++ include/bout_types.hxx | 4 ++++ include/boutcomm.hxx | 4 ++++ include/boutexception.hxx | 4 ++++ include/cyclic_reduction.hxx | 4 ++++ include/dcomplex.hxx | 4 ++++ include/derivs.hxx | 4 ++++ include/difops.hxx | 4 ++++ include/fft.hxx | 4 ++++ include/field.hxx | 4 ++++ include/field2d.hxx | 4 ++++ include/field3d.hxx | 4 ++++ include/field_data.hxx | 4 ++++ include/field_factory.hxx | 4 ++++ include/fieldperp.hxx | 4 ++++ include/globals.hxx | 4 ++++ include/gyro_average.hxx | 4 ++++ include/initialprofiles.hxx | 4 ++++ include/interpolation.hxx | 4 ++++ include/interpolation_xz.hxx | 4 ++++ include/interpolation_z.hxx | 4 ++++ include/invert_laplace.hxx | 4 ++++ include/invert_parderiv.hxx | 4 ++++ include/lapack_routines.hxx | 4 ++++ include/mask.hxx | 4 ++++ include/msg_stack.hxx | 4 ++++ include/multiostream.hxx | 4 ++++ include/options.hxx | 4 ++++ include/options_netcdf.hxx | 4 ++++ include/optionsreader.hxx | 4 ++++ include/output.hxx | 4 ++++ include/parallel_boundary_op.hxx | 4 ++++ include/parallel_boundary_region.hxx | 4 ++++ include/smoothing.hxx | 4 ++++ include/sourcex.hxx | 4 ++++ include/stencils.hxx | 4 ++++ include/unused.hxx | 4 ++++ include/utils.hxx | 4 ++++ include/vecops.hxx | 4 ++++ include/vector2d.hxx | 4 ++++ include/vector3d.hxx | 4 ++++ include/where.hxx | 4 ++++ 46 files changed, 184 insertions(+) create mode 100644 include/boundary_factory.hxx create mode 100644 include/boundary_op.hxx create mode 100644 include/boundary_region.hxx create mode 100644 include/boundary_standard.hxx create mode 100644 include/bout.hxx create mode 100644 include/bout_types.hxx create mode 100644 include/boutcomm.hxx create mode 100644 include/boutexception.hxx create mode 100644 include/cyclic_reduction.hxx create mode 100644 include/dcomplex.hxx create mode 100644 include/derivs.hxx create mode 100644 include/difops.hxx create mode 100644 include/fft.hxx create mode 100644 include/field.hxx create mode 100644 include/field2d.hxx create mode 100644 include/field3d.hxx create mode 100644 include/field_data.hxx create mode 100644 include/field_factory.hxx create mode 100644 include/fieldperp.hxx create mode 100644 include/globals.hxx create mode 100644 include/gyro_average.hxx create mode 100644 include/initialprofiles.hxx create mode 100644 include/interpolation.hxx create mode 100644 include/interpolation_xz.hxx create mode 100644 include/interpolation_z.hxx create mode 100644 include/invert_laplace.hxx create mode 100644 include/invert_parderiv.hxx create mode 100644 include/lapack_routines.hxx create mode 100644 include/mask.hxx create mode 100644 include/msg_stack.hxx create mode 100644 include/multiostream.hxx create mode 100644 include/options.hxx create mode 100644 include/options_netcdf.hxx create mode 100644 include/optionsreader.hxx create mode 100644 include/output.hxx create mode 100644 include/parallel_boundary_op.hxx create mode 100644 include/parallel_boundary_region.hxx create mode 100644 include/smoothing.hxx create mode 100644 include/sourcex.hxx create mode 100644 include/stencils.hxx create mode 100644 include/unused.hxx create mode 100644 include/utils.hxx create mode 100644 include/vecops.hxx create mode 100644 include/vector2d.hxx create mode 100644 include/vector3d.hxx create mode 100644 include/where.hxx diff --git a/include/boundary_factory.hxx b/include/boundary_factory.hxx new file mode 100644 index 0000000000..abbead8fc4 --- /dev/null +++ b/include/boundary_factory.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_factory.hxx" has moved to "bout/boundary_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_factory.hxx" diff --git a/include/boundary_op.hxx b/include/boundary_op.hxx new file mode 100644 index 0000000000..c96310f2d4 --- /dev/null +++ b/include/boundary_op.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_op.hxx" has moved to "bout/boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_op.hxx" diff --git a/include/boundary_region.hxx b/include/boundary_region.hxx new file mode 100644 index 0000000000..f487e88aeb --- /dev/null +++ b/include/boundary_region.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_region.hxx" has moved to "bout/boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_region.hxx" diff --git a/include/boundary_standard.hxx b/include/boundary_standard.hxx new file mode 100644 index 0000000000..b7f17cf363 --- /dev/null +++ b/include/boundary_standard.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_standard.hxx" has moved to "bout/boundary_standard.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_standard.hxx" diff --git a/include/bout.hxx b/include/bout.hxx new file mode 100644 index 0000000000..926f035d2f --- /dev/null +++ b/include/bout.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "bout.hxx" has moved to "bout/bout.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/bout.hxx" diff --git a/include/bout_types.hxx b/include/bout_types.hxx new file mode 100644 index 0000000000..e6048eb885 --- /dev/null +++ b/include/bout_types.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "bout_types.hxx" has moved to "bout/bout_types.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/bout_types.hxx" diff --git a/include/boutcomm.hxx b/include/boutcomm.hxx new file mode 100644 index 0000000000..256df49c4f --- /dev/null +++ b/include/boutcomm.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boutcomm.hxx" has moved to "bout/boutcomm.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boutcomm.hxx" diff --git a/include/boutexception.hxx b/include/boutexception.hxx new file mode 100644 index 0000000000..9189babfb3 --- /dev/null +++ b/include/boutexception.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boutexception.hxx" has moved to "bout/boutexception.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boutexception.hxx" diff --git a/include/cyclic_reduction.hxx b/include/cyclic_reduction.hxx new file mode 100644 index 0000000000..3ff098b062 --- /dev/null +++ b/include/cyclic_reduction.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "cyclic_reduction.hxx" has moved to "bout/cyclic_reduction.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/cyclic_reduction.hxx" diff --git a/include/dcomplex.hxx b/include/dcomplex.hxx new file mode 100644 index 0000000000..a91c5485bf --- /dev/null +++ b/include/dcomplex.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "dcomplex.hxx" has moved to "bout/dcomplex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/dcomplex.hxx" diff --git a/include/derivs.hxx b/include/derivs.hxx new file mode 100644 index 0000000000..d0a6eb5831 --- /dev/null +++ b/include/derivs.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "derivs.hxx" has moved to "bout/derivs.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/derivs.hxx" diff --git a/include/difops.hxx b/include/difops.hxx new file mode 100644 index 0000000000..a61d9712a9 --- /dev/null +++ b/include/difops.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "difops.hxx" has moved to "bout/difops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/difops.hxx" diff --git a/include/fft.hxx b/include/fft.hxx new file mode 100644 index 0000000000..d67b257388 --- /dev/null +++ b/include/fft.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "fft.hxx" has moved to "bout/fft.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/fft.hxx" diff --git a/include/field.hxx b/include/field.hxx new file mode 100644 index 0000000000..a2fcb2464e --- /dev/null +++ b/include/field.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field.hxx" has moved to "bout/field.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field.hxx" diff --git a/include/field2d.hxx b/include/field2d.hxx new file mode 100644 index 0000000000..3b148b3a50 --- /dev/null +++ b/include/field2d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field2d.hxx" has moved to "bout/field2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field2d.hxx" diff --git a/include/field3d.hxx b/include/field3d.hxx new file mode 100644 index 0000000000..300cec057b --- /dev/null +++ b/include/field3d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field3d.hxx" has moved to "bout/field3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field3d.hxx" diff --git a/include/field_data.hxx b/include/field_data.hxx new file mode 100644 index 0000000000..90f5c96c40 --- /dev/null +++ b/include/field_data.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field_data.hxx" has moved to "bout/field_data.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field_data.hxx" diff --git a/include/field_factory.hxx b/include/field_factory.hxx new file mode 100644 index 0000000000..c6302ee298 --- /dev/null +++ b/include/field_factory.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field_factory.hxx" has moved to "bout/field_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field_factory.hxx" diff --git a/include/fieldperp.hxx b/include/fieldperp.hxx new file mode 100644 index 0000000000..1994e53060 --- /dev/null +++ b/include/fieldperp.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "fieldperp.hxx" has moved to "bout/fieldperp.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/fieldperp.hxx" diff --git a/include/globals.hxx b/include/globals.hxx new file mode 100644 index 0000000000..f07488c10c --- /dev/null +++ b/include/globals.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "globals.hxx" has moved to "bout/globals.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/globals.hxx" diff --git a/include/gyro_average.hxx b/include/gyro_average.hxx new file mode 100644 index 0000000000..c0d454eb50 --- /dev/null +++ b/include/gyro_average.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "gyro_average.hxx" has moved to "bout/gyro_average.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/gyro_average.hxx" diff --git a/include/initialprofiles.hxx b/include/initialprofiles.hxx new file mode 100644 index 0000000000..7bc1595261 --- /dev/null +++ b/include/initialprofiles.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "initialprofiles.hxx" has moved to "bout/initialprofiles.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/initialprofiles.hxx" diff --git a/include/interpolation.hxx b/include/interpolation.hxx new file mode 100644 index 0000000000..80ad60b4e4 --- /dev/null +++ b/include/interpolation.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "interpolation.hxx" has moved to "bout/interpolation.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/interpolation.hxx" diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx new file mode 100644 index 0000000000..8845e34b80 --- /dev/null +++ b/include/interpolation_xz.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "interpolation_xz.hxx" has moved to "bout/interpolation_xz.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/interpolation_xz.hxx" diff --git a/include/interpolation_z.hxx b/include/interpolation_z.hxx new file mode 100644 index 0000000000..a88b486026 --- /dev/null +++ b/include/interpolation_z.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "interpolation_z.hxx" has moved to "bout/interpolation_z.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/interpolation_z.hxx" diff --git a/include/invert_laplace.hxx b/include/invert_laplace.hxx new file mode 100644 index 0000000000..fbb04acaf1 --- /dev/null +++ b/include/invert_laplace.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "invert_laplace.hxx" has moved to "bout/invert_laplace.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/invert_laplace.hxx" diff --git a/include/invert_parderiv.hxx b/include/invert_parderiv.hxx new file mode 100644 index 0000000000..81a8ca4f49 --- /dev/null +++ b/include/invert_parderiv.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "invert_parderiv.hxx" has moved to "bout/invert_parderiv.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/invert_parderiv.hxx" diff --git a/include/lapack_routines.hxx b/include/lapack_routines.hxx new file mode 100644 index 0000000000..97fa2c6be9 --- /dev/null +++ b/include/lapack_routines.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "lapack_routines.hxx" has moved to "bout/lapack_routines.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/lapack_routines.hxx" diff --git a/include/mask.hxx b/include/mask.hxx new file mode 100644 index 0000000000..cbeab65d85 --- /dev/null +++ b/include/mask.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "mask.hxx" has moved to "bout/mask.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/mask.hxx" diff --git a/include/msg_stack.hxx b/include/msg_stack.hxx new file mode 100644 index 0000000000..2503961748 --- /dev/null +++ b/include/msg_stack.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "msg_stack.hxx" has moved to "bout/msg_stack.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/msg_stack.hxx" diff --git a/include/multiostream.hxx b/include/multiostream.hxx new file mode 100644 index 0000000000..7e7101aad0 --- /dev/null +++ b/include/multiostream.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "multiostream.hxx" has moved to "bout/multiostream.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/multiostream.hxx" diff --git a/include/options.hxx b/include/options.hxx new file mode 100644 index 0000000000..4693422c13 --- /dev/null +++ b/include/options.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "options.hxx" has moved to "bout/options.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/options.hxx" diff --git a/include/options_netcdf.hxx b/include/options_netcdf.hxx new file mode 100644 index 0000000000..c0d14c536a --- /dev/null +++ b/include/options_netcdf.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "options_netcdf.hxx" has moved to "bout/options_netcdf.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/options_netcdf.hxx" diff --git a/include/optionsreader.hxx b/include/optionsreader.hxx new file mode 100644 index 0000000000..2c0f8344bf --- /dev/null +++ b/include/optionsreader.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "optionsreader.hxx" has moved to "bout/optionsreader.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/optionsreader.hxx" diff --git a/include/output.hxx b/include/output.hxx new file mode 100644 index 0000000000..7eebcad478 --- /dev/null +++ b/include/output.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "output.hxx" has moved to "bout/output.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/output.hxx" diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx new file mode 100644 index 0000000000..e82a88d98f --- /dev/null +++ b/include/parallel_boundary_op.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "parallel_boundary_op.hxx" has moved to "bout/parallel_boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/parallel_boundary_op.hxx" diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx new file mode 100644 index 0000000000..dee2277007 --- /dev/null +++ b/include/parallel_boundary_region.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "parallel_boundary_region.hxx" has moved to "bout/parallel_boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/parallel_boundary_region.hxx" diff --git a/include/smoothing.hxx b/include/smoothing.hxx new file mode 100644 index 0000000000..b1a36adfb2 --- /dev/null +++ b/include/smoothing.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "smoothing.hxx" has moved to "bout/smoothing.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/smoothing.hxx" diff --git a/include/sourcex.hxx b/include/sourcex.hxx new file mode 100644 index 0000000000..e09f3e89e4 --- /dev/null +++ b/include/sourcex.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "sourcex.hxx" has moved to "bout/sourcex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/sourcex.hxx" diff --git a/include/stencils.hxx b/include/stencils.hxx new file mode 100644 index 0000000000..fc877f3e1c --- /dev/null +++ b/include/stencils.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "stencils.hxx" has moved to "bout/stencils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/stencils.hxx" diff --git a/include/unused.hxx b/include/unused.hxx new file mode 100644 index 0000000000..fa5ea7b6d1 --- /dev/null +++ b/include/unused.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "unused.hxx" has moved to "bout/unused.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/unused.hxx" diff --git a/include/utils.hxx b/include/utils.hxx new file mode 100644 index 0000000000..d1a095e491 --- /dev/null +++ b/include/utils.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "utils.hxx" has moved to "bout/utils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/utils.hxx" diff --git a/include/vecops.hxx b/include/vecops.hxx new file mode 100644 index 0000000000..1773418077 --- /dev/null +++ b/include/vecops.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "vecops.hxx" has moved to "bout/vecops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/vecops.hxx" diff --git a/include/vector2d.hxx b/include/vector2d.hxx new file mode 100644 index 0000000000..6746d3f163 --- /dev/null +++ b/include/vector2d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "vector2d.hxx" has moved to "bout/vector2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/vector2d.hxx" diff --git a/include/vector3d.hxx b/include/vector3d.hxx new file mode 100644 index 0000000000..747b6a75dd --- /dev/null +++ b/include/vector3d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "vector3d.hxx" has moved to "bout/vector3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/vector3d.hxx" diff --git a/include/where.hxx b/include/where.hxx new file mode 100644 index 0000000000..e5b2bd9d30 --- /dev/null +++ b/include/where.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "where.hxx" has moved to "bout/where.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/where.hxx" From 55f967385c16b1e7c51c7d0db4ed938822abdbb6 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 11:44:42 +0100 Subject: [PATCH 059/412] Update all files for new headers --- .clang-format | 3 +- examples/2Dturbulence_multigrid/esel.cxx | 20 +- examples/6field-simple/elm_6f.cxx | 16 +- examples/IMEX/advection-diffusion/imex.cxx | 18 +- .../advection-reaction/split_operator.cxx | 4 +- examples/IMEX/diffusion-nl/diffusion-nl.cxx | 15 +- .../IMEX/drift-wave-constraint/test-drift.cxx | 53 +- examples/IMEX/drift-wave/test-drift.cxx | 41 +- examples/advdiff/advdiff.cxx | 30 +- examples/advdiff2/init.cxx | 2 +- examples/advdiff2/rhs.cxx | 4 +- examples/backtrace/backtrace.cxx | 2 +- examples/blob2d-laplacexz/blob2d.cxx | 13 +- examples/blob2d-outerloop/blob2d.cxx | 4 +- examples/blob2d/blob2d.cxx | 16 +- .../advection/advection.cxx | 11 +- examples/conducting-wall-mode/cwm.cxx | 21 +- examples/conduction-snb/conduction-snb.cxx | 2 +- examples/conduction/conduction.cxx | 17 +- examples/constraints/alfven-wave/alfven.cxx | 146 +- .../constraints/laplace-dae/laplace_dae.cxx | 8 +- examples/dalf3/dalf3.cxx | 334 ++-- examples/eigen-box/eigen-box.cxx | 7 +- .../elm-pb-outerloop/elm_pb_outerloop.cxx | 26 +- examples/elm-pb/elm_pb.cxx | 72 +- examples/em-drift/2fluid.cxx | 30 +- examples/fci-wave-logn/fci-wave.cxx | 115 +- examples/fci-wave/fci-wave.cxx | 34 +- .../finite-volume/diffusion/diffusion.cxx | 11 +- examples/finite-volume/fluid/fluid.cxx | 43 +- examples/finite-volume/test/finite_volume.cxx | 6 +- examples/gas-compress/gas_compress.cxx | 42 +- examples/gas-compress/gas_compress.hxx | 11 +- examples/gravity_reduced/gravity_reduced.cxx | 195 ++- examples/gyro-gem/gem.cxx | 742 ++++----- examples/hasegawa-wakatani-3d/hw.cxx | 2 +- examples/hasegawa-wakatani/hw.cxx | 71 +- .../invertable_operator.cxx | 22 +- examples/jorek-compare/jorek_compare.cxx | 14 +- examples/lapd-drift/lapd_drift.cxx | 549 +++--- .../create-initial-profiles.cxx | 6 +- examples/laplace-petsc3d/test-laplace3d.cxx | 42 +- examples/laplacexy/alfven-wave/alfven.cxx | 10 +- examples/laplacexy/laplace_perp/test.cxx | 31 +- .../simple-hypre/test-laplacexy-hypre.cxx | 4 +- examples/laplacexy/simple/test-laplacexy.cxx | 9 +- examples/make-script/test.cxx | 5 +- examples/monitor-newapi/monitor.cxx | 14 +- examples/monitor/monitor.cxx | 5 +- examples/orszag-tang/mhd.cxx | 2 +- .../performance/arithmetic/arithmetic.cxx | 53 +- .../arithmetic_3d2d/arithmetic_3d2d.cxx | 60 +- examples/performance/bracket/bracket.cxx | 32 +- .../communications/communications.cxx | 4 +- examples/performance/ddx/ddx.cxx | 152 +- examples/performance/ddy/ddy.cxx | 152 +- examples/performance/ddz/ddz.cxx | 152 +- .../iterator-offsets/iterator-offsets.cxx | 239 ++- examples/performance/iterator/iterator.cxx | 145 +- examples/performance/laplace/laplace.cxx | 24 +- .../tuning_regionblocksize.cxx | 22 +- examples/preconditioning/wave/test_precon.cxx | 4 +- examples/reconnect-2field/2field.cxx | 41 +- examples/shear-alfven-wave/2fluid.cxx | 30 +- examples/staggered_grid/test_staggered.cxx | 4 +- examples/subsampling/monitor.cxx | 2 +- examples/tokamak-2fluid/2fluid.cxx | 445 ++--- examples/uedge-benchmark/ue_bmark.cxx | 67 +- examples/wave-slab/wave_slab.cxx | 50 +- include/bout/array.hxx | 17 +- include/bout/assert.hxx | 30 +- include/bout/boundary_factory.hxx | 49 +- include/bout/boundary_op.hxx | 66 +- include/bout/boundary_region.hxx | 53 +- include/bout/boundary_standard.hxx | 439 ++--- include/bout/bout.hxx | 28 +- include/bout/bout_enum_class.hxx | 85 +- include/bout/bout_types.hxx | 20 +- include/bout/boutcomm.hxx | 9 +- include/bout/boutexception.hxx | 4 +- include/bout/constants.hxx | 28 +- include/bout/coordinates.hxx | 33 +- include/bout/cyclic_reduction.hxx | 95 +- include/bout/dcomplex.hxx | 4 +- include/bout/deriv_store.hxx | 31 +- include/bout/derivs.hxx | 104 +- include/bout/difops.hxx | 6 +- include/bout/expr.hxx | 117 +- include/bout/fft.hxx | 18 +- include/bout/field.hxx | 200 +-- include/bout/field2d.hxx | 26 +- include/bout/field3d.hxx | 258 +-- include/bout/field_accessor.hxx | 8 +- include/bout/field_data.hxx | 31 +- include/bout/field_factory.hxx | 22 +- include/bout/fieldgroup.hxx | 88 +- include/bout/fieldperp.hxx | 220 +-- include/bout/format.hxx | 4 +- include/bout/fv_ops.hxx | 773 ++++----- include/bout/generic_factory.hxx | 12 +- include/bout/globalfield.hxx | 87 +- include/bout/globalindexer.hxx | 6 +- include/bout/globals.hxx | 64 +- include/bout/griddata.hxx | 107 +- include/bout/gyro_average.hxx | 17 +- include/bout/hypre_interface.hxx | 18 +- include/bout/index_derivs.hxx | 45 +- include/bout/index_derivs_interface.hxx | 6 +- include/bout/interpolation.hxx | 21 +- include/bout/interpolation_xz.hxx | 44 +- include/bout/interpolation_z.hxx | 4 +- include/bout/invert/laplacexy.hxx | 49 +- include/bout/invert/laplacexy2.hxx | 8 +- include/bout/invert/laplacexy2_hypre.hxx | 6 +- include/bout/invert/laplacexz.hxx | 26 +- include/bout/invert_laplace.hxx | 107 +- include/bout/invert_parderiv.hxx | 59 +- include/bout/invert_pardiv.hxx | 8 +- include/bout/invertable_operator.hxx | 51 +- include/bout/lapack_routines.hxx | 17 +- include/bout/macro_for_each.hxx | 60 +- include/bout/mask.hxx | 20 +- include/bout/mesh.hxx | 195 +-- include/bout/monitor.hxx | 22 +- include/bout/msg_stack.hxx | 10 +- include/bout/multiostream.hxx | 47 +- include/bout/openmpwrap.hxx | 3 +- include/bout/options.hxx | 323 ++-- include/bout/options_netcdf.hxx | 24 +- include/bout/optionsreader.hxx | 25 +- include/bout/output.hxx | 75 +- include/bout/output_bout_types.hxx | 2 +- include/bout/parallel_boundary_op.hxx | 148 +- include/bout/parallel_boundary_region.hxx | 23 +- include/bout/paralleltransform.hxx | 32 +- include/bout/petsc_interface.hxx | 15 +- include/bout/petsclib.hxx | 45 +- include/bout/physicsmodel.hxx | 143 +- include/bout/rajalib.hxx | 2 +- include/bout/region.hxx | 310 ++-- include/bout/rkscheme.hxx | 21 +- include/bout/rvec.hxx | 2 +- include/bout/scorepwrapper.hxx | 8 +- include/bout/slepclib.hxx | 24 +- include/bout/smoothing.hxx | 28 +- include/bout/snb.hxx | 2 +- include/bout/solver.hxx | 48 +- include/bout/solverfactory.hxx | 4 +- include/bout/sourcex.hxx | 19 +- include/bout/stencils.hxx | 29 +- include/bout/sundials_backports.hxx | 2 +- include/bout/surfaceiter.hxx | 28 +- include/bout/sys/expressionparser.hxx | 12 +- include/bout/sys/generator_context.hxx | 36 +- include/bout/sys/range.hxx | 26 +- include/bout/sys/timer.hxx | 10 +- include/bout/sys/type_name.hxx | 60 +- include/bout/sys/uncopyable.hxx | 4 +- include/bout/sys/variant.hxx | 20 +- include/bout/template_combinations.hxx | 4 +- include/bout/traits.hxx | 8 +- include/bout/unused.hxx | 18 +- include/bout/utils.hxx | 181 +- include/bout/vecops.hxx | 10 +- include/bout/vector2d.hxx | 72 +- include/bout/vector3d.hxx | 101 +- include/bout/where.hxx | 14 +- src/bout++-time.cxx | 4 +- src/bout++-time.hxx | 4 +- src/bout++.cxx | 58 +- src/field/field.cxx | 24 +- src/field/field2d.cxx | 135 +- src/field/field3d.cxx | 227 +-- src/field/field_data.cxx | 34 +- src/field/field_factory.cxx | 117 +- src/field/fieldgenerators.cxx | 50 +- src/field/fieldgenerators.hxx | 33 +- src/field/fieldgroup.cxx | 2 +- src/field/fieldperp.cxx | 56 +- src/field/generated_fieldops.cxx | 296 ++-- src/field/globalfield.cxx | 347 ++-- src/field/initialprofiles.cxx | 12 +- src/field/vecops.cxx | 143 +- src/field/vector2d.cxx | 170 +- src/field/vector3d.cxx | 246 ++- src/field/where.cxx | 2 +- src/invert/fft_fftw.cxx | 203 ++- src/invert/lapack_routines.cxx | 121 +- .../laplace/impls/cyclic/cyclic_laplace.cxx | 13 +- .../laplace/impls/cyclic/cyclic_laplace.hxx | 42 +- .../laplace/impls/hypre3d/hypre3d_laplace.cxx | 30 +- .../laplace/impls/hypre3d/hypre3d_laplace.hxx | 10 +- .../iterative_parallel_tri.cxx | 48 +- .../iterative_parallel_tri.hxx | 8 +- .../laplace/impls/multigrid/multigrid_alg.cxx | 2 +- .../impls/multigrid/multigrid_laplace.cxx | 984 +++++------ .../impls/multigrid/multigrid_laplace.hxx | 138 +- .../impls/multigrid/multigrid_solver.cxx | 938 ++++++----- .../laplace/impls/naulin/naulin_laplace.cxx | 100 +- .../laplace/impls/naulin/naulin_laplace.hxx | 58 +- src/invert/laplace/impls/pcr/pcr.cxx | 49 +- src/invert/laplace/impls/pcr/pcr.hxx | 8 +- .../laplace/impls/pcr_thomas/pcr_thomas.cxx | 14 +- .../laplace/impls/pcr_thomas/pcr_thomas.hxx | 8 +- .../laplace/impls/petsc/petsc_laplace.cxx | 1418 ++++++++-------- .../laplace/impls/petsc/petsc_laplace.hxx | 130 +- .../laplace/impls/petsc3damg/petsc3damg.cxx | 37 +- .../laplace/impls/petsc3damg/petsc3damg.hxx | 60 +- .../laplace/impls/serial_band/serial_band.cxx | 298 ++-- .../laplace/impls/serial_band/serial_band.hxx | 27 +- .../laplace/impls/serial_tri/serial_tri.cxx | 39 +- .../laplace/impls/serial_tri/serial_tri.hxx | 21 +- src/invert/laplace/impls/spt/spt.cxx | 381 +++-- src/invert/laplace/impls/spt/spt.hxx | 54 +- src/invert/laplace/invert_laplace.cxx | 431 ++--- src/invert/laplacexy/laplacexy.cxx | 714 ++++---- src/invert/laplacexy2/laplacexy2.cxx | 8 +- src/invert/laplacexy2/laplacexy2_hypre.cxx | 23 +- .../impls/cyclic/laplacexz-cyclic.cxx | 115 +- .../impls/cyclic/laplacexz-cyclic.hxx | 21 +- .../laplacexz/impls/petsc/laplacexz-petsc.cxx | 323 ++-- .../laplacexz/impls/petsc/laplacexz-petsc.hxx | 35 +- src/invert/parderiv/impls/cyclic/cyclic.cxx | 59 +- src/invert/parderiv/impls/cyclic/cyclic.hxx | 22 +- src/invert/parderiv/invert_parderiv.cxx | 6 +- .../pardiv/impls/cyclic/pardiv_cyclic.cxx | 14 +- .../pardiv/impls/cyclic/pardiv_cyclic.hxx | 6 +- src/mesh/boundary_factory.cxx | 153 +- src/mesh/boundary_region.cxx | 137 +- src/mesh/boundary_standard.cxx | 381 +++-- src/mesh/coordinates.cxx | 170 +- src/mesh/data/gridfromfile.cxx | 189 ++- src/mesh/data/gridfromoptions.cxx | 34 +- src/mesh/difops.cxx | 301 ++-- src/mesh/fv_ops.cxx | 681 ++++---- src/mesh/impls/bout/boutmesh.cxx | 305 ++-- src/mesh/impls/bout/boutmesh.hxx | 27 +- src/mesh/index_derivs.cxx | 50 +- src/mesh/interpolation/bilinear_xz.cxx | 20 +- src/mesh/interpolation/hermite_spline_xz.cxx | 24 +- src/mesh/interpolation/hermite_spline_z.cxx | 33 +- src/mesh/interpolation/interpolation_z.cxx | 21 +- src/mesh/interpolation/lagrange_4pt_xz.cxx | 24 +- .../monotonic_hermite_spline_xz.cxx | 11 +- src/mesh/interpolation_xz.cxx | 39 +- src/mesh/mesh.cxx | 222 +-- src/mesh/parallel/fci.cxx | 52 +- src/mesh/parallel/fci.hxx | 24 +- src/mesh/parallel/identity.cxx | 11 +- src/mesh/parallel/shiftedmetric.cxx | 28 +- src/mesh/parallel/shiftedmetricinterp.cxx | 14 +- src/mesh/parallel/shiftedmetricinterp.hxx | 2 +- src/mesh/parallel_boundary_op.cxx | 104 +- src/mesh/parallel_boundary_region.cxx | 35 +- src/mesh/surfaceiter.cxx | 56 +- src/physics/gyro_average.cxx | 48 +- src/physics/physicsmodel.cxx | 22 +- src/physics/smoothing.cxx | 386 +++-- src/physics/snb.cxx | 2 +- src/physics/sourcex.cxx | 44 +- .../impls/adams_bashforth/adams_bashforth.cxx | 10 +- .../impls/adams_bashforth/adams_bashforth.hxx | 10 +- src/solver/impls/arkode/arkode.cxx | 109 +- src/solver/impls/arkode/arkode.hxx | 8 +- src/solver/impls/cvode/cvode.cxx | 133 +- src/solver/impls/cvode/cvode.hxx | 4 +- src/solver/impls/euler/euler.cxx | 77 +- src/solver/impls/euler/euler.hxx | 5 +- src/solver/impls/ida/ida.cxx | 43 +- src/solver/impls/ida/ida.hxx | 2 +- src/solver/impls/imex-bdf2/imex-bdf2.cxx | 61 +- src/solver/impls/imex-bdf2/imex-bdf2.hxx | 9 +- src/solver/impls/petsc/petsc.cxx | 709 +++++--- src/solver/impls/petsc/petsc.hxx | 34 +- src/solver/impls/power/power.cxx | 32 +- src/solver/impls/power/power.hxx | 3 +- src/solver/impls/pvode/pvode.cxx | 107 +- src/solver/impls/pvode/pvode.hxx | 6 +- src/solver/impls/rk3-ssp/rk3-ssp.cxx | 46 +- src/solver/impls/rk3-ssp/rk3-ssp.hxx | 2 +- src/solver/impls/rk4/rk4.cxx | 115 +- src/solver/impls/rk4/rk4.hxx | 2 +- .../rkgeneric/impls/cashkarp/cashkarp.cxx | 19 +- .../rkgeneric/impls/cashkarp/cashkarp.hxx | 2 +- .../rkgeneric/impls/rk4simple/rk4simple.cxx | 91 +- .../rkgeneric/impls/rk4simple/rk4simple.hxx | 9 +- .../impls/rkgeneric/impls/rkf34/rkf34.cxx | 18 +- .../impls/rkgeneric/impls/rkf34/rkf34.hxx | 2 +- .../impls/rkgeneric/impls/rkf45/rkf45.cxx | 19 +- .../impls/rkgeneric/impls/rkf45/rkf45.hxx | 2 +- src/solver/impls/rkgeneric/rkgeneric.cxx | 104 +- src/solver/impls/rkgeneric/rkgeneric.hxx | 2 +- src/solver/impls/rkgeneric/rkscheme.cxx | 208 +-- src/solver/impls/slepc/slepc.cxx | 16 +- src/solver/impls/slepc/slepc.hxx | 35 +- src/solver/impls/snes/snes.cxx | 10 +- src/solver/impls/snes/snes.hxx | 8 +- src/solver/impls/split-rk/split-rk.cxx | 115 +- src/solver/impls/split-rk/split-rk.hxx | 36 +- src/solver/solver.cxx | 446 ++--- src/sys/bout_types.cxx | 24 +- src/sys/boutcomm.cxx | 32 +- src/sys/boutexception.cxx | 36 +- src/sys/derivs.cxx | 153 +- src/sys/expressionparser.cxx | 196 ++- src/sys/generator_context.cxx | 50 +- src/sys/hyprelib.cxx | 8 +- src/sys/msg_stack.cxx | 13 +- src/sys/options.cxx | 126 +- src/sys/options/optionparser.hxx | 13 +- src/sys/options/options_ini.cxx | 77 +- src/sys/options/options_ini.hxx | 12 +- src/sys/options/options_netcdf.cxx | 6 +- src/sys/optionsreader.cxx | 39 +- src/sys/output.cxx | 6 +- src/sys/petsclib.cxx | 51 +- src/sys/range.cxx | 108 +- src/sys/slepclib.cxx | 22 +- src/sys/type_name.cxx | 12 +- src/sys/utils.cxx | 60 +- tests/MMS/GBS/gbs.cxx | 468 +++--- tests/MMS/GBS/gbs.hxx | 43 +- tests/MMS/advection/advection.cxx | 21 +- tests/MMS/diffusion/diffusion.cxx | 31 +- tests/MMS/diffusion2/diffusion.cxx | 15 +- tests/MMS/elm-pb/elm_pb.cxx | 368 +++-- tests/MMS/fieldalign/fieldalign.cxx | 16 +- tests/MMS/hw/hw.cxx | 8 +- tests/MMS/laplace/laplace.cxx | 22 +- tests/MMS/spatial/advection/advection.cxx | 6 +- tests/MMS/spatial/d2dx2/test_d2dx2.cxx | 6 +- tests/MMS/spatial/d2dz2/test_d2dz2.cxx | 6 +- tests/MMS/spatial/diffusion/diffusion.cxx | 15 +- tests/MMS/spatial/fci/fci_mms.cxx | 6 +- tests/MMS/time/time.cxx | 19 +- tests/MMS/tokamak/tokamak.cxx | 82 +- tests/MMS/wave-1d-y/wave.cxx | 19 +- tests/MMS/wave-1d/wave.cxx | 36 +- .../integrated/test-backtrace/boutexcept.cxx | 4 +- tests/integrated/test-beuler/test_beuler.cxx | 2 +- .../test-bout-override-default-option.cxx | 12 +- .../integrated/test-collect/test-collect.cxx | 2 +- .../test-command-args/command-args.cxx | 4 +- .../test-communications.cxx | 50 +- .../test-coordinates-initialization.cxx | 8 +- tests/integrated/test-cyclic/test_cyclic.cxx | 58 +- .../test-dataformat/test_dataformat.cxx | 5 +- tests/integrated/test-delp2/test_delp2.cxx | 6 +- .../test-drift-instability/2fluid.cxx | 34 +- .../test-fci-boundary/get_par_bndry.cxx | 8 +- .../test_fieldgroupcomm.cxx | 11 +- .../test-globalfield/test_globalfield.cxx | 103 +- .../test_griddata.cxx | 4 +- .../test-griddata/test_griddata.cxx | 2 +- tests/integrated/test-gyro/test_gyro.cxx | 10 +- .../integrated/test-initial/test_initial.cxx | 2 +- .../test-integrate/test_integrate.cxx | 35 +- .../test-interchange-instability/2fluid.cxx | 30 +- .../test-interpolate-z/test_interpolate.cxx | 16 +- .../test-interpolate/test_interpolate.cxx | 16 +- .../invertable_operator.cxx | 4 +- tests/integrated/test-invpar/test_invpar.cxx | 14 +- .../test-laplace-hypre3d/test-laplace3d.cxx | 6 +- .../test-laplace-petsc3d/test-laplace3d.cxx | 24 +- .../integrated/test-laplace/test_laplace.cxx | 6 +- .../integrated/test-laplace2/test_laplace.cxx | 32 +- .../test-laplacexy-fv/test-laplacexy.cxx | 16 +- .../test-laplacexy-short/test-laplacexy.cxx | 18 +- .../integrated/test-laplacexy/loadmetric.cxx | 68 +- .../integrated/test-laplacexy/loadmetric.hxx | 2 +- .../test-laplacexy/test-laplacexy.cxx | 27 +- .../test-laplacexy2-hypre/test-laplacexy.cxx | 8 +- .../test-laplacexz/test-laplacexz.cxx | 10 +- .../test_multigrid_laplace.cxx | 143 +- .../test_naulin_laplace.cxx | 134 +- .../integrated/test-nonuniform/test_delp2.cxx | 25 +- .../test-options-netcdf.cxx | 26 +- .../test-petsc_laplace/test_petsc_laplace.cxx | 1467 +++++++++-------- .../test_petsc_laplace_MAST_grid.cxx | 1459 +++++++++------- .../test_region_iterator.cxx | 67 +- .../test-restarting/test_restarting.cxx | 9 +- .../test-slepc-solver/test-slepc-solver.cxx | 1 + tests/integrated/test-smooth/test_smooth.cxx | 6 +- tests/integrated/test-snb/test_snb.cxx | 8 +- tests/integrated/test-solver/test_solver.cxx | 2 +- tests/integrated/test-squash/squash.cxx | 6 +- .../test-stopCheck-file/test_stopCheck.cxx | 8 +- .../test-stopCheck/test_stopCheck.cxx | 8 +- tests/integrated/test-subdir/bar/bar.cxx | 6 +- tests/integrated/test-subdir/fuu/fuu.cxx | 4 +- tests/integrated/test-subdir/fuu/fuu.hxx | 2 +- tests/integrated/test-subdir/subdirs.cxx | 9 +- .../test-twistshift.cxx | 12 +- .../test-twistshift/test-twistshift.cxx | 12 +- tests/integrated/test-vec/testVec.cxx | 3 +- .../test_yupdown_weights.cxx | 47 +- .../integrated/test-yupdown/test_yupdown.cxx | 13 +- tests/unit/bout_test_main.cxx | 4 +- tests/unit/fake_parallel_mesh.hxx | 22 +- tests/unit/field/test_field.cxx | 6 +- tests/unit/field/test_field2d.cxx | 75 +- tests/unit/field/test_field3d.cxx | 98 +- tests/unit/field/test_field_factory.cxx | 41 +- tests/unit/field/test_fieldgroup.cxx | 10 +- tests/unit/field/test_fieldperp.cxx | 60 +- tests/unit/field/test_initialprofiles.cxx | 8 +- tests/unit/field/test_vector2d.cxx | 47 +- tests/unit/field/test_vector3d.cxx | 42 +- tests/unit/field/test_where.cxx | 4 +- tests/unit/include/bout/test_array.cxx | 2 +- tests/unit/include/bout/test_assert.cxx | 2 +- .../include/bout/test_bout_enum_class.cxx | 2 +- tests/unit/include/bout/test_deriv_store.cxx | 8 +- .../include/bout/test_generic_factory.cxx | 5 +- .../include/bout/test_hypre_interface.cxx | 16 +- .../unit/include/bout/test_macro_for_each.cxx | 11 +- tests/unit/include/bout/test_monitor.cxx | 2 +- .../unit/include/bout/test_petsc_indexer.cxx | 263 +-- tests/unit/include/bout/test_petsc_matrix.cxx | 36 +- tests/unit/include/bout/test_petsc_vector.cxx | 26 +- tests/unit/include/bout/test_region.cxx | 186 +-- .../include/bout/test_single_index_ops.cxx | 42 +- .../bout/test_template_combinations.cxx | 4 +- tests/unit/include/bout/test_traits.cxx | 8 +- tests/unit/include/test_cyclic_reduction.cxx | 4 +- tests/unit/include/test_derivs.cxx | 263 +-- tests/unit/include/test_mask.cxx | 16 +- .../invert/laplace/test_laplace_cyclic.cxx | 22 +- .../invert/laplace/test_laplace_hypre3d.cxx | 94 +- .../laplace/test_laplace_petsc3damg.cxx | 244 ++- tests/unit/invert/test_fft.cxx | 4 +- tests/unit/mesh/data/test_gridfromoptions.cxx | 105 +- .../unit/mesh/parallel/test_shiftedmetric.cxx | 15 +- tests/unit/mesh/test_boundary_factory.cxx | 22 +- tests/unit/mesh/test_boutmesh.cxx | 7 +- tests/unit/mesh/test_coordinates.cxx | 193 +-- tests/unit/mesh/test_interpolation.cxx | 60 +- tests/unit/mesh/test_mesh.cxx | 14 +- tests/unit/solver/test_solver.cxx | 13 +- tests/unit/solver/test_solverfactory.cxx | 2 +- tests/unit/src/test_bout++.cxx | 10 +- tests/unit/sys/test_boutexception.cxx | 12 +- tests/unit/sys/test_expressionparser.cxx | 68 +- tests/unit/sys/test_msg_stack.cxx | 6 +- tests/unit/sys/test_options.cxx | 159 +- tests/unit/sys/test_options_fields.cxx | 33 +- tests/unit/sys/test_options_netcdf.cxx | 76 +- tests/unit/sys/test_optionsreader.cxx | 62 +- tests/unit/sys/test_output.cxx | 12 +- tests/unit/sys/test_raja.cxx | 2 +- tests/unit/sys/test_range.cxx | 2 +- tests/unit/sys/test_timer.cxx | 2 +- tests/unit/sys/test_type_name.cxx | 30 +- tests/unit/sys/test_utils.cxx | 51 +- tests/unit/test_extras.cxx | 6 +- tests/unit/test_extras.hxx | 44 +- tools/archiving/dumpsample/pdbsample.cxx | 295 ++-- tools/archiving/pdb2cdf/pdb2cdf.cxx | 555 +++---- .../_boutpp_build/boutexception_helper.cxx | 2 +- .../_boutpp_build/boutpp_openmpi_compat.hxx | 45 +- tools/tokamak_grids/coils/coils.cxx | 211 ++- 461 files changed, 18918 insertions(+), 17054 deletions(-) diff --git a/.clang-format b/.clang-format index f51c5bde87..eb5e7992cb 100644 --- a/.clang-format +++ b/.clang-format @@ -61,6 +61,7 @@ ForEachMacros: - foreach - Q_FOREACH - BOOST_FOREACH + - BOUT_FOR # IncludeBlocks: Regroup IncludeCategories: - Regex: '^(<|")bout/' @@ -107,7 +108,7 @@ SpacesInContainerLiterals: true SpacesInCStyleCastParentheses: false SpacesInParentheses: false SpacesInSquareBrackets: false -StatementMacros: +StatementAttributeLikeMacros: - BOUT_OMP Standard: c++14 TabWidth: 8 diff --git a/examples/2Dturbulence_multigrid/esel.cxx b/examples/2Dturbulence_multigrid/esel.cxx index 9b10731ac7..55a773df45 100644 --- a/examples/2Dturbulence_multigrid/esel.cxx +++ b/examples/2Dturbulence_multigrid/esel.cxx @@ -1,20 +1,20 @@ #include -#include -#include -#include -#include +#include +#include +#include +#include class ESEL : public PhysicsModel { private: Field3D n, vort; // Evolving density, temp and vorticity Field3D N; // ln(n) Field3D phi; - Field2D B; // Magnetic field - BoutReal D, mu; // Diffusion coefficients - Field2D sigma_n, sigma_T, sigma_vort; // dissipation terms - BoutReal zeta; // rho/R0 - BRACKET_METHOD bm; // Bracket method for advection terms - std::unique_ptr phiSolver{nullptr}; // Laplacian solver for vort -> phi + Field2D B; // Magnetic field + BoutReal D, mu; // Diffusion coefficients + Field2D sigma_n, sigma_T, sigma_vort; // dissipation terms + BoutReal zeta; // rho/R0 + BRACKET_METHOD bm; // Bracket method for advection terms + std::unique_ptr phiSolver{nullptr}; // Laplacian solver for vort -> phi bool test_laplacian; // If true, compute the error on the Laplacian inversion and abort Field3D vort_error; diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx index 940a024f69..651aa8cdb8 100644 --- a/examples/6field-simple/elm_6f.cxx +++ b/examples/6field-simple/elm_6f.cxx @@ -6,14 +6,14 @@ * T. Xia *******************************************************************************/ -#include "bout.hxx" -#include "derivs.hxx" -#include "initialprofiles.hxx" -#include "interpolation_xz.hxx" -#include "invert_laplace.hxx" -#include "invert_parderiv.hxx" -#include "msg_stack.hxx" -#include "sourcex.hxx" +#include "bout/bout.hxx" +#include "bout/derivs.hxx" +#include "bout/initialprofiles.hxx" +#include "bout/interpolation_xz.hxx" +#include "bout/invert_laplace.hxx" +#include "bout/invert_parderiv.hxx" +#include "bout/msg_stack.hxx" +#include "bout/sourcex.hxx" #include "bout/constants.hxx" #include "bout/physicsmodel.hxx" diff --git a/examples/IMEX/advection-diffusion/imex.cxx b/examples/IMEX/advection-diffusion/imex.cxx index d8e6a9b2ca..7ec927e471 100644 --- a/examples/IMEX/advection-diffusion/imex.cxx +++ b/examples/IMEX/advection-diffusion/imex.cxx @@ -8,17 +8,17 @@ * *******************************************************************/ #include -#include +#include class IMEXexample : public PhysicsModel { private: - Field3D U; // Evolving variable and auxilliary variable + Field3D U; // Evolving variable and auxilliary variable Field3D Vx, Dz; // Velocity, diffusion protected: int init(bool) { setSplitOperator(); // Split into convective and diffusive - + // Get options auto& options = Options::root()["imex"]; Vx = options["Vx"].doc("Velocity in X").withDefault(Field3D(100.0)); @@ -32,19 +32,19 @@ class IMEXexample : public PhysicsModel { int convective(BoutReal) { // Need communication mesh->communicate(U); - + // Passive advection - ddt(U) = -VDDX(Vx,U); - + ddt(U) = -VDDX(Vx, U); + return 0; } - + int diffusive(BoutReal) { mesh->communicate(U); // Diffusion - ddt(U) = Dz*D2DZ2(U); - + ddt(U) = Dz * D2DZ2(U); + return 0; } }; diff --git a/examples/IMEX/advection-reaction/split_operator.cxx b/examples/IMEX/advection-reaction/split_operator.cxx index 47330fecf7..c847e47ee6 100644 --- a/examples/IMEX/advection-reaction/split_operator.cxx +++ b/examples/IMEX/advection-reaction/split_operator.cxx @@ -20,8 +20,8 @@ *************************************************************/ #include -#include -#include +#include +#include class Split_operator : public PhysicsModel { Field3D U; // Evolving variable diff --git a/examples/IMEX/diffusion-nl/diffusion-nl.cxx b/examples/IMEX/diffusion-nl/diffusion-nl.cxx index 9598258713..fcb6aa165d 100644 --- a/examples/IMEX/diffusion-nl/diffusion-nl.cxx +++ b/examples/IMEX/diffusion-nl/diffusion-nl.cxx @@ -15,9 +15,9 @@ * */ -#include #include -#include +#include +#include class DiffusionNL : public PhysicsModel { protected: @@ -46,7 +46,7 @@ class DiffusionNL : public PhysicsModel { ddt(f) = 0.0; return 0; } - + /*! * Diffusive part of the problem. In an IMEX scheme * this will be treated implicitly @@ -98,7 +98,7 @@ class DiffusionNL : public PhysicsModel { */ int precon(BoutReal, BoutReal gamma, BoutReal) { // Preconditioner - + static std::unique_ptr inv{nullptr}; if (!inv) { // Initialise parallel inversion class @@ -107,13 +107,14 @@ class DiffusionNL : public PhysicsModel { } // Set the coefficient in front of Grad2_par2 - inv->setCoefB(-gamma*D); + inv->setCoefB(-gamma * D); //mesh->communicate(ddt(f)); - + ddt(f) = inv->solve(ddt(f)); - + return 0; } + private: Field3D f; // Evolving quantity BoutReal alpha; // Input parameter, D = f^alpha diff --git a/examples/IMEX/drift-wave-constraint/test-drift.cxx b/examples/IMEX/drift-wave-constraint/test-drift.cxx index 44747330be..e3bf88acfc 100644 --- a/examples/IMEX/drift-wave-constraint/test-drift.cxx +++ b/examples/IMEX/drift-wave-constraint/test-drift.cxx @@ -1,60 +1,60 @@ #include -#include +#include -#include +#include -class DriftWave : public PhysicsModel { +class DriftWave : public PhysicsModel { protected: int init(bool UNUSED(restart)) { // Specify evolving variables solver->add(Vort, "Vort"); // Vorticity solver->add(Ne, "Ne"); // Electron density - + // Get the normalised resistivity Options::getRoot()->getSection("drift")->get("nu", nu, 1.0); // Read background profile mesh->get(Ne0, "Ne0"); - + // Split into convective and diffusive (stiff) setSplitOperator(); // Solve potential as a constraint solver->constraint(phi, ddt(phi), "phi"); phi = 0.0; - + // Coordinate system coord = mesh->getCoordinates(); return 0; } - + int convective(BoutReal UNUSED(time)) { // Non-stiff parts of the problem here // Here just the nonlinear advection - + mesh->communicate(phi, Vort, Ne); - + // Linear advection ddt(Ne) = -bracket(phi, Ne0, BRACKET_ARAKAWA); - + // Non-linear advection of density and vorticity ddt(Ne) -= bracket(phi, Ne, BRACKET_ARAKAWA); - + ddt(Vort) = -bracket(phi, Vort, BRACKET_ARAKAWA); // potential is not evolved, // but solved as a constraint in the implicit stage ddt(phi) = 0.0; - + return 0; } - + int diffusive(BoutReal UNUSED(time)) { // Parallel dynamics treated implicitly - + mesh->communicate(phi, Vort, Ne); /* @@ -68,37 +68,36 @@ class DriftWave : public PhysicsModel { ddt(Ne) = -Div_par(Ve); ddt(Vort) = -Div_par(Ve); */ - + // This version uses only y+1, y-1 - ddt(Ne) = Grad2_par2(Ne - phi)/nu; + ddt(Ne) = Grad2_par2(Ne - phi) / nu; ddt(Vort) = ddt(Ne); - + // Calculate the constraint on potential // which is that ddt(phi) = 0 - + phi.applyBoundary("dirichlet_o2"); - + // This version uses FFTs, introducing dependencies in Z // ddt(phi) = Delp2(phi) - Vort; // This version uses central differencing for Delp2 - ddt(phi) = (coord->g11*D2DX2(phi) + coord->g33*D2DZ2(phi)) - Vort; - + ddt(phi) = (coord->g11 * D2DX2(phi) + coord->g33 * D2DZ2(phi)) - Vort; + return 0; } - + private: Field2D Ne0; // Background density profile - + Field3D Vort, Ne; // Vorticity and density Field3D phi; // Electrostatic potential Field3D Ve; // parallel electron velocity - + BoutReal nu; // Resistivity parameter - - Coordinates *coord; // Coordinate system metrics -}; + Coordinates* coord; // Coordinate system metrics +}; BOUTMAIN(DriftWave); diff --git a/examples/IMEX/drift-wave/test-drift.cxx b/examples/IMEX/drift-wave/test-drift.cxx index a91b9abecc..4e1099adae 100644 --- a/examples/IMEX/drift-wave/test-drift.cxx +++ b/examples/IMEX/drift-wave/test-drift.cxx @@ -1,9 +1,9 @@ #include -#include +#include -class DriftWave : public PhysicsModel { +class DriftWave : public PhysicsModel { protected: int init(bool) { // Specify evolving variables @@ -11,7 +11,7 @@ class DriftWave : public PhysicsModel { solver->add(Ne, "Ne"); // Electron density SAVE_REPEAT(phi); - + // Get the normalised resistivity nu = Options::root()["drift"]["nu"].doc("Normalised resistivity").withDefault(1.0); @@ -19,60 +19,59 @@ class DriftWave : public PhysicsModel { mesh->get(Ne0, "Ne0"); setSplitOperator(); // Split into convective and diffusive (stiff) - + // Laplacian solver for potential - phiSolver = Laplacian::create(); + phiSolver = Laplacian::create(); return 0; } - + int convective(BoutReal) { // Non-stiff parts of the problem here // Here just the nonlinear advection - + // Solve for potential phi = phiSolver->solve(Vort); mesh->communicate(phi, Vort, Ne); - + // Linear advection ddt(Ne) = -bracket(phi, Ne0, BRACKET_ARAKAWA); - + // Non-linear advection of density and vorticity ddt(Ne) -= bracket(phi, Ne, BRACKET_ARAKAWA); - + ddt(Vort) = -bracket(phi, Vort, BRACKET_ARAKAWA); - + return 0; } - + int diffusive(BoutReal) { // Parallel dynamics treated implicitly - + // Solve for potential phi = phiSolver->solve(Vort); mesh->communicate(phi, Vort, Ne); - - Ve = ( Grad_par(phi) - Grad_par(Ne) ) / nu; + + Ve = (Grad_par(phi) - Grad_par(Ne)) / nu; mesh->communicate(Ve); - + ddt(Ne) = -Div_par(Ve); ddt(Vort) = -Div_par(Ve); - + return 0; } - + private: Field2D Ne0; // Background density profile - + Field3D Vort, Ne; // Vorticity and density Field3D phi; // Electrostatic potential Field3D Ve; // parallel electron velocity - + std::unique_ptr phiSolver{nullptr}; BoutReal nu; // Resistivity parameter }; - BOUTMAIN(DriftWave); diff --git a/examples/advdiff/advdiff.cxx b/examples/advdiff/advdiff.cxx index ac540e52c9..063d5076de 100644 --- a/examples/advdiff/advdiff.cxx +++ b/examples/advdiff/advdiff.cxx @@ -5,46 +5,46 @@ *******************************************************************/ #include -#include +#include class AdvDiff : public PhysicsModel { private: - // Evolving variables + // Evolving variables Field3D V; protected: int init(bool restarting) { // 2D initial profiles Field2D V0; - + // Read initial conditions - - Coordinates *coord = mesh->getCoordinates(); - + + Coordinates* coord = mesh->getCoordinates(); + mesh->get(V0, "V0"); - mesh->get(coord->dx, "dx"); - mesh->get(coord->dy, "dy"); - + mesh->get(coord->dx, "dx"); + mesh->get(coord->dy, "dy"); + // read options - + // Set evolving variables SOLVE_FOR(V); - - if(!restarting) { + + if (!restarting) { // Set variables to these values (+ the initial perturbation) // NOTE: This must be after the calls to bout_solve V += V0; } return 0; } - + int rhs(BoutReal UNUSED(t)) { // Run communications mesh->communicate(V); - + //ddt(V) = D2DX2(V) + 0.5*DDX(V) + D2DY2(V); ddt(V) = DDX(V); - + return 0; } }; diff --git a/examples/advdiff2/init.cxx b/examples/advdiff2/init.cxx index 614f949544..196e261c6c 100644 --- a/examples/advdiff2/init.cxx +++ b/examples/advdiff2/init.cxx @@ -1,5 +1,5 @@ #include -#include +#include #include "header.hxx" diff --git a/examples/advdiff2/rhs.cxx b/examples/advdiff2/rhs.cxx index 511dccbc73..9799175b4b 100644 --- a/examples/advdiff2/rhs.cxx +++ b/examples/advdiff2/rhs.cxx @@ -1,5 +1,5 @@ -#include -#include +#include +#include #include "header.hxx" diff --git a/examples/backtrace/backtrace.cxx b/examples/backtrace/backtrace.cxx index f01a8ccad9..116120f8a9 100644 --- a/examples/backtrace/backtrace.cxx +++ b/examples/backtrace/backtrace.cxx @@ -3,7 +3,7 @@ */ #include -#include +#include void f1() { BoutReal a = 1; diff --git a/examples/blob2d-laplacexz/blob2d.cxx b/examples/blob2d-laplacexz/blob2d.cxx index ede9503319..e51019a8c6 100644 --- a/examples/blob2d-laplacexz/blob2d.cxx +++ b/examples/blob2d-laplacexz/blob2d.cxx @@ -4,9 +4,9 @@ NR Walkden, B Dudson 20 January 2012 *******************************************************************/ -#include "bout.hxx" // Commonly used BOUT++ components +#include "bout/bout.hxx" // Commonly used BOUT++ components +#include "bout/derivs.hxx" // To use DDZ() #include "bout/invert/laplacexz.hxx" // Laplacian inversion -#include "derivs.hxx" // To use DDZ() class Blob2D : public PhysicsModel { private: @@ -18,7 +18,7 @@ class Blob2D : public PhysicsModel { // Parameters // Bohm gyro radius, Ion cyclotron frequency, Bohm sound speed - BoutReal rho_s, Omega_i, c_s, n0; + BoutReal rho_s, Omega_i, c_s, n0; // Constants to calculate the parameters BoutReal Te0, e, B0, D_n, D_vort, m_i, m_e; @@ -76,9 +76,10 @@ class Blob2D : public PhysicsModel { c_s = sqrt(e * Te0 / m_i); // Bohm sound speed rho_s = c_s / Omega_i; // Bohm gyro-radius - output.write("\n\n\t----------Parameters: ------------ \n\tOmega_i = {:e} /s,\n\tc_s = " - "{:e} m/s,\n\trho_s = {:e} m\n", - Omega_i, c_s, rho_s); + output.write( + "\n\n\t----------Parameters: ------------ \n\tOmega_i = {:e} /s,\n\tc_s = " + "{:e} m/s,\n\trho_s = {:e} m\n", + Omega_i, c_s, rho_s); // Calculate delta_*, blob size scaling output.write("\tdelta_* = rho_s * (dn/n) * {:e}\n", diff --git a/examples/blob2d-outerloop/blob2d.cxx b/examples/blob2d-outerloop/blob2d.cxx index de49ca032d..c52984e2f1 100644 --- a/examples/blob2d-outerloop/blob2d.cxx +++ b/examples/blob2d-outerloop/blob2d.cxx @@ -7,8 +7,8 @@ *******************************************************************/ #include // Commonly used BOUT++ components -#include // To use DDZ() -#include // Laplacian inversion +#include // To use DDZ() +#include // Laplacian inversion #include "bout/single_index_ops.hxx" // Operators at a single index diff --git a/examples/blob2d/blob2d.cxx b/examples/blob2d/blob2d.cxx index c1f496c88a..f48e3bc03a 100644 --- a/examples/blob2d/blob2d.cxx +++ b/examples/blob2d/blob2d.cxx @@ -7,8 +7,8 @@ *******************************************************************/ #include // Commonly used BOUT++ components -#include // To use DDZ() -#include // Laplacian inversion +#include // To use DDZ() +#include // Laplacian inversion /// 2D drift-reduced model, mainly used for blob studies /// @@ -43,7 +43,8 @@ class Blob2D : public PhysicsModel { bool compressible; ///< If allow inclusion of n grad phi term in density evolution bool sheath; ///< Sheath connected? - std::unique_ptr phiSolver{nullptr}; ///< Performs Laplacian inversions to calculate phi + std::unique_ptr phiSolver{ + nullptr}; ///< Performs Laplacian inversions to calculate phi protected: int init(bool UNUSED(restarting)) { @@ -55,7 +56,7 @@ class Blob2D : public PhysicsModel { // Load system parameters Te0 = options["Te0"].doc("Temperature in eV").withDefault(30.0); - + e = options["e"].withDefault(1.602e-19); m_i = options["m_i"].withDefault(2 * 1.667e-27); m_e = options["m_e"].withDefault(9.11e-31); @@ -85,9 +86,10 @@ class Blob2D : public PhysicsModel { c_s = sqrt(e * Te0 / m_i); // Bohm sound speed rho_s = c_s / Omega_i; // Bohm gyro-radius - output.write("\n\n\t----------Parameters: ------------ \n\tOmega_i = {:e} /s,\n\tc_s = " - "{:e} m/s,\n\trho_s = {:e} m\n", - Omega_i, c_s, rho_s); + output.write( + "\n\n\t----------Parameters: ------------ \n\tOmega_i = {:e} /s,\n\tc_s = " + "{:e} m/s,\n\trho_s = {:e} m\n", + Omega_i, c_s, rho_s); // Calculate delta_*, blob size scaling output.write("\tdelta_* = rho_s * (dn/n) * {:e} ", diff --git a/examples/boundary-conditions/advection/advection.cxx b/examples/boundary-conditions/advection/advection.cxx index 93dc3e2c63..9442083b8b 100644 --- a/examples/boundary-conditions/advection/advection.cxx +++ b/examples/boundary-conditions/advection/advection.cxx @@ -8,7 +8,7 @@ class Advection : public PhysicsModel { private: Field3D f; ///< The evolving field - + protected: /// Initialise, specify evolving variables int init(bool) { @@ -18,19 +18,18 @@ class Advection : public PhysicsModel { } /// Calculate time derivatives - /// + /// /// df/dt = 1 * df/dy /// - /// Implemented using Vpar_Grad_par so + /// Implemented using Vpar_Grad_par so /// the method can be changed in the input int rhs(BoutReal) { mesh->communicate(f); - + ddt(f) = -Vpar_Grad_par(Field2D(1.0), f); - + return 0; } }; BOUTMAIN(Advection); - diff --git a/examples/conducting-wall-mode/cwm.cxx b/examples/conducting-wall-mode/cwm.cxx index 09ad7b780b..3b3fba1a45 100644 --- a/examples/conducting-wall-mode/cwm.cxx +++ b/examples/conducting-wall-mode/cwm.cxx @@ -6,10 +6,10 @@ *******************************************************************************/ #include -#include -#include -#include -#include +#include +#include +#include +#include class CWM : public PhysicsModel { private: @@ -124,8 +124,8 @@ class CWM : public PhysicsModel { /************* SHIFTED RADIAL COORDINATES ************/ // Check type of parallel transform std::string ptstr = - Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + Options::root()["mesh"]["paralleltransform"]["type"].withDefault( + "identity"); if (lowercase(ptstr) == "shifted") { ShearFactor = 0.0; // I disappears from metric @@ -151,8 +151,9 @@ class CWM : public PhysicsModel { BoutReal hthe0; if (mesh->get(hthe0, "hthe0") == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", - hthe0 / rho_s); + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } /************** NORMALISE QUANTITIES *****************/ @@ -235,10 +236,10 @@ class CWM : public PhysicsModel { dump.addOnce(mesh->LocalNy, "ngy"); dump.addOnce(mesh->LocalNz, "ngz"); SAVE_ONCE(nu_hat, hthe0); - + // Create a solver for the Laplacian phiSolver = Laplacian::create(); - + return 0; } diff --git a/examples/conduction-snb/conduction-snb.cxx b/examples/conduction-snb/conduction-snb.cxx index 179c8ee41a..6ebb853c83 100644 --- a/examples/conduction-snb/conduction-snb.cxx +++ b/examples/conduction-snb/conduction-snb.cxx @@ -1,7 +1,7 @@ // SNB heat conduction model #include -#include +#include int main(int argc, char** argv) { using bout::HeatFluxSNB; diff --git a/examples/conduction/conduction.cxx b/examples/conduction/conduction.cxx index 72ecfae5fd..7831b223de 100644 --- a/examples/conduction/conduction.cxx +++ b/examples/conduction/conduction.cxx @@ -7,34 +7,33 @@ class Conduction : public PhysicsModel { private: - Field3D T; // Evolving temperature equation only - + BoutReal chi; // Parallel conduction coefficient protected: - // This is called once at the start int init(bool UNUSED(restarting)) override { - + // Get the options auto& options = Options::root()["conduction"]; - + // Read from BOUT.inp, setting default to 1.0 // The doc() provides some documentation in BOUT.settings chi = options["chi"].doc("Conduction coefficient").withDefault(1.0); // Tell BOUT++ to solve T SOLVE_FOR(T); - + return 0; } int rhs(BoutReal UNUSED(time)) override { mesh->communicate(T); // Communicate guard cells - - ddt(T) = Div_par_K_Grad_par(chi, T); // Parallel diffusion Div_{||}( chi * Grad_{||}(T) ) - + + ddt(T) = + Div_par_K_Grad_par(chi, T); // Parallel diffusion Div_{||}( chi * Grad_{||}(T) ) + return 0; } }; diff --git a/examples/constraints/alfven-wave/alfven.cxx b/examples/constraints/alfven-wave/alfven.cxx index e39564d950..8d74794cf2 100644 --- a/examples/constraints/alfven-wave/alfven.cxx +++ b/examples/constraints/alfven-wave/alfven.cxx @@ -1,24 +1,24 @@ -#include #include -#include -#include +#include +#include +#include /// Fundamental constants const BoutReal PI = 3.14159265; -const BoutReal e0 = 8.854e-12; // Permittivity of free space -const BoutReal mu0 = 4.e-7*PI; // Permeability of free space -const BoutReal qe = 1.602e-19; // Electron charge -const BoutReal Me = 9.109e-31; // Electron mass -const BoutReal Mp = 1.67262158e-27; // Proton mass +const BoutReal e0 = 8.854e-12; // Permittivity of free space +const BoutReal mu0 = 4.e-7 * PI; // Permeability of free space +const BoutReal qe = 1.602e-19; // Electron charge +const BoutReal Me = 9.109e-31; // Electron mass +const BoutReal Mp = 1.67262158e-27; // Proton mass class Alfven : public PhysicsModel { private: Field3D Vort, Apar; // Evolving fields - + Field3D phi; // Electrostatic potential Field3D jpar; // Parallel current - + Field2D phi2D; // Axisymmetric phi BoutReal Tnorm, Nnorm, Bnorm, AA; // Normalisation options @@ -26,8 +26,8 @@ class Alfven : public PhysicsModel { BoutReal mu_epar; // Electron parallel viscosity BoutReal resistivity; - - bool newXZsolver; + + bool newXZsolver; std::unique_ptr phiSolver{nullptr}; // Old Laplacian in X-Z std::unique_ptr newSolver{nullptr}; // New Laplacian in X-Z protected: @@ -41,22 +41,22 @@ class Alfven : public PhysicsModel { output.write("Normalisation Te={:e}, Ne={:e}, B={:e}\n", Tnorm, Nnorm, Bnorm); SAVE_ONCE4(Tnorm, Nnorm, Bnorm, AA); // Save - - Cs0 = sqrt(qe*Tnorm / (AA*Mp)); // Reference sound speed [m/s] - Omega_ci = qe*Bnorm / (AA*Mp); // Ion cyclotron frequency [1/s] - rho_s0 = Cs0 / Omega_ci; - mi_me = AA*Mp/Me; - beta_e = qe*Tnorm*Nnorm / (SQ(Bnorm)/mu0); + Cs0 = sqrt(qe * Tnorm / (AA * Mp)); // Reference sound speed [m/s] + Omega_ci = qe * Bnorm / (AA * Mp); // Ion cyclotron frequency [1/s] + rho_s0 = Cs0 / Omega_ci; + + mi_me = AA * Mp / Me; + beta_e = qe * Tnorm * Nnorm / (SQ(Bnorm) / mu0); output.write("\tmi_me={:e}, beta_e={:e}\n", mi_me, beta_e); SAVE_ONCE2(mi_me, beta_e); - + output.write("\t Cs={:e}, rho_s={:e}, Omega_ci={:e}\n", Cs0, rho_s0, Omega_ci); SAVE_ONCE3(Cs0, rho_s0, Omega_ci); - mu_epar = opt["mu_epar"].withDefault(-1e7); // Electron parallel viscosity [m^2/s] - mu_epar /= rho_s0*rho_s0*Omega_ci * mi_me; // Normalise + mu_epar = opt["mu_epar"].withDefault(-1e7); // Electron parallel viscosity [m^2/s] + mu_epar /= rho_s0 * rho_s0 * Omega_ci * mi_me; // Normalise resistivity = opt["resistivity"].withDefault(1e-7); @@ -65,44 +65,44 @@ class Alfven : public PhysicsModel { // Specify evolving variables SOLVE_FOR2(Vort, Apar); - + ////////////////////////////////////////// // Solve potential as a constraint solver->constraint(phi, ddt(phi), "phi"); phi = 0.0; - + // Specify the preconditioner function setPrecon(&Alfven::precon); // Create an XZ solver newXZsolver = opt["newXZsolver"].withDefault(false); - if(newXZsolver) { + if (newXZsolver) { // Test new LaplaceXZ solver newSolver = LaplaceXZ::create(mesh); - }else { + } else { // Use older Laplacian solver - phiSolver = Laplacian::create(); + phiSolver = Laplacian::create(); } // Set boundary condition on jpar from input file jpar.setBoundary("jpar"); phi.setBoundary("phi"); - + SAVE_REPEAT(jpar); - + return 0; } int rhs(BoutReal time) { // Communicate evolving variables mesh->communicate(Vort, Apar); - + // Calculate parallel current from Apar - jpar = Delp2(Apar / (0.5*beta_e)); + jpar = Delp2(Apar / (0.5 * beta_e)); // Apply boundary condition on jpar and phi jpar.applyBoundary(time); - + // Communicate jpar and phi mesh->communicate(jpar, phi); @@ -113,21 +113,21 @@ class Alfven : public PhysicsModel { // Vorticity equation ddt(Vort) = Div_par(jpar); - + // Parallel electric field ddt(Apar) = Grad_par(phi); - if(resistivity > 0.0) { - ddt(Apar) += resistivity * jpar; - } + if (resistivity > 0.0) { + ddt(Apar) += resistivity * jpar; + } - if(mu_epar > 0.0) { + if (mu_epar > 0.0) { ddt(Apar) -= mu_epar * Laplace_par(jpar); // Parallel electron viscosity } - + return 0; } - + /*! * Preconditioner. This inverts the operator (1 - gamma*J) * where J is the Jacobian of the system @@ -150,9 +150,9 @@ class Alfven : public PhysicsModel { * ddt(f) = Result of the inversion */ int precon(BoutReal, BoutReal, BoutReal) { - if(newXZsolver) { + if (newXZsolver) { ddt(phi) = newSolver->solve(ddt(phi) - ddt(Vort), 0.0); - }else { + } else { ddt(phi) = phiSolver->solve(ddt(phi) - ddt(Vort), 0.0); } return 0; @@ -162,65 +162,63 @@ class Alfven : public PhysicsModel { // Load metric coefficients from the mesh Field2D Rxy, Bpxy, Btxy, hthe, sinty; GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics - + // Get the coordinates object - Coordinates *coord = mesh->getCoordinates(); + Coordinates* coord = mesh->getCoordinates(); // Checking for dpsi and qinty used in BOUT grids - Field2D dx; - if(!mesh->get(dx, "dpsi")) { + Field2D dx; + if (!mesh->get(dx, "dpsi")) { output << "\tUsing dpsi as the x grid spacing\n"; coord->dx = dx; // Only use dpsi if found - }else { + } else { // dx will have been read already from the grid output << "\tUsing dx as the x grid spacing\n"; } - - Rxy /= Lnorm; - hthe /= Lnorm; - sinty *= SQ(Lnorm)*Bnorm; - coord->dx /= SQ(Lnorm)*Bnorm; - + + Rxy /= Lnorm; + hthe /= Lnorm; + sinty *= SQ(Lnorm) * Bnorm; + coord->dx /= SQ(Lnorm) * Bnorm; + Bpxy /= Bnorm; Btxy /= Bnorm; - coord->Bxy /= Bnorm; - + coord->Bxy /= Bnorm; + // Check type of parallel transform - std::string ptstr = Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + std::string ptstr = + Options::root()["mesh"]["paralleltransform"]["type"].withDefault("identity"); - if(lowercase(ptstr) == "shifted") { + if (lowercase(ptstr) == "shifted") { // Using shifted metric method - sinty = 0.0; // I disappears from metric + sinty = 0.0; // I disappears from metric } - + BoutReal sbp = 1.0; // Sign of Bp if (min(Bpxy, true) < 0.0) { sbp = -1.0; } // Calculate metric components - - coord->g11 = SQ(Rxy*Bpxy); + + coord->g11 = SQ(Rxy * Bpxy); coord->g22 = 1.0 / SQ(hthe); - coord->g33 = SQ(sinty)*coord->g11 + SQ(coord->Bxy)/coord->g11; + coord->g33 = SQ(sinty) * coord->g11 + SQ(coord->Bxy) / coord->g11; coord->g12 = 0.0; - coord->g13 = -sinty*coord->g11; - coord->g23 = -sbp*Btxy/(hthe*Bpxy*Rxy); - + coord->g13 = -sinty * coord->g11; + coord->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy); + coord->J = hthe / Bpxy; - - coord->g_11 = 1.0/coord->g11 + SQ(sinty*Rxy); - coord->g_22 = SQ(coord->Bxy*hthe/Bpxy); - coord->g_33 = Rxy*Rxy; - coord->g_12 = sbp*Btxy*hthe*sinty*Rxy/Bpxy; - coord->g_13 = sinty*Rxy*Rxy; - coord->g_23 = sbp*Btxy*hthe*Rxy/Bpxy; - + + coord->g_11 = 1.0 / coord->g11 + SQ(sinty * Rxy); + coord->g_22 = SQ(coord->Bxy * hthe / Bpxy); + coord->g_33 = Rxy * Rxy; + coord->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy; + coord->g_13 = sinty * Rxy * Rxy; + coord->g_23 = sbp * Btxy * hthe * Rxy / Bpxy; + coord->geometry(); } }; BOUTMAIN(Alfven); - - diff --git a/examples/constraints/laplace-dae/laplace_dae.cxx b/examples/constraints/laplace-dae/laplace_dae.cxx index 6b36e3821d..20a9ffdbd8 100644 --- a/examples/constraints/laplace-dae/laplace_dae.cxx +++ b/examples/constraints/laplace-dae/laplace_dae.cxx @@ -4,10 +4,10 @@ *************************************************************/ #include -#include -#include -#include -#include +#include +#include +#include +#include class Laplace_dae : public PhysicsModel { Field3D U, Apar; // Evolving variables diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx index d44b066573..7f9422a60f 100644 --- a/examples/dalf3/dalf3.cxx +++ b/examples/dalf3/dalf3.cxx @@ -20,106 +20,106 @@ #include -#include -#include -#include #include +#include +#include #include +#include #include // Constants -const BoutReal MU0 = 4.0e-7*PI; -const BoutReal Charge = SI::qe; // electron charge e (C) -const BoutReal Mi = 2.0*SI::Mp; // Ion mass -const BoutReal Me = SI::Me; // Electron mass -const BoutReal Me_Mi = Me / Mi; // Electron mass / Ion mass +const BoutReal MU0 = 4.0e-7 * PI; +const BoutReal Charge = SI::qe; // electron charge e (C) +const BoutReal Mi = 2.0 * SI::Mp; // Ion mass +const BoutReal Me = SI::Me; // Electron mass +const BoutReal Me_Mi = Me / Mi; // Electron mass / Ion mass class DALF3 : public PhysicsModel { private: // Normalisation factors BoutReal Tenorm, Nenorm, Bnorm; BoutReal Cs, rho_s, wci; - + // Poisson brackets: b0 x Grad(f) dot Grad(g) / B = [f, g] // Method to use: BRACKET_ARAKAWA, BRACKET_STD or BRACKET_SIMPLE BRACKET_METHOD bm; // Bracket method for advection terms - + // Evolving quantities Field3D Vort, Ajpar, Pe, Vpar; - + Field3D phi, apar, jpar; - + Field2D B0, Pe0, Jpar0; Vector2D b0xcv; - + Field2D eta; // Collisional damping (resistivity) BoutReal beta_hat, mu_hat; BoutReal viscosity_par; - + bool split_n0; - bool ZeroElMass, estatic; + bool ZeroElMass, estatic; bool curv_kappa; bool flat_resist; BoutReal mul_resist; bool parallel_lc; bool nonlinear; bool jpar_noderiv; // Don't take Delp2(apar) to get jpar - + bool filter_z; - + BoutReal viscosity, hyper_viscosity; - + bool smooth_separatrix; - + FieldGroup comms; - std::unique_ptr phiSolver{nullptr}; // Laplacian solver in X-Z + std::unique_ptr phiSolver{nullptr}; // Laplacian solver in X-Z std::unique_ptr aparSolver{nullptr}; // Laplacian solver in X-Z for Apar - LaplaceXY *laplacexy; // Laplacian solver in X-Y (n=0) - Field2D phi2D; // Axisymmetric potential, used when split_n0=true + LaplaceXY* laplacexy; // Laplacian solver in X-Y (n=0) + Field2D phi2D; // Axisymmetric potential, used when split_n0=true protected: int init(bool UNUSED(restarting)) { - + ///////////////////////////////////////////////////// // Load data from the grid - + GRID_LOAD(Jpar0); SAVE_ONCE(Jpar0); - + Field2D Ni0, Te0; GRID_LOAD2(Ni0, Te0); - Ni0 *= 1e20; // To m^-3 - Pe0 = 2.*Charge * Ni0 * Te0; // Electron pressure in Pascals + Ni0 *= 1e20; // To m^-3 + Pe0 = 2. * Charge * Ni0 * Te0; // Electron pressure in Pascals SAVE_ONCE(Pe0); - + // Load curvature term - b0xcv.covariant = false; // Read contravariant components + b0xcv.covariant = false; // Read contravariant components mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2 - + // Metric coefficients Field2D Rxy, Bpxy, Btxy, hthe; Field2D I; // Shear factor - - if(mesh->get(Rxy, "Rxy")) { // m + + if (mesh->get(Rxy, "Rxy")) { // m output_error.write("Error: Cannot read Rxy from grid\n"); return 1; } - if(mesh->get(Bpxy, "Bpxy")) { // T + if (mesh->get(Bpxy, "Bpxy")) { // T output_error.write("Error: Cannot read Bpxy from grid\n"); return 1; } mesh->get(Btxy, "Btxy"); // T - mesh->get(B0, "Bxy"); // T + mesh->get(B0, "Bxy"); // T mesh->get(hthe, "hthe"); // m - mesh->get(I, "sinty");// m^-2 T^-1 + mesh->get(I, "sinty"); // m^-2 T^-1 // Set locations of staggered variables jpar.setLocation(CELL_YLOW); Ajpar.setLocation(CELL_YLOW); apar.setLocation(CELL_YLOW); - + ////////////////////////////////////////////////////////////// // Options @@ -145,24 +145,24 @@ class DALF3 : public PhysicsModel { int bracket_method; bracket_method = options["bracket_method"].withDefault(0); - switch(bracket_method) { + switch (bracket_method) { case 0: { - bm = BRACKET_STD; + bm = BRACKET_STD; output << "\tBrackets: default differencing\n"; break; } case 1: { - bm = BRACKET_SIMPLE; + bm = BRACKET_SIMPLE; output << "\tBrackets: simplified operator\n"; break; } case 2: { - bm = BRACKET_ARAKAWA; + bm = BRACKET_ARAKAWA; output << "\tBrackets: Arakawa scheme\n"; break; } case 3: { - bm = BRACKET_CTU; + bm = BRACKET_CTU; output << "\tBrackets: Corner Transport Upwind method\n"; break; } @@ -171,105 +171,105 @@ class DALF3 : public PhysicsModel { return 1; } - Coordinates *coord = mesh->getCoordinates(); - + Coordinates* coord = mesh->getCoordinates(); + // SHIFTED RADIAL COORDINATES // Check type of parallel transform - std::string ptstr = Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + std::string ptstr = + Options::root()["mesh"]["paralleltransform"]["type"].withDefault("identity"); - if(lowercase(ptstr) == "shifted") { + if (lowercase(ptstr) == "shifted") { // Dimits style, using local coordinate system - b0xcv.z += I*b0xcv.x; - I = 0.0; // I disappears from metric + b0xcv.z += I * b0xcv.x; + I = 0.0; // I disappears from metric } - + /////////////////////////////////////////////////// // Normalisation - + Tenorm = max(Te0, true); Nenorm = max(Ni0, true); - Bnorm = max(B0, true); - + Bnorm = max(B0, true); + // Sound speed in m/s - Cs = sqrt(Charge*Tenorm / Mi); - + Cs = sqrt(Charge * Tenorm / Mi); + // drift scale rho_s = Cs * Mi / (Charge * Bnorm); - + // Ion cyclotron frequency wci = Charge * Bnorm / Mi; - - beta_hat = 4.e-7*PI * Charge*Tenorm * Nenorm / (Bnorm*Bnorm); - + + beta_hat = 4.e-7 * PI * Charge * Tenorm * Nenorm / (Bnorm * Bnorm); + if (ZeroElMass) { mu_hat = 0.; } else { mu_hat = Me / Mi; } - + SAVE_ONCE3(Tenorm, Nenorm, Bnorm); SAVE_ONCE3(Cs, rho_s, wci); SAVE_ONCE2(beta_hat, mu_hat); - - // Spitzer resistivity + + // Spitzer resistivity if (flat_resist) { // eta in Ohm-m. NOTE: ln(Lambda) = 20 - eta = 0.51*1.03e-4*20.*pow(Tenorm, -1.5); + eta = 0.51 * 1.03e-4 * 20. * pow(Tenorm, -1.5); } else { - eta = 0.51*1.03e-4*20.*pow(Te0,-1.5); + eta = 0.51 * 1.03e-4 * 20. * pow(Te0, -1.5); } if (mul_resist < 0.0) { mul_resist = 0.0; } eta *= mul_resist; - + // Plasma quantities - Jpar0 /= Nenorm*Charge*Cs; - Pe0 /= Nenorm*Charge*Tenorm; - + Jpar0 /= Nenorm * Charge * Cs; + Pe0 /= Nenorm * Charge * Tenorm; + // Coefficients eta *= Charge * Nenorm / Bnorm; - - viscosity /= wci*SQ(rho_s); - hyper_viscosity /= wci*SQ(SQ(rho_s)); - viscosity_par /= wci*SQ(rho_s); - + + viscosity /= wci * SQ(rho_s); + hyper_viscosity /= wci * SQ(SQ(rho_s)); + viscosity_par /= wci * SQ(rho_s); + b0xcv.x /= Bnorm; - b0xcv.y *= rho_s*rho_s; - b0xcv.z *= rho_s*rho_s; - + b0xcv.y *= rho_s * rho_s; + b0xcv.z *= rho_s * rho_s; + // Metrics Rxy /= rho_s; hthe /= rho_s; - I *= rho_s*rho_s*Bnorm; + I *= rho_s * rho_s * Bnorm; Bpxy /= Bnorm; Btxy /= Bnorm; B0 /= Bnorm; - - coord->dx /= rho_s*rho_s*Bnorm; - + + coord->dx /= rho_s * rho_s * Bnorm; + /////////////////////////////////////////////////// // CALCULATE METRICS - - coord->g11 = SQ(Rxy*Bpxy); + + coord->g11 = SQ(Rxy * Bpxy); coord->g22 = 1.0 / SQ(hthe); - coord->g33 = SQ(I)*coord->g11 + SQ(B0)/coord->g11; + coord->g33 = SQ(I) * coord->g11 + SQ(B0) / coord->g11; coord->g12 = 0.0; - coord->g13 = -I*coord->g11; - coord->g23 = -Btxy/(hthe*Bpxy*Rxy); - + coord->g13 = -I * coord->g11; + coord->g23 = -Btxy / (hthe * Bpxy * Rxy); + coord->J = hthe / Bpxy; coord->Bxy = B0; - - coord->g_11 = 1.0/coord->g11 + SQ(I*Rxy); - coord->g_22 = SQ(B0*hthe/Bpxy); - coord->g_33 = Rxy*Rxy; - coord->g_12 = Btxy*hthe*I*Rxy/Bpxy; - coord->g_13 = I*Rxy*Rxy; - coord->g_23 = Btxy*hthe*Rxy/Bpxy; - + + coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy); + coord->g_22 = SQ(B0 * hthe / Bpxy); + coord->g_33 = Rxy * Rxy; + coord->g_12 = Btxy * hthe * I * Rxy / Bpxy; + coord->g_13 = I * Rxy * Rxy; + coord->g_23 = Btxy * hthe * Rxy / Bpxy; + coord->geometry(); // Calculate quantities from metric tensor SOLVE_FOR3(Vort, Pe, Vpar); @@ -284,24 +284,24 @@ class DALF3 : public PhysicsModel { // Need to communicate apar first then jpar comms.add(apar); } - + comms.add(phi); - + phi.setBoundary("phi"); apar.setBoundary("apar"); jpar.setBoundary("jpar"); - + SAVE_REPEAT3(jpar, apar, phi); - + if (nonlinear) { SAVE_REPEAT(eta); } else { SAVE_ONCE(eta); } - + // Create a solver for the Laplacian phiSolver = Laplacian::create(&options["phiSolver"]); - + // LaplaceXY for n=0 solve if (split_n0) { // Create an XY solver for n=0 component @@ -314,53 +314,53 @@ class DALF3 : public PhysicsModel { aparSolver = Laplacian::create(&options["aparSolver"]); aparSolver->setCoefA(beta_hat); aparSolver->setCoefD(-mu_hat); - + return 0; } - + // Curvature operator - const Field3D Kappa(const Field3D &f) { + const Field3D Kappa(const Field3D& f) { if (curv_kappa) { // Use the b0xcv vector from grid file - return -2.*b0xcv*Grad(f) / B0; + return -2. * b0xcv * Grad(f) / B0; } - - return 2.*bracket(log(B0), f, bm); + + return 2. * bracket(log(B0), f, bm); } - - const Field3D Grad_parP(const Field3D &f, CELL_LOC loc) { + + const Field3D Grad_parP(const Field3D& f, CELL_LOC loc) { Field3D result; if (mesh->StaggerGrids) { result = Grad_par(f, loc); if (nonlinear) { - result -= beta_hat * bracket(interp_to(apar, loc), interp_to(f, loc), - BRACKET_ARAKAWA); + result -= + beta_hat * bracket(interp_to(apar, loc), interp_to(f, loc), BRACKET_ARAKAWA); } } else { if (nonlinear) { - result = ::Grad_parP(apar*beta_hat, f); + result = ::Grad_parP(apar * beta_hat, f); } else { result = Grad_par(f, loc); } } return result; } - + int rhs(BoutReal UNUSED(time)) { - + // Invert vorticity to get electrostatic potential if (split_n0) { Field2D Vort2D = DC(Vort); // n=0 component phi2D = laplacexy->solve(Vort2D, phi2D); - + // Solve non-axisymmetric part using X-Z solver - phi = phiSolver->solve((Vort-Vort2D)*B0); + phi = phiSolver->solve((Vort - Vort2D) * B0); phi += phi2D; // Add axisymmetric part } else { - phi = phiSolver->solve(Vort*B0); + phi = phiSolver->solve(Vort * B0); } phi.applyBoundary(); - + // Calculate apar and jpar if (estatic) { // Electrostatic @@ -378,7 +378,7 @@ class DALF3 : public PhysicsModel { if (ZeroElMass) { // Ignore electron inertia term apar = Ajpar / beta_hat; - + mesh->communicate(comms); jpar = -Delp2(apar); jpar.applyBoundary(); @@ -388,11 +388,11 @@ class DALF3 : public PhysicsModel { // ajpar = beta_hat*apar + mu_hat*jpar apar = aparSolver->solve(Ajpar); apar.applyBoundary(); - + mesh->communicate(comms); if (jpar_noderiv) { // Already applied boundaries on Ajpar and apar - jpar = (Ajpar - beta_hat*apar) / mu_hat; + jpar = (Ajpar - beta_hat * apar) / mu_hat; } else { jpar = -Delp2(apar); jpar.applyBoundary(); @@ -400,18 +400,18 @@ class DALF3 : public PhysicsModel { } } } - + Field3D Pet = Pe0; if (nonlinear) { Pet += Pe; } - + // Boundary in jpar if (mesh->firstX()) { for (int i = 4; i >= 0; i--) { for (int j = 0; j < mesh->LocalNy; j++) { - for (int k=0;kLocalNz;k++) { - jpar(i,j,k) = 0.5*jpar(i+1,j,k); + for (int k = 0; k < mesh->LocalNz; k++) { + jpar(i, j, k) = 0.5 * jpar(i + 1, j, k); } } } @@ -419,33 +419,30 @@ class DALF3 : public PhysicsModel { if (mesh->lastX()) { for (int i = mesh->LocalNx - 5; i < mesh->LocalNx; i++) { for (int j = 0; j < mesh->LocalNy; j++) { - for (int k=0;kLocalNz;k++) { - jpar(i,j,k) = 0.5*jpar(i-1,j,k); + for (int k = 0; k < mesh->LocalNz; k++) { + jpar(i, j, k) = 0.5 * jpar(i - 1, j, k); } } } } - - + // Vorticity equation - ddt(Vort) = - B0*B0*Grad_parP(jpar/interp_to(B0, CELL_YLOW), CELL_CENTRE) - - B0*Kappa(Pe) - ; - + ddt(Vort) = B0 * B0 * Grad_parP(jpar / interp_to(B0, CELL_YLOW), CELL_CENTRE) + - B0 * Kappa(Pe); + if (nonlinear) { - ddt(Vort) -= bracket(phi, Vort, bm); // ExB advection + ddt(Vort) -= bracket(phi, Vort, bm); // ExB advection } - + if (viscosity > 0.0) { - ddt(Vort) += viscosity * Delp2(Vort); + ddt(Vort) += viscosity * Delp2(Vort); } if (hyper_viscosity > 0.0) { Field3D delp2_vort = Delp2(Vort); delp2_vort.applyBoundary("neumann"); mesh->communicate(delp2_vort); - - ddt(Vort) += hyper_viscosity*Delp2(delp2_vort); + + ddt(Vort) += hyper_viscosity * Delp2(delp2_vort); } if (filter_z) { @@ -455,31 +452,26 @@ class DALF3 : public PhysicsModel { // Parallel Ohm's law if (!(estatic && ZeroElMass)) { // beta_hat*apar + mu_hat*jpar - ddt(Ajpar) = - Grad_parP(Pe - phi, CELL_YLOW) - - beta_hat * bracket(apar, Pe0, BRACKET_ARAKAWA) - - eta*jpar - ; - + ddt(Ajpar) = Grad_parP(Pe - phi, CELL_YLOW) + - beta_hat * bracket(apar, Pe0, BRACKET_ARAKAWA) - eta * jpar; + if (nonlinear) { - ddt(Ajpar) -= mu_hat*bracket(phi, jpar, bm); + ddt(Ajpar) -= mu_hat * bracket(phi, jpar, bm); } if (filter_z) { ddt(Ajpar) = filter(ddt(Ajpar), 1); } } - + // Parallel velocity - ddt(Vpar) = - - Grad_parP(Pe, CELL_YLOW) - + beta_hat * bracket(apar, interp_to(Pe0, CELL_YLOW), BRACKET_ARAKAWA) - ; - + ddt(Vpar) = -Grad_parP(Pe, CELL_YLOW) + + beta_hat * bracket(apar, interp_to(Pe0, CELL_YLOW), BRACKET_ARAKAWA); + if (nonlinear) { ddt(Vpar) -= bracket(phi, Vpar, bm); } - + if (viscosity_par > 0.) { ddt(Vpar) += viscosity_par * Grad2_par2(Vpar); } @@ -490,13 +482,11 @@ class DALF3 : public PhysicsModel { // Electron pressure ddt(Pe) = - - bracket(phi, Pet, bm) - + Pet * ( - Kappa(phi - Pe) - + B0*Grad_parP( (jpar - Vpar)/interp_to(B0, CELL_YLOW) , CELL_YLOW) - ) - ; - + -bracket(phi, Pet, bm) + + Pet + * (Kappa(phi - Pe) + + B0 * Grad_parP((jpar - Vpar) / interp_to(B0, CELL_YLOW), CELL_YLOW)); + if (smooth_separatrix) { // Experimental smoothing across separatrix ddt(Vort) += mesh->smoothSeparatrix(Vort); @@ -507,46 +497,44 @@ class DALF3 : public PhysicsModel { } // Boundary in Vpar and vorticity - + if (mesh->firstX()) { for (int i = 3; i >= 0; i--) { for (int j = 0; j < mesh->LocalNy; j++) { - for (int k=0;kLocalNz;k++) { - ddt(Vpar)(i,j,k) = ddt(Vpar)(i+1,j,k); - ddt(Vort)(i,j,k) = ddt(Vort)(i+1,j,k); + for (int k = 0; k < mesh->LocalNz; k++) { + ddt(Vpar)(i, j, k) = ddt(Vpar)(i + 1, j, k); + ddt(Vort)(i, j, k) = ddt(Vort)(i + 1, j, k); } } } // Subtract DC component for (int i = 0; i < 10; i++) { - for (int j=0;jLocalNy;j++) { + for (int j = 0; j < mesh->LocalNy; j++) { BoutReal avg = 0.; for (int k = 0; k < mesh->LocalNz; k++) { - avg += ddt(Vort)(i,j,k); + avg += ddt(Vort)(i, j, k); } - avg /= (BoutReal) mesh->LocalNz; + avg /= (BoutReal)mesh->LocalNz; for (int k = 0; k < mesh->LocalNz; k++) { - ddt(Vort)(i,j,k) -= avg; + ddt(Vort)(i, j, k) -= avg; } - } + } } } if (mesh->lastX()) { for (int i = mesh->LocalNx - 3; i < mesh->LocalNx; i++) { for (int j = 0; j < mesh->LocalNy; j++) { - for (int k=0;kLocalNz;k++) { - ddt(Vpar)(i,j,k) = ddt(Vpar)(i-1,j,k); - ddt(Vort)(i,j,k) = ddt(Vort)(i-1,j,k); + for (int k = 0; k < mesh->LocalNz; k++) { + ddt(Vpar)(i, j, k) = ddt(Vpar)(i - 1, j, k); + ddt(Vort)(i, j, k) = ddt(Vort)(i - 1, j, k); } } } } - + return 0; } - }; BOUTMAIN(DALF3); - diff --git a/examples/eigen-box/eigen-box.cxx b/examples/eigen-box/eigen-box.cxx index 57c87f5667..c3eb738f8a 100644 --- a/examples/eigen-box/eigen-box.cxx +++ b/examples/eigen-box/eigen-box.cxx @@ -6,7 +6,7 @@ */ #include -#include +#include class EigenBox : public PhysicsModel { protected: @@ -17,12 +17,13 @@ class EigenBox : public PhysicsModel { } int rhs(BoutReal) override { mesh->communicate(f); - + ddt(g) = D2DX2(f); ddt(f) = g; - + return 0; } + private: Field3D f, g; }; diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx index 4f5d3b1047..41dcc75eda 100644 --- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx +++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx @@ -30,23 +30,23 @@ #include #include -#include -#include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include +#include +#include #include #include #include -#include -#include -#include +#include +#include +#include #include // Defines BOUT_FOR_RAJA @@ -54,7 +54,7 @@ #include #endif -#include +#include CELL_LOC loc = CELL_CENTRE; diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index eda8528351..78042ae364 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -7,15 +7,15 @@ #include #include -#include -#include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include +#include +#include #include @@ -23,7 +23,7 @@ #include #endif -#include +#include CELL_LOC loc = CELL_CENTRE; @@ -37,11 +37,11 @@ BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xout", "none"); class ELMpb : public PhysicsModel { private: // 2D inital profiles - Field2D J0, P0; // Current and pressure - Vector2D b0xcv; // Curvature term - Field2D beta; // Used for Vpar terms + Field2D J0, P0; // Current and pressure + Vector2D b0xcv; // Curvature term + Field2D beta; // Used for Vpar terms Coordinates::FieldMetric gradparB; - Field2D phi0; // When diamagnetic terms used + Field2D phi0; // When diamagnetic terms used Field2D Psixy, x; Coordinates::FieldMetric U0; // 0th vorticity of equilibrium flow, // radial flux coordinate, normalized radial flux coordinate @@ -205,11 +205,11 @@ class ELMpb : public PhysicsModel { bool phi_constraint; // Solver for phi using a solver constraint - bool include_rmp; // Include RMP coil perturbation - bool simple_rmp; // Just use a simple form for the perturbation + bool include_rmp; // Include RMP coil perturbation + bool simple_rmp; // Just use a simple form for the perturbation - BoutReal rmp_factor; // Multiply amplitude by this factor - BoutReal rmp_ramp; // Ramp-up time for RMP [s]. negative -> instant + BoutReal rmp_factor; // Multiply amplitude by this factor + BoutReal rmp_ramp; // Ramp-up time for RMP [s]. negative -> instant BoutReal rmp_freq; // Amplitude oscillation frequency [Hz] (negative -> no oscillation) BoutReal rmp_rotate; // Rotation rate [Hz] bool rmp_vac_mask; @@ -371,9 +371,8 @@ class ELMpb : public PhysicsModel { density = options["density"].doc("Number density [m^-3]").withDefault(1.0e19); - evolve_jpar = options["evolve_jpar"] - .doc("If true, evolve J raher than Psi") - .withDefault(false); + evolve_jpar = + options["evolve_jpar"].doc("If true, evolve J raher than Psi").withDefault(false); phi_constraint = options["phi_constraint"] .doc("Use solver constraint for phi?") .withDefault(false); @@ -419,7 +418,8 @@ class ELMpb : public PhysicsModel { throw BoutException("Invalid choice of bracket method. Must be 0 - 3\n"); } - bm_mag_flag = options["bm_mag_flag"].doc("magnetic flutter Poisson Bracket").withDefault(0); + bm_mag_flag = + options["bm_mag_flag"].doc("magnetic flutter Poisson Bracket").withDefault(0); switch (bm_mag_flag) { case 0: { bm_mag = BRACKET_STD; @@ -454,7 +454,8 @@ class ELMpb : public PhysicsModel { diamag_grad_t = options["diamag_grad_t"] .doc("Grad_par(Te) term in Psi equation") .withDefault(diamag); - diamag_phi0 = options["diamag_phi0"].doc("Include equilibrium phi0").withDefault(diamag); + diamag_phi0 = + options["diamag_phi0"].doc("Include equilibrium phi0").withDefault(diamag); dia_fact = options["dia_fact"] .doc("Scale diamagnetic effects by this factor") .withDefault(1.0); @@ -553,16 +554,20 @@ class ELMpb : public PhysicsModel { rmp_rotate = options["rmp_rotate"].withDefault(0.0); // Vacuum region control - vacuum_pressure = options["vacuum_pressure"] + vacuum_pressure = + options["vacuum_pressure"] .doc("Fraction of peak pressure, below which is considered vacuum.") .withDefault(0.02); - vacuum_trans = options["vacuum_trans"] + vacuum_trans = + options["vacuum_trans"] .doc("Vacuum boundary transition width, as fraction of peak pressure.") .withDefault(0.005); // Resistivity and hyper-resistivity options - vac_lund = options["vac_lund"].doc("Lundquist number in vacuum region").withDefault(0.0); - core_lund = options["core_lund"].doc("Lundquist number in core region").withDefault(0.0); + vac_lund = + options["vac_lund"].doc("Lundquist number in vacuum region").withDefault(0.0); + core_lund = + options["core_lund"].doc("Lundquist number in core region").withDefault(0.0); hyperresist = options["hyperresist"].withDefault(-1.0); ehyperviscos = options["ehyperviscos"].withDefault(-1.0); spitzer_resist = options["spitzer_resist"] @@ -574,7 +579,8 @@ class ELMpb : public PhysicsModel { damp_width = options["damp_width"] .doc("Width of the radial damping regions, in grid cells") .withDefault(0); - damp_t_const = options["damp_t_const"] + damp_t_const = + options["damp_t_const"] .doc("Time constant for damping in radial regions. Normalised time units.") .withDefault(0.1); @@ -583,7 +589,8 @@ class ELMpb : public PhysicsModel { viscos_perp = options["viscos_perp"].doc("Perpendicular viscosity").withDefault(-1.0); hyperviscos = options["hyperviscos"].doc("Radial hyperviscosity").withDefault(-1.0); - diffusion_par = options["diffusion_par"].doc("Parallel pressure diffusion").withDefault(-1.0); + diffusion_par = + options["diffusion_par"].doc("Parallel pressure diffusion").withDefault(-1.0); diffusion_p4 = options["diffusion_p4"] .doc("parallel hyper-viscous diffusion for pressure") .withDefault(-1.0); @@ -1107,7 +1114,7 @@ class ELMpb : public PhysicsModel { setPrecon(&ELMpb::precon); // Set Jacobian - setJacobian( (jacobianfunc) &ELMpb::jacobian ); + setJacobian((jacobianfunc)&ELMpb::jacobian); } // Diamagnetic phi0 @@ -1484,8 +1491,7 @@ class ELMpb : public PhysicsModel { if (eHall) { // electron parallel pressure ddt(Psi) += 0.25 * delta_i - * (Grad_parP(P, loc) - + bracket(interp_to(P0, loc), Psi, bm_mag)); + * (Grad_parP(P, loc) + bracket(interp_to(P0, loc), Psi, bm_mag)); } if (diamag_phi0) { // Equilibrium flow @@ -1532,7 +1538,7 @@ class ELMpb : public PhysicsModel { //////////////////////////////////////////////////// // Vorticity equation - Psi_loc = interp_to(Psi, CELL_CENTRE,"RGN_ALL"); + Psi_loc = interp_to(Psi, CELL_CENTRE, "RGN_ALL"); Psi_loc.applyBoundary(); // Grad j term ddt(U) = SQ(B0) * b0xGrad_dot_Grad(Psi_loc, J0, CELL_CENTRE); diff --git a/examples/em-drift/2fluid.cxx b/examples/em-drift/2fluid.cxx index d65a193827..00bd7e206c 100644 --- a/examples/em-drift/2fluid.cxx +++ b/examples/em-drift/2fluid.cxx @@ -8,9 +8,9 @@ #include -#include -#include -#include +#include +#include +#include class EMdrift : public PhysicsModel { private: @@ -48,11 +48,11 @@ class EMdrift : public PhysicsModel { // Inverts a Laplacian to get potential std::unique_ptr phiSolver; - + // Solves the electromagnetic potential std::unique_ptr aparSolver; Field2D acoef; // Coefficient in the Helmholtz equation - + int init(bool UNUSED(restarting)) override { Field2D I; // Shear factor @@ -106,12 +106,13 @@ class EMdrift : public PhysicsModel { if (ZeroElMass) { evolve_ajpar = 0; // Don't need ajpar - calculated from ohm's law } - + /************* SHIFTED RADIAL COORDINATES ************/ // Check type of parallel transform - std::string ptstr = Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + std::string ptstr = + Options::root()["mesh"]["paralleltransform"]["type"].withDefault( + "identity"); if (lowercase(ptstr) == "shifted") { ShearFactor = 0.0; // I disappears from metric @@ -150,8 +151,9 @@ class EMdrift : public PhysicsModel { BoutReal hthe0; if (mesh->get(hthe0, "hthe0") == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", - hthe0 / rho_s); + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } /************** NORMALISE QUANTITIES *****************/ @@ -223,14 +225,14 @@ class EMdrift : public PhysicsModel { // Add any other variables to be dumped to file SAVE_REPEAT(phi, Apar, jpar); - + SAVE_ONCE(Ni0, Te0, Ti0); SAVE_ONCE(Te_x, Ti_x, Ni_x, rho_s, wci, zeff, AA); - + // Create a solver for the Laplacian phiSolver = Laplacian::create(&globalOptions["phiSolver"]); - if (! (estatic || ZeroElMass)) { + if (!(estatic || ZeroElMass)) { // Create a solver for the electromagnetic potential aparSolver = Laplacian::create(&globalOptions["aparSolver"]); acoef = (-0.5 * beta_p / fmei) * Ni0; @@ -238,7 +240,7 @@ class EMdrift : public PhysicsModel { } else { globalOptions["aparSolver"].setConditionallyUsed(); } - + return 0; } diff --git a/examples/fci-wave-logn/fci-wave.cxx b/examples/fci-wave-logn/fci-wave.cxx index 8c801dfefa..731897ad4e 100644 --- a/examples/fci-wave-logn/fci-wave.cxx +++ b/examples/fci-wave-logn/fci-wave.cxx @@ -5,17 +5,17 @@ class FCIwave : public PhysicsModel { private: Field3D logn, v; //< Evolving density, momentum Field3D n; - + Field3D Bxyz; ///< Total magnetic field bool expand_divergence; - BoutReal background; ///< background density floor + BoutReal background; ///< background density floor BoutReal log_background; // Log(background) - + /// Parallel divergence, using integration over projected cells - Field3D Div_par_integrate(const Field3D &f) { + Field3D Div_par_integrate(const Field3D& f) { Field3D f_B = f / Bxyz; - + f_B.splitParallelSlices(); mesh->getCoordinates()->getParallelTransform().integrateParallelSlices(f_B); @@ -24,39 +24,36 @@ class FCIwave : public PhysicsModel { // then the boundary condition is simpler since f = 0 gives f_B=0 boundary condition. /// Loop over the mesh boundary regions - for (const auto ® : mesh->getBoundariesPar()) { - Field3D &f_B_next = f_B.ynext(reg->dir); - const Field3D &f_next = f.ynext(reg->dir); - const Field3D &B_next = Bxyz.ynext(reg->dir); - + for (const auto& reg : mesh->getBoundariesPar()) { + Field3D& f_B_next = f_B.ynext(reg->dir); + const Field3D& f_next = f.ynext(reg->dir); + const Field3D& B_next = Bxyz.ynext(reg->dir); + for (reg->first(); !reg->isDone(); reg->next()) { - f_B_next(reg->x, reg->y+reg->dir, reg->z) = - f_next(reg->x, reg->y+reg->dir, reg->z) / B_next(reg->x, reg->y+reg->dir, reg->z); + f_B_next(reg->x, reg->y + reg->dir, reg->z) = + f_next(reg->x, reg->y + reg->dir, reg->z) + / B_next(reg->x, reg->y + reg->dir, reg->z); } } - + Field3D result; result.allocate(); - - Coordinates *coord = mesh->getCoordinates(); - - for(auto i : result.getRegion(RGN_NOBNDRY)) { + + Coordinates* coord = mesh->getCoordinates(); + + for (auto i : result.getRegion(RGN_NOBNDRY)) { result[i] = Bxyz[i] * (f_B.yup()[i.yp()] - f_B.ydown()[i.ym()]) - / (2.*coord->dy[i] * sqrt(coord->g_22[i])); + / (2. * coord->dy[i] * sqrt(coord->g_22[i])); if (!finite(result[i])) { - output.write("[{:d},{:d},{:d}]: {:e}, {:e} -> {:e}\n", - i.x(), i.y(), i.z(), - f_B.yup()[i.yp()], - f_B.ydown()[i.ym()], - result[i]); - + output.write("[{:d},{:d},{:d}]: {:e}, {:e} -> {:e}\n", i.x(), i.y(), i.z(), + f_B.yup()[i.yp()], f_B.ydown()[i.ym()], result[i]); } } return result; } - + protected: int init(bool UNUSED(restarting)) override { @@ -68,67 +65,64 @@ class FCIwave : public PhysicsModel { Bxyz.applyParallelBoundary("parallel_neumann"); SAVE_ONCE(Bxyz); - Options::getRoot()->getSection("fciwave")->get("expand_divergence", expand_divergence, true); + Options::getRoot()->getSection("fciwave")->get("expand_divergence", expand_divergence, + true); Options::getRoot()->getSection("fciwave")->get("background", background, 1e-6); log_background = log(background); - - SOLVE_FOR2(logn,v); + + SOLVE_FOR2(logn, v); SAVE_REPEAT(n); - + SAVE_REPEAT2(ddt(logn), ddt(v)); - + return 0; } - + int rhs(BoutReal UNUSED(t)) override { - mesh->communicate(logn,v); + mesh->communicate(logn, v); // Boundary condition applied to log(n) to prevent negative densities logn.applyParallelBoundary(); v.applyParallelBoundary(); n = exp(logn); - + // Momentum - ddt(v) = - - v*Grad_par(v) - - Grad_par(logn) - + Grad2_par2(v) - ; + ddt(v) = -v * Grad_par(v) - Grad_par(logn) + Grad2_par2(v); if (expand_divergence) { - // Split the divergence of flux into two terms - ddt(logn) = - -v * Grad_par(logn) - Div_par(v); - + // Split the divergence of flux into two terms + ddt(logn) = -v * Grad_par(logn) - Div_par(v); + } else { // Calculate the flux divergence using Div_par_integrate - + Field3D nv = n * v; nv.splitParallelSlices(); - for (const auto ® : mesh->getBoundariesPar()) { - Field3D &nv_next = nv.ynext(reg->dir); + for (const auto& reg : mesh->getBoundariesPar()) { + Field3D& nv_next = nv.ynext(reg->dir); nv_next.allocate(); - - const Field3D &logn_next = logn.ynext(reg->dir); - const Field3D &v_next = v.ynext(reg->dir); - + + const Field3D& logn_next = logn.ynext(reg->dir); + const Field3D& v_next = v.ynext(reg->dir); + for (reg->first(); !reg->isDone(); reg->next()) { - BoutReal n_b = exp(0.5*(logn_next(reg->x, reg->y+reg->dir, reg->z) + - logn(reg->x, reg->y, reg->z))); - BoutReal v_b = 0.5*(v_next(reg->x, reg->y+reg->dir, reg->z) + - v(reg->x, reg->y, reg->z)); - - nv_next(reg->x, reg->y+reg->dir, reg->z) = - 2.*n_b*v_b - nv(reg->x, reg->y, reg->z); + BoutReal n_b = exp(0.5 + * (logn_next(reg->x, reg->y + reg->dir, reg->z) + + logn(reg->x, reg->y, reg->z))); + BoutReal v_b = + 0.5 + * (v_next(reg->x, reg->y + reg->dir, reg->z) + v(reg->x, reg->y, reg->z)); + + nv_next(reg->x, reg->y + reg->dir, reg->z) = + 2. * n_b * v_b - nv(reg->x, reg->y, reg->z); } } - + // Logarithm of density - ddt(logn) = - - Div_par_integrate(nv) / floor(n, background); - + ddt(logn) = -Div_par_integrate(nv) / floor(n, background); + // Apply a soft floor to the density // Hard floors (setting ddt = 0) can slow convergence of solver for (auto i : logn.getRegion(RGN_NOBNDRY)) { @@ -138,7 +132,6 @@ class FCIwave : public PhysicsModel { } } - return 0; } }; diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx index 62cfd4d3d9..226b52c808 100644 --- a/examples/fci-wave/fci-wave.cxx +++ b/examples/fci-wave/fci-wave.cxx @@ -14,7 +14,7 @@ class FCIwave : public PhysicsModel { BoutReal log_background; // Log(background) /// Parallel divergence, using integration over projected cells - Field3D Div_par_integrate(const Field3D &f) { + Field3D Div_par_integrate(const Field3D& f) { Field3D f_B = f / Bxyz; f_B.splitParallelSlices(); @@ -25,30 +25,30 @@ class FCIwave : public PhysicsModel { // then the boundary condition is simpler since f = 0 gives f_B=0 boundary condition. /// Loop over the mesh boundary regions - for (const auto ® : mesh->getBoundariesPar()) { - Field3D &f_B_next = f_B.ynext(reg->dir); - const Field3D &f_next = f.ynext(reg->dir); - const Field3D &B_next = Bxyz.ynext(reg->dir); + for (const auto& reg : mesh->getBoundariesPar()) { + Field3D& f_B_next = f_B.ynext(reg->dir); + const Field3D& f_next = f.ynext(reg->dir); + const Field3D& B_next = Bxyz.ynext(reg->dir); for (reg->first(); !reg->isDone(); reg->next()) { f_B_next(reg->x, reg->y + reg->dir, reg->z) = - f_next(reg->x, reg->y + reg->dir, reg->z) / - B_next(reg->x, reg->y + reg->dir, reg->z); + f_next(reg->x, reg->y + reg->dir, reg->z) + / B_next(reg->x, reg->y + reg->dir, reg->z); } } Field3D result; result.allocate(); - Coordinates *coord = mesh->getCoordinates(); + Coordinates* coord = mesh->getCoordinates(); for (auto i : result.getRegion(RGN_NOBNDRY)) { - result[i] = Bxyz[i] * (f_B.yup()[i.yp()] - f_B.ydown()[i.ym()]) / - (2. * coord->dy[i] * sqrt(coord->g_22[i])); + result[i] = Bxyz[i] * (f_B.yup()[i.yp()] - f_B.ydown()[i.ym()]) + / (2. * coord->dy[i] * sqrt(coord->g_22[i])); if (!finite(result[i])) { - output.write("[{:d},{:d},{:d}]: {:e}, {:e} -> {:e}\n", i.x(), i.y(), i.z(), f_B.yup()[i.yp()], - f_B.ydown()[i.ym()], result[i]); + output.write("[{:d},{:d},{:d}]: {:e}, {:e} -> {:e}\n", i.x(), i.y(), i.z(), + f_B.yup()[i.yp()], f_B.ydown()[i.ym()], result[i]); } } @@ -116,14 +116,14 @@ class FCIwave : public PhysicsModel { // between v, nv and momentum flux momflux.splitParallelSlices(); - for (const auto ® : mesh->getBoundariesPar()) { + for (const auto& reg : mesh->getBoundariesPar()) { // Using the values of density and velocity on the boundary - const Field3D &n_next = n.ynext(reg->dir); - const Field3D &v_next = v.ynext(reg->dir); + const Field3D& n_next = n.ynext(reg->dir); + const Field3D& v_next = v.ynext(reg->dir); // Set the momentum and momentum flux - Field3D &nv_next = nv.ynext(reg->dir); - Field3D &momflux_next = momflux.ynext(reg->dir); + Field3D& nv_next = nv.ynext(reg->dir); + Field3D& momflux_next = momflux.ynext(reg->dir); momflux_next.allocate(); for (reg->first(); !reg->isDone(); reg->next()) { diff --git a/examples/finite-volume/diffusion/diffusion.cxx b/examples/finite-volume/diffusion/diffusion.cxx index 8613e4e378..db3b438b93 100644 --- a/examples/finite-volume/diffusion/diffusion.cxx +++ b/examples/finite-volume/diffusion/diffusion.cxx @@ -1,15 +1,15 @@ /// Finite Volume parallel diffusion example /// -#include #include +#include class Diffusion : public PhysicsModel { protected: int init(bool UNUSED(restarting)) override { GRID_LOAD(k); mesh->communicate(k); - + SOLVE_FOR(f); return 0; @@ -17,16 +17,15 @@ class Diffusion : public PhysicsModel { int rhs(BoutReal UNUSED(time)) override { mesh->communicate(f); - + ddt(f) = FV::Div_par_K_Grad_par(k, f); - + return 0; } - + private: Field3D f; // Evolving field Field3D k; // Diffusion coefficient }; BOUTMAIN(Diffusion); - diff --git a/examples/finite-volume/fluid/fluid.cxx b/examples/finite-volume/fluid/fluid.cxx index 547996dc91..edbaae8ef2 100644 --- a/examples/finite-volume/fluid/fluid.cxx +++ b/examples/finite-volume/fluid/fluid.cxx @@ -3,57 +3,52 @@ #include -/// A 1D fluid equation (in y) -/// +/// A 1D fluid equation (in y) +/// /// Evolves density, pressure and momentum /// class Fluid : public PhysicsModel { protected: - int init(bool UNUSED(restart)) override { auto& opt = Options::root()["fluid"]; - gamma = opt["gamma"] - .doc("Adiabatic index (ratio of specific heats)") - .withDefault(5. / 3); + gamma = + opt["gamma"].doc("Adiabatic index (ratio of specific heats)").withDefault(5. / 3); SOLVE_FOR(n, p, nv); return 0; } - + int rhs(BoutReal UNUSED(time)) override { mesh->communicate(n, p, nv); // Calculate velocity from momentum Field3D v = nv / n; - + // Calculate sound speed Field3D cs = sqrt(gamma * p / n); - + // Density equation - ddt(n) = - - FV::Div_par(n, v, cs) // Limiter, flux conserving - ; - + ddt(n) = -FV::Div_par(n, v, cs) // Limiter, flux conserving + ; + // Pressure equation - ddt(p) = - - FV::Div_par(p, v, cs) // Limiter, flux conserving - - (gamma - 1.0) * p * Div_par(v) // Standard central differencing - ; - + ddt(p) = -FV::Div_par(p, v, cs) // Limiter, flux conserving + - (gamma - 1.0) * p * Div_par(v) // Standard central differencing + ; + // Momentum equation - ddt(nv) = - - FV::Div_par(nv, v, cs) // Limiter, flux conserving - - Grad_par(p) // Central differencing - ; + ddt(nv) = -FV::Div_par(nv, v, cs) // Limiter, flux conserving + - Grad_par(p) // Central differencing + ; return 0; } - + private: - Field3D n, p, nv; ///< Density, pressure, parallel momentum + Field3D n, p, nv; ///< Density, pressure, parallel momentum BoutReal gamma; ///< Adiabatic index }; diff --git a/examples/finite-volume/test/finite_volume.cxx b/examples/finite-volume/test/finite_volume.cxx index c5dd3bbd2c..3fefb43975 100644 --- a/examples/finite-volume/test/finite_volume.cxx +++ b/examples/finite-volume/test/finite_volume.cxx @@ -1,17 +1,17 @@ -#include +#include #include int main(int argc, char** argv) { BoutInitialise(argc, argv); - + Field3D f = 0.0; f.getMesh()->communicate(f); Field3D g = FV::D4DY4_Index(f); - + BoutFinalise(); return 0; }; diff --git a/examples/gas-compress/gas_compress.cxx b/examples/gas-compress/gas_compress.cxx index 1db8a8e7f2..812f17b4c0 100644 --- a/examples/gas-compress/gas_compress.cxx +++ b/examples/gas-compress/gas_compress.cxx @@ -8,49 +8,49 @@ int GasCompress::init(bool restarting) { mesh->get(N0, "density"); mesh->get(P0, "pressure"); V0.covariant = false; // Read contravariant components - V.covariant = false; // Evolve contravariant components + V.covariant = false; // Evolve contravariant components mesh->get(V0, "v"); g.covariant = false; mesh->get(g, "g"); - + // read options - + auto& options = Options::root()["gas"]; gamma_ratio = options["gamma"].withDefault(0.1); include_viscosity = options["include_viscosity"].withDefault(false); nu = options["viscosity"].withDefault(0.0); - + BoutReal v0_multiply = options["v0_multiply"].withDefault(1.0); V0 *= v0_multiply; - + sub_initial = options["sub_initial"].withDefault(false); - + V.y.setLocation(CELL_YLOW); // Stagger - + // Set evolving variables - + solver->add(N, "density", "description"); solver->add(P, "pressure"); solver->add(V, "v"); - - if(!restarting) { + + if (!restarting) { // Set variables to these values (+ the initial perturbation) // NOTE: This must be after the calls to bout_solve N += N0; P += P0; V += V0; } - + return 0; } int GasCompress::rhs(BoutReal UNUSED(time)) { // Run communications - mesh->communicate(N,P,V); - + mesh->communicate(N, P, V); + // Density ddt(N) = -Div(V, N); - + // Velocity if (sub_initial) { @@ -60,16 +60,16 @@ int GasCompress::rhs(BoutReal UNUSED(time)) { ddt(V) = -V_dot_Grad(V, V) - Grad(P, CELL_VSHIFT) / N + g; } - if(include_viscosity) { + if (include_viscosity) { // Add viscosity - - ddt(V).y += nu*Laplace(V.y); - ddt(V).z += nu*Laplace(V.z); + + ddt(V).y += nu * Laplace(V.y); + ddt(V).z += nu * Laplace(V.z); } - + // Pressure - ddt(P) = -Div(V, P) - (gamma_ratio-1.)*P*Div(V); - + ddt(P) = -Div(V, P) - (gamma_ratio - 1.) * P * Div(V); + return 0; } diff --git a/examples/gas-compress/gas_compress.hxx b/examples/gas-compress/gas_compress.hxx index bfca2caa12..05b5823f29 100644 --- a/examples/gas-compress/gas_compress.hxx +++ b/examples/gas-compress/gas_compress.hxx @@ -4,20 +4,21 @@ class GasCompress : public PhysicsModel { protected: int init(bool restarting); int rhs(BoutReal t); + private: - // Evolving variables + // Evolving variables Field3D N, P; // Density, Pressure Vector3D V; // velocity // 2D initial profiles Field2D N0, P0; Vector2D V0; - + // parameters - BoutReal gamma_ratio; // Ratio of specific heats - BoutReal nu; // Viscosity + BoutReal gamma_ratio; // Ratio of specific heats + BoutReal nu; // Viscosity bool include_viscosity; bool sub_initial; // Subtract initial force balance from momentum equation - + Vector2D g; // Acceleration }; diff --git a/examples/gravity_reduced/gravity_reduced.cxx b/examples/gravity_reduced/gravity_reduced.cxx index 4c4864f91e..2d4fb7ec94 100644 --- a/examples/gravity_reduced/gravity_reduced.cxx +++ b/examples/gravity_reduced/gravity_reduced.cxx @@ -5,20 +5,19 @@ * Have included compressional terms in Vpar and in pressure and density evolution equations. *******************************************************************************/ - #include -#include -#include -#include -#include +#include +#include +#include +#include const BoutReal PI = 3.14159265; class GravityReduced : public PhysicsModel { private: // 2D initial profiles - + Field2D rho0, p0; Field2D Jpar0; //calculated from equilibrium B field used in bbmhd Jpar0=b.curlB0 Vector2D B0_vec; @@ -29,39 +28,38 @@ class GravityReduced : public PhysicsModel { // Field3D U0; //calculated from intial velocity perturbation used in bbmhd. Field3D Vpar0; //parallel component of intial velocity perturbation. Field3D phi0; - + //3D evolving fields Field3D U, rho, p, Vpar, Psi; - + //Derived variables Field3D Jpar, phi; - + // Group of fields for communication FieldGroup comms; - + bool nonlinear; - + // metric coeffictients - Coordinates *coord; - + Coordinates* coord; + // parameters BoutReal mu_0, Gamma; - + BoutReal viscos_par; // Parallel viscosity BoutReal viscos_perp; // Perpendicular viscosity BoutReal hyperviscos; // Hyper-viscosity (radial) - + BRACKET_METHOD bm = BRACKET_ARAKAWA; /// Solver for inverting Laplacian std::unique_ptr phiSolver{nullptr}; - + int init(bool restarting) override { output << "Solving flute reduced MHD in a slab with gravity\n"; - + //*************** LOAD DATE FROM GRID FILE ******************** - // GRID_LOAD(U0); // output << "Loaded U0\n"; @@ -80,25 +78,25 @@ class GravityReduced : public PhysicsModel { output << "Loaded B0_vec\n"; GRID_LOAD(B0); output << "Loaded B0\n"; - + GRID_LOAD(phi0); output << "Loaded phi0\n"; // Set locations of staggered fields Psi.setLocation(CELL_YLOW); Vpar.setLocation(CELL_YLOW); - + // options stuff - + auto globalOptions = Options::root(); auto options = globalOptions["gravity"]; nonlinear = options["nonlinear"].withDefault(false); if (nonlinear) { - output <<"Solving WITH nonlinear terms\n"; + output << "Solving WITH nonlinear terms\n"; } else { - output <<"Solving WITHOUT nonlinear terms\n"; + output << "Solving WITHOUT nonlinear terms\n"; } phi.setBoundary("phi"); @@ -111,41 +109,41 @@ class GravityReduced : public PhysicsModel { // load metric tensor components coord = mesh->getCoordinates(); - + BoutReal Lz; // Size of the Z box Lz = options["Lz"].withDefault(1.); // Set the metric tensor components to get Lz - coord->g33 = SQ(2.*PI/Lz); + coord->g33 = SQ(2. * PI / Lz); coord->g_33 = 1. / coord->g33; - + /**************** SET EVOLVING VARIABLES *************/ - + // Tell BOUT++ which variables to evolve // add evolving variables to the communication object - + SOLVE_FOR(rho, p, U, Psi, Vpar); if (!restarting) { // Set initial perturbation // U = U0; // U = Delp2(phi0); - U = coord->g11*D2DX2(phi0) + coord->g33*D2DZ2(phi0); + U = coord->g11 * D2DX2(phi0) + coord->g33 * D2DZ2(phi0); Vpar = Vpar0; } - + //******************Set up comms*************** - + comms.add(rho, p, U, Psi, Vpar); - + // extra variables comms.add(phi); Jpar.setBoundary("jpar"); - + // Add variables to output file - SAVE_REPEAT(phi, Jpar); // Save every output + SAVE_REPEAT(phi, Jpar); // Save every output SAVE_ONCE(G, p0, rho0); // Save time derivatives @@ -155,108 +153,105 @@ class GravityReduced : public PhysicsModel { // Create a solver for the Laplacian phiSolver = Laplacian::create(); - + return 0; } - + int rhs(BoutReal UNUSED(t)) override { // U = Delp2(phi); phi = phiSolver->solve(U); // Invert Laplacian - phi.applyBoundary(); // Apply boundary condition in Y - + phi.applyBoundary(); // Apply boundary condition in Y + mesh->communicate(comms); - - Jpar = -(B0/mu_0)*Delp2(Psi); + + Jpar = -(B0 / mu_0) * Delp2(Psi); Jpar.applyBoundary(); - + mesh->communicate(Jpar); - + //Parallel electric field - ddt(Psi) = -(1/B0)*Grad_par(B0*phi, CELL_YLOW);// + 1e-2*Jpar; - + ddt(Psi) = -(1 / B0) * Grad_par(B0 * phi, CELL_YLOW); // + 1e-2*Jpar; + if (nonlinear) { - ddt(Psi) += (1/B0)*bracket(Psi, B0*phi, bm)*coord->Bxy; + ddt(Psi) += (1 / B0) * bracket(Psi, B0 * phi, bm) * coord->Bxy; } - + //Parallel vorticity - - ddt(U) = (SQ(B0)/rho0)*(Grad_par(Jpar/interp_to(B0, CELL_YLOW), CELL_CENTRE) ); - - ddt(U) -= (1/rho0)*bracket(G,rho, bm)*coord->Bxy; - - ddt(U) -= (SQ(B0)/rho0)*bracket(Psi,Jpar0/B0, bm)*coord->Bxy; + + ddt(U) = (SQ(B0) / rho0) * (Grad_par(Jpar / interp_to(B0, CELL_YLOW), CELL_CENTRE)); + + ddt(U) -= (1 / rho0) * bracket(G, rho, bm) * coord->Bxy; + + ddt(U) -= (SQ(B0) / rho0) * bracket(Psi, Jpar0 / B0, bm) * coord->Bxy; if (nonlinear) { - ddt(U) -= bracket(phi,U, bm)*coord->Bxy; - - ddt(U) -= (SQ(B0)/rho0)*bracket(Psi,Jpar/B0, bm)*coord->Bxy; + ddt(U) -= bracket(phi, U, bm) * coord->Bxy; + + ddt(U) -= (SQ(B0) / rho0) * bracket(Psi, Jpar / B0, bm) * coord->Bxy; } - - // Viscosity terms + + // Viscosity terms if (viscos_par > 0.0) { ddt(U) += viscos_par * Grad2_par2(U); // Parallel viscosity } - + if (viscos_perp > 0.0) { - ddt(U) += viscos_perp * Delp2(U); // Perpendicular viscosity + ddt(U) += viscos_perp * Delp2(U); // Perpendicular viscosity } - + // Parallel velocity - ddt(Vpar) = bracket(Psi,p0, bm)*coord->Bxy / rho0; - - ddt(Vpar) += -(Grad_par(p, CELL_YLOW))/rho0; - - ddt(Vpar) += bracket(G,Psi, bm)*coord->Bxy; - + ddt(Vpar) = bracket(Psi, p0, bm) * coord->Bxy / rho0; + + ddt(Vpar) += -(Grad_par(p, CELL_YLOW)) / rho0; + + ddt(Vpar) += bracket(G, Psi, bm) * coord->Bxy; + if (nonlinear) { - ddt(Vpar) -= bracket(phi,Vpar,bm)*coord->Bxy; - - ddt(Vpar) += bracket(Psi,p,bm)*coord->Bxy / rho0; + ddt(Vpar) -= bracket(phi, Vpar, bm) * coord->Bxy; + + ddt(Vpar) += bracket(Psi, p, bm) * coord->Bxy / rho0; } - + //Pressure - ddt(p) = -bracket(phi,p0,bm); - - ddt(p) += -((Gamma*p0)/(1 + Gamma*p0*mu_0/SQ(B0))) - * ( - (rho0*mu_0/SQ(B0))*bracket(G,phi,bm)*coord->Bxy - + Grad_par(Vpar, CELL_CENTRE) - (Vpar/B0)*Grad_par(B0) - ); - + ddt(p) = -bracket(phi, p0, bm); + + ddt(p) += -((Gamma * p0) / (1 + Gamma * p0 * mu_0 / SQ(B0))) + * ((rho0 * mu_0 / SQ(B0)) * bracket(G, phi, bm) * coord->Bxy + + Grad_par(Vpar, CELL_CENTRE) - (Vpar / B0) * Grad_par(B0)); + if (nonlinear) { - ddt(p) -= bracket(phi,p,bm)*coord->Bxy; - ddt(p) += ((Gamma*p0) / (1 + Gamma*p0*mu_0/SQ(B0))) * bracket(Psi, Vpar, bm)*coord->Bxy; + ddt(p) -= bracket(phi, p, bm) * coord->Bxy; + ddt(p) += ((Gamma * p0) / (1 + Gamma * p0 * mu_0 / SQ(B0))) * bracket(Psi, Vpar, bm) + * coord->Bxy; } - + //Density - ddt(rho) = -bracket(phi, rho0, bm)*coord->Bxy; - - ddt(rho) -= (rho0/(1 + Gamma*p0*mu_0/SQ(B0))) - * ( - (rho0*mu_0/SQ(B0))*bracket(G,phi,bm)*coord->Bxy - + Grad_par(Vpar, CELL_CENTRE) - - bracket(Psi,Vpar,bm)*coord->Bxy - - (Vpar/B0)*Grad_par(B0) - ); - + ddt(rho) = -bracket(phi, rho0, bm) * coord->Bxy; + + ddt(rho) -= (rho0 / (1 + Gamma * p0 * mu_0 / SQ(B0))) + * ((rho0 * mu_0 / SQ(B0)) * bracket(G, phi, bm) * coord->Bxy + + Grad_par(Vpar, CELL_CENTRE) - bracket(Psi, Vpar, bm) * coord->Bxy + - (Vpar / B0) * Grad_par(B0)); + if (nonlinear) { - ddt(rho) -= bracket(phi, rho, bm)*coord->Bxy; - ddt(rho) += ((rho0)/(1 + Gamma*p0*mu_0/SQ(B0)))*bracket(Psi, Vpar, bm)*coord->Bxy; + ddt(rho) -= bracket(phi, rho, bm) * coord->Bxy; + ddt(rho) += ((rho0) / (1 + Gamma * p0 * mu_0 / SQ(B0))) * bracket(Psi, Vpar, bm) + * coord->Bxy; } - + // Iterate over the lower Y boundary RangeIterator rlow = mesh->iterateBndryLowerY(); - for(rlow.first(); !rlow.isDone(); rlow.next()) { + for (rlow.first(); !rlow.isDone(); rlow.next()) { int x = rlow.ind; for (int y = 2; y >= 0; y--) { - for(int z=0;zLocalNz;z++) { - ddt(rho)(x,y,z) = ddt(rho)(x,y+1,z); - ddt(p)(x,y,z) = ddt(p)(x,y+1,z); - ddt(Psi)(x,y,z) = ddt(Psi)(x,y+1,z); + for (int z = 0; z < mesh->LocalNz; z++) { + ddt(rho)(x, y, z) = ddt(rho)(x, y + 1, z); + ddt(p)(x, y, z) = ddt(p)(x, y + 1, z); + ddt(Psi)(x, y, z) = ddt(Psi)(x, y + 1, z); } } } - + return 0; } }; diff --git a/examples/gyro-gem/gem.cxx b/examples/gyro-gem/gem.cxx index c82f3f7ec0..1a056c1c08 100644 --- a/examples/gyro-gem/gem.cxx +++ b/examples/gyro-gem/gem.cxx @@ -9,30 +9,30 @@ * This version uses global parameters for collisionality etc. ****************************************************************/ -#include #include +#include -#include -#include -#include +#include +#include +#include /// Fundamental constants -const BoutReal e0 = 8.854e-12; // Permittivity of free space -const BoutReal qe = 1.602e-19; // Electron charge -const BoutReal Me = 9.109e-31; // Electron mass +const BoutReal e0 = 8.854e-12; // Permittivity of free space +const BoutReal qe = 1.602e-19; // Electron charge +const BoutReal Me = 9.109e-31; // Electron mass const BoutReal Mp = 1.67262158e-27; // Proton mass class GEM : public PhysicsModel { ////////////////////////////////////////// // Evolving quantities - + // Ion species - Field3D Ni; // Gyro-center density - Field3D ApUi; // beta_e*Apar + mu_i * Ui + Field3D Ni; // Gyro-center density + Field3D ApUi; // beta_e*Apar + mu_i * Ui Field3D Tipar, Tiperp; // Parallel or perpendicular temp Field3D qipar, qiperp; // Parallel and perpendicular heat flux - + // Electron species Field3D Ne; Field3D ApUe; // beta_e*Apar + mu_e * Ue @@ -41,23 +41,23 @@ class GEM : public PhysicsModel { ////////////////////////////////////////// // Derived quantities - - Field3D phi; // Electrostatic potential - Field3D Apar; // Parallel vector potential - + + Field3D phi; // Electrostatic potential + Field3D Apar; // Parallel vector potential + Field3D Ui, Ue; // Ion and electron parallel velocity - - Field3D Jpar; // Parallel current - + + Field3D Jpar; // Parallel current + Field3D phi_G, Phi_G; // Gyro-reduced potential - + ////////////////////////////////////////// // Equilibrium - Coordinates *coord; - - Vector3D B0vec; // Equilibrium B field vector - Field2D logB; // For curvature + Coordinates* coord; + + Vector3D B0vec; // Equilibrium B field vector + Field2D logB; // For curvature Coordinates::FieldMetric Grad_par_logB; // Grad_par(log(B)) Field2D Ni0, Ne0; // Gyro-center densities @@ -72,24 +72,24 @@ class GEM : public PhysicsModel { BoutReal rho_s, delta; // Collisional transport coefficients - const BoutReal eta = 0.51; + const BoutReal eta = 0.51; const BoutReal alpha_e = 0.71; const BoutReal kappa_e = 3.2; - const BoutReal pi_e = 0.73; + const BoutReal pi_e = 0.73; // alpha_i = 0 const BoutReal kappa_i = 3.9; - const BoutReal pi_i = 0.73; + const BoutReal pi_i = 0.73; Field3D Rei; ////////////////////////////////////////// // Options - bool adiabatic_electrons; // Solve adiabatic electrons - bool small_rho_e; // Neglect electron gyro-radius - bool include_grad_par_B; // Include terms like Grad_par(log(B)) + bool adiabatic_electrons; // Solve adiabatic electrons + bool small_rho_e; // Neglect electron gyro-radius + bool include_grad_par_B; // Include terms like Grad_par(log(B)) bool curv_logB; @@ -97,11 +97,11 @@ class GEM : public PhysicsModel { BoutReal nu_e, nu_i; // Collisional dissipation - BoutReal nu_perp, nu_par; // Artificial dissipation + BoutReal nu_perp, nu_par; // Artificial dissipation bool fix_profiles; // Subtract toroidal averages - int jpar_bndry_width; // Set jpar = 0 in a boundary region + int jpar_bndry_width; // Set jpar = 0 in a boundary region bool nonlinear; // Include nonlinear terms @@ -138,22 +138,22 @@ class GEM : public PhysicsModel { BoutReal Lbar; // Perpendicular scale length BoutReal Tenorm; // Typical value of Te for normalisation BoutReal Ninorm; // Typical density value for normalisation - BoutReal Bbar; // Magnetic field + BoutReal Bbar; // Magnetic field - BoutReal Cs; // Sound speed sqrt(Tenorm / Mi) - BoutReal Tbar; // Timescale Lbar / Cs + BoutReal Cs; // Sound speed sqrt(Tenorm / Mi) + BoutReal Tbar; // Timescale Lbar / Cs FieldGroup comms; // Communications /// Solver for inverting Laplacian std::unique_ptr phiSolver{nullptr}; std::unique_ptr aparSolver{nullptr}; - + //////////////////////////////////////////////////////////////////////// // Initialisation - + //Field3D xzdamp; - + int init(bool restarting) override { ////////////////////////////////// // Read options @@ -184,37 +184,37 @@ class GEM : public PhysicsModel { ////////////////////////////////// // Read profiles - + // Mesh Field2D Rxy, Bpxy, Btxy, Bxy, hthe; - GRID_LOAD(Rxy); // Major radius [m] - GRID_LOAD(Bpxy); // Poloidal B field [T] - GRID_LOAD(Btxy); // Toroidal B field [T] - GRID_LOAD(Bxy); // Total B field [T] - GRID_LOAD(hthe); // Poloidal arc length [m / radian] - + GRID_LOAD(Rxy); // Major radius [m] + GRID_LOAD(Bpxy); // Poloidal B field [T] + GRID_LOAD(Btxy); // Toroidal B field [T] + GRID_LOAD(Bxy); // Total B field [T] + GRID_LOAD(hthe); // Poloidal arc length [m / radian] + GRID_LOAD(Te0); // Electron temperature in eV GRID_LOAD(Ni0); // Ion number density in 10^20 m^-3 - + Ni0 *= 1.e20; // Convert to m^-3 - + Ti0 = Te0; Ne0 = Ni0; - + Field2D p_e = qe * Te0 * Ne0; // Electron pressure in Pascals - + if (flat_temp > 0.) { Te0 = flat_temp; Ti0 = flat_temp; - - Ne0 = Ni0 = p_e / (qe*Te0); + + Ne0 = Ni0 = p_e / (qe * Te0); } else if (flat_dens > 0.) { Ne0 = flat_dens; Ni0 = flat_dens; - - Te0 = Ti0 = p_e / (qe*Ne0); + + Te0 = Ti0 = p_e / (qe * Ne0); } - + if (curv_logB) { GRID_LOAD(logB); } @@ -224,32 +224,35 @@ class GEM : public PhysicsModel { ApUi.setLocation(CELL_YLOW); qepar.setLocation(CELL_YLOW); qipar.setLocation(CELL_YLOW); - + ////////////////////////////////// // Pick normalisation factors - - if (mesh->get(Lbar, "Lbar")) {// Try to read from grid file + + if (mesh->get(Lbar, "Lbar")) { // Try to read from grid file if (mesh->get(Lbar, "rmag")) { Lbar = 1.0; } } Lbar = options["Lbar"].withDefault(Lbar); // Override in options file - SAVE_ONCE(Lbar); // Save in output file + SAVE_ONCE(Lbar); // Save in output file - BoutReal AA; // Ion atomic mass - BoutReal ZZ; // Ion charge + BoutReal AA; // Ion atomic mass + BoutReal ZZ; // Ion charge AA = options["AA"].withDefault(2.0); // Deuterium by default ZZ = options["ZZ"].withDefault(1.0); - Tenorm = max(Te0,true); SAVE_ONCE(Tenorm); // Maximum value over the grid - Ninorm = max(Ni0, true); SAVE_ONCE(Ninorm); - - Cs = sqrt(qe*Tenorm / (AA*Mp)); SAVE_ONCE(Cs); // Sound speed in m/s - + Tenorm = max(Te0, true); + SAVE_ONCE(Tenorm); // Maximum value over the grid + Ninorm = max(Ni0, true); + SAVE_ONCE(Ninorm); + + Cs = sqrt(qe * Tenorm / (AA * Mp)); + SAVE_ONCE(Cs); // Sound speed in m/s + Tbar = Lbar / Cs; Tbar = options["Tbar"].withDefault(Tbar); // Override in options file - SAVE_ONCE(Tbar); // Timescale in seconds - + SAVE_ONCE(Tbar); // Timescale in seconds + if (mesh->get(Bbar, "Bbar")) { if (mesh->get(Bbar, "bmag")) { Bbar = max(Bxy, true); @@ -257,33 +260,37 @@ class GEM : public PhysicsModel { } Bbar = options["Bbar"].withDefault(Bbar); // Override in options file SAVE_ONCE(Bbar); - - beta_e = 4.e-7*PI * max(p_e,true) / (Bbar*Bbar); SAVE_ONCE(beta_e); - + + beta_e = 4.e-7 * PI * max(p_e, true) / (Bbar * Bbar); + SAVE_ONCE(beta_e); + // Mass to charge ratios mu_i = 1. / ZZ; mu_e = -1. / (AA * 1860.); - + tau_e = -1; - tau_i = 1. /ZZ; - + tau_i = 1. / ZZ; + // Gyro-radii (SI units) - rho_s = Cs * AA * Mp / (qe * Bbar); + rho_s = Cs * AA * Mp / (qe * Bbar); rho_e = rho_s * sqrt(fabs(mu_e * tau_e)); rho_i = rho_s * sqrt(fabs(mu_i * tau_i)); SAVE_ONCE3(rho_s, rho_e, rho_i); - - delta = rho_s / Lbar; SAVE_ONCE(delta); // This should be small - + + delta = rho_s / Lbar; + SAVE_ONCE(delta); // This should be small + //////////////////////////////////////////////////// // Terms in equations jpar_bndry_width = options["jpar_bndry_width"].withDefault(-1); OPTION4(options, ne_ddt, ne_te0, ne_ue, ne_curv, true); // Linear - OPTION2(options, ne_ne1, ne_te1, nonlinear); // Nonlinear - OPTION6(options, apue_ddt, apue_phi1, apue_pet, apue_curv, apue_gradB, apue_Rei, true); - OPTION4(options, apue_ue1_phi1, apue_qe1_phi1, apue_apar1_phi1, apue_apar1_pe1, nonlinear); + OPTION2(options, ne_ne1, ne_te1, nonlinear); // Nonlinear + OPTION6(options, apue_ddt, apue_phi1, apue_pet, apue_curv, apue_gradB, apue_Rei, + true); + OPTION4(options, apue_ue1_phi1, apue_qe1_phi1, apue_apar1_phi1, apue_apar1_pe1, + nonlinear); tepar_ddt = options["tepar_ddt"].withDefault(true); teperp_ddt = options["teperp_ddt"].withDefault(true); @@ -291,9 +298,11 @@ class GEM : public PhysicsModel { qeperp_ddt = options["qeperp_ddt"].withDefault(true); OPTION4(options, ni_ddt, ni_ti0, ni_ui, ni_curv, true); // Linear - OPTION2(options, ni_ni1, ni_ti1, nonlinear); // Nonlinear - OPTION6(options, apui_ddt, apui_phi1, apui_pit, apui_curv, apui_gradB, apui_Rei, true); - OPTION4(options, apui_ui1_phi1, apui_qi1_phi1, apui_apar1_phi1, apui_apar1_pi1, nonlinear); + OPTION2(options, ni_ni1, ni_ti1, nonlinear); // Nonlinear + OPTION6(options, apui_ddt, apui_phi1, apui_pit, apui_curv, apui_gradB, apui_Rei, + true); + OPTION4(options, apui_ui1_phi1, apui_qi1_phi1, apui_apar1_phi1, apui_apar1_pi1, + nonlinear); tipar_ddt = options["tipar_ddt"].withDefault(true); tiperp_ddt = options["tiperp_ddt"].withDefault(true); qipar_ddt = options["qipar_ddt"].withDefault(true); @@ -301,80 +310,86 @@ class GEM : public PhysicsModel { //////////////////////////////////////////////////// // Collisional parameters - + /// Coulomb logarithm - BoutReal Coulomb = 6.6 - 0.5*log(Ninorm * 1e-20) + 1.5*log(Tenorm); - + BoutReal Coulomb = 6.6 - 0.5 * log(Ninorm * 1e-20) + 1.5 * log(Tenorm); + BoutReal t_e, t_i; // Braginskii collision times - - t_e = 1. / (2.91e-6 * (Ninorm / 1e6) * Coulomb * pow(Tenorm, -3./2)); - - t_i = pow(ZZ, -4.) * sqrt(AA) / (4.80e-8 * (Ninorm / 1e6) * Coulomb * pow(Tenorm, -3./2)); - + + t_e = 1. / (2.91e-6 * (Ninorm / 1e6) * Coulomb * pow(Tenorm, -3. / 2)); + + t_i = pow(ZZ, -4.) * sqrt(AA) + / (4.80e-8 * (Ninorm / 1e6) * Coulomb * pow(Tenorm, -3. / 2)); + output << "\n\tParameters\n"; output.write("\tt_e = {:e} [s], t_i = {:e} [s]\n", t_e, t_i); - output.write("\tLbar = {:e} [m], Cs = {:e} [m/s]\n", - Lbar, Cs); + output.write("\tLbar = {:e} [m], Cs = {:e} [m/s]\n", Lbar, Cs); output.write("\tTbar = {:e} [s]\n", Tbar); - nu_e = Lbar / (Cs*t_e); SAVE_ONCE(nu_e); - nu_i = Lbar / (Cs*t_i); SAVE_ONCE(nu_i); + nu_e = Lbar / (Cs * t_e); + SAVE_ONCE(nu_e); + nu_i = Lbar / (Cs * t_i); + SAVE_ONCE(nu_i); output.write("\tNormalised nu_e = {:e}, nu_i = {:e}\n", nu_e, nu_i); output << "\tbeta_e = " << beta_e << endl; output << "\tdelta = " << delta << endl; - + //////////////////////////////////////////////////// // Normalise - - Te0 /= Tenorm * delta; SAVE_ONCE(Te0); - Ti0 /= Tenorm * delta; SAVE_ONCE(Ti0); - - Ni0 /= Ninorm * delta; SAVE_ONCE(Ni0); - Ne0 /= Ninorm * delta; SAVE_ONCE(Ne0); - + + Te0 /= Tenorm * delta; + SAVE_ONCE(Te0); + Ti0 /= Tenorm * delta; + SAVE_ONCE(Ti0); + + Ni0 /= Ninorm * delta; + SAVE_ONCE(Ni0); + Ne0 /= Ninorm * delta; + SAVE_ONCE(Ne0); + rho_e /= rho_s; rho_i /= rho_s; - + output << "\tNormalised rho_e = " << rho_e << endl; output << "\tNormalised rho_i = " << rho_i << endl; - + ////////////////////////////////// // Metric tensor components coord = mesh->getCoordinates(); - + // Normalise hthe /= Lbar; // parallel derivatives normalised to Lperp - + Bpxy /= Bbar; Btxy /= Bbar; - Bxy /= Bbar; - - Rxy /= rho_s; // Perpendicular derivatives normalised to rho_s - coord->dx /= rho_s*rho_s*Bbar; - + Bxy /= Bbar; + + Rxy /= rho_s; // Perpendicular derivatives normalised to rho_s + coord->dx /= rho_s * rho_s * Bbar; + // Metric components - - coord->g11 = SQ(Rxy*Bpxy); + + coord->g11 = SQ(Rxy * Bpxy); coord->g22 = 1.0 / SQ(hthe); - coord->g33 = SQ(Bxy)/coord->g11; + coord->g33 = SQ(Bxy) / coord->g11; coord->g12 = 0.0; coord->g13 = 0.; - coord->g23 = -Btxy/(hthe*Bpxy*Rxy); - + coord->g23 = -Btxy / (hthe * Bpxy * Rxy); + coord->J = hthe / Bpxy; coord->Bxy = Bxy; - - coord->g_11 = 1.0/coord->g11; - coord->g_22 = SQ(Bxy*hthe/Bpxy); - coord->g_33 = Rxy*Rxy; + + coord->g_11 = 1.0 / coord->g11; + coord->g_22 = SQ(Bxy * hthe / Bpxy); + coord->g_33 = Rxy * Rxy; coord->g_12 = 0.; coord->g_13 = 0.; - coord->g_23 = Btxy*hthe*Rxy/Bpxy; - + coord->g_23 = Btxy * hthe * Rxy / Bpxy; + coord->geometry(); - + // Set B field vector - + B0vec.covariant = false; B0vec.x = 0.; B0vec.y = Bpxy / hthe; @@ -390,9 +405,9 @@ class GEM : public PhysicsModel { } else { Grad_par_logB = 0.; } - + ////////////////////////////////// - + // Add ion equations if (ni_ddt) { SOLVE_FOR(Ni); @@ -438,14 +453,14 @@ class GEM : public PhysicsModel { /// Split operator, with artificial dissipation in second function setSplitOperator(); // Split into convective and diffusive (stiff) - + if (adiabatic_electrons) { // Solving with adiabatic electrons output << "Error: no adiabatic electrons yet\n"; return 1; } else { // Add electron equations - + if (ne_ddt) { SOLVE_FOR(Ne); comms.add(Ne); @@ -488,26 +503,26 @@ class GEM : public PhysicsModel { qeperp = 0.; } } - + bool output_ddt; output_ddt = options["output_ddt"].withDefault(false); if (output_ddt) { // Output the time derivatives if (ni_ddt) { - dump.add(ddt(Ni), "F_Ni", 1); + dump.add(ddt(Ni), "F_Ni", 1); } if (apui_ddt) { - dump.add(ddt(ApUi), "F_ApUi", 1); + dump.add(ddt(ApUi), "F_ApUi", 1); } if (tipar_ddt) { - dump.add(ddt(Tipar), "F_Tipar", 1); + dump.add(ddt(Tipar), "F_Tipar", 1); } if (tiperp_ddt) { dump.add(ddt(Tiperp), "F_Tiperp", 1); } if (qipar_ddt) { - dump.add(ddt(qipar), "F_qipar", 1); + dump.add(ddt(qipar), "F_qipar", 1); } if (qiperp_ddt) { dump.add(ddt(qiperp), "F_qiperp", 1); @@ -515,158 +530,156 @@ class GEM : public PhysicsModel { if (!adiabatic_electrons) { if (ne_ddt) { - dump.add(ddt(Ne), "F_Ne", 1); + dump.add(ddt(Ne), "F_Ne", 1); } if (apue_ddt) { - dump.add(ddt(ApUe), "F_ApUe", 1); + dump.add(ddt(ApUe), "F_ApUe", 1); } if (tepar_ddt) { - dump.add(ddt(Tepar), "F_Tepar", 1); + dump.add(ddt(Tepar), "F_Tepar", 1); } if (teperp_ddt) { dump.add(ddt(Teperp), "F_Teperp", 1); } if (qepar_ddt) { - dump.add(ddt(qepar), "F_qepar", 1); + dump.add(ddt(qepar), "F_qepar", 1); } if (qeperp_ddt) { dump.add(ddt(qeperp), "F_qeperp", 1); } } } - + dump.add(phi, "phi", 1); dump.add(Apar, "Apar", 1); dump.add(Ui, "Ui", 1); dump.add(Ue, "Ue", 1); dump.add(Jpar, "Jpar", 1); - + // To ensure X periodicity mesh->communicate(comms); - + comms.add(phi, Apar, Ui, Ue, Jpar); - + dump.add(phi_G, "phi_G", 1); - + ////////////////////////////////// - + if (!restarting) { // Initial current - + Field2D Jpar0; if (mesh->get(Jpar0, "Jpar0") == 0) { // Initial current specified. Set parallel electron velocity - } - + // Initial potential - + Field2D phi0; if (mesh->get(phi0, "phi0") == 0) { - } } - + phi.setBoundary("phi"); Apar.setBoundary("Apar"); - + // Create a solver for the Laplacian phiSolver = Laplacian::create(&globalOptions["phiSolver"]); aparSolver = Laplacian::create(&globalOptions["aparSolver"], CELL_YLOW); - aparSolver->setCoefA(beta_e * (1./mu_e - 1./mu_i)); - + aparSolver->setCoefA(beta_e * (1. / mu_e - 1. / mu_i)); + return 0; } //////////////////////////////////////////////////////////////////////// // Calculate auxilliary quantities - + void calc_aux() { //////////////////////////////////////////// // Adiabatic electrons - + if (adiabatic_electrons) { // Solve adiabatic electrons using surface-averaged phi - + Field2D phi_zonal = averageY(DC(phi)); // Average over Y and Z Ne = phi - phi_zonal; - + // Need to solve with polarisation! } - + //////////////////////////////////////////// // Polarisation equation (quasi-neutrality) - + if (small_rho_e) { // Neglect electron Larmor radius - + Field3D dn = Ne - gyroPade1(Ni, rho_i) - gyroPade2(Tiperp, rho_i); - + phi = phiSolver->solve(tau_i * dn / SQ(rho_i)); phi -= tau_i * dn; } else { - Field3D dn = gyroPade1(Ne, rho_e) + gyroPade2(Teperp, rho_e) - - gyroPade1(Ni, rho_i) - gyroPade2(Tiperp, rho_i); - + Field3D dn = gyroPade1(Ne, rho_e) + gyroPade2(Teperp, rho_e) - gyroPade1(Ni, rho_i) + - gyroPade2(Tiperp, rho_i); + // Neglect electron gyroscreening phi = phiSolver->solve(tau_i * dn / (rho_i * rho_i)); phi -= tau_i * dn; } - + phi.applyBoundary(); - + //////////////////////////////////////////// // Helmholtz equation for Apar - - Field2D a = beta_e * (1./mu_e - 1./mu_i); - Apar = aparSolver->solve(ApUe/mu_e - ApUi/mu_i); - + + Field2D a = beta_e * (1. / mu_e - 1. / mu_i); + Apar = aparSolver->solve(ApUe / mu_e - ApUi / mu_i); + Apar.applyBoundary(); - - Ui = (ApUi - beta_e*Apar) / mu_i; - Ue = (ApUe - beta_e*Apar) / mu_e; - + + Ui = (ApUi - beta_e * Apar) / mu_i; + Ue = (ApUe - beta_e * Apar) / mu_e; + if (jpar_bndry_width > 0) { // Zero j in boundary regions. Prevents vorticity drive // at the boundary for (int i = 0; i < jpar_bndry_width; i++) { for (int j = 0; j < mesh->LocalNy; j++) { - for (int k=0;kLocalNz;k++) { + for (int k = 0; k < mesh->LocalNz; k++) { if (mesh->firstX()) { - Ui(i,j,k) = 0.0; - Ue(i,j,k) = 0.0; + Ui(i, j, k) = 0.0; + Ue(i, j, k) = 0.0; } if (mesh->lastX()) { - Ui(mesh->LocalNx-1-i,j,k) = 0.0; - Ue(mesh->LocalNx-1-i,j,k) = 0.0; + Ui(mesh->LocalNx - 1 - i, j, k) = 0.0; + Ue(mesh->LocalNx - 1 - i, j, k) = 0.0; } } } } } - + Jpar = Ui - Ue; } - + //////////////////////////////////////////////////////////////////////// // Non-stiff part of the RHS function - + int convective(BoutReal UNUSED(time)) override { calc_aux(); - + //////////////////////////////////////////// // Communicate - + mesh->communicate(comms); - + //////////////////////////////////////////// // Electron equations - + if (!adiabatic_electrons) { // Electron equations - + if (small_rho_e) { // No gyro-averaging for small rho_e phi_G = phi; @@ -675,10 +688,10 @@ class GEM : public PhysicsModel { // Gyro-reduced potentials phi_G = gyroPade1(phi, rho_e, INVERT_RHS, INVERT_RHS); Phi_G = gyroPade2(phi, rho_e, INVERT_RHS, INVERT_RHS); - + mesh->communicate(phi_G, Phi_G); } - + if (ne_ddt) { ddt(Ne) = -UE_Grad(Ne0, phi_G); if (ne_ne1) { @@ -696,7 +709,8 @@ class GEM : public PhysicsModel { } if (ne_curv) { - ddt(Ne) += curvature(phi_G + tau_e*Ne + 0.5*(tau_e*Tepar + tau_e*Teperp + Phi_G)); + ddt(Ne) += curvature(phi_G + tau_e * Ne + + 0.5 * (tau_e * Tepar + tau_e * Teperp + Phi_G)); } if (low_pass_z > 0) { @@ -707,39 +721,39 @@ class GEM : public PhysicsModel { ddt(Ne) -= DC(ddt(Ne)); } } - + if (apue_ddt) { if (apue_ue1_phi1) { - ddt(ApUe) = -mu_e*UE_Grad(Ue, phi_G); + ddt(ApUe) = -mu_e * UE_Grad(Ue, phi_G); } else { ddt(ApUe) = 0.0; } if (apue_qe1_phi1) { - ddt(ApUe) -= mu_e*WE_Grad(qeperp, Phi_G); + ddt(ApUe) -= mu_e * WE_Grad(qeperp, Phi_G); } if (apue_phi1) { // Linear term ddt(ApUe) -= Grad_par(phi_G, CELL_YLOW); } if (apue_apar1_phi1) { // Nonlinear term - ddt(ApUe) += beta_e*bracket(Apar, phi_G, BRACKET_ARAKAWA); + ddt(ApUe) += beta_e * bracket(Apar, phi_G, BRACKET_ARAKAWA); } if (apue_pet) { // Linear terms - ddt(ApUe) -= tau_i*Grad_parP(Ne0 + Te0, CELL_YLOW) - + tau_i*Grad_par(Ne+Tepar, CELL_YLOW); + ddt(ApUe) -= tau_i * Grad_parP(Ne0 + Te0, CELL_YLOW) + + tau_i * Grad_par(Ne + Tepar, CELL_YLOW); } if (apue_apar1_pe1) { // Nonlinear terms - ddt(ApUe) += tau_i*beta_e*bracket(Apar, Ne+Tepar, BRACKET_ARAKAWA); + ddt(ApUe) += tau_i * beta_e * bracket(Apar, Ne + Tepar, BRACKET_ARAKAWA); } if (apue_curv) { - ddt(ApUe) += mu_e * tau_e * curvature(2.*Ue + qepar + 0.5*qeperp); + ddt(ApUe) += mu_e * tau_e * curvature(2. * Ue + qepar + 0.5 * qeperp); } if (apue_gradB) { - ddt(ApUe) -= tau_e * (Phi_G + tau_e*Teperp - tau_e*Tepar)*Grad_par_logB; + ddt(ApUe) -= tau_e * (Phi_G + tau_e * Teperp - tau_e * Tepar) * Grad_par_logB; } if (low_pass_z > 0) { @@ -750,18 +764,16 @@ class GEM : public PhysicsModel { ddt(ApUe) -= DC(ddt(ApUe)); } } - + if (tepar_ddt) { - ddt(Tepar) = curvature(phi_G + tau_e*(Ne+Tepar) + 2.*tau_e*Tepar) - - (Ue + qeperp)*Grad_par_logB - ; - + ddt(Tepar) = curvature(phi_G + tau_e * (Ne + Tepar) + 2. * tau_e * Tepar) + - (Ue + qeperp) * Grad_par_logB; + if (nonlinear) { - ddt(Tepar) += -UE_Grad(Te0 + Tepar, phi_G) - - 2.*Div_parP(Ue + qepar, CELL_CENTRE); + ddt(Tepar) += + -UE_Grad(Te0 + Tepar, phi_G) - 2. * Div_parP(Ue + qepar, CELL_CENTRE); } else { - ddt(Tepar) += -UE_Grad(Te0, phi_G) - - 2.*Div_par(Ue + qepar, CELL_CENTRE); + ddt(Tepar) += -UE_Grad(Te0, phi_G) - 2. * Div_par(Ue + qepar, CELL_CENTRE); } if (low_pass_z > 0) { @@ -772,24 +784,20 @@ class GEM : public PhysicsModel { ddt(Tepar) -= DC(ddt(Tepar)); } } - + if (teperp_ddt) { - ddt(Teperp) = - + 0.5*curvature(phi_G + Phi_G + tau_e*(Ne + Teperp) - + 3.*(Phi_G + tau_e*Teperp)) - + (Ue + qeperp)*Grad_par_logB - ; - + ddt(Teperp) = +0.5 + * curvature(phi_G + Phi_G + tau_e * (Ne + Teperp) + + 3. * (Phi_G + tau_e * Teperp)) + + (Ue + qeperp) * Grad_par_logB; + if (nonlinear) { - ddt(Teperp) += - - UE_Grad(Te0 + Teperp, phi_G) - - WE_Grad(Ne0 + Ne + 2.*(Te0 + Teperp), Phi_G) - - Div_parP(qeperp, CELL_CENTRE); + ddt(Teperp) += -UE_Grad(Te0 + Teperp, phi_G) + - WE_Grad(Ne0 + Ne + 2. * (Te0 + Teperp), Phi_G) + - Div_parP(qeperp, CELL_CENTRE); } else { - ddt(Teperp) += - - UE_Grad(Te0, phi_G) - - WE_Grad(Ne0 + 2.*Te0, Phi_G) - - Div_par(qeperp, CELL_CENTRE); + ddt(Teperp) += -UE_Grad(Te0, phi_G) - WE_Grad(Ne0 + 2. * Te0, Phi_G) + - Div_par(qeperp, CELL_CENTRE); } if (low_pass_z > 0) { @@ -800,20 +808,16 @@ class GEM : public PhysicsModel { ddt(Teperp) -= DC(ddt(Teperp)); } } - + if (qepar_ddt) { - ddt(qepar) = - - 1.5*(1./mu_e)*Grad_parP(tau_e*Te0, CELL_YLOW) - + 0.5*mu_e*tau_e*curvature(3.*Ue + 8.*qepar) - ; - + ddt(qepar) = -1.5 * (1. / mu_e) * Grad_parP(tau_e * Te0, CELL_YLOW) + + 0.5 * mu_e * tau_e * curvature(3. * Ue + 8. * qepar); + if (nonlinear) { - ddt(qepar) += - - UE_Grad(qepar, phi_G) - - 1.5*(1./mu_e)*Grad_parP(tau_e*Tepar, CELL_YLOW); + ddt(qepar) += -UE_Grad(qepar, phi_G) + - 1.5 * (1. / mu_e) * Grad_parP(tau_e * Tepar, CELL_YLOW); } else { - ddt(qepar) += - - 1.5*(1./mu_e)*Grad_par(tau_e*Tepar, CELL_YLOW); + ddt(qepar) += -1.5 * (1. / mu_e) * Grad_par(tau_e * Tepar, CELL_YLOW); } if (low_pass_z > 0) { @@ -824,22 +828,18 @@ class GEM : public PhysicsModel { ddt(qepar) -= DC(ddt(qepar)); } } - + if (qeperp_ddt) { - ddt(qeperp) = - + (1./mu_e)*beta_e*bracket(Apar, tau_e*Te0, BRACKET_ARAKAWA) - + 0.5*tau_e*curvature(Ue + 6.*qeperp) - - (tau_e/mu_e)*(Phi_G + tau_e*Teperp - tau_e*Tepar)*Grad_par_logB - ; - + ddt(qeperp) = + +(1. / mu_e) * beta_e * bracket(Apar, tau_e * Te0, BRACKET_ARAKAWA) + + 0.5 * tau_e * curvature(Ue + 6. * qeperp) + - (tau_e / mu_e) * (Phi_G + tau_e * Teperp - tau_e * Tepar) * Grad_par_logB; + if (nonlinear) { - ddt(qeperp) += - - UE_Grad(qeperp, phi_G) - - WE_Grad(Ue + 2.*qeperp, Phi_G) - - (1./mu_e)*Grad_parP(Phi_G + tau_e*Teperp, CELL_YLOW); + ddt(qeperp) += -UE_Grad(qeperp, phi_G) - WE_Grad(Ue + 2. * qeperp, Phi_G) + - (1. / mu_e) * Grad_parP(Phi_G + tau_e * Teperp, CELL_YLOW); } else { - ddt(qeperp) += - -(1./mu_e)*Grad_par(Phi_G + tau_e*Teperp, CELL_YLOW); + ddt(qeperp) += -(1. / mu_e) * Grad_par(Phi_G + tau_e * Teperp, CELL_YLOW); } if (low_pass_z > 0) { @@ -851,16 +851,16 @@ class GEM : public PhysicsModel { } } } - + //////////////////////////////////////////// // Ion equations - + // Calculate gyroreduced potentials phi_G = gyroPade1(phi, rho_i, INVERT_RHS, INVERT_RHS); Phi_G = gyroPade2(phi, rho_i, INVERT_RHS, INVERT_RHS); - + mesh->communicate(phi_G, Phi_G); - + if (ni_ddt) { ddt(Ni) = -UE_Grad(Ni0, phi_G); if (ni_ni1) { @@ -878,7 +878,8 @@ class GEM : public PhysicsModel { } if (ni_curv) { - ddt(Ni) += curvature(phi_G + tau_i*Ni + 0.5*(tau_i*Tipar + tau_i*Tiperp + Phi_G)); + ddt(Ni) += curvature(phi_G + tau_i * Ni + + 0.5 * (tau_i * Tipar + tau_i * Tiperp + Phi_G)); } if (low_pass_z > 0) { @@ -889,39 +890,39 @@ class GEM : public PhysicsModel { ddt(Ni) -= DC(ddt(Ni)); } } - + if (apui_ddt) { if (apui_ui1_phi1) { - ddt(ApUi) = -mu_i*UE_Grad(Ui, phi_G); + ddt(ApUi) = -mu_i * UE_Grad(Ui, phi_G); } else { ddt(ApUi) = 0.0; } if (apui_qi1_phi1) { - ddt(ApUi) -= mu_i*WE_Grad(qiperp, Phi_G); + ddt(ApUi) -= mu_i * WE_Grad(qiperp, Phi_G); } if (apui_phi1) { ddt(ApUi) -= Grad_par(phi_G, CELL_YLOW); } if (apui_apar1_phi1) { // Nonlinear term - ddt(ApUi) += beta_e*bracket(Apar, phi_G, BRACKET_ARAKAWA); + ddt(ApUi) += beta_e * bracket(Apar, phi_G, BRACKET_ARAKAWA); } if (apui_pit) { // Linear terms - ddt(ApUi) -= tau_i*Grad_parP(Ni0 + Ti0, CELL_YLOW) - + tau_i*Grad_par(Ni+Tipar, CELL_YLOW); + ddt(ApUi) -= tau_i * Grad_parP(Ni0 + Ti0, CELL_YLOW) + + tau_i * Grad_par(Ni + Tipar, CELL_YLOW); } if (apui_apar1_pi1) { // Nonlinear terms - ddt(ApUi) += tau_i*beta_e*bracket(Apar, Ni+Tipar, BRACKET_ARAKAWA); + ddt(ApUi) += tau_i * beta_e * bracket(Apar, Ni + Tipar, BRACKET_ARAKAWA); } if (apui_curv) { - ddt(ApUi) += mu_i * tau_i * curvature(2.*Ui + qipar + 0.5*qiperp); + ddt(ApUi) += mu_i * tau_i * curvature(2. * Ui + qipar + 0.5 * qiperp); } if (apui_gradB) { - ddt(ApUi) -= tau_i * (Phi_G + tau_i*Tiperp - tau_i*Tipar)*Grad_par_logB; + ddt(ApUi) -= tau_i * (Phi_G + tau_i * Tiperp - tau_i * Tipar) * Grad_par_logB; } if (low_pass_z > 0) { @@ -932,21 +933,16 @@ class GEM : public PhysicsModel { ddt(ApUi) -= DC(ddt(ApUi)); } } - + if (tipar_ddt) { - ddt(Tipar) = - + curvature(phi_G + tau_i*(Ni+Tipar) + 2.*tau_i*Tipar) - - (Ui + qiperp)*Grad_par_logB - ; - + ddt(Tipar) = +curvature(phi_G + tau_i * (Ni + Tipar) + 2. * tau_i * Tipar) + - (Ui + qiperp) * Grad_par_logB; + if (nonlinear) { - ddt(Tipar) += - -UE_Grad(Ti0 + Tipar, phi_G) - - 2.*Div_parP(Ui + qipar, CELL_CENTRE); + ddt(Tipar) += + -UE_Grad(Ti0 + Tipar, phi_G) - 2. * Div_parP(Ui + qipar, CELL_CENTRE); } else { - ddt(Tipar) += - -UE_Grad(Ti0, phi_G) - - 2.*Div_par(Ui + qipar, CELL_CENTRE); + ddt(Tipar) += -UE_Grad(Ti0, phi_G) - 2. * Div_par(Ui + qipar, CELL_CENTRE); } if (low_pass_z > 0) { @@ -957,24 +953,20 @@ class GEM : public PhysicsModel { ddt(Tipar) -= DC(ddt(Tipar)); } } - + if (tiperp_ddt) { - ddt(Tiperp) = - + 0.5*curvature(phi_G + Phi_G + tau_i*(Ni + Tiperp) - + 3.*(Phi_G + tau_i*Tiperp)) - + (Ui + qiperp)*Grad_par_logB - ; - + ddt(Tiperp) = +0.5 + * curvature(phi_G + Phi_G + tau_i * (Ni + Tiperp) + + 3. * (Phi_G + tau_i * Tiperp)) + + (Ui + qiperp) * Grad_par_logB; + if (nonlinear) { - ddt(Tiperp) += - - UE_Grad(Ti0 + Tiperp, phi_G) - - WE_Grad(Ni0 + Ni + 2.*(Ti0 + Tiperp), Phi_G) - - Div_parP(qiperp, CELL_CENTRE); + ddt(Tiperp) += -UE_Grad(Ti0 + Tiperp, phi_G) + - WE_Grad(Ni0 + Ni + 2. * (Ti0 + Tiperp), Phi_G) + - Div_parP(qiperp, CELL_CENTRE); } else { - ddt(Tiperp) += - - UE_Grad(Ti0, phi_G) - - WE_Grad(Ni0 + 2.*Ti0, Phi_G) - - Div_par(qiperp, CELL_CENTRE); + ddt(Tiperp) += -UE_Grad(Ti0, phi_G) - WE_Grad(Ni0 + 2. * Ti0, Phi_G) + - Div_par(qiperp, CELL_CENTRE); } if (low_pass_z > 0) { @@ -985,19 +977,17 @@ class GEM : public PhysicsModel { ddt(Tiperp) -= DC(ddt(Tiperp)); } } - + if (qipar_ddt) { - ddt(qipar) = - + 1.5*(1./mu_i)*beta_e*bracket(Apar, tau_i*Ti0, BRACKET_ARAKAWA) - + 0.5*tau_i*curvature(3.*Ui + 8.*qipar); - + ddt(qipar) = + +1.5 * (1. / mu_i) * beta_e * bracket(Apar, tau_i * Ti0, BRACKET_ARAKAWA) + + 0.5 * tau_i * curvature(3. * Ui + 8. * qipar); + if (nonlinear) { - ddt(qipar) += - - UE_Grad(qipar, phi_G) - - 1.5*(1./mu_i)*Grad_parP(tau_i*Tipar, CELL_YLOW); + ddt(qipar) += -UE_Grad(qipar, phi_G) + - 1.5 * (1. / mu_i) * Grad_parP(tau_i * Tipar, CELL_YLOW); } else { - ddt(qipar) += - - 1.5*(1./mu_i)*Grad_par(tau_i*Tipar, CELL_YLOW); + ddt(qipar) += -1.5 * (1. / mu_i) * Grad_par(tau_i * Tipar, CELL_YLOW); } if (low_pass_z > 0) { @@ -1008,21 +998,18 @@ class GEM : public PhysicsModel { ddt(qipar) -= DC(ddt(qipar)); } } - + if (qiperp_ddt) { - ddt(qiperp) = - + (1./mu_i)*beta_e*bracket(Apar, tau_i*Ti0, BRACKET_ARAKAWA) - + 0.5*tau_i*curvature(Ui + 6.*qiperp) - - (tau_i/mu_i)*(Phi_G + tau_i*Tiperp - tau_i*Tipar)*Grad_par_logB; - + ddt(qiperp) = + +(1. / mu_i) * beta_e * bracket(Apar, tau_i * Ti0, BRACKET_ARAKAWA) + + 0.5 * tau_i * curvature(Ui + 6. * qiperp) + - (tau_i / mu_i) * (Phi_G + tau_i * Tiperp - tau_i * Tipar) * Grad_par_logB; + if (nonlinear) { - ddt(qiperp) += - - UE_Grad(qiperp, phi_G) - - WE_Grad(Ui + 2.*qiperp, Phi_G) - - (1./mu_i)*Grad_parP(Phi_G + tau_i*Tiperp, CELL_YLOW); + ddt(qiperp) += -UE_Grad(qiperp, phi_G) - WE_Grad(Ui + 2. * qiperp, Phi_G) + - (1. / mu_i) * Grad_parP(Phi_G + tau_i * Tiperp, CELL_YLOW); } else { - ddt(qiperp) += - - (1./mu_i)*Grad_par(Phi_G + tau_i*Tiperp, CELL_YLOW); + ddt(qiperp) += -(1. / mu_i) * Grad_par(Phi_G + tau_i * Tiperp, CELL_YLOW); } if (low_pass_z > 0) { @@ -1033,7 +1020,7 @@ class GEM : public PhysicsModel { ddt(qiperp) -= DC(ddt(qiperp)); } } - + return 0; } @@ -1041,23 +1028,23 @@ class GEM : public PhysicsModel { // Artificial dissipation terms int diffusive(BoutReal UNUSED(time)) override { Field3D S_D, K_par, K_perp, K_D; // Collisional dissipation terms - + calc_aux(); - + //////////////////////////////////////////// // Communicate - + mesh->communicate(comms); - + //////////////////////////////////////////// // Resistivity - - Rei = mu_e*nu_e*(eta*Jpar + - (alpha_e/kappa_e)*(qepar + qeperp + alpha_e*Jpar)); - + + Rei = mu_e * nu_e + * (eta * Jpar + (alpha_e / kappa_e) * (qepar + qeperp + alpha_e * Jpar)); + //////////////////////////////////////////// // Electron equations - + if (!adiabatic_electrons) { if (small_rho_e) { // No gyro-averaging for small rho_e @@ -1067,16 +1054,18 @@ class GEM : public PhysicsModel { // Gyro-reduced potentials phi_G = gyroPade1(phi, rho_e, INVERT_RHS, INVERT_RHS); Phi_G = gyroPade2(phi, rho_e, INVERT_RHS, INVERT_RHS); - + mesh->communicate(phi_G, Phi_G); } - + // Collisional dissipation - S_D = (nu_e / (3.*pi_e)) * (Tepar - Teperp); - K_par = mu_e*tau_e*nu_e*((5./2.)/kappa_e)*(qepar + 0.6*alpha_e*Jpar); - K_perp = mu_e*tau_e*nu_e*((5./2.)/kappa_e)*(qeperp + 0.4*alpha_e*Jpar); - K_D = 1.28*mu_e*tau_e*nu_e*((5./2.)/kappa_e)*(qepar - 1.5*qeperp); - + S_D = (nu_e / (3. * pi_e)) * (Tepar - Teperp); + K_par = + mu_e * tau_e * nu_e * ((5. / 2.) / kappa_e) * (qepar + 0.6 * alpha_e * Jpar); + K_perp = + mu_e * tau_e * nu_e * ((5. / 2.) / kappa_e) * (qeperp + 0.4 * alpha_e * Jpar); + K_D = 1.28 * mu_e * tau_e * nu_e * ((5. / 2.) / kappa_e) * (qepar - 1.5 * qeperp); + if (ne_ddt) { ddt(Ne) = 0.; if (ne_ne1) { @@ -1086,47 +1075,44 @@ class GEM : public PhysicsModel { if (apue_ddt) { ddt(ApUe) = 0.0; if (apue_ue1_phi1) { - ddt(ApUe) -= mu_e*UE_Grad_D(Ue, phi_G); + ddt(ApUe) -= mu_e * UE_Grad_D(Ue, phi_G); } if (apue_Rei) { ddt(ApUe) -= Rei; } } if (tepar_ddt) { - ddt(Tepar) = -UE_Grad_D(Tepar, phi_G) - 2.*S_D; - + ddt(Tepar) = -UE_Grad_D(Tepar, phi_G) - 2. * S_D; } if (teperp_ddt) { ddt(Teperp) = -UE_Grad_D(Teperp, phi_G) + S_D; } if (qepar_ddt) { ddt(qepar) = -UE_Grad_D(qepar, phi_G) - //- Landau*(tau_e/mu_e)*(1. - 0.125*Grad2_par2(qepar)) - - (1./mu_e)*K_par - - (1./mu_e)*K_D; + //- Landau*(tau_e/mu_e)*(1. - 0.125*Grad2_par2(qepar)) + - (1. / mu_e) * K_par - (1. / mu_e) * K_D; } if (qeperp_ddt) { - ddt(qeperp) = -UE_Grad_D(qeperp, phi_G) - - (1./mu_e)*K_perp - + (1./mu_e)*K_D; + ddt(qeperp) = + -UE_Grad_D(qeperp, phi_G) - (1. / mu_e) * K_perp + (1. / mu_e) * K_D; } } - + //////////////////////////////////////////// // Ion equations - + // Calculate gyroreduced potentials phi_G = gyroPade1(phi, rho_i, INVERT_RHS, INVERT_RHS); Phi_G = gyroPade2(phi, rho_i, INVERT_RHS, INVERT_RHS); - + mesh->communicate(phi_G, Phi_G); - + // Collisional dissipation - S_D = (nu_i / (3.*pi_i)) * (Tipar - Tiperp); - K_par = mu_i*tau_i*nu_i*((5./2.)/kappa_i)*qipar; - K_perp = mu_i*tau_i*nu_i*((5./2.)/kappa_i)*qiperp; - K_D = 1.28*mu_i*tau_i*nu_i*((5./2.)/kappa_i)*(qipar - 1.5*qiperp); - + S_D = (nu_i / (3. * pi_i)) * (Tipar - Tiperp); + K_par = mu_i * tau_i * nu_i * ((5. / 2.) / kappa_i) * qipar; + K_perp = mu_i * tau_i * nu_i * ((5. / 2.) / kappa_i) * qiperp; + K_D = 1.28 * mu_i * tau_i * nu_i * ((5. / 2.) / kappa_i) * (qipar - 1.5 * qiperp); + if (ni_ddt) { ddt(Ni) = 0.; if (ni_ni1) { @@ -1136,81 +1122,71 @@ class GEM : public PhysicsModel { if (apui_ddt) { ddt(ApUi) = 0.0; if (apui_ui1_phi1) { - ddt(ApUi) = -mu_i*UE_Grad_D(Ui, phi_G); + ddt(ApUi) = -mu_i * UE_Grad_D(Ui, phi_G); } if (apui_Rei) { ddt(ApUi) -= Rei; } } if (tipar_ddt) { - ddt(Tipar) = - UE_Grad_D(Tipar, phi_G) - 2.*S_D; + ddt(Tipar) = -UE_Grad_D(Tipar, phi_G) - 2. * S_D; } if (tiperp_ddt) { - ddt(Tiperp) = - UE_Grad_D(Tiperp, phi_G) + S_D; + ddt(Tiperp) = -UE_Grad_D(Tiperp, phi_G) + S_D; } if (qipar_ddt) { - ddt(qipar) = - UE_Grad_D(qipar, phi_G) - - (1./mu_e)*K_par - - (1./mu_e)*K_D; + ddt(qipar) = -UE_Grad_D(qipar, phi_G) - (1. / mu_e) * K_par - (1. / mu_e) * K_D; } if (qiperp_ddt) { - ddt(qiperp) = - UE_Grad_D(qiperp, phi_G) - - (1./mu_e)*K_perp - + (1./mu_e)*K_D; + ddt(qiperp) = -UE_Grad_D(qiperp, phi_G) - (1. / mu_e) * K_perp + (1. / mu_e) * K_D; } - + return 0; } - + //////////////////////////////////////////////////////////////////////// // Curvature operator - + // K(f) = Div((c/B^2) B x Grad(f)) // Simple implementation. Could be improved to eliminate the communication - const Field3D curvature(const Field3D &f) { + const Field3D curvature(const Field3D& f) { if (curv_logB) { - return -bracket(2.*logB, f, BRACKET_ARAKAWA); + return -bracket(2. * logB, f, BRACKET_ARAKAWA); } - return -bracket(2.*log(coord->Bxy), f, BRACKET_ARAKAWA); + return -bracket(2. * log(coord->Bxy), f, BRACKET_ARAKAWA); } - + //////////////////////////////////////////////////////////////////////// // Advection terms - + /// ExB advection - const Field3D UE_Grad(const Field3D &f, const Field3D &p) { - return bracket(p, f, bm); - } - + const Field3D UE_Grad(const Field3D& f, const Field3D& p) { return bracket(p, f, bm); } + /// Artificial dissipation terms in advection - const Field3D UE_Grad_D(const Field3D &f, const Field3D &UNUSED(p)) { + const Field3D UE_Grad_D(const Field3D& f, const Field3D& UNUSED(p)) { Field3D delp2 = Delp2(f); delp2.applyBoundary("neumann"); mesh->communicate(delp2); - - return nu_perp*Delp2( delp2 * SQ(SQ(1./coord->Bxy)) ) - - nu_par*Grad2_par2(f) // NB: This should be changed for variable B - ; - } - - const Field3D WE_Grad(const Field3D &f, const Field3D &p) { - return bracket(p, f, bm); + + return nu_perp * Delp2(delp2 * SQ(SQ(1. / coord->Bxy))) + - nu_par * Grad2_par2(f) // NB: This should be changed for variable B + ; } - + + const Field3D WE_Grad(const Field3D& f, const Field3D& p) { return bracket(p, f, bm); } + //////////////////////////////////////////////////////////////////////// // Parallel derivative - - const Field3D Grad_parP(const Field3D &f, CELL_LOC loc = CELL_DEFAULT) { + + const Field3D Grad_parP(const Field3D& f, CELL_LOC loc = CELL_DEFAULT) { return Grad_par(f, loc) - - beta_e*bracket(interp_to(Apar, loc), interp_to(f, loc), BRACKET_ARAKAWA); + - beta_e * bracket(interp_to(Apar, loc), interp_to(f, loc), BRACKET_ARAKAWA); } - - const Field3D Div_parP(const Field3D &f, CELL_LOC loc = CELL_DEFAULT) { + + const Field3D Div_parP(const Field3D& f, CELL_LOC loc = CELL_DEFAULT) { return interp_to(coord->Bxy, loc) - *Grad_parP(f/interp_to(coord->Bxy, f.getLocation()), loc); + * Grad_parP(f / interp_to(coord->Bxy, f.getLocation()), loc); } - }; BOUTMAIN(GEM); - diff --git a/examples/hasegawa-wakatani-3d/hw.cxx b/examples/hasegawa-wakatani-3d/hw.cxx index b9101bf4f2..0405d1dbe3 100644 --- a/examples/hasegawa-wakatani-3d/hw.cxx +++ b/examples/hasegawa-wakatani-3d/hw.cxx @@ -11,7 +11,7 @@ #include #include -#include +#include #define DISABLE_RAJA 0 #include diff --git a/examples/hasegawa-wakatani/hw.cxx b/examples/hasegawa-wakatani/hw.cxx index 72f1d78d82..dcd7533f35 100644 --- a/examples/hasegawa-wakatani/hw.cxx +++ b/examples/hasegawa-wakatani/hw.cxx @@ -1,28 +1,28 @@ #include -#include -#include -#include +#include +#include +#include class HW : public PhysicsModel { private: - Field3D n, vort; // Evolving density and vorticity - Field3D phi; // Electrostatic potential + Field3D n, vort; // Evolving density and vorticity + Field3D phi; // Electrostatic potential // Model parameters - BoutReal alpha; // Adiabaticity (~conductivity) - BoutReal kappa; // Density gradient drive - BoutReal Dvort, Dn; // Diffusion - bool modified; // Modified H-W equations? - + BoutReal alpha; // Adiabaticity (~conductivity) + BoutReal kappa; // Density gradient drive + BoutReal Dvort, Dn; // Diffusion + bool modified; // Modified H-W equations? + // Poisson brackets: b0 x Grad(f) dot Grad(g) / B = [f, g] // Method to use: BRACKET_ARAKAWA, BRACKET_STD or BRACKET_SIMPLE BRACKET_METHOD bm; // Bracket method for advection terms - + std::unique_ptr phiSolver; // Laplacian solver for vort -> phi // Simple implementation of 4th order perpendicular Laplacian - Field3D Delp4(const Field3D &var) { + Field3D Delp4(const Field3D& var) { Field3D tmp; tmp = Delp2(var); mesh->communicate(tmp); @@ -31,7 +31,7 @@ class HW : public PhysicsModel { //return Delp2(var); } - + protected: int init(bool UNUSED(restart)) { @@ -48,31 +48,31 @@ class HW : public PhysicsModel { // Split into convective and diffusive parts setSplitOperator(); - + phiSolver = Laplacian::create(); phi = 0.; // Starting phi - - // Use default flags - + + // Use default flags + // Choose method to use for Poisson bracket advection terms - switch(options["bracket"].withDefault(0)) { + switch (options["bracket"].withDefault(0)) { case 0: { - bm = BRACKET_STD; + bm = BRACKET_STD; output << "\tBrackets: default differencing\n"; break; } case 1: { - bm = BRACKET_SIMPLE; + bm = BRACKET_SIMPLE; output << "\tBrackets: simplified operator\n"; break; } case 2: { - bm = BRACKET_ARAKAWA; + bm = BRACKET_ARAKAWA; output << "\tBrackets: Arakawa scheme\n"; break; } case 3: { - bm = BRACKET_CTU; + bm = BRACKET_CTU; output << "\tBrackets: Corner Transport Upwind method\n"; break; } @@ -80,40 +80,41 @@ class HW : public PhysicsModel { output << "ERROR: Invalid choice of bracket method. Must be 0 - 3\n"; return 1; } - + return 0; } int convective(BoutReal UNUSED(time)) { // Non-stiff, convective part of the problem - + // Solve for potential phi = phiSolver->solve(vort, phi); - + // Communicate variables mesh->communicate(n, vort, phi); - + // Modified H-W equations, with zonal component subtracted from resistive coupling term Field3D nonzonal_n = n; Field3D nonzonal_phi = phi; - if(modified) { + if (modified) { // Subtract average in Y and Z nonzonal_n -= averageY(DC(n)); nonzonal_phi -= averageY(DC(phi)); } - - ddt(n) = -bracket(phi, n, bm) + alpha*(nonzonal_phi - nonzonal_n) - kappa*DDZ(phi); - - ddt(vort) = -bracket(phi, vort, bm) + alpha*(nonzonal_phi - nonzonal_n); - + + ddt(n) = + -bracket(phi, n, bm) + alpha * (nonzonal_phi - nonzonal_n) - kappa * DDZ(phi); + + ddt(vort) = -bracket(phi, vort, bm) + alpha * (nonzonal_phi - nonzonal_n); + return 0; } - + int diffusive(BoutReal UNUSED(time)) { // Diffusive terms mesh->communicate(n, vort); - ddt(n) = -Dn*Delp4(n); - ddt(vort) = -Dvort*Delp4(vort); + ddt(n) = -Dn * Delp4(n); + ddt(vort) = -Dvort * Delp4(vort); return 0; } }; diff --git a/examples/invertable_operator/invertable_operator.cxx b/examples/invertable_operator/invertable_operator.cxx index d4d429b61e..064cc1719c 100644 --- a/examples/invertable_operator/invertable_operator.cxx +++ b/examples/invertable_operator/invertable_operator.cxx @@ -1,15 +1,15 @@ -#include -#include +#include +#include #include #include #include -#include +#include -#include +#include -Field3D minus(const Field3D &input) { return -1.0 * input; }; -Field3D delp(const Field3D &input) { return input + Delp2(input); }; +Field3D minus(const Field3D& input) { return -1.0 * input; }; +Field3D delp(const Field3D& input) { return input + Delp2(input); }; class HW : public PhysicsModel { private: @@ -17,7 +17,7 @@ class HW : public PhysicsModel { struct myOp { BoutReal factor = 1.; - Field3D operator()(const Field3D &input) { return factor * input + Delp2(input); }; + Field3D operator()(const Field3D& input) { return factor * input + Delp2(input); }; }; myOp myDelp; @@ -25,7 +25,7 @@ class HW : public PhysicsModel { Field3D D = 1.0, C = 1.0, A = 0.0; // Drop C term for now - Field3D operator()(const Field3D &input) { + Field3D operator()(const Field3D& input) { TRACE("myLaplacian::operator()"); Timer timer("invertable_operator_operate"); Field3D result = A * input + D * Delp2(input); @@ -42,7 +42,7 @@ class HW : public PhysicsModel { bool withDiv = false; // Drop C term for now - Field3D operator()(const Field3D &input) { + Field3D operator()(const Field3D& input) { TRACE("myLaplacian::operator()"); Timer timer("invertable_operator_operate"); Field3D result = A * input + B * Laplace_perp(input); @@ -112,7 +112,7 @@ class HW : public PhysicsModel { solutionInv = mySolver.invert(n, solutionInv); // mesh->communicate(solutionInv); } - } catch (BoutException &e) { + } catch (BoutException& e) { }; mesh->communicate(solutionInv); @@ -128,7 +128,7 @@ class HW : public PhysicsModel { for (int i = 0; i < nits; i++) { solutionLap = laplacianSolver->solve(n); } - } catch (BoutException &e) { + } catch (BoutException& e) { }; } diff --git a/examples/jorek-compare/jorek_compare.cxx b/examples/jorek-compare/jorek_compare.cxx index d4ef79c57a..5963fbd7ca 100644 --- a/examples/jorek-compare/jorek_compare.cxx +++ b/examples/jorek-compare/jorek_compare.cxx @@ -6,7 +6,7 @@ #include #include -#include +#include class Jorek : public PhysicsModel { private: @@ -114,7 +114,8 @@ class Jorek : public PhysicsModel { Field2D factor = P0 / (Charge * (Ti0 + Te0) * rho0); - output.write("\tPressure factor {:e} -> {:e}\n", min(factor, true), max(factor, true)); + output.write("\tPressure factor {:e} -> {:e}\n", min(factor, true), + max(factor, true)); // Multiply temperatures by this factor Te0 *= factor; @@ -239,8 +240,8 @@ class Jorek : public PhysicsModel { // Check type of parallel transform std::string ptstr = - Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + Options::root()["mesh"]["paralleltransform"]["type"].withDefault( + "identity"); if (lowercase(ptstr) == "shifted") { // Dimits style, using local coordinate system @@ -334,7 +335,8 @@ class Jorek : public PhysicsModel { eta = eta0; tau_e = tau_enorm * pow(Te0, 1.5) / rho0; - output.write("\tNormalised tau_e = {:e} -> {:e}\n", min(tau_e, true), max(tau_e, true)); + output.write("\tNormalised tau_e = {:e} -> {:e}\n", min(tau_e, true), + max(tau_e, true)); // Set locations for staggered grids vD.setLocation(CELL_VSHIFT); @@ -356,7 +358,7 @@ class Jorek : public PhysicsModel { SAVE_REPEAT(phi, Jpar); // Save each timestep SAVE_REPEAT(divExB); - + // Create a solver for the Laplacian phiSolver = Laplacian::create(); if (vorticity_momentum) { diff --git a/examples/lapd-drift/lapd_drift.cxx b/examples/lapd-drift/lapd_drift.cxx index da7980bb95..b7579dacb1 100644 --- a/examples/lapd-drift/lapd_drift.cxx +++ b/examples/lapd-drift/lapd_drift.cxx @@ -5,44 +5,44 @@ *******************************************************************************/ #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include #include #include /// Solves 2-fluid equations for turbulence in a linear device -/// +/// class LAPDdrift : public PhysicsModel { private: // 2D initial profiles Field2D Ni0, Ti0, Te0, Vi0, phi0, Ve0, Ajpar0, src_ni0; Coordinates::FieldMetric rho0; Vector2D b0xcv; // for curvature terms - + // 3D evolving fields Field3D rho, ni, ajpar, te; - + // Derived 3D variables Field3D phi, Apar, Ve, jpar; - + // Non-linear coefficients Field3D nu, mu_i, kapa_Te, kapa_Ti; - + // 3D total values Field3D Nit, Tit, Tet, Vit, phit, VEt, dphi_bc_ydown, dphi_bc_yup; // pressures Field3D pei, pe; Field2D pei0, pe0; - + // Metric coefficients - Field2D Rxy, Bpxy, Btxy, hthe,Zxy; - + Field2D Rxy, Bpxy, Btxy, hthe, Zxy; + // parameters BoutReal Te_x, Ti_x, Ni_x, Vi_x, bmag, rho_s, fmei, AA, ZZ; BoutReal lambda_ei, lambda_ii; @@ -50,118 +50,118 @@ class LAPDdrift : public PhysicsModel { BoutReal ni_perpdiff, rho_perpdiff, te_perpdiff; BoutReal beta_p; BoutReal nuIonNeutral; // Ion-neutral collision rate (normalised by wci) - + // settings bool estatic, ZeroElMass; // Switch for electrostatic operation (true = no Apar) - - bool arakawa; // Use Arakawa scheme for ExB advection - bool bout_exb; // Use BOUT-06 expression for ExB velocity - + + bool arakawa; // Use Arakawa scheme for ExB advection + bool bout_exb; // Use BOUT-06 expression for ExB velocity + BoutReal zeff, nu_perp; bool evolve_rho, evolve_ni, evolve_ajpar, evolve_te; BoutReal ShearFactor; BoutReal time_step; - + bool nonlinear; bool neg_fix; - + BoutReal ni_floor, minNit; - + bool filter_z; int filter_z_mode; - - bool log_density; // Evolve logarithm of the density - + + bool log_density; // Evolve logarithm of the density + bool niprofile; - + bool evolve_source_ni, evolve_source_te; // If true, evolve a source/sink profile - BoutReal source_response; // Initial source response (inverse timescale) - BoutReal source_converge; // Timescale for convergence - Field2D Sn,St; // Density source (inverse timescale) - bool input_source; // Read Sn from the input file + BoutReal source_response; // Initial source response (inverse timescale) + BoutReal source_converge; // Timescale for convergence + Field2D Sn, St; // Density source (inverse timescale) + bool input_source; // Read Sn from the input file bool remove_tor_av_ni, remove_tor_av_te; // Subtract the toroidal averages - + // Switches for terms in the ni equation bool ni_jpar1, ni_ni0_phi1, ni_ni1_phi0, ni_ni1_phi1, ni_src_ni0, ni_diff; - + // Switches for terms in the rho equation bool rho_jpar1, rho_nuin_rho1, rho_rho1, rho_rho1_phi1, rho_ve2t, rho_diff; bool rho_rho0_phi1, rho_rho1_phi0, rho_ve2lin; - + // Switches for terms in the ajpar equation - bool ajpar_phi1, ajpar_jpar1, ajpar_te_ni, ajpar_te; + bool ajpar_phi1, ajpar_jpar1, ajpar_te_ni, ajpar_te; bool ajpar_ajpar1_phi1, ajpar_ajpar1_phi0, ajpar_ve1_ve1; - + // Switches for terms in the te equation bool te_te1_phi0, te_te0_phi1, te_te1_phi1, te_ajpar_te; bool te_te_ajpar, te_nu_te1, te_nu_tet, te_jpar, te_diff; - + // Coefficients for linear sheath problem Field2D LAMBDA1, LAMBDA2; - + // My ixseps variables int my_ixseps; - + // Communication object FieldGroup comms; // Laplacian inversion object std::unique_ptr phiSolver; + protected: - /// Function called once at the start of the simulation /// /// @param[in] restarting True if simulation is restarting int init(bool UNUSED(restarting)) { - Field2D I; // Shear factor - + Field2D I; // Shear factor + output.write("Solving LAPD drift test case\n"); - + /************* LOAD DATA FROM GRID FILE ****************/ - + // Load 2D profiles (set to zero if not found) - mesh->get(Ni0, "Ni0"); - mesh->get(Ti0, "Ti0"); - mesh->get(Te0, "Te0"); - mesh->get(Vi0, "Vi0"); - mesh->get(Ve0, "Ve0"); - mesh->get(phi0, "phi0"); - mesh->get(rho0, "rho0"); + mesh->get(Ni0, "Ni0"); + mesh->get(Ti0, "Ti0"); + mesh->get(Te0, "Te0"); + mesh->get(Vi0, "Vi0"); + mesh->get(Ve0, "Ve0"); + mesh->get(phi0, "phi0"); + mesh->get(rho0, "rho0"); mesh->get(Ajpar0, "Ajpar0"); mesh->get(src_ni0, "src_ni0"); - + // Load magnetic curvature term - b0xcv.covariant = false; // Read contravariant components + b0xcv.covariant = false; // Read contravariant components mesh->get(b0xcv, "bxcv"); // b0xkappa terms - Coordinates *coord = mesh->getCoordinates(); - + Coordinates* coord = mesh->getCoordinates(); + // Load metrics - mesh->get(Rxy, "Rxy"); - mesh->get(Zxy, "Zxy"); + mesh->get(Rxy, "Rxy"); + mesh->get(Zxy, "Zxy"); mesh->get(Bpxy, "Bpxy"); mesh->get(Btxy, "Btxy"); mesh->get(hthe, "hthe"); - mesh->get(coord->dx, "dpsi"); - mesh->get(I, "sinty"); - + mesh->get(coord->dx, "dpsi"); + mesh->get(I, "sinty"); + // Load normalisation values mesh->get(Te_x, "Te_x"); mesh->get(Ti_x, "Ti_x"); mesh->get(Ni_x, "Ni_x"); mesh->get(bmag, "bmag"); - + // Get separatrix location mesh->get(my_ixseps, "ixseps1"); - + Ni_x *= 1.0e14; bmag *= 1.0e4; /*************** READ OPTIONS *************************/ // Read some parameters - + auto& globalOptions = Options::root(); - + time_step = globalOptions["TIMESTEP"].withDefault(1.0); auto& options = globalOptions["2fluid"]; @@ -245,113 +245,115 @@ class LAPDdrift : public PhysicsModel { if (ZeroElMass) { evolve_ajpar = false; // Don't need ajpar - calculated from ohm's law } - + /************* SHIFTED RADIAL COORDINATES ************/ - + // Check type of parallel transform - std::string ptstr = Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + std::string ptstr = + Options::root()["mesh"]["paralleltransform"]["type"].withDefault( + "identity"); if (lowercase(ptstr) == "shifted") { - ShearFactor = 0.0; // I disappears from metric - b0xcv.z += I*b0xcv.x; + ShearFactor = 0.0; // I disappears from metric + b0xcv.z += I * b0xcv.x; } - + /************** CALCULATE PARAMETERS *****************/ - - rho_s = 1.02*sqrt(AA*Te_x)/ZZ/bmag; - fmei = 1./1836.2/AA; - - lambda_ei = 24.-log(sqrt(Ni_x)/Te_x); - lambda_ii = 23.-log(ZZ*ZZ*ZZ*sqrt(2.*Ni_x)/pow(Ti_x, 1.5)); - wci = 9.58e3*ZZ*bmag/AA; - nueix = 2.91e-6*Ni_x*lambda_ei/pow(Te_x, 1.5); - nuiix = 4.78e-8*pow(ZZ,4.)*Ni_x*lambda_ii/pow(Ti_x, 1.5)/sqrt(AA); - nu_hat = zeff*nueix/wci; - mui_hat = 0.96*wci/nuiix*pow(Ti_x/Te_x, -1.5); - - + + rho_s = 1.02 * sqrt(AA * Te_x) / ZZ / bmag; + fmei = 1. / 1836.2 / AA; + + lambda_ei = 24. - log(sqrt(Ni_x) / Te_x); + lambda_ii = 23. - log(ZZ * ZZ * ZZ * sqrt(2. * Ni_x) / pow(Ti_x, 1.5)); + wci = 9.58e3 * ZZ * bmag / AA; + nueix = 2.91e-6 * Ni_x * lambda_ei / pow(Te_x, 1.5); + nuiix = 4.78e-8 * pow(ZZ, 4.) * Ni_x * lambda_ii / pow(Ti_x, 1.5) / sqrt(AA); + nu_hat = zeff * nueix / wci; + mui_hat = 0.96 * wci / nuiix * pow(Ti_x / Te_x, -1.5); + if (estatic) { - beta_p = 1.e-29; + beta_p = 1.e-29; } else { - beta_p = 4.03e-11*Ni_x*Te_x/bmag/bmag; + beta_p = 4.03e-11 * Ni_x * Te_x / bmag / bmag; } Vi_x = wci * rho_s; - + output.write("Collisions: nueix = {:e}, nu_hat = {:e}\n", nueix, nu_hat); - + /************** PRINT Z INFORMATION ******************/ - + BoutReal hthe0; - if(mesh->get(hthe0, "hthe0") == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", hthe0/rho_s); + if (mesh->get(hthe0, "hthe0") == 0) { + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } - + /************** SHIFTED GRIDS LOCATION ***************/ - + // Velocities defined on cell boundaries ajpar.setLocation(CELL_YLOW); // Apar and jpar too - Apar.setLocation(CELL_YLOW); + Apar.setLocation(CELL_YLOW); jpar.setLocation(CELL_YLOW); - + /************** NORMALISE QUANTITIES *****************/ - + output.write("\tNormalising to rho_s = {:e}\n", rho_s); // Normalise profiles - Ni0 /= Ni_x/1.0e14; - Ti0 /= Te_x; - Te0 /= Te_x; + Ni0 /= Ni_x / 1.0e14; + Ti0 /= Te_x; + Te0 /= Te_x; phi0 /= Te_x; - Vi0 /= Vi_x; - + Vi0 /= Vi_x; + // Normalise curvature term - b0xcv.x /= (bmag/1e4); - b0xcv.y *= rho_s*rho_s; - b0xcv.z *= rho_s*rho_s; - - // Normalise geometry + b0xcv.x /= (bmag / 1e4); + b0xcv.y *= rho_s * rho_s; + b0xcv.z *= rho_s * rho_s; + + // Normalise geometry Rxy /= rho_s; hthe /= rho_s; - I *= rho_s*rho_s*(bmag/1e4)*ShearFactor; - coord->dx /= rho_s*rho_s*(bmag/1e4); - + I *= rho_s * rho_s * (bmag / 1e4) * ShearFactor; + coord->dx /= rho_s * rho_s * (bmag / 1e4); + // Normalise magnetic field - Bpxy /= (bmag/1.e4); - Btxy /= (bmag/1.e4); - coord->Bxy /= (bmag/1.e4); - + Bpxy /= (bmag / 1.e4); + Btxy /= (bmag / 1.e4); + coord->Bxy /= (bmag / 1.e4); + // calculate pressures - pei0 = (Ti0 + Te0)*Ni0; - pe0 = Te0*Ni0; - + pei0 = (Ti0 + Te0) * Ni0; + pe0 = Te0 * Ni0; + /**************** CALCULATE METRICS ******************/ - - coord->g11 = SQ(Rxy*Bpxy); + + coord->g11 = SQ(Rxy * Bpxy); coord->g22 = 1.0 / SQ(hthe); - coord->g33 = SQ(I)*coord->g11 + SQ(coord->Bxy)/coord->g11; + coord->g33 = SQ(I) * coord->g11 + SQ(coord->Bxy) / coord->g11; coord->g12 = 0.0; - coord->g13 = -I*coord->g11; - coord->g23 = -Btxy/(hthe*Bpxy*Rxy); - + coord->g13 = -I * coord->g11; + coord->g23 = -Btxy / (hthe * Bpxy * Rxy); + coord->J = hthe / Bpxy; - - coord->g_11 = 1.0/coord->g11 + SQ(I*Rxy); - coord->g_22 = SQ(coord->Bxy*hthe/Bpxy); - coord->g_33 = Rxy*Rxy; - coord->g_12 = Btxy*hthe*I*Rxy/Bpxy; - coord->g_13 = I*Rxy*Rxy; - coord->g_23 = Btxy*hthe*Rxy/Bpxy; - + + coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy); + coord->g_22 = SQ(coord->Bxy * hthe / Bpxy); + coord->g_33 = Rxy * Rxy; + coord->g_12 = Btxy * hthe * I * Rxy / Bpxy; + coord->g_13 = I * Rxy * Rxy; + coord->g_23 = Btxy * hthe * Rxy / Bpxy; + coord->geometry(); - - rho0 = Ni0*Delp2(phi0) + Perp_Grad_dot_Grad(phi0,Ni0); - + + rho0 = Ni0 * Delp2(phi0) + Perp_Grad_dot_Grad(phi0, Ni0); + /**************** SET EVOLVING VARIABLES *************/ - + // Tell BOUT++ which variables to evolve // add evolving variables to the communication object if (evolve_rho) { @@ -377,7 +379,7 @@ class LAPDdrift : public PhysicsModel { dump.add(ajpar, "ajpar", 1); // output calculated Ajpar } } - + if (evolve_te) { SOLVE_FOR(te); comms.add(te); @@ -388,7 +390,7 @@ class LAPDdrift : public PhysicsModel { // Set boundary conditions on jpar and VEt jpar.setBoundary("jpar"); VEt.setBoundary("VEt"); - + if (evolve_source_ni) { SOLVE_FOR(Sn); } @@ -396,63 +398,63 @@ class LAPDdrift : public PhysicsModel { mesh->get(Sn, "Sn"); dump.add(Sn, "Sn"); } - + if (evolve_source_te) { SOLVE_FOR(St); } /************** SETUP COMMUNICATIONS **************/ - + // add extra variables to communication comms.add(phi); - + /*************** DUMP VARIABLES TO OUTPUT**********/ - dump.add(phi, "phi", 1); dump.add(jpar, "jpar", 1); - - SAVE_ONCE(Ni0,Te0,phi0,rho0); - SAVE_ONCE(Rxy,Bpxy,Btxy,Zxy,hthe); + dump.add(phi, "phi", 1); + dump.add(jpar, "jpar", 1); + + SAVE_ONCE(Ni0, Te0, phi0, rho0); + SAVE_ONCE(Rxy, Bpxy, Btxy, Zxy, hthe); dump.addOnce(coord->Bxy, "Bxy"); dump.addOnce(my_ixseps, "ixseps"); - - SAVE_ONCE(Te_x,Ti_x,Ni_x); - SAVE_ONCE(AA,ZZ,zeff,rho_s,wci,bmag); + + SAVE_ONCE(Te_x, Ti_x, Ni_x); + SAVE_ONCE(AA, ZZ, zeff, rho_s, wci, bmag); dump.addOnce(mesh->LocalNx, "ngx"); - dump.addOnce(mesh->LocalNy, "ngy"); + dump.addOnce(mesh->LocalNy, "ngy"); dump.addOnce(mesh->LocalNz, "ngz"); - SAVE_ONCE(mui_hat,nu_hat,nuIonNeutral,beta_p,time_step,hthe0); - SAVE_ONCE(ni_perpdiff,rho_perpdiff,te_perpdiff); + SAVE_ONCE(mui_hat, nu_hat, nuIonNeutral, beta_p, time_step, hthe0); + SAVE_ONCE(ni_perpdiff, rho_perpdiff, te_perpdiff); // Laplacian inversion solver phiSolver = Laplacian::create(); phiSolver->setCoefC(Ni0); - + return 0; } ////////////////////////////////////// - ////////////////////////////////////// /// Function called at each time step /// Time derivatives calculated here int rhs(BoutReal t) { - Coordinates *coord = mesh->getCoordinates(); - + Coordinates* coord = mesh->getCoordinates(); + // Invert vorticity to get phi - + // Solves \nabla^2_\perp x + (1./c)*\nabla_perp c\cdot\nabla_\perp x + a x = b // Arguments are: (b, bit-field, a, c) // Passing NULL -> missing term if (nonlinear) { - phi = phiSolver->solve(rho/(Ni0+ni)); + phi = phiSolver->solve(rho / (Ni0 + ni)); } else { - phi = phiSolver->solve(rho/Ni0); + phi = phiSolver->solve(rho / Ni0); } - + // Communicate variables mesh->communicate(comms); - + // Update profiles if (nonlinear) { Nit = Ni0 + ni; @@ -465,132 +467,132 @@ class LAPDdrift : public PhysicsModel { Tit = Ti0; Tet = Te0; } - + BoutReal source_alpha; - + // Calculate source response if (source_converge > 0.) { - source_alpha = source_response * exp(-1.*t/source_converge); + source_alpha = source_response * exp(-1. * t / source_converge); } else { source_alpha = source_response; } // Exit if the density goes negative if (nonlinear && min(Nit) < 0.0) { - output.enable(); // Use stdout for the next line + output.enable(); // Use stdout for the next line throw BoutException("Unphysical negative density encountered. Exiting...\n"); } - // Exit if the temperature goes negative or make negatives zero if (nonlinear && evolve_te && min(Tet) < 0.0) { - output.enable(); // Use stdout for the next line + output.enable(); // Use stdout for the next line throw BoutException("Unphysical negative temperature encountered. Exiting...\n"); } - + // Update non-linear coefficients - nu = nu_hat * Nit / pow(Tet,1.5); - mu_i = mui_hat * pow(Tit,2.5)/Nit; + nu = nu_hat * Nit / pow(Tet, 1.5); + mu_i = mui_hat * pow(Tit, 2.5) / Nit; //kapa_Te = 3.2*(1./fmei)*(wci/nueix)*pow(Tet,2.5); //kapa_Ti = 3.9*(wci/nuiix)*(Tit^2.5); - + // Calculate pressures //pei = (Tet+Tit)*Nit; //pe = Tet*Nit; - + // Calculate E cross B velocity if (nonlinear) { - VEt = sqrt(coord->g11*DDX(phit)*DDX(phit) + coord->g33*DDZ(phit)*DDZ(phit)); - + VEt = sqrt(coord->g11 * DDX(phit) * DDX(phit) + coord->g33 * DDZ(phit) * DDZ(phit)); + // Set boundary condition on VEt VEt.applyBoundary(); - + // Communicate VEt mesh->communicate(VEt); } - + if (ZeroElMass) { // Set jpar,Ve,Ajpar neglecting the electron inertia term - jpar = (interp_to(Tet, CELL_YLOW)*Grad_par(ni, CELL_YLOW) - - interp_to(Nit, CELL_YLOW)*Grad_par(phi, CELL_YLOW))/(fmei*0.51*nu); - + jpar = (interp_to(Tet, CELL_YLOW) * Grad_par(ni, CELL_YLOW) + - interp_to(Nit, CELL_YLOW) * Grad_par(phi, CELL_YLOW)) + / (fmei * 0.51 * nu); + // Set boundary condition on jpar jpar.applyBoundary(); - + // Need to communicate jpar mesh->communicate(jpar); - - Ve = -jpar/interp_to(Nit, CELL_YLOW); + + Ve = -jpar / interp_to(Nit, CELL_YLOW); ajpar = Ve; } else { - + Ve = ajpar; - jpar = -interp_to(Nit, CELL_YLOW)*Ve; + jpar = -interp_to(Nit, CELL_YLOW) * Ve; //jpar = -Ni0*Ve; //Linearize as in BOUT06 } ////////////////////////////////////////////////////////////////////////////////////////// // DENSITY EQUATION - + ddt(ni) = 0.0; if (evolve_ni) { - + if (ni_ni0_phi1) { - ddt(ni) -= DDX(Ni0)*DDZ(phi); + ddt(ni) -= DDX(Ni0) * DDZ(phi); } - + if (ni_ni1_phi0) { ddt(ni) -= vE_Grad(ni, phi0); } - + if (ni_ni1_phi1) { ddt(ni) -= vE_Grad(ni, phi); } - + if (ni_jpar1) { ddt(ni) += Grad_par(jpar, CELL_CENTRE); // Left hand differencing } - + if (ni_src_ni0) { ddt(ni) += src_ni0; } - + if (ni_diff) { ddt(ni) += ni_perpdiff * Delp2(ni); } if (evolve_source_ni) { ddt(Sn) = averageY(-1. * source_alpha * DC(ni) / Ni0); - + // Add density source/sink - ddt(ni) += Sn*where(Sn, Ni0, Nit); // Sn*Ni0 if Sn > 0, Sn*Nit if Sn < 0 + ddt(ni) += Sn * where(Sn, Ni0, Nit); // Sn*Ni0 if Sn > 0, Sn*Nit if Sn < 0 } - - if(remove_tor_av_ni) { + + if (remove_tor_av_ni) { ddt(ni) -= DC(ddt(ni)); // REMOVE TOROIDAL AVERAGE DENSITY } } /////////////////////////////////////////////////////////////////////////////////////////// // VORTICITY - + ddt(rho) = 0.0; if (evolve_rho) { - - if (rho_jpar1) { + + if (rho_jpar1) { ddt(rho) += Grad_par(jpar, CELL_CENTRE); // Left hand differencing } - + if (rho_nuin_rho1) { ddt(rho) -= nuIonNeutral * rho; } - + if (rho_rho1) { ddt(rho) += mu_i * Delp2(rho); } - + if (rho_diff) { ddt(rho) += rho_perpdiff * Delp2(rho); } - + if (rho_rho1_phi1) { ddt(rho) -= vE_Grad(rho, phi); } @@ -598,146 +600,140 @@ class LAPDdrift : public PhysicsModel { if (rho_rho0_phi1) { ddt(rho) -= vE_Grad(rho0, phi); } - + if (rho_rho1_phi0) { ddt(rho) -= vE_Grad(rho, phi0); } - + if (rho_ve2lin) { - ddt(rho) -= coord->g11*coord->g33 * DDX(phi0)*(DDX(Ni0)*D2DXDZ(phi) - D2DX2(phi0)*DDZ(ni)); + ddt(rho) -= coord->g11 * coord->g33 * DDX(phi0) + * (DDX(Ni0) * D2DXDZ(phi) - D2DX2(phi0) * DDZ(ni)); } - + if (rho_ve2t) { - ddt(rho) += VEt * vE_Grad(VEt,Nit); + ddt(rho) += VEt * vE_Grad(VEt, Nit); } - } - + ///////////////////////////////////////////////////////////////////////////////////// // AJPAR - + ddt(ajpar) = 0.0; if (evolve_ajpar) { if (ajpar_phi1) { - ddt(ajpar) += (1./fmei)*Grad_par(phi, CELL_YLOW); // Right-hand deriv with b.c. Necessary for sheath mode + ddt(ajpar) += + (1. / fmei) + * Grad_par(phi, + CELL_YLOW); // Right-hand deriv with b.c. Necessary for sheath mode } - + if (ajpar_jpar1) { - ddt(ajpar) -= 0.51*interp_to(nu, CELL_YLOW)*ajpar; + ddt(ajpar) -= 0.51 * interp_to(nu, CELL_YLOW) * ajpar; } - if (ajpar_te_ni) { - ddt(ajpar) -= (1./fmei)*interp_to(Tet/Nit, CELL_YLOW)*Grad_par(ni, CELL_YLOW); + ddt(ajpar) -= + (1. / fmei) * interp_to(Tet / Nit, CELL_YLOW) * Grad_par(ni, CELL_YLOW); } - + if (ajpar_te) { - ddt(ajpar) -= (1.71/fmei)*Grad_par(te, CELL_YLOW); + ddt(ajpar) -= (1.71 / fmei) * Grad_par(te, CELL_YLOW); } - + if (ajpar_ajpar1_phi0) { - ddt(ajpar) -= vE_Grad(ajpar,interp_to(phi0, CELL_YLOW)); + ddt(ajpar) -= vE_Grad(ajpar, interp_to(phi0, CELL_YLOW)); } - + if (ajpar_ajpar1_phi1) { - ddt(ajpar) -= vE_Grad(ajpar,interp_to(phi, CELL_YLOW)); + ddt(ajpar) -= vE_Grad(ajpar, interp_to(phi, CELL_YLOW)); } - + if (ajpar_ve1_ve1) { - ddt(ajpar) -= Vpar_Grad_par(ajpar,ajpar); + ddt(ajpar) -= Vpar_Grad_par(ajpar, ajpar); } - } - - + ///////////////////////////////////////////////////////////////////////////////////////// // TEMPERATURE EQUATION - + ddt(te) = 0.0; if (evolve_te) { if (te_te0_phi1) { ddt(te) -= vE_Grad(Te0, phi); } - - + if (te_te1_phi0) { ddt(te) -= vE_Grad(te, phi0); } - + if (te_te1_phi1) { ddt(te) -= vE_Grad(te, phi); } - + if (te_ajpar_te) { ddt(te) -= interp_to(ajpar, CELL_CENTRE) * Grad_par(te); } - + if (te_te_ajpar) { - ddt(te) -= 2./3. * Tet * Grad_par(ajpar, CELL_CENTRE); + ddt(te) -= 2. / 3. * Tet * Grad_par(ajpar, CELL_CENTRE); } - + if (te_nu_te1) { - ddt(te) -= 2.*fmei*nu_hat/sqrt(Te0)*(ni - 1./2.*Ni0/Te0*te); // Explicitly linear + ddt(te) -= 2. * fmei * nu_hat / sqrt(Te0) + * (ni - 1. / 2. * Ni0 / Te0 * te); // Explicitly linear } - + if (te_nu_tet) { - ddt(te) -= 2.*fmei*(nu*Tet - nu_hat*Ni0/sqrt(Te0)); // All Nonlinear + ddt(te) -= 2. * fmei * (nu * Tet - nu_hat * Ni0 / sqrt(Te0)); // All Nonlinear } if (te_jpar) { - ddt(te) += 0.71*2./3. * Tet/Nit * Grad_par(jpar, CELL_CENTRE); + ddt(te) += 0.71 * 2. / 3. * Tet / Nit * Grad_par(jpar, CELL_CENTRE); } - + if (te_diff) { ddt(te) += te_perpdiff * Delp2(te); } - + if (remove_tor_av_te) { ddt(te) -= DC(ddt(te)); // REMOVE TOROIDAL AVERAGE TEMPERATURE } - + if (evolve_source_te) { // Evolve source ddt(St) = averageY(-1. * source_alpha * DC(te) / Te0); - + // Add heat source/sink - ddt(te) += St*where(St, Te0, Tet); - + ddt(te) += St * where(St, Te0, Tet); } - - + // There is an ion collision term that can be added with finite T_i - } - + ///////////////////////////////////////////////////////////////////////////////////////// // Z filtering if (filter_z) { // Filter out all except filter_z_mode - + ddt(rho) = filter(ddt(rho), filter_z_mode); ddt(ni) = filter(ddt(ni), filter_z_mode); ddt(ajpar) = filter(ddt(ajpar), filter_z_mode); ddt(te) = filter(ddt(te), filter_z_mode); } - - + return 0; } ///////////////////////////////////////////////////////////////// - - - + /****************SPECIAL DIFFERENTIAL OPERATORS******************/ Coordinates::FieldMetric Perp_Grad_dot_Grad(const Field2D& p, const Field2D& f) { - return DDX(p)*DDX(f)*mesh->getCoordinates()->g11; + return DDX(p) * DDX(f) * mesh->getCoordinates()->g11; } - - + ///////////////////////////////////////////////////////////////// // ExB terms. These routines allow comparisons with BOUT-06 // if bout_exb=true is set in BOUT.inp @@ -749,27 +745,27 @@ class LAPDdrift : public PhysicsModel { result = 0.0; } else { // Use full expression with all terms - + result = b0xGrad_dot_Grad(p, f) / mesh->getCoordinates()->Bxy; } return result; } - const Field3D vE_Grad(const Field2D &f, const Field3D &p) { - Coordinates *coord = mesh->getCoordinates(); + const Field3D vE_Grad(const Field2D& f, const Field3D& p) { + Coordinates* coord = mesh->getCoordinates(); Field3D result; if (arakawa) { // Arakawa scheme for perpendicular flow. Here as a test - + result.allocate(); - + int ncz = mesh->LocalNz; for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { for (int jy = mesh->ystart; jy <= mesh->yend; jy++) { - for(int jz=0;jzdx(jx, jy, jz) * coord->dz(jx, jy, jz)); - result(jx,jy,jz) = (Jpp + Jpx + Jxp) / 3.; + result(jx, jy, jz) = (Jpp + Jpx + Jxp) / 3.; } } } - }else if(bout_exb) { + } else if (bout_exb) { // Use a subset of terms for comparison to BOUT-06 result = VDDX(DDZ(p), f); - }else { + } else { // Use full expression with all terms result = b0xGrad_dot_Grad(p, f) / coord->Bxy; } return result; } - - const Field3D vE_Grad(const Field3D &f, const Field2D &p) { + + const Field3D vE_Grad(const Field3D& f, const Field2D& p) { Field3D result; if (bout_exb) { // Use a subset of terms for comparison to BOUT-06 @@ -818,23 +814,23 @@ class LAPDdrift : public PhysicsModel { } return result; } - - const Field3D vE_Grad(const Field3D &f, const Field3D &p) { + + const Field3D vE_Grad(const Field3D& f, const Field3D& p) { Field3D result; - - Coordinates *coord = mesh->getCoordinates(); + + Coordinates* coord = mesh->getCoordinates(); if (arakawa) { // Arakawa scheme for perpendicular flow. Here as a test - + result.allocate(); - + int ncz = mesh->LocalNz; for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { for (int jy = mesh->ystart; jy <= mesh->yend; jy++) { - for(int jz=0;jzdx(jx, jy, jz) * coord->dz(jx, jy, jz)); - result(jx,jy,jz) = (Jpp + Jpx + Jxp) / 3.; + result(jx, jy, jz) = (Jpp + Jpx + Jxp) / 3.; } } } - }else if(bout_exb) { + } else if (bout_exb) { // Use a subset of terms for comparison to BOUT-06 result = VDDX(DDZ(p), f) + VDDZ(-DDX(p), f); - }else { + } else { // Use full expression with all terms result = b0xGrad_dot_Grad(p, f) / coord->Bxy; } return result; } - }; BOUTMAIN(LAPDdrift); diff --git a/examples/laplace-petsc3d/create-initial-profiles.cxx b/examples/laplace-petsc3d/create-initial-profiles.cxx index 941df06641..75a4e774b6 100644 --- a/examples/laplace-petsc3d/create-initial-profiles.cxx +++ b/examples/laplace-petsc3d/create-initial-profiles.cxx @@ -23,8 +23,8 @@ * **************************************************************************/ +#include "bout/initialprofiles.hxx" #include "bout/physicsmodel.hxx" -#include "initialprofiles.hxx" class CreateInitialProfiles : public PhysicsModel { int init(bool) { @@ -49,13 +49,13 @@ class CreateInitialProfiles : public PhysicsModel { mesh->get(jyseps2_2, "jyseps2_2"); // outboard midplane - int yind = mesh->getLocalYIndexNoBoundaries((jyseps1_2 + jyseps2_2)/2); + int yind = mesh->getLocalYIndexNoBoundaries((jyseps1_2 + jyseps2_2) / 2); if (yind >= mesh->ystart and yind <= mesh->yend) { initial = sliceXZ(input1, yind); } // inboard midplane - yind = mesh->getLocalYIndexNoBoundaries((jyseps1_1 + jyseps2_1)/2); + yind = mesh->getLocalYIndexNoBoundaries((jyseps1_1 + jyseps2_1) / 2); if (yind >= mesh->ystart and yind <= mesh->yend) { initial = sliceXZ(input2, yind); } diff --git a/examples/laplace-petsc3d/test-laplace3d.cxx b/examples/laplace-petsc3d/test-laplace3d.cxx index b36643196c..46bfce7859 100644 --- a/examples/laplace-petsc3d/test-laplace3d.cxx +++ b/examples/laplace-petsc3d/test-laplace3d.cxx @@ -23,10 +23,10 @@ * **************************************************************************/ -#include "bout.hxx" -#include "derivs.hxx" -#include "initialprofiles.hxx" -#include "invert_laplace.hxx" +#include "bout/bout.hxx" +#include "bout/derivs.hxx" +#include "bout/initialprofiles.hxx" +#include "bout/invert_laplace.hxx" // The discretisation used in the solver is subtly different from that // in Laplace_perp, which can introduce error with some grids @@ -36,13 +36,13 @@ Field3D this_Laplace_perp(const Field3D& f) { // dfdy not divided by dy yet auto dfdy = bout::derivatives::index::DDY(f, CELL_DEFAULT, "DEFAULT", "RGN_NOY"); - return coords->G1*DDX(f) - + (coords->G2 - DDY(coords->J/coords->g_22)/coords->J)*DDY(f) - + coords->G3*DDZ(f) - + coords->g11*D2DX2(f) + (coords->g22 - 1./coords->g_22)*D2DY2(f) - + coords->g33*D2DZ2(f) - + 2.*(coords->g12*DDX(dfdy)/coords->dy + coords->g13*D2DXDZ(f) - + coords->g23*D2DYDZ(f)); + return coords->G1 * DDX(f) + + (coords->G2 - DDY(coords->J / coords->g_22) / coords->J) * DDY(f) + + coords->G3 * DDZ(f) + coords->g11 * D2DX2(f) + + (coords->g22 - 1. / coords->g_22) * D2DY2(f) + coords->g33 * D2DZ2(f) + + 2. + * (coords->g12 * DDX(dfdy) / coords->dy + coords->g13 * D2DXDZ(f) + + coords->g23 * D2DYDZ(f)); } int main(int argc, char** argv) { @@ -65,15 +65,15 @@ int main(int argc, char** argv) { int y = mesh->ystart - 1; if (x == mesh->xstart) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x-1, y, z) = 0.5*(f(x-1, y - 1, z) + f(x-1, y, z)); + f(x - 1, y, z) = 0.5 * (f(x - 1, y - 1, z) + f(x - 1, y, z)); } } for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x, y, z) = 0.5*(f(x, y, z) + f(x, y + 1, z)); + f(x, y, z) = 0.5 * (f(x, y, z) + f(x, y + 1, z)); } if (x == mesh->xend) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x+1, y, z) = 0.5*(f(x+1, y - 1, z) + f(x+1, y, z)); + f(x + 1, y, z) = 0.5 * (f(x + 1, y - 1, z) + f(x + 1, y, z)); } } } @@ -82,15 +82,15 @@ int main(int argc, char** argv) { int y = mesh->yend + 1; if (x == mesh->xstart) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x-1, y, z) = 0.5*(f(x-1, y - 1, z) + f(x-1, y, z)); + f(x - 1, y, z) = 0.5 * (f(x - 1, y - 1, z) + f(x - 1, y, z)); } } for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x, y, z) = 0.5*(f(x, y - 1, z) + f(x, y, z)); + f(x, y, z) = 0.5 * (f(x, y - 1, z) + f(x, y, z)); } if (x == mesh->xend) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x+1, y, z) = 0.5*(f(x+1, y - 1, z) + f(x+1, y, z)); + f(x + 1, y, z) = 0.5 * (f(x + 1, y - 1, z) + f(x + 1, y, z)); } } } @@ -98,7 +98,7 @@ int main(int argc, char** argv) { int x = mesh->xstart - 1; for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x, y, z) = 0.5*(f(x, y, z) + f(x, y + 1, z)); + f(x, y, z) = 0.5 * (f(x, y, z) + f(x, y + 1, z)); } } } @@ -106,7 +106,7 @@ int main(int argc, char** argv) { int x = mesh->xend + 1; for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x, y, z) = 0.5*(f(x, y - 1, z) + f(x, y, z)); + f(x, y, z) = 0.5 * (f(x, y - 1, z) + f(x, y, z)); } } } @@ -137,8 +137,8 @@ int main(int argc, char** argv) { // Calculate error /////////////////////////////////////////////////////////////////////////////////////// auto& g_22 = mesh->getCoordinates()->g_22; - Field3D rhs_check = D*this_Laplace_perp(f) - + (Grad(f)*Grad(C2)-DDY(C2)*DDY(f)/g_22)/C1 + A*f; + Field3D rhs_check = D * this_Laplace_perp(f) + + (Grad(f) * Grad(C2) - DDY(C2) * DDY(f) / g_22) / C1 + A * f; // The usual way to do this would be // // Field3D rhs_check = D*Laplace_perp(f) + diff --git a/examples/laplacexy/alfven-wave/alfven.cxx b/examples/laplacexy/alfven-wave/alfven.cxx index f1523c9fb4..4f7de495ea 100644 --- a/examples/laplacexy/alfven-wave/alfven.cxx +++ b/examples/laplacexy/alfven-wave/alfven.cxx @@ -2,8 +2,8 @@ #include #include #include -#include -#include +#include +#include /// Fundamental constants const BoutReal PI = 3.14159265; @@ -32,10 +32,10 @@ class Alfven : public PhysicsModel { bool laplace_perp; // Use Laplace_perp or Delp2? bool split_n0; // Split solve into n=0 and n~=0? - LaplaceXY *laplacexy; // Laplacian solver in X-Y (n=0) + LaplaceXY* laplacexy; // Laplacian solver in X-Y (n=0) bool newXZsolver; - std::unique_ptr phiSolver; // Old Laplacian in X-Z + std::unique_ptr phiSolver; // Old Laplacian in X-Z std::unique_ptr newSolver{nullptr}; // New Laplacian in X-Z protected: int init(bool UNUSED(restarting)) { @@ -173,7 +173,7 @@ class Alfven : public PhysicsModel { Field2D Rxy, Bpxy, Btxy, hthe, sinty; GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics - Coordinates *coord = mesh->getCoordinates(); // Metric tensor + Coordinates* coord = mesh->getCoordinates(); // Metric tensor // Checking for dpsi and qinty used in BOUT grids Field2D dx; diff --git a/examples/laplacexy/laplace_perp/test.cxx b/examples/laplacexy/laplace_perp/test.cxx index b35128767a..104aaedf10 100644 --- a/examples/laplacexy/laplace_perp/test.cxx +++ b/examples/laplacexy/laplace_perp/test.cxx @@ -1,28 +1,28 @@ -#include +#include #include -#include -#include +#include +#include using bout::globals::mesh; int main(int argc, char** argv) { BoutInitialise(argc, argv); - + /////////////////////////////////////// bool calc_metric; calc_metric = Options::root()["calc_metric"].withDefault(false); - if(calc_metric) { + if (calc_metric) { // Read metric tensor Field2D Rxy, Btxy, Bpxy, B0, hthe, I; - mesh->get(Rxy, "Rxy"); // m + mesh->get(Rxy, "Rxy"); // m mesh->get(Btxy, "Btxy"); // T mesh->get(Bpxy, "Bpxy"); // T - mesh->get(B0, "Bxy"); // T + mesh->get(B0, "Bxy"); // T mesh->get(hthe, "hthe"); // m - mesh->get(I, "sinty");// m^-2 T^-1 + mesh->get(I, "sinty"); // m^-2 T^-1 - Coordinates *coord = mesh->getCoordinates(); + Coordinates* coord = mesh->getCoordinates(); // Calculate metrics coord->g11 = SQ(Rxy * Bpxy); @@ -45,19 +45,19 @@ int main(int argc, char** argv) { coord->geometry(); } /////////////////////////////////////// - + // Read an analytic input Field2D input = FieldFactory::get()->create2D("input", Options::getRoot(), mesh); - + // Create a LaplaceXY solver - LaplaceXY *laplacexy = new LaplaceXY(mesh); - + LaplaceXY* laplacexy = new LaplaceXY(mesh); + // Solve, using 0.0 as starting guess Field2D solved = laplacexy->solve(input, 0.0); - + // Need to communicate guard cells mesh->communicate(solved); - + // Now differentiate using Laplace_perp Options::root()["result"] = Laplace_perp(solved); @@ -70,4 +70,3 @@ int main(int argc, char** argv) { BoutFinalise(); return 0; } - diff --git a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx b/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx index cc3e347126..e90ccfc2e9 100644 --- a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx +++ b/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx @@ -1,6 +1,6 @@ #include -#include -#include +#include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/examples/laplacexy/simple/test-laplacexy.cxx b/examples/laplacexy/simple/test-laplacexy.cxx index b511b60493..c21d47d947 100644 --- a/examples/laplacexy/simple/test-laplacexy.cxx +++ b/examples/laplacexy/simple/test-laplacexy.cxx @@ -1,11 +1,11 @@ -#include #include -#include +#include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); - + /// Create a LaplaceXY object LaplaceXY laplacexy(bout::globals::mesh); @@ -15,7 +15,7 @@ int main(int argc, char** argv) { /// Solution Field2D x = 0.0; - + x = laplacexy.solve(rhs, x); Options dump; @@ -26,4 +26,3 @@ int main(int argc, char** argv) { BoutFinalise(); return 0; } - diff --git a/examples/make-script/test.cxx b/examples/make-script/test.cxx index 008c9480f5..8086e7a9e3 100644 --- a/examples/make-script/test.cxx +++ b/examples/make-script/test.cxx @@ -6,13 +6,13 @@ class Test : public PhysicsModel { private: Field2D f; - + public: int init(bool) override { SOLVE_FOR(f); return 0; } - + int rhs(BoutReal) override { ddt(f) = -f; return 0; @@ -20,4 +20,3 @@ class Test : public PhysicsModel { }; BOUTMAIN(Test); - diff --git a/examples/monitor-newapi/monitor.cxx b/examples/monitor-newapi/monitor.cxx index ef3091a14e..753728a639 100644 --- a/examples/monitor-newapi/monitor.cxx +++ b/examples/monitor-newapi/monitor.cxx @@ -10,26 +10,26 @@ class MonitorExample : public PhysicsModel { solver->add(f, "f"); return 0; } - + // Calculate time-derivatives int rhs(BoutReal UNUSED(t)) { ddt(f) = -f; return 0; - } - + } + // This called every output timestep int outputMonitor(BoutReal simtime, int iter, int NOUT) { - output.write("\nOutput monitor, time = {:e}, step {:d} of {:d}\n", - simtime, iter, NOUT); + output.write("\nOutput monitor, time = {:e}, step {:d} of {:d}\n", simtime, iter, + NOUT); return 0; } - + // This called every timestep int timestepMonitor(BoutReal simtime, BoutReal dt) { output.write("\nTimestep monitor, time = {:e}, dt = {:e}\n", simtime, dt); return 0; } - + private: Field2D f; }; diff --git a/examples/monitor/monitor.cxx b/examples/monitor/monitor.cxx index 0db85b01c6..8a8825bad1 100644 --- a/examples/monitor/monitor.cxx +++ b/examples/monitor/monitor.cxx @@ -2,7 +2,7 @@ */ #include -#include +#include /// Create a function to be called every timestep int my_timestep_monitor(Solver* UNUSED(solver), BoutReal simtime, BoutReal dt) { @@ -15,7 +15,8 @@ class MyOutputMonitor : public Monitor { public: explicit MyOutputMonitor(BoutReal timestep = -1) : Monitor(timestep){}; int call(Solver* UNUSED(solver), BoutReal simtime, int iter, int NOUT) override { - output.write("\nOutput monitor, time = {:e}, step {:d} of {:d}\n", simtime, iter, NOUT); + output.write("\nOutput monitor, time = {:e}, step {:d} of {:d}\n", simtime, iter, + NOUT); return 0; } }; diff --git a/examples/orszag-tang/mhd.cxx b/examples/orszag-tang/mhd.cxx index 02e93efa36..0e12db0cf4 100644 --- a/examples/orszag-tang/mhd.cxx +++ b/examples/orszag-tang/mhd.cxx @@ -46,7 +46,7 @@ class MHD : public PhysicsModel { B.covariant = false; // evolve contravariant components solver->add(B, "B"); - Coordinates *coord = mesh->getCoordinates(); + Coordinates* coord = mesh->getCoordinates(); output.write("dx(0,0,0) = {:e}, dy(0,0,0) = {:e}, dz(0,0,0) = {:e}\n", coord->dx(0, 0, 0), coord->dy(0, 0, 0), coord->dz(0, 0, 0)); diff --git a/examples/performance/arithmetic/arithmetic.cxx b/examples/performance/arithmetic/arithmetic.cxx index 30d2a72893..583c857e28 100644 --- a/examples/performance/arithmetic/arithmetic.cxx +++ b/examples/performance/arithmetic/arithmetic.cxx @@ -13,17 +13,15 @@ using SteadyClock = std::chrono::time_point; using Duration = std::chrono::duration; using namespace std::chrono; -#define TIMEIT(elapsed, ...) \ - { \ - SteadyClock start = steady_clock::now(); \ - { \ - __VA_ARGS__ ; \ - } \ - Duration diff = steady_clock::now() - start; \ - elapsed.min = diff > elapsed.min ? elapsed.min : diff; \ - elapsed.max = diff < elapsed.max ? elapsed.max : diff; \ - elapsed.count++; \ - elapsed.avg = elapsed.avg * (1 - 1. / elapsed.count) + diff / elapsed.count; \ +#define TIMEIT(elapsed, ...) \ + { \ + SteadyClock start = steady_clock::now(); \ + { __VA_ARGS__; } \ + Duration diff = steady_clock::now() - start; \ + elapsed.min = diff > elapsed.min ? elapsed.min : diff; \ + elapsed.max = diff < elapsed.max ? elapsed.max : diff; \ + elapsed.count++; \ + elapsed.avg = elapsed.avg * (1 - 1. / elapsed.count) + diff / elapsed.count; \ } struct Durations { @@ -55,19 +53,20 @@ class Arithmetic : public PhysicsModel { // Using C loops result2.allocate(); - BoutReal *rd = &result2(0, 0, 0); - BoutReal *ad = &a(0, 0, 0); - BoutReal *bd = &b(0, 0, 0); - BoutReal *cd = &c(0, 0, 0); - TIMEIT(elapsed2, - for (int i = 0, iend = (mesh->LocalNx * mesh->LocalNy * mesh->LocalNz) - 1; - i != iend; i++) { - *rd = 2. * (*ad) + (*bd) * (*cd); - rd++; - ad++; - bd++; - cd++; - }); + BoutReal* rd = &result2(0, 0, 0); + BoutReal* ad = &a(0, 0, 0); + BoutReal* bd = &b(0, 0, 0); + BoutReal* cd = &c(0, 0, 0); + TIMEIT( + elapsed2, + for (int i = 0, iend = (mesh->LocalNx * mesh->LocalNy * mesh->LocalNz) - 1; + i != iend; i++) { + *rd = 2. * (*ad) + (*bd) * (*cd); + rd++; + ad++; + bd++; + cd++; + }); // Template expressions TIMEIT(elapsed3, result3 = eval3D(add(mul(2, a), mul(b, c)));); @@ -81,9 +80,9 @@ class Arithmetic : public PhysicsModel { output << "TIMING\n======\n"; //#define PRINT(str,elapsed) output << str << elapsed.min.count()<< //elapsed.avg.count()<< elapsed.max.count() << endl; -#define PRINT(str, elapsed) \ - output.write("{:s} {:8.3g} {:8.3g} {:8.3g}\n", str, elapsed.min.count(), elapsed.avg.count(), \ - elapsed.max.count()) +#define PRINT(str, elapsed) \ + output.write("{:s} {:8.3g} {:8.3g} {:8.3g}\n", str, elapsed.min.count(), \ + elapsed.avg.count(), elapsed.max.count()) PRINT("Fields: ", elapsed1); PRINT("C loop: ", elapsed2); PRINT("Templates: ", elapsed3); diff --git a/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx b/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx index 6743f46b0b..83167a5b42 100644 --- a/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx +++ b/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx @@ -57,21 +57,21 @@ class Arithmetic : public PhysicsModel { // Using C loops result2.allocate(); - BoutReal *rd = &result2(0, 0, 0); - BoutReal *ad = &a(0, 0, 0); - BoutReal *bd = &b(0, 0, 0); - BoutReal *cd = &c(0, 0, 0); - TIMEIT("C loop", - for (int i = 0, iend = (mesh->LocalNx * mesh->LocalNy) -1; - i != iend; i++) { - for (int j = 0, jend = mesh->LocalNz - 1; j != jend; j++){ - *rd = 2. * (*ad) + (*bd) * (*cd); - rd++; - ad++; - bd++; - } - cd++; - }); + BoutReal* rd = &result2(0, 0, 0); + BoutReal* ad = &a(0, 0, 0); + BoutReal* bd = &b(0, 0, 0); + BoutReal* cd = &c(0, 0, 0); + TIMEIT( + "C loop", + for (int i = 0, iend = (mesh->LocalNx * mesh->LocalNy) - 1; i != iend; i++) { + for (int j = 0, jend = mesh->LocalNz - 1; j != jend; j++) { + *rd = 2. * (*ad) + (*bd) * (*cd); + rd++; + ad++; + bd++; + } + cd++; + }); // Template expressions result3.allocate(); @@ -84,20 +84,22 @@ class Arithmetic : public PhysicsModel { output.enable(); constexpr int width = 15; - output< +#include #include #include @@ -12,8 +12,8 @@ #include #include -#include -#include +#include +#include #include "bout/openmpwrap.hxx" #include "bout/region.hxx" @@ -23,18 +23,18 @@ using Duration = std::chrono::duration; using namespace std::chrono; using bout::globals::mesh; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); std::vector names; std::vector times; @@ -74,8 +74,7 @@ int main(int argc, char **argv) { ITERATOR_TEST_BLOCK("Bracket [2D,3D] SIMPLE", result = bracket(a, c, BRACKET_SIMPLE);); - ITERATOR_TEST_BLOCK("Bracket [2D,3D] DEFAULT", - result = bracket(a, c, BRACKET_STD);); + ITERATOR_TEST_BLOCK("Bracket [2D,3D] DEFAULT", result = bracket(a, c, BRACKET_STD);); } if (do3D3D) { @@ -88,8 +87,7 @@ int main(int argc, char **argv) { ITERATOR_TEST_BLOCK("Bracket [3D,3D] SIMPLE", result = bracket(a, b, BRACKET_SIMPLE);); - ITERATOR_TEST_BLOCK("Bracket [3D,3D] DEFAULT", - result = bracket(a, b, BRACKET_STD);); + ITERATOR_TEST_BLOCK("Bracket [3D,3D] DEFAULT", result = bracket(a, b, BRACKET_STD);); } // Uncomment below for a "correctness" check diff --git a/examples/performance/communications/communications.cxx b/examples/performance/communications/communications.cxx index 96e170b8cb..1360f45e77 100644 --- a/examples/performance/communications/communications.cxx +++ b/examples/performance/communications/communications.cxx @@ -1,6 +1,6 @@ -#include #include -#include +#include +#include int main(int argc, char** argv) { diff --git a/examples/performance/ddx/ddx.cxx b/examples/performance/ddx/ddx.cxx index a610cbc31b..3e4a7803f6 100644 --- a/examples/performance/ddx/ddx.cxx +++ b/examples/performance/ddx/ddx.cxx @@ -3,43 +3,41 @@ * */ -#include +#include #include #include +#include #include #include #include -#include +#include "bout/derivs.hxx" #include "bout/openmpwrap.hxx" #include "bout/region.hxx" -#include "derivs.hxx" using SteadyClock = std::chrono::time_point; using Duration = std::chrono::duration; using namespace std::chrono; using bout::globals::mesh; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } -BoutReal test_ddy(stencil &s) { - return (s.p - s.m); -} +BoutReal test_ddy(stencil& s) { return (s.p - s.m); } -using deriv_func = BoutReal (*)(stencil &); +using deriv_func = BoutReal (*)(stencil&); deriv_func func_ptr = &test_ddy; -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); std::vector names; std::vector times; @@ -62,13 +60,10 @@ int main(int argc, char **argv) { Field3D result; result.allocate(); - const int len = mesh->LocalNx*mesh->LocalNy*mesh->LocalNz; + const int len = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz; // Nested loops over block data - ITERATOR_TEST_BLOCK( - "DDX Default", - result = DDX(a); - ); + ITERATOR_TEST_BLOCK("DDX Default", result = DDX(a);); ITERATOR_TEST_BLOCK("DDX C2", result = DDX(a, CELL_DEFAULT, "DIFF_C2");); @@ -81,58 +76,69 @@ int main(int argc, char **argv) { ITERATOR_TEST_BLOCK("DDX W3", result = DDX(a, CELL_DEFAULT, "DIFF_W3");); if (profileMode) { - int nthreads = 0; + int nthreads = 0; #if BOUT_USE_OPENMP - nthreads = omp_get_max_threads(); + nthreads = omp_get_max_threads(); #endif - int width = 12; - if (includeHeader) { - time_output << "\n------------------------------------------------\n"; - time_output << "Case legend"; - time_output << "\n------------------------------------------------\n"; - - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; - } - time_output << "\n"; - time_output << std::setw(width) << "Nprocs" << "\t"; - time_output << std::setw(width) << "Nthreads" << "\t"; - time_output << std::setw(width) << "Num_loops" << "\t"; - time_output << std::setw(width) << "Local grid" << "\t"; - time_output << std::setw(width) << "Nx (global)" << "\t"; - time_output << std::setw(width) << "Ny (global)" << "\t"; - time_output << std::setw(width) << "Nz (global)" << "\t"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << "\t"; - } - time_output << "\n"; - } - - time_output << std::setw(width) << BoutComm::size() << "\t"; - time_output << std::setw(width) << nthreads << "\t"; - time_output << std::setw(width) << NUM_LOOPS << "\t"; - time_output << std::setw(width) << len << "\t"; - time_output << std::setw(width) << mesh->GlobalNx << "\t"; - time_output << std::setw(width) << mesh->GlobalNy << "\t"; - time_output << std::setw(width) << mesh->GlobalNz << "\t"; - for (const auto &time : times) { - time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; - } - time_output << "\n"; - } else { - std::vector sizes(names.size()); - std::transform(names.begin(), names.end(), sizes.begin(), - [](const std::string &name) -> int { return static_cast(name.size()); }); - int width = *std::max_element(sizes.begin(), sizes.end()); - width += 5; - time_output << std::setw(width) << "Case name" << "\t" << "Time per iteration (s)" << "\n"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS - << "\n"; - } - }; - - BoutFinalise(); - return 0; + int width = 12; + if (includeHeader) { + time_output << "\n------------------------------------------------\n"; + time_output << "Case legend"; + time_output << "\n------------------------------------------------\n"; + + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; + } + time_output << "\n"; + time_output << std::setw(width) << "Nprocs" + << "\t"; + time_output << std::setw(width) << "Nthreads" + << "\t"; + time_output << std::setw(width) << "Num_loops" + << "\t"; + time_output << std::setw(width) << "Local grid" + << "\t"; + time_output << std::setw(width) << "Nx (global)" + << "\t"; + time_output << std::setw(width) << "Ny (global)" + << "\t"; + time_output << std::setw(width) << "Nz (global)" + << "\t"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << "\t"; + } + time_output << "\n"; + } + + time_output << std::setw(width) << BoutComm::size() << "\t"; + time_output << std::setw(width) << nthreads << "\t"; + time_output << std::setw(width) << NUM_LOOPS << "\t"; + time_output << std::setw(width) << len << "\t"; + time_output << std::setw(width) << mesh->GlobalNx << "\t"; + time_output << std::setw(width) << mesh->GlobalNy << "\t"; + time_output << std::setw(width) << mesh->GlobalNz << "\t"; + for (const auto& time : times) { + time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; + } + time_output << "\n"; + } else { + std::vector sizes(names.size()); + std::transform( + names.begin(), names.end(), sizes.begin(), + [](const std::string& name) -> int { return static_cast(name.size()); }); + int width = *std::max_element(sizes.begin(), sizes.end()); + width += 5; + time_output << std::setw(width) << "Case name" + << "\t" + << "Time per iteration (s)" + << "\n"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS + << "\n"; + } + }; + + BoutFinalise(); + return 0; } diff --git a/examples/performance/ddy/ddy.cxx b/examples/performance/ddy/ddy.cxx index 02e1368ffc..a11e1d52bc 100644 --- a/examples/performance/ddy/ddy.cxx +++ b/examples/performance/ddy/ddy.cxx @@ -3,43 +3,41 @@ * */ -#include +#include #include #include +#include #include #include #include -#include +#include "bout/derivs.hxx" #include "bout/openmpwrap.hxx" #include "bout/region.hxx" -#include "derivs.hxx" using SteadyClock = std::chrono::time_point; using Duration = std::chrono::duration; using namespace std::chrono; using bout::globals::mesh; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } -BoutReal test_ddy(stencil &s) { - return (s.p - s.m); -} +BoutReal test_ddy(stencil& s) { return (s.p - s.m); } -using deriv_func = BoutReal (*)(stencil &); +using deriv_func = BoutReal (*)(stencil&); deriv_func func_ptr = &test_ddy; -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); std::vector names; std::vector times; @@ -62,13 +60,10 @@ int main(int argc, char **argv) { Field3D result; result.allocate(); - const int len = mesh->LocalNx*mesh->LocalNy*mesh->LocalNz; + const int len = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz; // Nested loops over block data - ITERATOR_TEST_BLOCK( - "DDY Default", - result = DDY(a); - ); + ITERATOR_TEST_BLOCK("DDY Default", result = DDY(a);); ITERATOR_TEST_BLOCK("DDY C2", result = DDY(a, CELL_DEFAULT, "DIFF_C2");); @@ -81,58 +76,69 @@ int main(int argc, char **argv) { ITERATOR_TEST_BLOCK("DDY W3", result = DDY(a, CELL_DEFAULT, "DIFF_W3");); if (profileMode) { - int nthreads = 0; + int nthreads = 0; #if BOUT_USE_OPENMP - nthreads = omp_get_max_threads(); + nthreads = omp_get_max_threads(); #endif - int width = 12; - if (includeHeader) { - time_output << "\n------------------------------------------------\n"; - time_output << "Case legend"; - time_output << "\n------------------------------------------------\n"; - - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; - } - time_output << "\n"; - time_output << std::setw(width) << "Nprocs" << "\t"; - time_output << std::setw(width) << "Nthreads" << "\t"; - time_output << std::setw(width) << "Num_loops" << "\t"; - time_output << std::setw(width) << "Local grid" << "\t"; - time_output << std::setw(width) << "Nx (global)" << "\t"; - time_output << std::setw(width) << "Ny (global)" << "\t"; - time_output << std::setw(width) << "Nz (global)" << "\t"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << "\t"; - } - time_output << "\n"; - } - - time_output << std::setw(width) << BoutComm::size() << "\t"; - time_output << std::setw(width) << nthreads << "\t"; - time_output << std::setw(width) << NUM_LOOPS << "\t"; - time_output << std::setw(width) << len << "\t"; - time_output << std::setw(width) << mesh->GlobalNx << "\t"; - time_output << std::setw(width) << mesh->GlobalNy << "\t"; - time_output << std::setw(width) << mesh->GlobalNz << "\t"; - for (const auto &time : times) { - time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; - } - time_output << "\n"; - } else { - std::vector sizes(names.size()); - std::transform(names.begin(), names.end(), sizes.begin(), - [](const std::string &name) -> int { return static_cast(name.size()); }); - int width = *std::max_element(sizes.begin(), sizes.end()); - width += 5; - time_output << std::setw(width) << "Case name" << "\t" << "Time per iteration (s)" << "\n"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS - << "\n"; - } - }; - - BoutFinalise(); - return 0; + int width = 12; + if (includeHeader) { + time_output << "\n------------------------------------------------\n"; + time_output << "Case legend"; + time_output << "\n------------------------------------------------\n"; + + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; + } + time_output << "\n"; + time_output << std::setw(width) << "Nprocs" + << "\t"; + time_output << std::setw(width) << "Nthreads" + << "\t"; + time_output << std::setw(width) << "Num_loops" + << "\t"; + time_output << std::setw(width) << "Local grid" + << "\t"; + time_output << std::setw(width) << "Nx (global)" + << "\t"; + time_output << std::setw(width) << "Ny (global)" + << "\t"; + time_output << std::setw(width) << "Nz (global)" + << "\t"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << "\t"; + } + time_output << "\n"; + } + + time_output << std::setw(width) << BoutComm::size() << "\t"; + time_output << std::setw(width) << nthreads << "\t"; + time_output << std::setw(width) << NUM_LOOPS << "\t"; + time_output << std::setw(width) << len << "\t"; + time_output << std::setw(width) << mesh->GlobalNx << "\t"; + time_output << std::setw(width) << mesh->GlobalNy << "\t"; + time_output << std::setw(width) << mesh->GlobalNz << "\t"; + for (const auto& time : times) { + time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; + } + time_output << "\n"; + } else { + std::vector sizes(names.size()); + std::transform( + names.begin(), names.end(), sizes.begin(), + [](const std::string& name) -> int { return static_cast(name.size()); }); + int width = *std::max_element(sizes.begin(), sizes.end()); + width += 5; + time_output << std::setw(width) << "Case name" + << "\t" + << "Time per iteration (s)" + << "\n"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS + << "\n"; + } + }; + + BoutFinalise(); + return 0; } diff --git a/examples/performance/ddz/ddz.cxx b/examples/performance/ddz/ddz.cxx index 4feb46d137..8a7262b1cb 100644 --- a/examples/performance/ddz/ddz.cxx +++ b/examples/performance/ddz/ddz.cxx @@ -3,43 +3,41 @@ * */ -#include +#include #include #include +#include #include #include #include -#include +#include "bout/derivs.hxx" #include "bout/openmpwrap.hxx" #include "bout/region.hxx" -#include "derivs.hxx" using SteadyClock = std::chrono::time_point; using Duration = std::chrono::duration; using namespace std::chrono; using bout::globals::mesh; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } -BoutReal test_ddy(stencil &s) { - return (s.p - s.m); -} +BoutReal test_ddy(stencil& s) { return (s.p - s.m); } -using deriv_func = BoutReal (*)(stencil &); +using deriv_func = BoutReal (*)(stencil&); deriv_func func_ptr = &test_ddy; -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); std::vector names; std::vector times; @@ -62,13 +60,10 @@ int main(int argc, char **argv) { Field3D result; result.allocate(); - const int len = mesh->LocalNx*mesh->LocalNy*mesh->LocalNz; + const int len = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz; // Nested loops over block data - ITERATOR_TEST_BLOCK( - "DDZ Default", - result = DDZ(a); - ); + ITERATOR_TEST_BLOCK("DDZ Default", result = DDZ(a);); ITERATOR_TEST_BLOCK("DDZ C2", result = DDZ(a, CELL_DEFAULT, "DIFF_C2");); @@ -83,58 +78,69 @@ int main(int argc, char **argv) { ITERATOR_TEST_BLOCK("DDZ FFT", result = DDZ(a, CELL_DEFAULT, "DIFF_FFT");); if (profileMode) { - int nthreads = 0; + int nthreads = 0; #if BOUT_USE_OPENMP - nthreads = omp_get_max_threads(); + nthreads = omp_get_max_threads(); #endif - int width = 12; - if (includeHeader) { - time_output << "\n------------------------------------------------\n"; - time_output << "Case legend"; - time_output << "\n------------------------------------------------\n"; - - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; - } - time_output << "\n"; - time_output << std::setw(width) << "Nprocs" << "\t"; - time_output << std::setw(width) << "Nthreads" << "\t"; - time_output << std::setw(width) << "Num_loops" << "\t"; - time_output << std::setw(width) << "Local grid" << "\t"; - time_output << std::setw(width) << "Nx (global)" << "\t"; - time_output << std::setw(width) << "Ny (global)" << "\t"; - time_output << std::setw(width) << "Nz (global)" << "\t"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << "\t"; - } - time_output << "\n"; - } - - time_output << std::setw(width) << BoutComm::size() << "\t"; - time_output << std::setw(width) << nthreads << "\t"; - time_output << std::setw(width) << NUM_LOOPS << "\t"; - time_output << std::setw(width) << len << "\t"; - time_output << std::setw(width) << mesh->GlobalNx << "\t"; - time_output << std::setw(width) << mesh->GlobalNy << "\t"; - time_output << std::setw(width) << mesh->GlobalNz << "\t"; - for (const auto &time : times) { - time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; - } - time_output << "\n"; - } else { - std::vector sizes(names.size()); - std::transform(names.begin(), names.end(), sizes.begin(), - [](const std::string &name) -> int { return static_cast(name.size()); }); - int width = *std::max_element(sizes.begin(), sizes.end()); - width += 5; - time_output << std::setw(width) << "Case name" << "\t" << "Time per iteration (s)" << "\n"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS - << "\n"; - } - }; - - BoutFinalise(); - return 0; + int width = 12; + if (includeHeader) { + time_output << "\n------------------------------------------------\n"; + time_output << "Case legend"; + time_output << "\n------------------------------------------------\n"; + + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; + } + time_output << "\n"; + time_output << std::setw(width) << "Nprocs" + << "\t"; + time_output << std::setw(width) << "Nthreads" + << "\t"; + time_output << std::setw(width) << "Num_loops" + << "\t"; + time_output << std::setw(width) << "Local grid" + << "\t"; + time_output << std::setw(width) << "Nx (global)" + << "\t"; + time_output << std::setw(width) << "Ny (global)" + << "\t"; + time_output << std::setw(width) << "Nz (global)" + << "\t"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << "\t"; + } + time_output << "\n"; + } + + time_output << std::setw(width) << BoutComm::size() << "\t"; + time_output << std::setw(width) << nthreads << "\t"; + time_output << std::setw(width) << NUM_LOOPS << "\t"; + time_output << std::setw(width) << len << "\t"; + time_output << std::setw(width) << mesh->GlobalNx << "\t"; + time_output << std::setw(width) << mesh->GlobalNy << "\t"; + time_output << std::setw(width) << mesh->GlobalNz << "\t"; + for (const auto& time : times) { + time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; + } + time_output << "\n"; + } else { + std::vector sizes(names.size()); + std::transform( + names.begin(), names.end(), sizes.begin(), + [](const std::string& name) -> int { return static_cast(name.size()); }); + int width = *std::max_element(sizes.begin(), sizes.end()); + width += 5; + time_output << std::setw(width) << "Case name" + << "\t" + << "Time per iteration (s)" + << "\n"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS + << "\n"; + } + }; + + BoutFinalise(); + return 0; } diff --git a/examples/performance/iterator-offsets/iterator-offsets.cxx b/examples/performance/iterator-offsets/iterator-offsets.cxx index 3ac7efa593..08149f855e 100644 --- a/examples/performance/iterator-offsets/iterator-offsets.cxx +++ b/examples/performance/iterator-offsets/iterator-offsets.cxx @@ -3,14 +3,14 @@ * */ -#include +#include #include #include +#include #include #include #include -#include #include "bout/openmpwrap.hxx" #include "bout/region.hxx" @@ -20,25 +20,23 @@ using Duration = std::chrono::duration; using namespace std::chrono; using bout::globals::mesh; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } -BoutReal test_ddy(stencil &s) { - return (s.p - s.m); -} +BoutReal test_ddy(stencil& s) { return (s.p - s.m); } -using deriv_func = BoutReal (*)(stencil &); +using deriv_func = BoutReal (*)(stencil&); deriv_func func_ptr = &test_ddy; -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); std::vector names; std::vector times; @@ -61,131 +59,132 @@ int main(int argc, char **argv) { Field3D result; result.allocate(); - const int len = mesh->LocalNx*mesh->LocalNy*mesh->LocalNz; + const int len = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz; // Nested loops over block data ITERATOR_TEST_BLOCK( - "Nested loop", - for(int i=0;iLocalNx;++i) { - for(int j=mesh->ystart;jyend;++j) { - for(int k=0;kLocalNz;++k) { - result(i,j,k) = (a(i,j+1,k) - a(i,j-1,k)); + "Nested loop", for (int i = 0; i < mesh->LocalNx; ++i) { + for (int j = mesh->ystart; j < mesh->yend; ++j) { + for (int k = 0; k < mesh->LocalNz; ++k) { + result(i, j, k) = (a(i, j + 1, k) - a(i, j - 1, k)); + } } - } - } - ); + }); #if BOUT_USE_OPENMP ITERATOR_TEST_BLOCK( "Nested loop (omp)", BOUT_OMP(parallel for) for(int i=0;iLocalNx;++i) { - for(int j=mesh->ystart;jyend;++j) { - for(int k=0;kLocalNz;++k) { - result(i,j,k) = (a(i,j+1,k) - a(i,j-1,k)); - } + for (int j = mesh->ystart; j < mesh->yend; ++j) { + for (int k = 0; k < mesh->LocalNz; ++k) { + result(i, j, k) = (a(i, j + 1, k) - a(i, j - 1, k)); } } + } ); #endif { - auto deriv = DerivativeStore::getInstance().getStandardDerivative("C2",DIRECTION::Y, STAGGER::None); - ITERATOR_TEST_BLOCK( - "DerivativeStore without fetching", - deriv(a, result, "RGN_NOY"); - ); + auto deriv = DerivativeStore::getInstance().getStandardDerivative( + "C2", DIRECTION::Y, STAGGER::None); + ITERATOR_TEST_BLOCK("DerivativeStore without fetching", deriv(a, result, "RGN_NOY");); }; - - ITERATOR_TEST_BLOCK( - "DerivativeStore with fetch", - auto deriv = DerivativeStore::getInstance().getStandardDerivative("C2",DIRECTION::Y, STAGGER::None); - deriv(a, result, "RGN_NOY"); - ); + + ITERATOR_TEST_BLOCK("DerivativeStore with fetch", + auto deriv = + DerivativeStore::getInstance().getStandardDerivative( + "C2", DIRECTION::Y, STAGGER::None); + deriv(a, result, "RGN_NOY");); ITERATOR_TEST_BLOCK( - "Region with stencil", - BOUT_OMP(parallel) - { - stencil s; - BOUT_FOR_INNER(i, mesh->getRegion3D("RGN_NOY")) { - s.m = a[i.ym()]; - s.c = a[i]; - s.p = a[i.yp()]; - - result[i] = (s.p - s.m); - } - } - ); - + "Region with stencil", BOUT_OMP(parallel) { + stencil s; + BOUT_FOR_INNER(i, mesh->getRegion3D("RGN_NOY")) { + s.m = a[i.ym()]; + s.c = a[i]; + s.p = a[i.yp()]; + + result[i] = (s.p - s.m); + } + }); + ITERATOR_TEST_BLOCK( - "Region with stencil and function pointer", - BOUT_OMP(parallel) - { - stencil s; - BOUT_FOR_INNER(i, mesh->getRegion3D("RGN_NOY")) { - s.m = a[i.ym()]; - s.c = a[i]; - s.p = a[i.yp()]; - - result[i] = func_ptr(s); - } - } - ); - - if (profileMode) { - int nthreads = 0; + "Region with stencil and function pointer", BOUT_OMP(parallel) { + stencil s; + BOUT_FOR_INNER(i, mesh->getRegion3D("RGN_NOY")) { + s.m = a[i.ym()]; + s.c = a[i]; + s.p = a[i.yp()]; + + result[i] = func_ptr(s); + } + }); + + if (profileMode) { + int nthreads = 0; #if BOUT_USE_OPENMP - nthreads = omp_get_max_threads(); + nthreads = omp_get_max_threads(); #endif - int width = 12; - if (includeHeader) { - time_output << "\n------------------------------------------------\n"; - time_output << "Case legend"; - time_output << "\n------------------------------------------------\n"; - - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; - } - time_output << "\n"; - time_output << std::setw(width) << "Nprocs" << "\t"; - time_output << std::setw(width) << "Nthreads" << "\t"; - time_output << std::setw(width) << "Num_loops" << "\t"; - time_output << std::setw(width) << "Local grid" << "\t"; - time_output << std::setw(width) << "Nx (global)" << "\t"; - time_output << std::setw(width) << "Ny (global)" << "\t"; - time_output << std::setw(width) << "Nz (global)" << "\t"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << "Case " << i << "\t"; - } - time_output << "\n"; - } - - time_output << std::setw(width) << BoutComm::size() << "\t"; - time_output << std::setw(width) << nthreads << "\t"; - time_output << std::setw(width) << NUM_LOOPS << "\t"; - time_output << std::setw(width) << len << "\t"; - time_output << std::setw(width) << mesh->GlobalNx << "\t"; - time_output << std::setw(width) << mesh->GlobalNy << "\t"; - time_output << std::setw(width) << mesh->GlobalNz << "\t"; - for (const auto &time : times) { - time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; - } - time_output << "\n"; - } else { - std::vector sizes(names.size()); - std::transform(names.begin(), names.end(), sizes.begin(), - [](const std::string &name) -> int { return static_cast(name.size()); }); - int width = *std::max_element(sizes.begin(), sizes.end()); - width += 5; - time_output << std::setw(width) << "Case name" << "\t" << "Time per iteration (s)" << "\n"; - for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS - << "\n"; - } - }; - - BoutFinalise(); - return 0; + int width = 12; + if (includeHeader) { + time_output << "\n------------------------------------------------\n"; + time_output << "Case legend"; + time_output << "\n------------------------------------------------\n"; + + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; + } + time_output << "\n"; + time_output << std::setw(width) << "Nprocs" + << "\t"; + time_output << std::setw(width) << "Nthreads" + << "\t"; + time_output << std::setw(width) << "Num_loops" + << "\t"; + time_output << std::setw(width) << "Local grid" + << "\t"; + time_output << std::setw(width) << "Nx (global)" + << "\t"; + time_output << std::setw(width) << "Ny (global)" + << "\t"; + time_output << std::setw(width) << "Nz (global)" + << "\t"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << "Case " << i << "\t"; + } + time_output << "\n"; + } + + time_output << std::setw(width) << BoutComm::size() << "\t"; + time_output << std::setw(width) << nthreads << "\t"; + time_output << std::setw(width) << NUM_LOOPS << "\t"; + time_output << std::setw(width) << len << "\t"; + time_output << std::setw(width) << mesh->GlobalNx << "\t"; + time_output << std::setw(width) << mesh->GlobalNy << "\t"; + time_output << std::setw(width) << mesh->GlobalNz << "\t"; + for (const auto& time : times) { + time_output << std::setw(width) << time.count() / NUM_LOOPS << "\t"; + } + time_output << "\n"; + } else { + std::vector sizes(names.size()); + std::transform( + names.begin(), names.end(), sizes.begin(), + [](const std::string& name) -> int { return static_cast(name.size()); }); + int width = *std::max_element(sizes.begin(), sizes.end()); + width += 5; + time_output << std::setw(width) << "Case name" + << "\t" + << "Time per iteration (s)" + << "\n"; + for (std::size_t i = 0; i < names.size(); i++) { + time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS + << "\n"; + } + }; + + BoutFinalise(); + return 0; } diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx index 4ed9cc5031..5e8df511d7 100644 --- a/examples/performance/iterator/iterator.cxx +++ b/examples/performance/iterator/iterator.cxx @@ -3,14 +3,14 @@ * */ -#include +#include #include +#include #include #include #include #include -#include #include "bout/openmpwrap.hxx" #include "bout/region.hxx" @@ -20,21 +20,22 @@ using Duration = std::chrono::duration; using namespace std::chrono; using bout::globals::mesh; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - {__VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0 ; repetitionIndex < NUM_LOOPS ; repetitionIndex++){ \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now()-start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); std::vector names; std::vector times; - + //Get options root auto globalOptions = Options::root(); auto modelOpts = globalOptions["performanceIterator"]; @@ -46,7 +47,7 @@ int main(int argc, char **argv) { ConditionalOutput time_output(Output::getInstance()); time_output.enable(true); - + Field3D a = 1.0; Field3D b = 2.0; @@ -54,98 +55,92 @@ int main(int argc, char **argv) { result.allocate(); //Some small setup for C loop case - BoutReal *ad = &a(0,0,0); - BoutReal *bd = &b(0,0,0); - BoutReal *rd = &result(0,0,0); - - const int len = mesh->LocalNx*mesh->LocalNy*mesh->LocalNz; + BoutReal* ad = &a(0, 0, 0); + BoutReal* bd = &b(0, 0, 0); + BoutReal* rd = &result(0, 0, 0); + + const int len = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz; //Raw C loop - ITERATOR_TEST_BLOCK("C loop", - for(int j=0;jLocalNx;++i) { - for(int j=0;jLocalNy;++j) { - for(int k=0;kLocalNz;++k) { - result(i,j,k) = a(i,j,k) + b(i,j,k); - } - } - } - ); + ITERATOR_TEST_BLOCK( + "Nested loop", for (int i = 0; i < mesh->LocalNx; ++i) { + for (int j = 0; j < mesh->LocalNy; ++j) { + for (int k = 0; k < mesh->LocalNz; ++k) { + result(i, j, k) = a(i, j, k) + b(i, j, k); + } + } + }); #if BOUT_USE_OPENMP ITERATOR_TEST_BLOCK("Nested loop (omp)", BOUT_OMP(parallel for) for(int i=0;iLocalNx;++i) { - for(int j=0;jLocalNy;++j) { - for(int k=0;kLocalNz;++k) { - result(i,j,k) = a(i,j,k) + b(i,j,k); - } - } + for (int j = 0; j < mesh->LocalNy; ++j) { + for (int k = 0; k < mesh->LocalNz; ++k) { + result(i, j, k) = a(i, j, k) + b(i, j, k); + } + } } ); #endif - + //Raw C loop - ITERATOR_TEST_BLOCK("C loop repeat", - for(int j=0;jgetRegion("RGN_ALL")) { - result[i] = a[i] + b[i]; - } - ); + "Region (serial)", + BOUT_FOR_SERIAL(i, mesh->getRegion("RGN_ALL")) { result[i] = a[i] + b[i]; }); #if BOUT_USE_OPENMP ITERATOR_TEST_BLOCK( - "Region (omp)", - BOUT_FOR(i, mesh->getRegion("RGN_ALL")) { - result[i] = a[i] + b[i]; - } - ); + "Region (omp)", + BOUT_FOR (i, mesh->getRegion("RGN_ALL")) { result[i] = a[i] + b[i]; }); #endif - - if(profileMode){ - int nthreads=0; + + if (profileMode) { + int nthreads = 0; #if BOUT_USE_OPENMP nthreads = omp_get_max_threads(); #endif constexpr int width = 12; - if(includeHeader){ + if (includeHeader) { time_output << "\n------------------------------------------------\n"; time_output << "Case legend"; - time_output <<"\n------------------------------------------------\n"; + time_output << "\n------------------------------------------------\n"; for (std::size_t i = 0; i < names.size(); i++) { time_output << std::setw(width) << "Case " << i << ".\t" << names[i] << "\n"; } time_output << "\n"; - time_output << std::setw(width) << "Nprocs" << "\t"; - time_output << std::setw(width) << "Nthreads" << "\t"; - time_output << std::setw(width) << "Num_loops" << "\t"; - time_output << std::setw(width) << "Local grid" << "\t"; - time_output << std::setw(width) << "Nx (global)" << "\t"; - time_output << std::setw(width) << "Ny (global)" << "\t"; - time_output << std::setw(width) << "Nz (global)" << "\t"; + time_output << std::setw(width) << "Nprocs" + << "\t"; + time_output << std::setw(width) << "Nthreads" + << "\t"; + time_output << std::setw(width) << "Num_loops" + << "\t"; + time_output << std::setw(width) << "Local grid" + << "\t"; + time_output << std::setw(width) << "Nx (global)" + << "\t"; + time_output << std::setw(width) << "Ny (global)" + << "\t"; + time_output << std::setw(width) << "Nz (global)" + << "\t"; for (std::size_t i = 0; i < names.size(); i++) { time_output << std::setw(width) << "Case " << i << "\t"; } @@ -160,16 +155,22 @@ int main(int argc, char **argv) { time_output << std::setw(width) << mesh->GlobalNy << "\t"; time_output << std::setw(width) << mesh->GlobalNz << "\t"; for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << times[i].count()/NUM_LOOPS << "\t"; + time_output << std::setw(width) << times[i].count() / NUM_LOOPS << "\t"; } time_output << "\n"; - }else{ + } else { std::size_t width = 0; - for (const auto i: names){ width = i.size() > width ? i.size() : width;}; + for (const auto i : names) { + width = i.size() > width ? i.size() : width; + }; width = width + 5; - time_output << std::setw(width) << "Case name" << "\t" << "Time per iteration (s)" << "\n"; + time_output << std::setw(width) << "Case name" + << "\t" + << "Time per iteration (s)" + << "\n"; for (std::size_t i = 0; i < names.size(); i++) { - time_output << std::setw(width) << names[i] << "\t" << times[i].count()/NUM_LOOPS << "\n"; + time_output << std::setw(width) << names[i] << "\t" << times[i].count() / NUM_LOOPS + << "\n"; } }; diff --git a/examples/performance/laplace/laplace.cxx b/examples/performance/laplace/laplace.cxx index 4d2cfc957a..1ebbfb7583 100644 --- a/examples/performance/laplace/laplace.cxx +++ b/examples/performance/laplace/laplace.cxx @@ -3,9 +3,9 @@ * */ -#include -#include -#include +#include +#include +#include #include #include @@ -20,15 +20,15 @@ using SteadyClock = std::chrono::time_point; using Duration = std::chrono::duration; using namespace std::chrono; -#define TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } int main(int argc, char** argv) { diff --git a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx index 9335d428d1..aa8fa7fe52 100644 --- a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx +++ b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx @@ -4,7 +4,7 @@ * */ -#include +#include #include #include @@ -22,15 +22,15 @@ using Duration = std::chrono::duration; using namespace std::chrono; using namespace bout::globals; -#define ITERATOR_TEST_BLOCK(NAME, ...) \ - { \ - __VA_ARGS__ \ - names.push_back(NAME); \ - SteadyClock start = steady_clock::now(); \ - for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ - __VA_ARGS__; \ - } \ - times.push_back(steady_clock::now() - start); \ +#define ITERATOR_TEST_BLOCK(NAME, ...) \ + { \ + __VA_ARGS__ \ + names.push_back(NAME); \ + SteadyClock start = steady_clock::now(); \ + for (int repetitionIndex = 0; repetitionIndex < NUM_LOOPS; repetitionIndex++) { \ + __VA_ARGS__; \ + } \ + times.push_back(steady_clock::now() - start); \ } int main(int argc, char** argv) { @@ -61,7 +61,7 @@ int main(int argc, char** argv) { mesh->LocalNy, mesh->LocalNz, blocksize); ITERATOR_TEST_BLOCK( - name, BOUT_FOR(i, region) { result[i] = a[i] + b[i]; }); + name, BOUT_FOR (i, region) { result[i] = a[i] + b[i]; }); } // Report diff --git a/examples/preconditioning/wave/test_precon.cxx b/examples/preconditioning/wave/test_precon.cxx index c270514826..639bbed344 100644 --- a/examples/preconditioning/wave/test_precon.cxx +++ b/examples/preconditioning/wave/test_precon.cxx @@ -7,8 +7,8 @@ */ #include -#include -#include +#include +#include class Test_precon : public PhysicsModel { Field3D u, v; // Evolving variables diff --git a/examples/reconnect-2field/2field.cxx b/examples/reconnect-2field/2field.cxx index bc998915a9..ed800e18dd 100644 --- a/examples/reconnect-2field/2field.cxx +++ b/examples/reconnect-2field/2field.cxx @@ -5,11 +5,11 @@ #include -#include -#include -#include -#include #include +#include +#include +#include +#include class TwoField : public PhysicsModel { private: @@ -45,26 +45,26 @@ class TwoField : public PhysicsModel { // Method to use: BRACKET_ARAKAWA, BRACKET_STD or BRACKET_SIMPLE BRACKET_METHOD bm; // Bracket method for advection terms - bool nonlinear; bool include_jpar0; int jpar_bndry; - std::unique_ptr inv{nullptr}; // Parallel inversion class used in preconditioner + std::unique_ptr inv{ + nullptr}; // Parallel inversion class used in preconditioner // Coordinate system metric Coordinates *coord, *coord_ylow; // Inverts a Laplacian to get potential std::unique_ptr phiSolver{nullptr}; - + protected: int init(bool UNUSED(restarting)) override { // Load 2D profiles GRID_LOAD(Jpar0, Te0, Ni0); Ni0 *= 1e20; // To m^-3 - + // Coordinate system coord = mesh->getCoordinates(); coord = mesh->getCoordinates(CELL_YLOW); @@ -120,12 +120,12 @@ class TwoField : public PhysicsModel { if (Tenorm < 1) { Tenorm = 1000; } - + Nenorm = max(Ni0, true); if (Nenorm < 1) { Nenorm = 1.e19; } - + Bnorm = max(coord->Bxy, true); // Sound speed in m/s @@ -213,11 +213,11 @@ class TwoField : public PhysicsModel { // Create a solver for the Laplacian phiSolver = Laplacian::create(); - + return 0; } - const Field3D Grad_parP(const Field3D &f, CELL_LOC loc = CELL_DEFAULT) { + const Field3D Grad_parP(const Field3D& f, CELL_LOC loc = CELL_DEFAULT) { Field3D result; if (nonlinear) { result = ::Grad_parP((Apar + Apar_ext) * beta_hat, f); @@ -269,11 +269,10 @@ class TwoField : public PhysicsModel { ddt(U) = SQ(coord->Bxy) * Grad_parP(jpar / coord_ylow->Bxy, CELL_CENTRE); if (include_jpar0) { - ddt(U) -= SQ(coord->Bxy) * beta_hat * - interp_to( - bracket(Apar + Apar_ext, Jpar0 / coord_ylow->Bxy, BRACKET_ARAKAWA), - CELL_CENTRE - ); + ddt(U) -= + SQ(coord->Bxy) * beta_hat + * interp_to(bracket(Apar + Apar_ext, Jpar0 / coord_ylow->Bxy, BRACKET_ARAKAWA), + CELL_CENTRE); } ddt(U) -= bracket(Phi0_ext, U, bm); // ExB advection @@ -319,7 +318,7 @@ class TwoField : public PhysicsModel { for (int i = jpar_bndry; i >= 0; i--) { for (int j = 0; j < mesh->LocalNy; j++) { for (int k = 0; k < mesh->LocalNz; k++) { - Jp(i,j,k) = Jp(i + 1,j,k); + Jp(i, j, k) = Jp(i + 1, j, k); } } } @@ -328,15 +327,15 @@ class TwoField : public PhysicsModel { for (int i = mesh->LocalNx - jpar_bndry - 1; i < mesh->LocalNx; i++) { for (int j = 0; j < mesh->LocalNy; j++) { for (int k = 0; k < mesh->LocalNz; k++) { - Jp(i,j,k) = Jp(i - 1,j,k); + Jp(i, j, k) = Jp(i - 1, j, k); } } } } } - Field3D U1 = ddt(U) + gamma * SQ(coord->Bxy) - * Grad_par(Jp / coord_ylow->Bxy, CELL_CENTRE); + Field3D U1 = + ddt(U) + gamma * SQ(coord->Bxy) * Grad_par(Jp / coord_ylow->Bxy, CELL_CENTRE); inv->setCoefB(-SQ(gamma * coord->Bxy) / beta_hat); ddt(U) = inv->solve(U1); diff --git a/examples/shear-alfven-wave/2fluid.cxx b/examples/shear-alfven-wave/2fluid.cxx index afeae37dfe..a38da9a22a 100644 --- a/examples/shear-alfven-wave/2fluid.cxx +++ b/examples/shear-alfven-wave/2fluid.cxx @@ -5,9 +5,9 @@ #include -#include -#include -#include +#include +#include +#include class ShearAlfven : public PhysicsModel { private: @@ -44,12 +44,12 @@ class ShearAlfven : public PhysicsModel { FieldGroup comms; // Coordinate system - Coordinates *coord; + Coordinates* coord; /// Solver for inverting Laplacian std::unique_ptr phiSolver; std::unique_ptr aparSolver; - + protected: int init(bool UNUSED(restarting)) override { Field2D I; // Shear factor @@ -85,7 +85,7 @@ class ShearAlfven : public PhysicsModel { mesh->get(coord->Bxy, "Bxy"); mesh->get(coord->dx, "dpsi"); mesh->get(I, "sinty"); - + // Load normalisation values GRID_LOAD(Te_x); GRID_LOAD(Ti_x); @@ -111,9 +111,10 @@ class ShearAlfven : public PhysicsModel { /************* SHIFTED RADIAL COORDINATES ************/ // Check type of parallel transform - std::string ptstr = Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); - + std::string ptstr = + Options::root()["mesh"]["paralleltransform"]["type"].withDefault( + "identity"); + if (lowercase(ptstr) == "shifted") { ShearFactor = 0.0; // I disappears from metric b0xcv.z += I * b0xcv.x; @@ -134,8 +135,9 @@ class ShearAlfven : public PhysicsModel { BoutReal hthe0; if (mesh->get(hthe0, "hthe0") == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", - hthe0 / rho_s); + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } /************** SHIFTED GRIDS LOCATION ***************/ @@ -222,7 +224,7 @@ class ShearAlfven : public PhysicsModel { SAVE_ONCE(Ni0, Te0, Ti0); SAVE_ONCE(Te_x, Ti_x, Ni_x, rho_s, wci); - + // Create a solver for the Laplacian phiSolver = Laplacian::create(&options["phiSolver"]); @@ -239,10 +241,10 @@ class ShearAlfven : public PhysicsModel { if (ZeroElMass) { mesh->communicate(comms); - + Apar = -Ajpar; jpar = -Delp2(Apar); - + mesh->communicate(jpar); } else { diff --git a/examples/staggered_grid/test_staggered.cxx b/examples/staggered_grid/test_staggered.cxx index 5a0abb9ca1..f6e368f20a 100644 --- a/examples/staggered_grid/test_staggered.cxx +++ b/examples/staggered_grid/test_staggered.cxx @@ -3,8 +3,8 @@ */ #include -#include -#include +#include +#include class TestStaggered : public PhysicsModel { Field3D n, v; diff --git a/examples/subsampling/monitor.cxx b/examples/subsampling/monitor.cxx index b1e6a009d9..c06886c26a 100644 --- a/examples/subsampling/monitor.cxx +++ b/examples/subsampling/monitor.cxx @@ -1,7 +1,7 @@ /* */ #include -#include +#include #include diff --git a/examples/tokamak-2fluid/2fluid.cxx b/examples/tokamak-2fluid/2fluid.cxx index 4bcc18915f..9108edb5bd 100644 --- a/examples/tokamak-2fluid/2fluid.cxx +++ b/examples/tokamak-2fluid/2fluid.cxx @@ -6,90 +6,90 @@ #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include class TwoFluid : public PhysicsModel { private: // 2D initial profiles Field2D Ni0, Ti0, Te0, Vi0, phi0, Ve0, rho0, Ajpar0; Vector2D b0xcv; // for curvature terms - + // 3D evolving fields Field3D rho, Te, Ni, Ajpar, Vi, Ti; - + // Derived 3D variables Field3D phi, Apar, Ve, jpar; - + // Non-linear coefficients Field3D nu, mu_i, kapa_Te, kapa_Ti; - + // 3D total values Field3D Nit, Tit, Tet, Vit; - + // pressures Field3D pei, pe; Field2D pei0, pe0; - + // Metric coefficients Field2D Rxy, Bpxy, Btxy, hthe; - + // parameters BoutReal Te_x, Ti_x, Ni_x, Vi_x, bmag, rho_s, fmei, AA, ZZ; BoutReal lambda_ei, lambda_ii; BoutReal nu_hat, mui_hat, wci, nueix, nuiix; BoutReal beta_p; BoutReal nuIonNeutral; // Ion-neutral collision rate (normalised by wci) - + // settings bool estatic, ZeroElMass; // Switch for electrostatic operation (true = no Apar) BoutReal zeff, nu_perp; bool evolve_rho, evolve_te, evolve_ni, evolve_ajpar, evolve_vi, evolve_ti; BoutReal ShearFactor; - + bool curv_upwind; // Use upwinding methods for curvature terms - + bool laplace_extra_rho_term; // An extra first-order term in the vorticity inversion - bool vort_include_pi; // Include Pi in vorticity - + bool vort_include_pi; // Include Pi in vorticity + bool bout_jpar; // Use BOUT-06 method for Jpar bool OhmPe; // Include the Pe term in Ohm's law - + int bkgd; // Profile options for coefficients (same options as BOUT-06) int iTe_dc; // Profile evolution options - + // Poisson brackets: b0 x Grad(f) dot Grad(g) / B = [f, g] // Method to use: BRACKET_ARAKAWA, BRACKET_STD or BRACKET_SIMPLE BRACKET_METHOD bm; // Bracket method for advection terms - + // Switches for the equation terms bool ni_ni1_phi0, ni_ni0_phi1, ni_ni1_phi1, ni_nit_phit; - bool ni_vi1_ni0, ni_vi0_ni1, ni_vi1_ni1, ni_vit_nit; + bool ni_vi1_ni0, ni_vi0_ni1, ni_vi1_ni1, ni_vit_nit; bool ni_jpar1, ni_pe1, ni_ni1; bool ni_ni0_curv_phi1, ni_ni1_curv_phi0, ni_ni1_curv_phi1, ni_nit_curv_phit; - + bool rho_rho0_phi1, rho_rho1_phi0, rho_rho1_phi1; bool rho_vi1_rho0, rho_vi0_rho1, rho_vi1_rho1; bool rho_pei1, rho_jpar1, rho_rho1; - + bool vi_vi0_phi1, vi_vi1_phi0, vi_vi1_phi1, vi_vit_phit; bool vi_vi1_vi0, vi_vi0_vi1, vi_vi1_vi1, vi_vit_vit; bool vi_pei1, vi_peit, vi_vi1; - + bool te_te1_phi0, te_te0_phi1, te_te1_phi1; - + bool ti_ti1_phi0, ti_ti0_phi1, ti_ti1_phi1; - + int lowPass_z; // Low-pass filter result - + // Group of objects for communications FieldGroup comms; // Coordinate system metrics - Coordinates *coord; + Coordinates* coord; // Inverts a Laplacian to get potential std::unique_ptr phiSolver; @@ -97,20 +97,20 @@ class TwoFluid : public PhysicsModel { // Solves the electromagnetic potential std::unique_ptr aparSolver; Field2D acoef; // Coefficient in the Helmholtz equation - + int init(bool UNUSED(restarting)) override { TRACE("int init(bool) "); - - Field2D I; // Shear factor + + Field2D I; // Shear factor // Get the coordinate system coord = mesh->getCoordinates(); - + output.write("Solving 6-variable 2-fluid equations\n"); - + //////////////////////////////////////////////////////// // LOAD DATA FROM GRID FILE - + // Load 2D profiles (set to zero if not found) GRID_LOAD(Ni0); GRID_LOAD(Ti0); @@ -120,9 +120,9 @@ class TwoFluid : public PhysicsModel { GRID_LOAD(phi0); GRID_LOAD(rho0); GRID_LOAD(Ajpar0); - + // Load magnetic curvature term - b0xcv.covariant = false; // Read contravariant components + b0xcv.covariant = false; // Read contravariant components mesh->get(b0xcv, "bxcv"); // b0xkappa terms // Load metrics @@ -130,29 +130,29 @@ class TwoFluid : public PhysicsModel { GRID_LOAD(Bpxy); GRID_LOAD(Btxy); GRID_LOAD(hthe); - + Field2D dx; - if(!mesh->get(dx, "dpsi")) { + if (!mesh->get(dx, "dpsi")) { output << "\tUsing dpsi as the x grid spacing\n"; coord->dx = dx; // Only use dpsi if found - }else { + } else { // dx will have been read already from the grid output << "\tUsing dx as the x grid spacing\n"; } - mesh->get(I, "sinty"); - + mesh->get(I, "sinty"); + // Load normalisation values GRID_LOAD(Te_x); GRID_LOAD(Ti_x); GRID_LOAD(Ni_x); GRID_LOAD(bmag); - + Ni_x *= 1.0e14; bmag *= 1.0e4; - + //////////////////////////////////////////////////////// // READ OPTIONS - + // Read some parameters auto globalOptions = Options::root(); auto options = globalOptions["2fluid"]; @@ -172,24 +172,24 @@ class TwoFluid : public PhysicsModel { // Choose method to use for Poisson bracket advection terms int bracket_method; bracket_method = options["bracket_method"].withDefault(0); - switch(bracket_method) { + switch (bracket_method) { case 0: { - bm = BRACKET_STD; + bm = BRACKET_STD; output << "\tBrackets: default differencing\n"; break; } case 1: { - bm = BRACKET_SIMPLE; + bm = BRACKET_SIMPLE; output << "\tBrackets: simplified operator\n"; break; } case 2: { - bm = BRACKET_ARAKAWA; + bm = BRACKET_ARAKAWA; output << "\tBrackets: Arakawa scheme\n"; break; } case 3: { - bm = BRACKET_CTU; + bm = BRACKET_CTU; output << "\tBrackets: Corner Transport Upwind method\n"; break; } @@ -213,11 +213,11 @@ class TwoFluid : public PhysicsModel { evolve_vi = globalOptions["vi"]["evolve"].withDefault(true); evolve_ti = globalOptions["ti"]["evolve"].withDefault(true); evolve_ajpar = globalOptions["Ajpar"]["evolve"].withDefault(true); - + if (ZeroElMass) { evolve_ajpar = 0; // Don't need ajpar - calculated from ohm's law } - + //////////////////////////////////////////////////////// // Equation terms @@ -227,31 +227,31 @@ class TwoFluid : public PhysicsModel { options->get("ni0_phi1", ni_ni0_phi1, false); options->get("ni1_phi1", ni_ni1_phi1, false); options->get("nit_phit", ni_nit_phit, false); - options->get("vi1_ni0", ni_vi1_ni0, false); - options->get("vi0_ni1", ni_vi0_ni1, false); - options->get("vi1_ni1", ni_vi1_ni1, false); - options->get("vit_nit", ni_vit_nit, false); - options->get("jpar1", ni_jpar1, false); - options->get("pe1", ni_pe1, false); + options->get("vi1_ni0", ni_vi1_ni0, false); + options->get("vi0_ni1", ni_vi0_ni1, false); + options->get("vi1_ni1", ni_vi1_ni1, false); + options->get("vit_nit", ni_vit_nit, false); + options->get("jpar1", ni_jpar1, false); + options->get("pe1", ni_pe1, false); options->get("ni0_curv_phi1", ni_ni0_curv_phi1, false); options->get("ni1_curv_phi0", ni_ni1_curv_phi0, false); options->get("ni1_curv_phi1", ni_ni1_curv_phi1, false); options->get("nit_curv_phit", ni_nit_curv_phit, false); - } - + } + if (evolve_rho) { Options* options = &globalOptions["rho"]; options->get("rho0_phi1", rho_rho0_phi1, false); options->get("rho1_phi0", rho_rho1_phi0, false); options->get("rho1_phi1", rho_rho1_phi1, false); - options->get("vi1_rho0", rho_vi1_rho0, false); - options->get("vi0_rho1", rho_vi0_rho1, false); - options->get("vi1_rho1", rho_vi1_rho1, false); - options->get("pei1", rho_pei1, false); - options->get("jpar1", rho_jpar1, false); - options->get("rho1", rho_rho1, false); - } - + options->get("vi1_rho0", rho_vi1_rho0, false); + options->get("vi0_rho1", rho_vi0_rho1, false); + options->get("vi1_rho1", rho_vi1_rho1, false); + options->get("pei1", rho_pei1, false); + options->get("jpar1", rho_jpar1, false); + options->get("rho1", rho_rho1, false); + } + if (evolve_vi) { Options* options = &globalOptions["vi"]; options->get("vi0_phi1", vi_vi0_phi1, false); @@ -266,7 +266,7 @@ class TwoFluid : public PhysicsModel { options->get("peit", vi_peit, false); options->get("vi1", vi_vi1, false); } - + if (evolve_te) { Options* options = &globalOptions["te"]; options->get("te1_phi0", te_te1_phi0, false); @@ -280,56 +280,59 @@ class TwoFluid : public PhysicsModel { options->get("ti0_phi1", ti_ti0_phi1, false); options->get("ti1_phi1", ti_ti1_phi1, false); } - + //////////////////////////////////////////////////////// // SHIFTED RADIAL COORDINATES // Check type of parallel transform - std::string ptstr = Options::root()["mesh"]["paralleltransform"]["type"] - .withDefault("identity"); + std::string ptstr = + Options::root()["mesh"]["paralleltransform"]["type"].withDefault( + "identity"); if (lowercase(ptstr) == "shifted") { - ShearFactor = 0.0; // I disappears from metric - b0xcv.z += I*b0xcv.x; + ShearFactor = 0.0; // I disappears from metric + b0xcv.z += I * b0xcv.x; } //////////////////////////////////////////////////////// // CALCULATE PARAMETERS - - rho_s = 1.02*sqrt(AA*Te_x)/ZZ/bmag; - fmei = 1./1836.2/AA; - - lambda_ei = 24.-log(sqrt(Ni_x)/Te_x); - lambda_ii = 23.-log(ZZ*ZZ*ZZ*sqrt(2.*Ni_x)/pow(Ti_x, 1.5)); - wci = 9.58e3*ZZ*bmag/AA; - nueix = 2.91e-6*Ni_x*lambda_ei/pow(Te_x, 1.5); - nuiix = 4.78e-8*pow(ZZ,4.)*Ni_x*lambda_ii/pow(Ti_x, 1.5)/sqrt(AA); - nu_hat = zeff*nueix/wci; - + + rho_s = 1.02 * sqrt(AA * Te_x) / ZZ / bmag; + fmei = 1. / 1836.2 / AA; + + lambda_ei = 24. - log(sqrt(Ni_x) / Te_x); + lambda_ii = 23. - log(ZZ * ZZ * ZZ * sqrt(2. * Ni_x) / pow(Ti_x, 1.5)); + wci = 9.58e3 * ZZ * bmag / AA; + nueix = 2.91e-6 * Ni_x * lambda_ei / pow(Te_x, 1.5); + nuiix = 4.78e-8 * pow(ZZ, 4.) * Ni_x * lambda_ii / pow(Ti_x, 1.5) / sqrt(AA); + nu_hat = zeff * nueix / wci; + if (nu_perp < 1.e-10) { - mui_hat = (3./10.)*nuiix/wci; + mui_hat = (3. / 10.) * nuiix / wci; } else { - mui_hat = nu_perp; + mui_hat = nu_perp; } - + if (estatic) { - beta_p = 1.e-29; + beta_p = 1.e-29; } else { - beta_p = 4.03e-11*Ni_x*Te_x/bmag/bmag; + beta_p = 4.03e-11 * Ni_x * Te_x / bmag / bmag; } - + Vi_x = wci * rho_s; - + output.write("Collisions: nueix = {:e}, nu_hat = {:e}\n", nueix, nu_hat); - + //////////////////////////////////////////////////////// // PRINT Z INFORMATION - + BoutReal hthe0; - if(mesh->get(hthe0, "hthe0") == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", hthe0/rho_s); + if (mesh->get(hthe0, "hthe0") == 0) { + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } - + if (mesh->StaggerGrids) { //////////////////////////////////////////////////////// // SHIFTED GRIDS LOCATION @@ -342,61 +345,61 @@ class TwoFluid : public PhysicsModel { Apar.setLocation(CELL_YLOW); jpar.setLocation(CELL_YLOW); } - + //////////////////////////////////////////////////////// // NORMALISE QUANTITIES - + output.write("\tNormalising to rho_s = {:e}\n", rho_s); - + // Normalise profiles - Ni0 /= Ni_x/1.0e14; + Ni0 /= Ni_x / 1.0e14; Ti0 /= Te_x; Te0 /= Te_x; phi0 /= Te_x; Vi0 /= Vi_x; - + // Normalise curvature term - b0xcv.x /= (bmag/1e4); - b0xcv.y *= rho_s*rho_s; - b0xcv.z *= rho_s*rho_s; - - // Normalise geometry + b0xcv.x /= (bmag / 1e4); + b0xcv.y *= rho_s * rho_s; + b0xcv.z *= rho_s * rho_s; + + // Normalise geometry Rxy /= rho_s; hthe /= rho_s; - I *= rho_s*rho_s*(bmag/1e4)*ShearFactor; - coord->dx /= rho_s*rho_s*(bmag/1e4); + I *= rho_s * rho_s * (bmag / 1e4) * ShearFactor; + coord->dx /= rho_s * rho_s * (bmag / 1e4); // Normalise magnetic field - Bpxy /= (bmag/1.e4); - Btxy /= (bmag/1.e4); - coord->Bxy /= (bmag/1.e4); - + Bpxy /= (bmag / 1.e4); + Btxy /= (bmag / 1.e4); + coord->Bxy /= (bmag / 1.e4); + // calculate pressures - pei0 = (Ti0 + Te0)*Ni0; - pe0 = Te0*Ni0; - + pei0 = (Ti0 + Te0) * Ni0; + pe0 = Te0 * Ni0; + //////////////////////////////////////////////////////// // CALCULATE METRICS - - coord->g11 = SQ(Rxy*Bpxy); + + coord->g11 = SQ(Rxy * Bpxy); coord->g22 = 1.0 / SQ(hthe); - coord->g33 = SQ(I)*coord->g11 + SQ(coord->Bxy)/coord->g11; + coord->g33 = SQ(I) * coord->g11 + SQ(coord->Bxy) / coord->g11; coord->g12 = 0.0; - coord->g13 = -I*coord->g11; - coord->g23 = -Btxy/(hthe*Bpxy*Rxy); - + coord->g13 = -I * coord->g11; + coord->g23 = -Btxy / (hthe * Bpxy * Rxy); + coord->J = hthe / Bpxy; - - coord->g_11 = 1.0/coord->g11 + SQ(I*Rxy); - coord->g_22 = SQ(coord->Bxy*hthe/Bpxy); - coord->g_33 = Rxy*Rxy; - coord->g_12 = Btxy*hthe*I*Rxy/Bpxy; - coord->g_13 = I*Rxy*Rxy; - coord->g_23 = Btxy*hthe*Rxy/Bpxy; - + + coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy); + coord->g_22 = SQ(coord->Bxy * hthe / Bpxy); + coord->g_33 = Rxy * Rxy; + coord->g_12 = Btxy * hthe * I * Rxy / Bpxy; + coord->g_13 = I * Rxy * Rxy; + coord->g_23 = Btxy * hthe * Rxy / Bpxy; + //////////////////////////////////////////////////////// // SET EVOLVING VARIABLES - + // Tell BOUT++ which variables to evolve // add evolving variables to the communication object if (evolve_rho) { @@ -408,7 +411,7 @@ class TwoFluid : public PhysicsModel { rho.setBoundary("rho"); rho.applyBoundary(); } - + if (evolve_ni) { SOLVE_FOR(Ni); comms.add(Ni); @@ -418,7 +421,7 @@ class TwoFluid : public PhysicsModel { Ni.setBoundary("Ni"); Ni.applyBoundary(); } - + if (evolve_te) { SOLVE_FOR(Te); comms.add(Te); @@ -428,12 +431,12 @@ class TwoFluid : public PhysicsModel { Te.setBoundary("Te"); Te.applyBoundary(); } - + if (evolve_ajpar) { SOLVE_FOR(Ajpar); comms.add(Ajpar); output.write("ajpar\n"); - }else { + } else { initial_profile("Ajpar", Ajpar); if (ZeroElMass) { dump.add(Ajpar, "Ajpar", 1); // output calculated Ajpar @@ -441,7 +444,7 @@ class TwoFluid : public PhysicsModel { Ajpar.setBoundary("Ajpar"); Ajpar.applyBoundary(); } - + if (evolve_vi) { SOLVE_FOR(Vi); comms.add(Vi); @@ -451,7 +454,7 @@ class TwoFluid : public PhysicsModel { Vi.setBoundary("Vi"); Vi.applyBoundary(); } - + if (evolve_ti) { SOLVE_FOR(Ti); comms.add(Ti); @@ -461,31 +464,31 @@ class TwoFluid : public PhysicsModel { Ti.setBoundary("Ti"); Ti.applyBoundary(); } - + jpar.setBoundary("jpar"); - + //////////////////////////////////////////////////////// // SETUP COMMUNICATIONS - + // add extra variables to communication comms.add(phi); comms.add(Apar); - + // Add any other variables to be dumped to file - dump.addRepeat(phi, "phi"); + dump.addRepeat(phi, "phi"); dump.addRepeat(Apar, "Apar"); dump.addRepeat(jpar, "jpar"); - + dump.addOnce(Ni0, "Ni0"); dump.addOnce(Te0, "Te0"); dump.addOnce(Ti0, "Ti0"); - - dump.addOnce(Te_x, "Te_x"); - dump.addOnce(Ti_x, "Ti_x"); - dump.addOnce(Ni_x, "Ni_x"); + + dump.addOnce(Te_x, "Te_x"); + dump.addOnce(Ti_x, "Ti_x"); + dump.addOnce(Ni_x, "Ni_x"); dump.addOnce(rho_s, "rho_s"); - dump.addOnce(wci, "wci"); - + dump.addOnce(wci, "wci"); + // Create a solver for the Laplacian phiSolver = Laplacian::create(&options["phiSolver"]); if (laplace_extra_rho_term) { @@ -493,7 +496,7 @@ class TwoFluid : public PhysicsModel { phiSolver->setCoefC(Ni0); } - if (! (estatic || ZeroElMass)) { + if (!(estatic || ZeroElMass)) { // Create a solver for the electromagnetic potential aparSolver = Laplacian::create(&options["aparSolver"], mesh->StaggerGrids ? CELL_YLOW : CELL_CENTRE); @@ -504,30 +507,30 @@ class TwoFluid : public PhysicsModel { } aparSolver->setCoefA(acoef); } - + return 0; } - + // ExB terms using Poisson bracket -#define vE_Grad(f, p) ( bracket(p, f, bm) ) +#define vE_Grad(f, p) (bracket(p, f, bm)) int rhs(BoutReal UNUSED(t)) override { - + //////////////////////////////////////////////////////// // Invert vorticity to get phi // // Solves \nabla^2_\perp x + \nabla_perp c\cdot\nabla_\perp x + a x = b // Arguments are: (b, bit-field, a, c) // Passing NULL -> missing term - + { TRACE("Solving for phi"); - - phi = phiSolver->solve(rho/Ni0); - + + phi = phiSolver->solve(rho / Ni0); + if (vort_include_pi) { // Include Pi term in vorticity - phi -= (Ti*Ni0 + Ni*Te0) / Ni0; + phi -= (Ti * Ni0 + Ni * Te0) / Ni0; } } @@ -540,17 +543,17 @@ class TwoFluid : public PhysicsModel { // Electrostatic operation Apar = 0.0; } else { - Apar = aparSolver->solve(acoef*(Vi - Ajpar)); + Apar = aparSolver->solve(acoef * (Vi - Ajpar)); } } - + //////////////////////////////////////////////////////// // Communicate variables mesh->communicate(comms); //////////////////////////////////////////////////////// // Update profiles for calculating nu, mu_i, kapa_Te,i - switch(bkgd) { + switch (bkgd) { case 0: { // Toroidal averages Nit = Ni0 + DC(Ni); Tit = Ti0 + DC(Ti); @@ -563,7 +566,7 @@ class TwoFluid : public PhysicsModel { Tit = Ti0 + Ti; Tet = Te0 + Te; Vit = Vi0 + Vi; - break; + break; } case 2: { // Unperturbed values Nit = Ni0; @@ -576,55 +579,55 @@ class TwoFluid : public PhysicsModel { throw BoutException("ERROR: Invalid bkgd option\n"); } } - + //////////////////////////////////////////////////////// // Update non-linear coefficients on the mesh if (mesh->StaggerGrids) { - nu = nu_hat * interp_to(Nit / pow(Tet,1.5), CELL_YLOW); + nu = nu_hat * interp_to(Nit / pow(Tet, 1.5), CELL_YLOW); } else { - nu = nu_hat * Nit / pow(Tet,1.5); + nu = nu_hat * Nit / pow(Tet, 1.5); } - mu_i = mui_hat * Nit / sqrt(Tit); - kapa_Te = 3.2*(1./fmei)*(wci/nueix)*pow(Tet,2.5); - kapa_Ti = 3.9*(wci/nuiix)*pow(Tit,2.5); - + mu_i = mui_hat * Nit / sqrt(Tit); + kapa_Te = 3.2 * (1. / fmei) * (wci / nueix) * pow(Tet, 2.5); + kapa_Ti = 3.9 * (wci / nuiix) * pow(Tit, 2.5); + // note: nonlinear terms are not here - pei = (Te0+Ti0)*Ni + (Te + Ti)*Ni0; - pe = Te0*Ni + Te*Ni0; - + pei = (Te0 + Ti0) * Ni + (Te + Ti) * Ni0; + pe = Te0 * Ni + Te * Ni0; + //////////////////////////////////////////////////////// if (ZeroElMass) { // Set jpar,Ve,Ajpar neglecting the electron inertia term // Calculate Jpar, communicating across processors - jpar = -(Ni0*Grad_par(phi, CELL_YLOW)) / (fmei*0.51*nu); - + jpar = -(Ni0 * Grad_par(phi, CELL_YLOW)) / (fmei * 0.51 * nu); + if (OhmPe) { - jpar += (Te0*Grad_par(Ni, CELL_YLOW)) / (fmei*0.51*nu); + jpar += (Te0 * Grad_par(Ni, CELL_YLOW)) / (fmei * 0.51 * nu); } - + // Need to communicate jpar mesh->communicate(jpar); jpar.applyBoundary(); - + if (!mesh->StaggerGrids) { - Ve = Vi - jpar/Ni0; + Ve = Vi - jpar / Ni0; } else { - Ve = Vi - jpar/interp_to(Ni0, CELL_YLOW); + Ve = Vi - jpar / interp_to(Ni0, CELL_YLOW); } Ajpar = Ve; } else { - + Ve = Ajpar + Apar; if (!mesh->StaggerGrids) { - jpar = Ni0*(Vi - Ve); + jpar = Ni0 * (Vi - Ve); } else { - jpar = interp_to(Ni0, CELL_YLOW)*(Vi - Ve); + jpar = interp_to(Ni0, CELL_YLOW) * (Vi - Ve); } } - + //////////////////////////////////////////////////////// // DENSITY EQUATION - + ddt(Ni) = 0.0; if (evolve_ni) { TRACE("Density equation"); @@ -666,23 +669,24 @@ class TwoFluid : public PhysicsModel { } if (ni_pe1) { - ddt(Ni) += 2.0*V_dot_Grad(b0xcv, pe); + ddt(Ni) += 2.0 * V_dot_Grad(b0xcv, pe); } if (ni_ni0_curv_phi1) { - ddt(Ni) -= 2.0*Ni0*V_dot_Grad(b0xcv, phi); + ddt(Ni) -= 2.0 * Ni0 * V_dot_Grad(b0xcv, phi); } if (ni_ni1_curv_phi0) { - ddt(Ni) -= 2.0*Ni*V_dot_Grad(b0xcv, phi0); + ddt(Ni) -= 2.0 * Ni * V_dot_Grad(b0xcv, phi0); } if (ni_ni1_curv_phi1) { - ddt(Ni) -= 2.0*Ni*V_dot_Grad(b0xcv, phi); + ddt(Ni) -= 2.0 * Ni * V_dot_Grad(b0xcv, phi); } if (ni_nit_curv_phit) { - ddt(Ni) -= 2.0*Nit*V_dot_Grad(b0xcv, phi+phi0) - 2.0*Ni0*V_dot_Grad(b0xcv, phi0); + ddt(Ni) -= 2.0 * Nit * V_dot_Grad(b0xcv, phi + phi0) + - 2.0 * Ni0 * V_dot_Grad(b0xcv, phi0); } if (ni_ni1) { @@ -698,7 +702,7 @@ class TwoFluid : public PhysicsModel { //////////////////////////////////////////////////////// // ION VELOCITY - + ddt(Vi) = 0.0; if (evolve_vi) { TRACE("Ion velocity equation"); @@ -716,7 +720,7 @@ class TwoFluid : public PhysicsModel { } if (vi_vit_phit) { - ddt(Vi) -= vE_Grad(Vit, phi+phi0) - vE_Grad(Vi0, phi+phi0); + ddt(Vi) -= vE_Grad(Vit, phi + phi0) - vE_Grad(Vi0, phi + phi0); } if (vi_vi1_vi0) { @@ -736,25 +740,25 @@ class TwoFluid : public PhysicsModel { } if (vi_pei1) { - ddt(Vi) -= Grad_par(pei)/Ni0; + ddt(Vi) -= Grad_par(pei) / Ni0; } if (vi_peit) { - ddt(Vi) -= Grad_par(pei)/Nit; + ddt(Vi) -= Grad_par(pei) / Nit; } if (vi_vi1) { - ddt(Vi) -= mu_i*Delp2(Vi); + ddt(Vi) -= mu_i * Delp2(Vi); } if (lowPass_z > 0) { ddt(Vi) = lowPass(ddt(Vi), lowPass_z); } } - + //////////////////////////////////////////////////////// // ELECTRON TEMPERATURE - + ddt(Te) = 0.0; if (evolve_te) { TRACE("Electron temperature equation"); @@ -781,10 +785,10 @@ class TwoFluid : public PhysicsModel { ddt(Te) = lowPass(ddt(Te), lowPass_z); } } - + //////////////////////////////////////////////////////// // ION TEMPERATURE - + ddt(Ti) = 0.0; if (evolve_ti) { TRACE("Ion temperature equation"); @@ -811,10 +815,10 @@ class TwoFluid : public PhysicsModel { ddt(Ti) = lowPass(ddt(Ti), lowPass_z); } } - + //////////////////////////////////////////////////////// // VORTICITY - + ddt(rho) = 0.0; if (evolve_rho) { TRACE("Vorticity equation"); @@ -845,14 +849,14 @@ class TwoFluid : public PhysicsModel { if (rho_pei1) { if (curv_upwind) { - ddt(rho) += 2.0*coord->Bxy*V_dot_Grad(b0xcv, pei); // Use upwinding + ddt(rho) += 2.0 * coord->Bxy * V_dot_Grad(b0xcv, pei); // Use upwinding } else { - ddt(rho) += 2.0*coord->Bxy*b0xcv*Grad(pei); // Use central differencing + ddt(rho) += 2.0 * coord->Bxy * b0xcv * Grad(pei); // Use central differencing } - } - + } + if (rho_jpar1) { - ddt(rho) += SQ(coord->Bxy)*Div_par(jpar, CELL_CENTRE); + ddt(rho) += SQ(coord->Bxy) * Div_par(jpar, CELL_CENTRE); } if (rho_rho1) { @@ -863,38 +867,38 @@ class TwoFluid : public PhysicsModel { ddt(rho) = lowPass(ddt(rho), lowPass_z); } } - + //////////////////////////////////////////////////////// // AJPAR - + ddt(Ajpar) = 0.0; if (evolve_ajpar) { TRACE("Ajpar equation"); - + //ddt(Ajpar) -= vE_Grad(Ajpar0, phi) + vE_Grad(Ajpar, phi0) + vE_Grad(Ajpar, phi); //ddt(Ajpar) -= (1./fmei)*1.71*Grad_par(Te, CELL_YLOW); - - ddt(Ajpar) += (1./fmei)*Grad_par(phi, CELL_YLOW); - + + ddt(Ajpar) += (1. / fmei) * Grad_par(phi, CELL_YLOW); + if (OhmPe) { - ddt(Ajpar) -= (1./fmei)*(Te0/Ni0)*Grad_par(Ni, CELL_YLOW); + ddt(Ajpar) -= (1. / fmei) * (Te0 / Ni0) * Grad_par(Ni, CELL_YLOW); } - + if (mesh->StaggerGrids) { - ddt(Ajpar) += 0.51*nu*jpar/interp_to(Ni0, CELL_YLOW); + ddt(Ajpar) += 0.51 * nu * jpar / interp_to(Ni0, CELL_YLOW); } else { - ddt(Ajpar) += 0.51*nu*jpar/Ni0; + ddt(Ajpar) += 0.51 * nu * jpar / Ni0; } if (lowPass_z > 0) { ddt(Ajpar) = lowPass(ddt(Ajpar), lowPass_z); } } - + //////////////////////////////////////////////////////// // Profile evolution options - - switch(iTe_dc) { + + switch (iTe_dc) { case 1: { // subtacting out toroidal averages for all fields if (evolve_ni) { ddt(Ni) -= DC(ddt(Ni)); @@ -938,10 +942,9 @@ class TwoFluid : public PhysicsModel { throw BoutException("ERROR: invalid option for iTe_dc\n"); } } - - return(0); + + return (0); } }; BOUTMAIN(TwoFluid); - diff --git a/examples/uedge-benchmark/ue_bmark.cxx b/examples/uedge-benchmark/ue_bmark.cxx index 704964c875..969b4fc5db 100644 --- a/examples/uedge-benchmark/ue_bmark.cxx +++ b/examples/uedge-benchmark/ue_bmark.cxx @@ -10,9 +10,9 @@ * *******************************************************************************/ -#include #include -#include +#include +#include #include @@ -20,39 +20,38 @@ class UedgeBenchmark : public PhysicsModel { private: // 2D initial profiles Field2D Ni0, Ti0, Te0, Vi0; - + // 3D evolving fields Field3D Te, Ni, Vi, Ti; - + // Non-linear coefficients Field3D kapa_Te, kapa_Ti; - + // 3D total values Field3D Nit, Tit, Tet, Vit; - + // pressures Field3D peit, pe; Field2D pei0, pe0; // Metric coefficients Field2D Rxy, Bpxy, Btxy, hthe; - + // parameters BoutReal Te_x, Ti_x, Ni_x, Vi_x, bmag, rho_s, fmei, AA, ZZ; BoutReal lambda_ei, lambda_ii; BoutReal nu_hat, mui_hat, wci, nueix, nuiix; - + BoutReal chi_perp, D_perp, mu_perp; - + protected: - int init(bool UNUSED(restarting)) { Field2D I; // Shear factor - + output.write("Solving transport equations for Ni, Vi, Ti, Te\n"); - + /////////////// LOAD DATA FROM GRID FILE ////////////// - + // Load 2D profiles (set to zero if not found) GRID_LOAD(Ni0, Ti0, Te0, Vi0); @@ -97,21 +96,22 @@ class UedgeBenchmark : public PhysicsModel { BoutReal hthe0; if (GRID_LOAD1(hthe0) == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", - hthe0 / rho_s); + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } ///////////// NORMALISE QUANTITIES //////////////////// - + output.write("\tNormalising to rho_s = {:e}\n", rho_s); - + auto* coords = mesh->getCoordinates(); // Normalise profiles Ni0 /= Ni_x / 1.0e14; Ti0 /= Te_x; Te0 /= Te_x; Vi0 /= Vi_x; - + // Normalise geometry Rxy /= rho_s; hthe /= rho_s; @@ -135,7 +135,8 @@ class UedgeBenchmark : public PhysicsModel { D_perp = 0.1; mu_perp = 0.1; - output.write("Diffusion coefficients: chi {:e} D {:e} Mu {:e}\n", chi_perp, D_perp, mu_perp); + output.write("Diffusion coefficients: chi {:e} D {:e} Mu {:e}\n", chi_perp, D_perp, + mu_perp); /////////////// CALCULATE METRICS ///////////////// @@ -166,11 +167,11 @@ class UedgeBenchmark : public PhysicsModel { Tet.setBoundary("Te"); Tit.setBoundary("Ti"); Vit.setBoundary("Vi"); - + Ni0.applyBoundary("neumann"); Te0.applyBoundary("neumann"); Ti0.applyBoundary("neumann"); - + ///////////// SET EVOLVING VARIABLES ////////////// // // Tell BOUT++ which variables to evolve @@ -195,17 +196,17 @@ class UedgeBenchmark : public PhysicsModel { + DDX( difVi * sg ) * DDX(Vi) * sg; } */ - + // This version the same as in BOUT-06. Note the R's moved,and hthe added Field3D Div_X_K_Grad_X(const Field3D& difFi, const Field3D& Fi) { Field3D result; - + result = difFi * (pow(Rxy * Bpxy, 2.0)) * D2DX2(Fi) - + (Bpxy / hthe) * DDX(difFi * Rxy * Rxy * Bpxy * hthe) * DDX(Fi); - + + (Bpxy / hthe) * DDX(difFi * Rxy * Rxy * Bpxy * hthe) * DDX(Fi); + return result; } - + int rhs(BoutReal UNUSED(t)) { // Communicate variables mesh->communicate(Ni, Vi, Te, Ti); @@ -221,7 +222,7 @@ class UedgeBenchmark : public PhysicsModel { Tet.applyBoundary(); Tit.applyBoundary(); Vit.applyBoundary(); - + // Update non-linear coefficients on the mesh kapa_Te = 3.2 * (1. / fmei) * (wci / nueix) * pow(Tet, 2.5); kapa_Ti = 3.9 * (wci / nuiix) * pow(Tit, 2.5); @@ -230,21 +231,21 @@ class UedgeBenchmark : public PhysicsModel { // DENSITY EQUATION ddt(Ni) = -Vpar_Grad_par(Vit, Nit) - Nit * Div_par(Vit) - + Div_X_K_Grad_X(D_perp * (Nit * 0.0 + 1.0), Nit); + + Div_X_K_Grad_X(D_perp * (Nit * 0.0 + 1.0), Nit); // ION VELOCITY ddt(Vi) = (-Grad_par(peit) + Div_X_K_Grad_X(mu_perp * Nit, Vit)) / Nit - - Vpar_Grad_par(Vit, Nit * Vit) / Nit - ddt(Ni) * Vit / Nit; + - Vpar_Grad_par(Vit, Nit * Vit) / Nit - ddt(Ni) * Vit / Nit; // ELECTRON TEMPERATURE ddt(Te) = (Div_par_K_Grad_par(kapa_Te, Tet) + Div_X_K_Grad_X(chi_perp * Nit, Tet)) - / (1.5 * Nit) - - ddt(Ni) * Tet / Nit; + / (1.5 * Nit) + - ddt(Ni) * Tet / Nit; // ION TEMPERATURE ddt(Ti) = (Div_par_K_Grad_par(kapa_Ti, Tit) + Div_X_K_Grad_X(chi_perp * Nit, Tit)) - / (1.5 * Nit) - - ddt(Ni) * Tit / Nit; + / (1.5 * Nit) + - ddt(Ni) * Tit / Nit; return 0; } diff --git a/examples/wave-slab/wave_slab.cxx b/examples/wave-slab/wave_slab.cxx index 4226e2f6f5..4169b63dab 100644 --- a/examples/wave-slab/wave_slab.cxx +++ b/examples/wave-slab/wave_slab.cxx @@ -12,61 +12,59 @@ #include - class WaveTest : public PhysicsModel { public: int init(bool UNUSED(restarting)) { - auto *coords = mesh->getCoordinates(); + auto* coords = mesh->getCoordinates(); Field2D Rxy, Bpxy, Btxy, hthe, I; GRID_LOAD(Rxy); GRID_LOAD(Bpxy); GRID_LOAD(Btxy); GRID_LOAD(hthe); - mesh->get(coords->Bxy, "Bxy"); + mesh->get(coords->Bxy, "Bxy"); int ShiftXderivs = 0; mesh->get(ShiftXderivs, "false"); - if(ShiftXderivs) { + if (ShiftXderivs) { // No integrated shear in metric I = 0.0; } else { - mesh->get(I, "sinty"); + mesh->get(I, "sinty"); } - coords->g11 = pow(Rxy*Bpxy,2.0); - coords->g22 = 1.0 / pow(hthe,2.0); - coords->g33 = pow(I,2.0)*coords->g11 + pow(coords->Bxy,2.0)/coords->g11; + coords->g11 = pow(Rxy * Bpxy, 2.0); + coords->g22 = 1.0 / pow(hthe, 2.0); + coords->g33 = pow(I, 2.0) * coords->g11 + pow(coords->Bxy, 2.0) / coords->g11; coords->g12 = 0.0; - coords->g13 = -I*coords->g11; - coords->g23 = -Btxy/(hthe*Bpxy*Rxy); - + coords->g13 = -I * coords->g11; + coords->g23 = -Btxy / (hthe * Bpxy * Rxy); + coords->J = hthe / Bpxy; - - coords->g_11 = 1.0/coords->g11 + (pow(I*Rxy,2.0)); - coords->g_22 = pow(coords->Bxy*hthe/Bpxy,2.0); - coords->g_33 = Rxy*Rxy; - coords->g_12 = Btxy*hthe*I*Rxy/Bpxy; - coords->g_13 = I*Rxy*Rxy; - coords->g_23 = Btxy*hthe*Rxy/Bpxy; - + + coords->g_11 = 1.0 / coords->g11 + (pow(I * Rxy, 2.0)); + coords->g_22 = pow(coords->Bxy * hthe / Bpxy, 2.0); + coords->g_33 = Rxy * Rxy; + coords->g_12 = Btxy * hthe * I * Rxy / Bpxy; + coords->g_13 = I * Rxy * Rxy; + coords->g_23 = Btxy * hthe * Rxy / Bpxy; + coords->geometry(); - + solver->add(f, "f"); solver->add(g, "g"); - + return 0; } int rhs(BoutReal UNUSED(time)) { - mesh->communicate(f,g); - + mesh->communicate(f, g); + ddt(f) = Grad_par(g); ddt(g) = Grad_par(f); - + return 0; } - + private: Field3D f, g; }; - BOUTMAIN(WaveTest); diff --git a/include/bout/array.hxx b/include/bout/array.hxx index b9f1bc1bb1..e258f235b4 100644 --- a/include/bout/array.hxx +++ b/include/bout/array.hxx @@ -50,7 +50,7 @@ template using iterator = T*; template using const_iterator = const T*; -} +} // namespace /*! * ArrayData holds the actual data @@ -169,7 +169,7 @@ private: * - Arrays can't be used in GPU code. To access Array data * inside a RAJA loop, first extract the raw pointer */ -template> +template > class Array { public: using data_type = T; @@ -193,9 +193,7 @@ public: /*! * Destructor. Releases the underlying dataBlock */ - ~Array() noexcept { - release(ptr); - } + ~Array() noexcept { release(ptr); } /*! * Copy constructor @@ -216,9 +214,7 @@ public: /*! * Move constructor */ - Array(Array&& other) noexcept { - swap(*this, other); - } + Array(Array&& other) noexcept { swap(*this, other); } /*! * Reallocate the array with size = \p new_size @@ -271,9 +267,7 @@ public: /*! * Returns true if the Array is empty */ - bool empty() const noexcept { - return ptr == nullptr; - } + bool empty() const noexcept { return ptr == nullptr; } /*! * Return size of the array. Zero if the array is empty. @@ -492,4 +486,3 @@ bool operator==(const Array& lhs, const Array& rhs) { } #endif // __ARRAY_H__ - diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx index b851467c1e..233641966b 100644 --- a/include/bout/assert.hxx +++ b/include/bout/assert.hxx @@ -17,7 +17,7 @@ #ifndef __BOUT_ASSERT_H__ #define __BOUT_ASSERT_H__ -#include "../boutexception.hxx" +#include "bout/boutexception.hxx" #ifndef CHECK #define CHECKLEVEL 0 @@ -26,36 +26,40 @@ #endif #if CHECKLEVEL >= 0 -#define ASSERT0(condition) \ - if(!(condition)) { \ - throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, #condition); \ +#define ASSERT0(condition) \ + if (!(condition)) { \ + throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \ + #condition); \ } #else // CHECKLEVEL >= 0 #define ASSERT0(condition) #endif #if CHECKLEVEL >= 1 -#define ASSERT1(condition) \ - if(!(condition)) { \ - throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, #condition); \ +#define ASSERT1(condition) \ + if (!(condition)) { \ + throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \ + #condition); \ } #else // CHECKLEVEL >= 1 #define ASSERT1(condition) #endif #if CHECKLEVEL >= 2 -#define ASSERT2(condition) \ - if(!(condition)) { \ - throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, #condition); \ +#define ASSERT2(condition) \ + if (!(condition)) { \ + throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \ + #condition); \ } #else // CHECKLEVEL >= 2 #define ASSERT2(condition) #endif #if CHECKLEVEL >= 3 -#define ASSERT3(condition) \ - if(!(condition)) { \ - throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, #condition); \ +#define ASSERT3(condition) \ + if (!(condition)) { \ + throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \ + #condition); \ } #else // CHECKLEVEL >= 3 #define ASSERT3(condition) diff --git a/include/bout/boundary_factory.hxx b/include/bout/boundary_factory.hxx index bc5ff496b4..445f50068c 100644 --- a/include/bout/boundary_factory.hxx +++ b/include/bout/boundary_factory.hxx @@ -12,8 +12,8 @@ class BoundaryRegionPar; class BoundaryRegion; class BoundaryModifier; -#include #include +#include /// Create BoundaryOp objects on demand /*! @@ -62,7 +62,7 @@ class BoundaryModifier; * */ class BoundaryFactory { - public: +public: ~BoundaryFactory(); /// Return a pointer to the only instance static BoundaryFactory* getInstance(); @@ -70,45 +70,46 @@ class BoundaryFactory { static void cleanup(); ///< Frees all memory /// Create a boundary operation object - BoundaryOpBase* create(const std::string &name, BoundaryRegionBase *region); - BoundaryOpBase* create(const char* name, BoundaryRegionBase *region); + BoundaryOpBase* create(const std::string& name, BoundaryRegionBase* region); + BoundaryOpBase* create(const char* name, BoundaryRegionBase* region); /// Create a boundary object using the options file - BoundaryOpBase* createFromOptions(const std::string &varname, BoundaryRegionBase *region); - BoundaryOpBase* createFromOptions(const char* varname, BoundaryRegionBase *region); + BoundaryOpBase* createFromOptions(const std::string& varname, + BoundaryRegionBase* region); + BoundaryOpBase* createFromOptions(const char* varname, BoundaryRegionBase* region); /*! * Add available boundary conditions and modifiers * Supply an object, and the name to be used */ - void add(BoundaryOp* bop, const std::string &name); - + void add(BoundaryOp* bop, const std::string& name); + /*! * Add a boundary condition. * * Note: This method should be removed, as the string method is sufficient */ - void add(BoundaryOp* bop, const char *name); - + void add(BoundaryOp* bop, const char* name); + /*! * Add a boundary condition modifier */ - void addMod(BoundaryModifier* bmod, const std::string &name); - + void addMod(BoundaryModifier* bmod, const std::string& name); + /*! * Note: This method should be removed, as the string method is sufficient - */ - void addMod(BoundaryModifier* bmod, const char *name); - + */ + void addMod(BoundaryModifier* bmod, const char* name); + // Parallel boundaries - void add(BoundaryOpPar* bop, const std::string &name); - void add(BoundaryOpPar* bop, const char *name); + void add(BoundaryOpPar* bop, const std::string& name); + void add(BoundaryOpPar* bop, const char* name); - private: +private: /*! * Private constructor, preventing instantiation of this class - */ - BoundaryFactory(); + */ + BoundaryFactory(); static BoundaryFactory* instance; ///< The only instance of this class (Singleton) // Database of available boundary conditions and modifiers @@ -120,14 +121,12 @@ class BoundaryFactory { // map par_modmap; // Functions to look up operations and modifiers - BoundaryOp* findBoundaryOp(const std::string &s); - BoundaryModifier* findBoundaryMod(const std::string &s); + BoundaryOp* findBoundaryOp(const std::string& s); + BoundaryModifier* findBoundaryMod(const std::string& s); // Parallel boundary conditions - BoundaryOpPar* findBoundaryOpPar(const std::string &s); + BoundaryOpPar* findBoundaryOpPar(const std::string& s); // To be implemented... // BoundaryModifier* findBoundaryMod(const string &s); - }; #endif // __BNDRY_FACTORY_H__ - diff --git a/include/bout/boundary_op.hxx b/include/bout/boundary_op.hxx index c67d09e9b0..035caa2778 100644 --- a/include/bout/boundary_op.hxx +++ b/include/bout/boundary_op.hxx @@ -5,16 +5,16 @@ class BoundaryModifier; #ifndef __BNDRY_OP__ #define __BNDRY_OP__ -#include "boundary_region.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "vector2d.hxx" -#include "vector3d.hxx" -#include "unused.hxx" +#include "bout/boundary_region.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/unused.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" #include -#include #include +#include class BoundaryOpBase { public: @@ -22,18 +22,18 @@ public: virtual ~BoundaryOpBase() = default; /// Apply a boundary condition on field f - virtual void apply(Field2D &f) = 0; - virtual void apply(Field2D &f,BoutReal UNUSED(t)){return apply(f);}//JMAD - virtual void apply(Field3D &f) = 0; - virtual void apply(Field3D &f,BoutReal UNUSED(t)){return apply(f);}//JMAD + virtual void apply(Field2D& f) = 0; + virtual void apply(Field2D& f, BoutReal UNUSED(t)) { return apply(f); } //JMAD + virtual void apply(Field3D& f) = 0; + virtual void apply(Field3D& f, BoutReal UNUSED(t)) { return apply(f); } //JMAD - virtual void apply(Vector2D &f) { + virtual void apply(Vector2D& f) { apply(f.x); apply(f.y); apply(f.z); } - virtual void apply(Vector3D &f) { + virtual void apply(Vector3D& f) { apply(f.x); apply(f.y); apply(f.z); @@ -47,49 +47,47 @@ public: bndry = nullptr; apply_to_ddt = false; } - BoundaryOp(BoundaryRegion *region) {bndry = region; apply_to_ddt=false;} + BoundaryOp(BoundaryRegion* region) { + bndry = region; + apply_to_ddt = false; + } ~BoundaryOp() override = default; // Note: All methods must implement clone, except for modifiers (see below) - virtual BoundaryOp* clone(BoundaryRegion *UNUSED(region), const std::list &UNUSED(args)) { + virtual BoundaryOp* clone(BoundaryRegion* UNUSED(region), + const std::list& UNUSED(args)) { throw BoutException("BoundaryOp::clone not implemented"); } /// Clone using positional args and keywords /// If not implemented, check if keywords are passed, then call two-argument version - virtual BoundaryOp *clone(BoundaryRegion *region, const std::list &args, - const std::map &keywords) { + virtual BoundaryOp* clone(BoundaryRegion* region, const std::list& args, + const std::map& keywords) { if (!keywords.empty()) { // Given keywords, but not using throw BoutException("Keywords ignored in boundary : {:s}", keywords.begin()->first); } - + return clone(region, args); } /// Apply a boundary condition on ddt(f) - virtual void apply_ddt(Field2D &f) { - apply(ddt(f)); - } - virtual void apply_ddt(Field3D &f) { - apply(ddt(f)); - } - virtual void apply_ddt(Vector2D &f) { - apply(ddt(f)); - } - virtual void apply_ddt(Vector3D &f) { - apply(ddt(f)); - } + virtual void apply_ddt(Field2D& f) { apply(ddt(f)); } + virtual void apply_ddt(Field3D& f) { apply(ddt(f)); } + virtual void apply_ddt(Vector2D& f) { apply(ddt(f)); } + virtual void apply_ddt(Vector3D& f) { apply(ddt(f)); } - BoundaryRegion *bndry; - bool apply_to_ddt; // True if this boundary condition should be applied on the time derivatives, false if it should be applied to the field values + BoundaryRegion* bndry; + bool + apply_to_ddt; // True if this boundary condition should be applied on the time derivatives, false if it should be applied to the field values }; class BoundaryModifier : public BoundaryOp { public: BoundaryModifier() = default; - BoundaryModifier(BoundaryOp *operation) : BoundaryOp(operation->bndry), op(operation) {} - virtual BoundaryOp* cloneMod(BoundaryOp *op, const std::list &args) = 0; + BoundaryModifier(BoundaryOp* operation) : BoundaryOp(operation->bndry), op(operation) {} + virtual BoundaryOp* cloneMod(BoundaryOp* op, const std::list& args) = 0; + protected: BoundaryOp* op{nullptr}; }; diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx index dd24f48d3a..542460580c 100644 --- a/include/bout/boundary_region.hxx +++ b/include/bout/boundary_region.hxx @@ -10,20 +10,22 @@ class BoundaryRegion; class Mesh; namespace bout { namespace globals { - extern Mesh* mesh; ///< Global mesh -} // namespace bout +extern Mesh* mesh; ///< Global mesh } // namespace globals +} // namespace bout /// Location of boundary -enum class BndryLoc {xin, - xout, - ydown, - yup, - all, - par_fwd_xin, // Don't include parallel boundaries - par_bkwd_xin, - par_fwd_xout, // Don't include parallel boundaries - par_bkwd_xout}; +enum class BndryLoc { + xin, + xout, + ydown, + yup, + all, + par_fwd_xin, // Don't include parallel boundaries + par_bkwd_xin, + par_fwd_xout, // Don't include parallel boundaries + par_bkwd_xout +}; constexpr BndryLoc BNDRY_XIN = BndryLoc::xin; constexpr BndryLoc BNDRY_XOUT = BndryLoc::xout; constexpr BndryLoc BNDRY_YDOWN = BndryLoc::ydown; @@ -36,12 +38,12 @@ constexpr BndryLoc BNDRY_PAR_BKWD_XOUT = BndryLoc::par_bkwd_xout; class BoundaryRegionBase { public: - BoundaryRegionBase() = delete; - BoundaryRegionBase(std::string name, Mesh *passmesh = nullptr) + BoundaryRegionBase(std::string name, Mesh* passmesh = nullptr) : localmesh(passmesh ? passmesh : bout::globals::mesh), label(std::move(name)) {} - BoundaryRegionBase(std::string name, BndryLoc loc, Mesh *passmesh = nullptr) - : localmesh(passmesh ? passmesh : bout::globals::mesh), label(std::move(name)), location(loc) {} + BoundaryRegionBase(std::string name, BndryLoc loc, Mesh* passmesh = nullptr) + : localmesh(passmesh ? passmesh : bout::globals::mesh), label(std::move(name)), + location(loc) {} virtual ~BoundaryRegionBase() = default; @@ -49,27 +51,28 @@ public: std::string label; ///< Label for this boundary region - BndryLoc location; ///< Which side of the domain is it on? - bool isParallel = false; ///< Is this a parallel boundary? + BndryLoc location; ///< Which side of the domain is it on? + bool isParallel = false; ///< Is this a parallel boundary? - virtual void first() = 0; ///< Move the region iterator to the start - virtual void next() = 0; ///< Get the next element in the loop - /// over every element from inside out (in - /// X or Y first) - virtual bool isDone() = 0; ///< Returns true if outside domain. Can use this with nested nextX, nextY + virtual void first() = 0; ///< Move the region iterator to the start + virtual void next() = 0; ///< Get the next element in the loop + /// over every element from inside out (in + /// X or Y first) + virtual bool + isDone() = 0; ///< Returns true if outside domain. Can use this with nested nextX, nextY }; /// Describes a region of the boundary, and a means of iterating over it class BoundaryRegion : public BoundaryRegionBase { public: BoundaryRegion() = delete; - BoundaryRegion(std::string name, BndryLoc loc, Mesh *passmesh = nullptr) + BoundaryRegion(std::string name, BndryLoc loc, Mesh* passmesh = nullptr) : BoundaryRegionBase(name, loc, passmesh) {} - BoundaryRegion(std::string name, int xd, int yd, Mesh *passmesh = nullptr) + BoundaryRegion(std::string name, int xd, int yd, Mesh* passmesh = nullptr) : BoundaryRegionBase(name, passmesh), bx(xd), by(yd), width(2) {} ~BoundaryRegion() override = default; - int x,y; ///< Indices of the point in the boundary + int x, y; ///< Indices of the point in the boundary int bx, by; ///< Direction of the boundary [x+bx][y+by] is going outwards int width; ///< Width of the boundary diff --git a/include/bout/boundary_standard.hxx b/include/bout/boundary_standard.hxx index d11d8591ad..96d43de24d 100644 --- a/include/bout/boundary_standard.hxx +++ b/include/bout/boundary_standard.hxx @@ -3,366 +3,389 @@ #ifndef __BNDRY_STD_H__ #define __BNDRY_STD_H__ -#include "boundary_op.hxx" -#include "bout_types.hxx" -#include -#include "unused.hxx" +#include "bout/boundary_op.hxx" +#include "bout/bout_types.hxx" +#include "bout/unused.hxx" +#include #include /// Dirichlet boundary condition set half way between guard cell and grid cell at 2nd order accuracy class BoundaryDirichlet_2ndOrder : public BoundaryOp { - public: +public: BoundaryDirichlet_2ndOrder() : val(0.) {} - BoundaryDirichlet_2ndOrder(BoutReal setval ): val(setval) {} - BoundaryDirichlet_2ndOrder(BoundaryRegion *region, BoutReal setval=0.):BoundaryOp(region),val(setval) { } + BoundaryDirichlet_2ndOrder(BoutReal setval) : val(setval) {} + BoundaryDirichlet_2ndOrder(BoundaryRegion* region, BoutReal setval = 0.) + : BoundaryOp(region), val(setval) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: BoutReal val; }; /// Dirichlet (set to zero) boundary condition class BoundaryDirichlet : public BoundaryOp { - public: +public: BoundaryDirichlet() : gen(nullptr) {} - BoundaryDirichlet(BoundaryRegion *region, std::shared_ptr g) + BoundaryDirichlet(BoundaryRegion* region, std::shared_ptr g) : BoundaryOp(region), gen(std::move(g)) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field2D &f,BoutReal t) override; - void apply(Field3D &f) override; - void apply(Field3D &f,BoutReal t) override; + void apply(Field2D& f) override; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override; + void apply(Field3D& f, BoutReal t) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: - std::shared_ptr gen; // Generator + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: + std::shared_ptr gen; // Generator }; BoutReal default_func(BoutReal t, int x, int y, int z); /// 3nd-order boundary condition class BoundaryDirichlet_O3 : public BoundaryOp { - public: +public: BoundaryDirichlet_O3() : gen(nullptr) {} - BoundaryDirichlet_O3(BoundaryRegion *region, std::shared_ptr g) + BoundaryDirichlet_O3(BoundaryRegion* region, std::shared_ptr g) : BoundaryOp(region), gen(std::move(g)) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field2D &f,BoutReal t) override; - void apply(Field3D &f) override; - void apply(Field3D &f,BoutReal t) override; + void apply(Field2D& f) override; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override; + void apply(Field3D& f, BoutReal t) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: - std::shared_ptr gen; // Generator + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: + std::shared_ptr gen; // Generator }; /// 4th-order boundary condition class BoundaryDirichlet_O4 : public BoundaryOp { - public: +public: BoundaryDirichlet_O4() : gen(nullptr) {} - BoundaryDirichlet_O4(BoundaryRegion *region, std::shared_ptr g) + BoundaryDirichlet_O4(BoundaryRegion* region, std::shared_ptr g) : BoundaryOp(region), gen(std::move(g)) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field2D &f,BoutReal t) override; - void apply(Field3D &f) override; - void apply(Field3D &f,BoutReal t) override; + void apply(Field2D& f) override; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override; + void apply(Field3D& f, BoutReal t) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: - std::shared_ptr gen; // Generator + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: + std::shared_ptr gen; // Generator }; /// Dirichlet boundary condition set half way between guard cell and grid cell at 4th order accuracy class BoundaryDirichlet_4thOrder : public BoundaryOp { - public: +public: BoundaryDirichlet_4thOrder() : val(0.) {} - BoundaryDirichlet_4thOrder(BoutReal setval ): val(setval) {} - BoundaryDirichlet_4thOrder(BoundaryRegion *region, BoutReal setval=0.):BoundaryOp(region),val(setval) { } + BoundaryDirichlet_4thOrder(BoutReal setval) : val(setval) {} + BoundaryDirichlet_4thOrder(BoundaryRegion* region, BoutReal setval = 0.) + : BoundaryOp(region), val(setval) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: BoutReal val; }; /// Neumann (zero-gradient) boundary condition for non-orthogonal meshes class BoundaryNeumann_NonOrthogonal : public BoundaryOp { - public: - BoundaryNeumann_NonOrthogonal(): val(0.) {} - BoundaryNeumann_NonOrthogonal(BoutReal setval ): val(setval) {} - BoundaryNeumann_NonOrthogonal(BoundaryRegion *region, BoutReal setval=0.):BoundaryOp(region),val(setval) { } +public: + BoundaryNeumann_NonOrthogonal() : val(0.) {} + BoundaryNeumann_NonOrthogonal(BoutReal setval) : val(setval) {} + BoundaryNeumann_NonOrthogonal(BoundaryRegion* region, BoutReal setval = 0.) + : BoundaryOp(region), val(setval) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; - private: + void apply(Field2D& f) override; + void apply(Field3D& f) override; + +private: BoutReal val; }; /// Neumann (zero-gradient) boundary condition, using 2nd order on boundary class BoundaryNeumann2 : public BoundaryOp { - public: +public: BoundaryNeumann2() {} - BoundaryNeumann2(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryNeumann2(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; }; /// Neumann boundary condition set half way between guard cell and grid cell at 2nd order accuracy class BoundaryNeumann_2ndOrder : public BoundaryOp { - public: +public: BoundaryNeumann_2ndOrder() : val(0.) {} - BoundaryNeumann_2ndOrder(BoutReal setval ): val(setval) {} - BoundaryNeumann_2ndOrder(BoundaryRegion *region, BoutReal setval=0.):BoundaryOp(region),val(setval) { } + BoundaryNeumann_2ndOrder(BoutReal setval) : val(setval) {} + BoundaryNeumann_2ndOrder(BoundaryRegion* region, BoutReal setval = 0.) + : BoundaryOp(region), val(setval) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: BoutReal val; }; // Neumann boundary condition set half way between guard cell and grid cell at 2nd order accuracy class BoundaryNeumann : public BoundaryOp { - public: +public: BoundaryNeumann() : gen(nullptr) {} - BoundaryNeumann(BoundaryRegion *region, std::shared_ptr g) + BoundaryNeumann(BoundaryRegion* region, std::shared_ptr g) : BoundaryOp(region), gen(std::move(g)) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field2D &f, BoutReal t) override; - void apply(Field3D &f) override; - void apply(Field3D &f,BoutReal t) override; + void apply(Field2D& f) override; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override; + void apply(Field3D& f, BoutReal t) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: std::shared_ptr gen; }; /// Neumann boundary condition set half way between guard cell and grid cell at 4th order accuracy class BoundaryNeumann_4thOrder : public BoundaryOp { - public: +public: BoundaryNeumann_4thOrder() : val(0.) {} - BoundaryNeumann_4thOrder(BoutReal setval ): val(setval) {} - BoundaryNeumann_4thOrder(BoundaryRegion *region, BoutReal setval=0.):BoundaryOp(region),val(setval) { } + BoundaryNeumann_4thOrder(BoutReal setval) : val(setval) {} + BoundaryNeumann_4thOrder(BoundaryRegion* region, BoutReal setval = 0.) + : BoundaryOp(region), val(setval) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: BoutReal val; }; /// Neumann boundary condition set half way between guard cell and grid cell at 4th order accuracy class BoundaryNeumann_O4 : public BoundaryOp { - public: +public: BoundaryNeumann_O4() : gen(nullptr) {} - BoundaryNeumann_O4(BoundaryRegion *region, std::shared_ptr g) + BoundaryNeumann_O4(BoundaryRegion* region, std::shared_ptr g) : BoundaryOp(region), gen(std::move(g)) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field2D &f, BoutReal t) override; - void apply(Field3D &f) override; - void apply(Field3D &f,BoutReal t) override; + void apply(Field2D& f) override; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override; + void apply(Field3D& f, BoutReal t) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: std::shared_ptr gen; }; /// NeumannPar (zero-gradient) boundary condition on /// the variable / sqrt(g_22) class BoundaryNeumannPar : public BoundaryOp { - public: +public: BoundaryNeumannPar() {} - BoundaryNeumannPar(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryNeumannPar(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; }; /// Robin (mix of Dirichlet and Neumann) class BoundaryRobin : public BoundaryOp { - public: +public: BoundaryRobin() : aval(0.), bval(0.), gval(0.) {} - BoundaryRobin(BoundaryRegion *region, BoutReal a, BoutReal b, BoutReal g):BoundaryOp(region), aval(a), bval(b), gval(g) { } + BoundaryRobin(BoundaryRegion* region, BoutReal a, BoutReal b, BoutReal g) + : BoundaryOp(region), aval(a), bval(b), gval(g) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; + private: BoutReal aval, bval, gval; }; /// Constant gradient (zero second derivative) class BoundaryConstGradient : public BoundaryOp { - public: +public: BoundaryConstGradient() {} - BoundaryConstGradient(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryConstGradient(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; }; /// Zero Laplacian, decaying solution class BoundaryZeroLaplace : public BoundaryOp { - public: +public: BoundaryZeroLaplace() {} - BoundaryZeroLaplace(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryZeroLaplace(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; }; /// Zero Laplacian class BoundaryZeroLaplace2 : public BoundaryOp { - public: +public: BoundaryZeroLaplace2() {} - BoundaryZeroLaplace2(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryZeroLaplace2(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; }; /// Constant Laplacian, decaying solution class BoundaryConstLaplace : public BoundaryOp { - public: +public: BoundaryConstLaplace() {} - BoundaryConstLaplace(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryConstLaplace(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; }; /// Vector boundary condition Div(B) = 0, Curl(B) = 0 class BoundaryDivCurl : public BoundaryOp { - public: +public: BoundaryDivCurl() {} - BoundaryDivCurl(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryDivCurl(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &UNUSED(f)) override { throw BoutException("ERROR: DivCurl boundary only for vectors"); } - void apply(Field3D &UNUSED(f)) override { throw BoutException("ERROR: DivCurl boundary only for vectors"); } - void apply(Vector2D &f) override; - void apply(Vector3D &f) override; + void apply(Field2D& UNUSED(f)) override { + throw BoutException("ERROR: DivCurl boundary only for vectors"); + } + void apply(Field3D& UNUSED(f)) override { + throw BoutException("ERROR: DivCurl boundary only for vectors"); + } + void apply(Vector2D& f) override; + void apply(Vector3D& f) override; }; /// Free boundary condition (evolve the field in the guard cells, using non-centred derivatives to calculate the ddt) class BoundaryFree : public BoundaryOp { - public: - BoundaryFree() : val(0.) {apply_to_ddt = true;} - BoundaryFree(BoutReal setval): val(setval) {} - BoundaryFree(BoundaryRegion *region, BoutReal setval=0.):BoundaryOp(region),val(setval) { } +public: + BoundaryFree() : val(0.) { apply_to_ddt = true; } + BoundaryFree(BoutReal setval) : val(setval) {} + BoundaryFree(BoundaryRegion* region, BoutReal setval = 0.) + : BoundaryOp(region), val(setval) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: BoutReal val; }; @@ -370,60 +393,62 @@ class BoundaryFree : public BoundaryOp { /// Alternative free boundary condition (evolve the field in the guard cells, using non-centred derivatives to calculate the ddt) class BoundaryFree_O2 : public BoundaryOp { public: - BoundaryFree_O2() {} - BoundaryFree_O2(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryFree_O2() {} + BoundaryFree_O2(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; }; class BoundaryFree_O3 : public BoundaryOp { public: BoundaryFree_O3() {} - BoundaryFree_O3(BoundaryRegion *region):BoundaryOp(region) { } + BoundaryFree_O3(BoundaryRegion* region) : BoundaryOp(region) {} using BoundaryOp::clone; - BoundaryOp* clone(BoundaryRegion *region, const std::list &args) override; + BoundaryOp* clone(BoundaryRegion* region, const std::list& args) override; using BoundaryOp::apply; - void apply(Field2D &f) override; - void apply(Field3D &f) override; + void apply(Field2D& f) override; + void apply(Field3D& f) override; using BoundaryOp::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; }; // End L.Easy - ///////////////////////////////////////////////////////// /// Convert a boundary condition to a relaxing one class BoundaryRelax : public BoundaryModifier { - public: - BoundaryRelax() : r(10.) {apply_to_ddt = true;} // Set default rate - BoundaryRelax(BoundaryOp *operation, BoutReal rate) : BoundaryModifier(operation) {r = fabs(rate); apply_to_ddt = true;} - BoundaryOp* cloneMod(BoundaryOp *op, const std::list &args) override; +public: + BoundaryRelax() : r(10.) { apply_to_ddt = true; } // Set default rate + BoundaryRelax(BoundaryOp* operation, BoutReal rate) : BoundaryModifier(operation) { + r = fabs(rate); + apply_to_ddt = true; + } + BoundaryOp* cloneMod(BoundaryOp* op, const std::list& args) override; using BoundaryModifier::apply; - void apply(Field2D &f) override {apply(f, 0.);}; - void apply(Field2D &f, BoutReal t) override; - void apply(Field3D &f) override {apply(f, 0.);}; - void apply(Field3D &f, BoutReal t) override; + void apply(Field2D& f) override { apply(f, 0.); }; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override { apply(f, 0.); }; + void apply(Field3D& f, BoutReal t) override; using BoundaryModifier::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; - private: + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + +private: BoutReal r; }; @@ -431,18 +456,20 @@ class BoundaryRelax : public BoundaryModifier { class BoundaryWidth : public BoundaryModifier { public: BoundaryWidth() : width(2) {} - BoundaryWidth(BoundaryOp *operation, int wid) : BoundaryModifier(operation), width(wid) {} - BoundaryOp* cloneMod(BoundaryOp *op, const std::list &args) override; + BoundaryWidth(BoundaryOp* operation, int wid) + : BoundaryModifier(operation), width(wid) {} + BoundaryOp* cloneMod(BoundaryOp* op, const std::list& args) override; using BoundaryModifier::apply; - void apply(Field2D &f) override {apply(f, 0.);}; - void apply(Field2D &f, BoutReal t) override; - void apply(Field3D &f) override {apply(f, 0.);}; - void apply(Field3D &f, BoutReal t) override; + void apply(Field2D& f) override { apply(f, 0.); }; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override { apply(f, 0.); }; + void apply(Field3D& f, BoutReal t) override; using BoundaryModifier::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + private: int width; }; @@ -451,19 +478,20 @@ private: /// Equivalent to converting the boundary condition to "Field Aligned" from "orthogonal" class BoundaryToFieldAligned : public BoundaryModifier { public: - BoundaryToFieldAligned(){} - BoundaryToFieldAligned(BoundaryOp *operation) : BoundaryModifier(operation){} - BoundaryOp* cloneMod(BoundaryOp *op, const std::list &args) override; + BoundaryToFieldAligned() {} + BoundaryToFieldAligned(BoundaryOp* operation) : BoundaryModifier(operation) {} + BoundaryOp* cloneMod(BoundaryOp* op, const std::list& args) override; using BoundaryModifier::apply; - void apply(Field2D &f) override {apply(f, 0.);}; - void apply(Field2D &f, BoutReal t) override; - void apply(Field3D &f) override {apply(f, 0.);}; - void apply(Field3D &f, BoutReal t) override; + void apply(Field2D& f) override { apply(f, 0.); }; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override { apply(f, 0.); }; + void apply(Field3D& f, BoutReal t) override; using BoundaryModifier::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + private: }; @@ -471,19 +499,20 @@ private: /// Equivalent to converting the boundary condition from "Field Aligned" to "orthogonal" class BoundaryFromFieldAligned : public BoundaryModifier { public: - BoundaryFromFieldAligned(){} - BoundaryFromFieldAligned(BoundaryOp *operation) : BoundaryModifier(operation){} - BoundaryOp* cloneMod(BoundaryOp *op, const std::list &args) override; + BoundaryFromFieldAligned() {} + BoundaryFromFieldAligned(BoundaryOp* operation) : BoundaryModifier(operation) {} + BoundaryOp* cloneMod(BoundaryOp* op, const std::list& args) override; using BoundaryModifier::apply; - void apply(Field2D &f) override {apply(f, 0.);}; - void apply(Field2D &f, BoutReal t) override; - void apply(Field3D &f) override {apply(f, 0.);}; - void apply(Field3D &f, BoutReal t) override; + void apply(Field2D& f) override { apply(f, 0.); }; + void apply(Field2D& f, BoutReal t) override; + void apply(Field3D& f) override { apply(f, 0.); }; + void apply(Field3D& f, BoutReal t) override; using BoundaryModifier::apply_ddt; - void apply_ddt(Field2D &f) override; - void apply_ddt(Field3D &f) override; + void apply_ddt(Field2D& f) override; + void apply_ddt(Field3D& f) override; + private: }; diff --git a/include/bout/bout.hxx b/include/bout/bout.hxx index dc5b1f98d1..b1845b8f1b 100644 --- a/include/bout/bout.hxx +++ b/include/bout/bout.hxx @@ -38,20 +38,20 @@ #include "bout/build_config.hxx" -#include "boutcomm.hxx" -#include "difops.hxx" // Differential operators -#include "field2d.hxx" -#include "field3d.hxx" -#include "globals.hxx" -#include "options_netcdf.hxx" -#include "output.hxx" -#include "smoothing.hxx" // Smoothing functions -#include "sourcex.hxx" // source and mask functions -#include "utils.hxx" -#include "vecops.hxx" // Vector differential operations -#include "vector2d.hxx" -#include "vector3d.hxx" -#include "where.hxx" +#include "bout/boutcomm.hxx" +#include "bout/difops.hxx" // Differential operators +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/globals.hxx" +#include "bout/options_netcdf.hxx" +#include "bout/output.hxx" +#include "bout/smoothing.hxx" // Smoothing functions +#include "bout/sourcex.hxx" // source and mask functions +#include "bout/utils.hxx" +#include "bout/vecops.hxx" // Vector differential operations +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" +#include "bout/where.hxx" #include "bout/mesh.hxx" #include "bout/solver.hxx" #include "bout/version.hxx" diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx index 2b0950c109..451d97ccf1 100644 --- a/include/bout/bout_enum_class.hxx +++ b/include/bout/bout_enum_class.hxx @@ -22,10 +22,10 @@ #ifndef __BOUT_ENUM_CLASS_H__ #define __BOUT_ENUM_CLASS_H__ +#include "bout/boutexception.hxx" +#include "bout/msg_stack.hxx" +#include "bout/options.hxx" #include "bout/macro_for_each.hxx" -#include "boutexception.hxx" -#include "msg_stack.hxx" -#include "options.hxx" #include #include @@ -53,52 +53,51 @@ #define _ec_expand_10(_call, enumname, x, ...) \ _call(enumname, x) _ec_expand_9(_call, enumname, __VA_ARGS__) -#define BOUT_ENUM_CLASS_MAP_ARGS(mac, enumname, ...) \ - BOUT_EXPAND(_GET_FOR_EACH_EXPANSION( \ - __VA_ARGS__, _ec_expand_10, _ec_expand_9, _ec_expand_8, _ec_expand_7, _ec_expand_6, \ - _ec_expand_5, _ec_expand_4, _ec_expand_3, _ec_expand_2, _ec_expand_1) \ - (mac, enumname, __VA_ARGS__)) +#define BOUT_ENUM_CLASS_MAP_ARGS(mac, enumname, ...) \ + BOUT_EXPAND(_GET_FOR_EACH_EXPANSION( \ + __VA_ARGS__, _ec_expand_10, _ec_expand_9, _ec_expand_8, _ec_expand_7, \ + _ec_expand_6, _ec_expand_5, _ec_expand_4, _ec_expand_3, _ec_expand_2, \ + _ec_expand_1)(mac, enumname, __VA_ARGS__)) #define BOUT_ENUM_CLASS_STR(enumname, val) {enumname::val, lowercase(#val)}, #define BOUT_STR_ENUM_CLASS(enumname, val) {lowercase(#val), enumname::val}, -#define BOUT_MAKE_FROMSTRING_NAME(enumname) enumname ## FromString +#define BOUT_MAKE_FROMSTRING_NAME(enumname) enumname##FromString /// Create an enum class with toString and FromString functions, and an /// Options::as overload to read the enum -#define BOUT_ENUM_CLASS(enumname, ...) \ -enum class enumname { __VA_ARGS__ }; \ - \ -inline std::string toString(enumname e) { \ - AUTO_TRACE(); \ - const static std::map toString_map = { \ - BOUT_ENUM_CLASS_MAP_ARGS(BOUT_ENUM_CLASS_STR, enumname, __VA_ARGS__) \ - }; \ - auto found = toString_map.find(e); \ - if (found == toString_map.end()) { \ - throw BoutException("Did not find enum {:d}", static_cast(e)); \ - } \ - return found->second; \ -} \ - \ -inline enumname BOUT_MAKE_FROMSTRING_NAME(enumname)(const std::string& s) { \ - AUTO_TRACE(); \ - const static std::map fromString_map = { \ - BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__) \ - }; \ - auto found = fromString_map.find(s); \ - if (found == fromString_map.end()) { \ - throw BoutException("Did not find enum {:s}", s); \ - } \ - return found->second; \ -} \ - \ -template <> inline enumname Options::as(const enumname&) const { \ - return BOUT_MAKE_FROMSTRING_NAME(enumname)(this->as()); \ -} \ - \ -inline std::ostream& operator<<(std::ostream& out, const enumname& e) { \ - return out << toString(e); \ -} +#define BOUT_ENUM_CLASS(enumname, ...) \ + enum class enumname { __VA_ARGS__ }; \ + \ + inline std::string toString(enumname e) { \ + AUTO_TRACE(); \ + const static std::map toString_map = { \ + BOUT_ENUM_CLASS_MAP_ARGS(BOUT_ENUM_CLASS_STR, enumname, __VA_ARGS__)}; \ + auto found = toString_map.find(e); \ + if (found == toString_map.end()) { \ + throw BoutException("Did not find enum {:d}", static_cast(e)); \ + } \ + return found->second; \ + } \ + \ + inline enumname BOUT_MAKE_FROMSTRING_NAME(enumname)(const std::string& s) { \ + AUTO_TRACE(); \ + const static std::map fromString_map = { \ + BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__)}; \ + auto found = fromString_map.find(s); \ + if (found == fromString_map.end()) { \ + throw BoutException("Did not find enum {:s}", s); \ + } \ + return found->second; \ + } \ + \ + template <> \ + inline enumname Options::as(const enumname&) const { \ + return BOUT_MAKE_FROMSTRING_NAME(enumname)(this->as()); \ + } \ + \ + inline std::ostream& operator<<(std::ostream& out, const enumname& e) { \ + return out << toString(e); \ + } #endif // __BOUT_ENUM_CLASS_H__ diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx index 33cb2b0dce..e5c764aa66 100644 --- a/include/bout/bout_types.hxx +++ b/include/bout/bout_types.hxx @@ -31,11 +31,15 @@ using BoutReal = double; /// Quiet NaN constexpr BoutReal BoutNaN = std::numeric_limits::quiet_NaN(); -#define ENUMSTR(val) {val, #val} -#define STRENUM(val) {#val, val} +#define ENUMSTR(val) \ + { val, #val } +#define STRENUM(val) \ + { \ +#val, val \ + } /// 4 possible variable locations. Default is for passing to functions -enum class CELL_LOC {deflt, centre, xlow, ylow, zlow, vshift}; +enum class CELL_LOC { deflt, centre, xlow, ylow, zlow, vshift }; constexpr CELL_LOC CELL_DEFAULT = CELL_LOC::deflt; constexpr CELL_LOC CELL_CENTRE = CELL_LOC::centre; constexpr CELL_LOC CELL_CENTER = CELL_LOC::centre; @@ -48,7 +52,7 @@ std::string toString(CELL_LOC location); CELL_LOC CELL_LOCFromString(const std::string& location_string); /// Differential methods. Both central and upwind -enum class DIFF_METHOD {deflt, u1, u2, c2, w2, w3, c4, u3, fft, split, s2}; +enum class DIFF_METHOD { deflt, u1, u2, c2, w2, w3, c4, u3, fft, split, s2 }; constexpr DIFF_METHOD DIFF_DEFAULT = DIFF_METHOD::deflt; constexpr DIFF_METHOD DIFF_U1 = DIFF_METHOD::u1; constexpr DIFF_METHOD DIFF_U2 = DIFF_METHOD::u2; @@ -64,7 +68,7 @@ constexpr DIFF_METHOD DIFF_S2 = DIFF_METHOD::s2; std::string toString(DIFF_METHOD location); /// Specify grid region for looping -enum class REGION {all, nobndry, nox, noy, noz}; +enum class REGION { all, nobndry, nox, noy, noz }; constexpr REGION RGN_ALL = REGION::all; constexpr REGION RGN_NOBNDRY = REGION::nobndry; constexpr REGION RGN_NOX = REGION::nox; @@ -128,14 +132,14 @@ std::string toString(DERIV deriv); // A small struct that can be used to wrap a specific enum value, giving // it a unique type that can be passed as a valid type to templates and // which can be inspected to provide the actual value of the enum -template +template struct enumWrapper { using type = T; static const type value = val; - T lookup(){return val;}; + T lookup() { return val; }; }; /// Boundary condition function -using FuncPtr = BoutReal(*)(BoutReal t, BoutReal x, BoutReal y, BoutReal z); +using FuncPtr = BoutReal (*)(BoutReal t, BoutReal x, BoutReal y, BoutReal z); #endif // __BOUT_TYPES_H__ diff --git a/include/bout/boutcomm.hxx b/include/bout/boutcomm.hxx index 88ad07e2b6..77038844a8 100644 --- a/include/bout/boutcomm.hxx +++ b/include/bout/boutcomm.hxx @@ -42,8 +42,8 @@ public: /// Shortcut method static MPI_Comm get(); - static void setArgs(int &c, char** &v); - + static void setArgs(int& c, char**& v); + static void cleanup(); static int rank(); ///< Rank: my processor number @@ -56,7 +56,7 @@ public: MPI_Comm getComm(); bool isSet(); - private: +private: BoutComm(); int* pargc{nullptr}; @@ -64,9 +64,8 @@ public: ///< so pointers are used bool hasBeenSet{false}; MPI_Comm comm; - - static BoutComm* instance; ///< The only instance of this class (Singleton) + static BoutComm* instance; ///< The only instance of this class (Singleton) }; #endif // __BOUTCOMM_H__ diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx index ccd7e1d50a..5b8a421692 100644 --- a/include/bout/boutexception.hxx +++ b/include/bout/boutexception.hxx @@ -28,9 +28,7 @@ public: ~BoutException() override; - const char* what() const noexcept override { - return message.c_str(); - } + const char* what() const noexcept override { return message.c_str(); } /// Return the exception message along with the MsgStack and /// backtrace (if available) diff --git a/include/bout/constants.hxx b/include/bout/constants.hxx index c8799b4bcd..c811799aef 100644 --- a/include/bout/constants.hxx +++ b/include/bout/constants.hxx @@ -6,7 +6,7 @@ #ifndef __CONSTANTS_H__ #define __CONSTANTS_H__ -#include +#include /// Mathematical constant pi constexpr BoutReal PI = 3.141592653589793; @@ -14,18 +14,18 @@ constexpr BoutReal PI = 3.141592653589793; constexpr BoutReal TWOPI = 2 * PI; namespace SI { - // Constants in SI system of units - constexpr BoutReal c = 299792458; ///< Speed of light in vacuum - constexpr BoutReal mu0 = 4.e-7*PI; ///< Permeability of free space - constexpr BoutReal e0 = 1/(c*c*mu0); ///< Permittivity of free space - constexpr BoutReal qe = 1.602176634e-19; ///< Electron charge - constexpr BoutReal Me = 9.10938356e-31; ///< Electron mass - constexpr BoutReal Mp = 1.672621898e-27; ///< Proton mass - constexpr BoutReal kb = 1.38064852e-23; ///< Boltzmanns constant - constexpr BoutReal amu = 1.660539040e-27; ///< Unified atomic mass unit - constexpr BoutReal M_Hydrogen = 1.008 * amu; ///< Mass of a Hydrogen atom - constexpr BoutReal M_Deuterium = 2.01410178 * amu; ///< Mass of a Deuterium atom - constexpr BoutReal M_Tritium = 3.0160492 * amu; ///< Mass of a Tritium atom -} +// Constants in SI system of units +constexpr BoutReal c = 299792458; ///< Speed of light in vacuum +constexpr BoutReal mu0 = 4.e-7 * PI; ///< Permeability of free space +constexpr BoutReal e0 = 1 / (c * c * mu0); ///< Permittivity of free space +constexpr BoutReal qe = 1.602176634e-19; ///< Electron charge +constexpr BoutReal Me = 9.10938356e-31; ///< Electron mass +constexpr BoutReal Mp = 1.672621898e-27; ///< Proton mass +constexpr BoutReal kb = 1.38064852e-23; ///< Boltzmanns constant +constexpr BoutReal amu = 1.660539040e-27; ///< Unified atomic mass unit +constexpr BoutReal M_Hydrogen = 1.008 * amu; ///< Mass of a Hydrogen atom +constexpr BoutReal M_Deuterium = 2.01410178 * amu; ///< Mass of a Deuterium atom +constexpr BoutReal M_Tritium = 3.0160492 * amu; ///< Mass of a Tritium atom +} // namespace SI #endif // __CONSTANTS_H__ diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx index a5b996b250..625c07ec2e 100644 --- a/include/bout/coordinates.hxx +++ b/include/bout/coordinates.hxx @@ -33,11 +33,11 @@ #ifndef __COORDINATES_H__ #define __COORDINATES_H__ -#include "field2d.hxx" -#include "field3d.hxx" -#include "utils.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/utils.hxx" #include "bout/paralleltransform.hxx" -#include +#include class Datafile; class Mesh; @@ -46,7 +46,7 @@ class Mesh; * Represents a coordinate system, and associated operators * * This is a container for a collection of metric tensor components - */ + */ class Coordinates { public: #if BOUT_USE_METRIC_3D @@ -56,7 +56,7 @@ public: #endif /// Standard constructor from input - Coordinates(Mesh *mesh, Options* options = nullptr); + Coordinates(Mesh* mesh, Options* options = nullptr); /// Constructor interpolating from another Coordinates object /// By default attempts to read staggered Coordinates from grid data source, @@ -64,8 +64,8 @@ public: /// force_interpolate_from_centre argument to true to always interpolate /// (useful if CELL_CENTRE Coordinates have been changed, so reading from file /// would not be correct). - Coordinates(Mesh *mesh, Options* options, const CELL_LOC loc, const Coordinates* coords_in, - bool force_interpolate_from_centre=false); + Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc, + const Coordinates* coords_in, bool force_interpolate_from_centre = false); /// A constructor useful for testing purposes. To use it, inherit /// from Coordinates. If \p calculate_geometry is true (default), @@ -117,7 +117,7 @@ public: /// Calculate differential geometry quantities from the metric tensor int geometry(bool recalculate_staggered = true, - bool force_interpolate_from_centre = false); + bool force_interpolate_from_centre = false); /// Invert contravatiant metric to get covariant components int calcCovariant(const std::string& region = "RGN_ALL"); /// Invert covariant metric to get contravariant components @@ -173,7 +173,7 @@ public: const std::string& method = "DEFAULT"); Field3D Grad_par(const Field3D& var, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT"); + const std::string& method = "DEFAULT"); /// Advection along magnetic field V*b.Grad(f) FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f, @@ -181,21 +181,22 @@ public: const std::string& method = "DEFAULT"); Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, - CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT"); + CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT"); /// Divergence along magnetic field Div(b*f) = B.Grad(f/B) FieldMetric Div_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT"); Field3D Div_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT"); + const std::string& method = "DEFAULT"); // Second derivative along magnetic field FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT"); Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT"); + const std::string& method = "DEFAULT"); // Perpendicular Laplacian operator, using only X-Z derivatives // NOTE: This might be better bundled with the Laplacian inversion code // since it makes use of the same coefficients and FFT routines @@ -206,8 +207,8 @@ public: // Full parallel Laplacian operator on scalar field // Laplace_par(f) = Div( b (b dot Grad(f)) ) FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT); - Field3D Laplace_par(const Field3D &f, CELL_LOC outloc=CELL_DEFAULT); - + Field3D Laplace_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT); + // Full Laplacian operator on scalar field FieldMetric Laplace(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& dfdy_boundary_conditions = "free_o3", @@ -222,7 +223,7 @@ public: private: int nz; // Size of mesh in Z. This is mesh->ngz-1 - Mesh * localmesh; + Mesh* localmesh; CELL_LOC location; /// Handles calculation of yup and ydown diff --git a/include/bout/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx index 25e45cccc2..82ef283476 100644 --- a/include/bout/cyclic_reduction.hxx +++ b/include/bout/cyclic_reduction.hxx @@ -47,18 +47,19 @@ //#define DIAGNOSE 1 #include "mpi.h" -#include "utils.hxx" -#include "msg_stack.hxx" -#include +#include "bout/msg_stack.hxx" +#include "bout/utils.hxx" +#include +#include "bout/boutexception.hxx" #include "bout/assert.hxx" -#include "boutexception.hxx" -#include "output.hxx" +#include "bout/output.hxx" #include "bout/openmpwrap.hxx" -template class CyclicReduce { +template +class CyclicReduce { public: CyclicReduce() = default; @@ -76,8 +77,9 @@ public: int np, myp; MPI_Comm_size(c, &np); MPI_Comm_rank(c, &myp); - if ((size != N) || (np != nprocs) || (myp != myproc)) + if ((size != N) || (np != nprocs) || (myp != myproc)) { Nsys = 0; // Need to re-size + } N = size; periodic = false; nprocs = np; @@ -90,7 +92,7 @@ public: /// By default not periodic void setPeriodic(bool p = true) { periodic = p; } - void setCoefs(const Array &a, const Array &b, const Array &c) { + void setCoefs(const Array& a, const Array& b, const Array& c) { ASSERT2(a.size() == b.size()); ASSERT2(a.size() == c.size()); ASSERT2(a.size() == N); @@ -99,7 +101,7 @@ public: Matrix bMatrix(1, N); Matrix cMatrix(1, N); - BOUT_OMP(parallel for) + BOUT_OMP(parallel for) for (int i = 0; i < N; ++i) { aMatrix(0, i) = a[i]; bMatrix(0, i) = b[i]; @@ -139,7 +141,7 @@ public: /// /// @param[in] rhs Array storing Values of the rhs for a single system /// @param[out] x Array storing the result for a single system - void solve(const Array &rhs, Array &x) { + void solve(const Array& rhs, Array& x) { ASSERT2(rhs.size() == x.size()); ASSERT2(rhs.size() == N); @@ -166,7 +168,7 @@ public: /// /// @param[in] rhs Matrix storing Values of the rhs for each system /// @param[out] x Matrix storing the result for each system - void solve(const Matrix &rhs, Matrix &x) { + void solve(const Matrix& rhs, Matrix& x) { TRACE("CyclicReduce::solve"); ASSERT2(static_cast(std::get<0>(rhs.shape())) == Nsys); ASSERT2(static_cast(std::get<0>(x.shape())) == Nsys); @@ -176,8 +178,9 @@ public: // Multiple RHS int nrhs = std::get<0>(rhs.shape()); - if (nrhs != Nsys) + if (nrhs != Nsys) { throw BoutException("Sorry, can't yet handle nrhs != nsys"); + } // Insert RHS into coefs array. Ordered to allow efficient partitioning // for MPI send/receives @@ -227,10 +230,12 @@ public: if (p == myproc) { // Just copy the data - BOUT_OMP(parallel for) - for (int i = 0; i < myns; i++) - for (int j = 0; j < 8; j++) + BOUT_OMP(parallel for) + for (int i = 0; i < myns; i++) { + for (int j = 0; j < 8; j++) { ifcs(i, 8 * p + j) = myif(sys0 + i, j); + } + } } else { #ifdef DIAGNOSE output << "Expecting to receive " << len << " from " << p << endl; @@ -249,13 +254,15 @@ public: int s0 = 0; for (int p = 0; p < nprocs; p++) { // Loop over processor int nsp = ns; - if (p < nsextra) + if (p < nsextra) { nsp++; + } if ((p != myproc) && (nsp > 0)) { #ifdef DIAGNOSE output << "Sending to " << p << endl; - for (int i = 0; i < 8; i++) + for (int i = 0; i < 8; i++) { output << "value " << i << " : " << myif(s0, i) << endl; + } #endif MPI_Send(&myif(s0, 0), // Data pointer 8 * nsp * sizeof(T), // Number @@ -278,14 +285,15 @@ public: #ifdef DIAGNOSE output << "Copying received data from " << p << endl; #endif - BOUT_OMP(parallel for) - for (int i = 0; i < myns; i++) + BOUT_OMP(parallel for) + for (int i = 0; i < myns; i++) { for (int j = 0; j < 8; j++) { #ifdef DIAGNOSE output << "Value " << j << " : " << recvbuffer(p, 8 * i + j) << endl; #endif ifcs(i, 8 * p + j) = recvbuffer(p, 8 * i + j); } + } req[p] = MPI_REQUEST_NULL; } } while (p != MPI_UNDEFINED); @@ -308,7 +316,7 @@ public: if2x2.ensureUnique(); x1.ensureUnique(); xn.ensureUnique(); - + BOUT_OMP(parallel for) for (int i = 0; i < myns; ++i) { // (a b) (x1) = (b1) @@ -349,13 +357,14 @@ public: // Post receives for (int p = 0; p < nprocs; p++) { // Loop over processor int nsp = ns; - if (p < nsextra) + if (p < nsextra) { nsp++; + } int len = 2 * nsp * sizeof(T); // 2 values per system if (p == myproc) { // Just copy the data - BOUT_OMP(parallel for) + BOUT_OMP(parallel for) for (int i = 0; i < myns; i++) { x1[sys0 + i] = ifx(i, 2 * p); xn[sys0 + i] = ifx(i, 2 * p + 1); @@ -371,15 +380,16 @@ public: p, // Identifier comm, // Communicator &req[p]); // Request - } else + } else { req[p] = MPI_REQUEST_NULL; + } } if (myns > 0) { // Send data for (int p = 0; p < nprocs; p++) { // Loop over processor if (p != myproc) { - BOUT_OMP(parallel for) + BOUT_OMP(parallel for) for (int i = 0; i < myns; i++) { ifp[2 * i] = ifx(i, 2 * p); ifp[2 * i + 1] = ifx(i, 2 * p + 1); @@ -408,14 +418,16 @@ public: int s0 = fromproc * ns; if (fromproc > nsextra) { s0 += nsextra; - } else + } else { s0 += fromproc; + } nsp = ns; - if (fromproc < nsextra) + if (fromproc < nsextra) { nsp++; - - BOUT_OMP(parallel for) + } + + BOUT_OMP(parallel for) for (int i = 0; i < nsp; i++) { x1[s0 + i] = recvbuffer(fromproc, 2 * i); xn[s0 + i] = recvbuffer(fromproc, 2 * i + 1); @@ -461,8 +473,9 @@ private: /// @param[in] nsys Number of independent systems to solve /// @param[in] n Size of each system of equations void allocMemory(int np, int nsys, int n) { - if ((nsys == Nsys) && (n == N) && (np == nprocs)) + if ((nsys == Nsys) && (n == N) && (np == nprocs)) { return; // No need to allocate memory + } nprocs = np; Nsys = nsys; @@ -520,12 +533,13 @@ private: /// ( a3 b3 c3 ) => ( A2 B2 C2) /// ( ... ) /// ( an bn cn) - void reduce(int ns, int nloc, Matrix &co, Matrix &ifc) { + void reduce(int ns, int nloc, Matrix& co, Matrix& ifc) { #ifdef DIAGNOSE - if (nloc < 2) + if (nloc < 2) { throw BoutException("CyclicReduce::reduce nloc < 2"); + } #endif - + BOUT_OMP(parallel for) for (int j = 0; j < ns; j++) { // Calculate upper interface equation @@ -538,8 +552,9 @@ private: for (int i = nloc - 3; i >= 0; i--) { // Check for zero pivot - if (std::abs(ifc(j, 1)) < 1e-10) + if (std::abs(ifc(j, 1)) < 1e-10) { throw BoutException("Zero pivot in CyclicReduce::reduce"); + } // beta <- v_{i,i+1} / v_u,i T beta = co(j, 4 * i + 2) / ifc(j, 1); @@ -559,13 +574,15 @@ private: // v_l <- v_(k+1) // b_l <- b_{k+1} - for (int i = 0; i < 4; i++) + for (int i = 0; i < 4; i++) { ifc(j, 4 + i) = co(j, 4 + i); + } for (int i = 2; i < nloc; i++) { - if (std::abs(ifc(j, 4 + 1)) < 1e-10) + if (std::abs(ifc(j, 4 + 1)) < 1e-10) { throw BoutException("Zero pivot in CyclicReduce::reduce"); + } // alpha <- v_{i,i-1} / v_l,i-1 T alpha = co(j, 4 * i) / ifc(j, 4 + 1); @@ -598,20 +615,20 @@ private: const Array& xn, Matrix& xa) { xa.ensureUnique(); // Going to be modified, so call this outside parallel region - + // Tridiagonal system, solve using serial Thomas algorithm // xa -- Result for each system // co -- Coefficients & rhs for each system BOUT_OMP(parallel for) for (int i = 0; i < ns; i++) { // Loop over systems - Array gam(nloc); // Thread-local array + Array gam(nloc); // Thread-local array T bet = 1.0; xa(i, 0) = x1[i]; // Already know the first gam[1] = 0.; for (int j = 1; j < nloc - 1; j++) { bet = co(i, 4 * j + 1) - co(i, 4 * j) * gam[j]; // bet = b[j]-a[j]*gam[j] - xa(i, j) = (co(i, 4 * j + 3) - co(i, 4 * j) * xa(i, j - 1)) / - bet; // x[j] = (r[j]-a[j]*x[j-1])/bet; + xa(i, j) = (co(i, 4 * j + 3) - co(i, 4 * j) * xa(i, j - 1)) + / bet; // x[j] = (r[j]-a[j]*x[j-1])/bet; gam[j + 1] = co(i, 4 * j + 2) / bet; // gam[j+1] = c[j]/bet } xa(i, nloc - 1) = xn[i]; // Know the last value diff --git a/include/bout/dcomplex.hxx b/include/bout/dcomplex.hxx index 0b0ce50552..569b5f2c13 100644 --- a/include/bout/dcomplex.hxx +++ b/include/bout/dcomplex.hxx @@ -32,12 +32,12 @@ #ifndef __DCOMPLEX_H__ #define __DCOMPLEX_H__ +#include "bout/bout_types.hxx" #include -#include "bout_types.hxx" using dcomplex = std::complex; -const dcomplex Im(0,1); // 1i +const dcomplex Im(0, 1); // 1i /// Complex type for passing data to/from FORTRAN struct fcmplx { diff --git a/include/bout/deriv_store.hxx b/include/bout/deriv_store.hxx index 1c6504b2ec..6dc44c76ad 100644 --- a/include/bout/deriv_store.hxx +++ b/include/bout/deriv_store.hxx @@ -36,10 +36,10 @@ #include -#include -#include -#include -#include +#include +#include +#include +#include /// Here we have a templated singleton that is used to store DerivativeFunctions /// for all types of derivatives. It is templated on the FieldType (2D or 3D) as @@ -50,9 +50,10 @@ /// upwind and flux). template struct DerivativeStore { - using standardFunc = std::function; - using flowFunc = - std::function; + using standardFunc = + std::function; + using flowFunc = std::function; using upwindFunc = flowFunc; using fluxFunc = flowFunc; @@ -202,8 +203,7 @@ struct DerivativeStore { }; // Register this method name in lookup of known methods - registeredMethods[getKey(direction, stagger, toString(derivType))].insert( - methodName); + registeredMethods[getKey(direction, stagger, toString(derivType))].insert(methodName); }; /// Templated versions of the above registration routines. @@ -251,8 +251,9 @@ struct DerivativeStore { }; const auto resultOfFind = theMap->find(key); - if (resultOfFind != theMap->end()) + if (resultOfFind != theMap->end()) { return resultOfFind->second; + } throw BoutException("Couldn't find requested method {:s} in map for standard " "derivative of type {:s}.", @@ -293,8 +294,9 @@ struct DerivativeStore { }; const auto resultOfFind = theMap->find(key); - if (resultOfFind != theMap->end()) + if (resultOfFind != theMap->end()) { return resultOfFind->second; + } throw BoutException( "Couldn't find requested method {:s} in map for standard flow of type {:s}.", @@ -391,8 +393,8 @@ struct DerivativeStore { defaultMethods[getKey(theDirection, STAGGER::C2L, theDerivTypeString)] = theDefault; output_verbose << "The default method for staggered derivative type " - << theDerivTypeString << " in direction " - << toString(theDirection) << " is " << theDefault << "\n"; + << theDerivTypeString << " in direction " << toString(theDirection) + << " is " << theDefault << "\n"; } } } @@ -489,8 +491,7 @@ private: std::string getMethodName(std::string name, DIRECTION direction, STAGGER stagger = STAGGER::None) const { AUTO_TRACE(); - return name + " (" + toString(direction) + ", " + toString(stagger) - + ")"; + return name + " (" + toString(direction) + ", " + toString(stagger) + ")"; }; std::string nameLookup(const std::string name, const std::string defaultName) const { diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx index 9bbb570fac..c01e1562fc 100644 --- a/include/bout/derivs.hxx +++ b/include/bout/derivs.hxx @@ -29,12 +29,12 @@ #ifndef __DERIVS_H__ #define __DERIVS_H__ -#include "field2d.hxx" -#include "field3d.hxx" -#include "vector2d.hxx" -#include "vector3d.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" -#include "bout_types.hxx" +#include "bout/bout_types.hxx" ////////// FIRST DERIVATIVES ////////// @@ -50,8 +50,9 @@ /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D DDX(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D DDX(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate first partial derivative in X /// @@ -81,8 +82,9 @@ Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D DDY(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D DDY(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate first partial derivative in Y /// @@ -112,8 +114,9 @@ Coordinates::FieldMetric DDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D DDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D DDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate first partial derivative in Z /// @@ -143,8 +146,9 @@ Coordinates::FieldMetric DDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Vector3D DDZ(const Vector3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Vector3D DDZ(const Vector3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate first partial derivative in Z /// @@ -158,8 +162,9 @@ Vector3D DDZ(const Vector3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::strin /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Vector2D DDZ(const Vector2D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Vector2D DDZ(const Vector2D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); ////////// SECOND DERIVATIVES ////////// @@ -175,8 +180,9 @@ Vector2D DDZ(const Vector2D& f, CELL_LOC outloc = CELL_DEFAULT, const std::strin /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D2DX2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D2DX2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate second partial derivative in X /// @@ -206,8 +212,9 @@ Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D2DY2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D2DY2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate second partial derivative in Y /// @@ -237,8 +244,9 @@ Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D2DZ2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D2DZ2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate second partial derivative in Z /// @@ -270,8 +278,9 @@ Coordinates::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D4DX4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D4DX4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate forth partial derivative in X /// @@ -301,8 +310,9 @@ Coordinates::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D4DY4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D4DY4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate forth partial derivative in Y /// @@ -332,8 +342,9 @@ Coordinates::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D4DZ4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D4DZ4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate forth partial derivative in Z /// @@ -365,7 +376,8 @@ Coordinates::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY Field3D VDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// For terms of form v * grad(f) /// @@ -399,7 +411,8 @@ Coordinates::FieldMetric VDDX(const Field2D& v, const Field2D& f, /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY Field3D VDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// For terms of form v * grad(f) /// @@ -433,7 +446,8 @@ Coordinates::FieldMetric VDDY(const Field2D& v, const Field2D& f, /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY Field3D VDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// For terms of form v * grad(f) /// @@ -485,7 +499,8 @@ Coordinates::FieldMetric VDDZ(const Field3D& v, const Field2D& f, /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY Field3D FDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// for terms of form div(v * f) /// @@ -519,7 +534,8 @@ Coordinates::FieldMetric FDDX(const Field2D& v, const Field2D& f, /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY Field3D FDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// for terms of form div(v * f) /// @@ -553,7 +569,8 @@ Coordinates::FieldMetric FDDY(const Field2D& v, const Field2D& f, /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY Field3D FDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// for terms of form div(v * f) /// @@ -614,11 +631,11 @@ Field3D D2DXDY(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, /// (default) then the same as the region for the calculation as a /// whole. If dfdy_region < region in size then this will cause /// errors. -Coordinates::FieldMetric -D2DXDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, - const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY", - const std::string& dfdy_boundary_condition = "free_o3", - const std::string& dfdy_region = ""); +Coordinates::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY", + const std::string& dfdy_boundary_condition = "free_o3", + const std::string& dfdy_region = ""); /// Calculate mixed partial derivative in x and z /// @@ -632,8 +649,9 @@ D2DXDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate mixed partial derivative in x and z /// @@ -663,8 +681,9 @@ Coordinates::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT /// If not given, defaults to DIFF_DEFAULT /// @param[in] region What region is expected to be calculated /// If not given, defaults to RGN_NOBNDRY -Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& - method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); +Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, + const std::string& method = "DEFAULT", + const std::string& region = "RGN_NOBNDRY"); /// Calculate mixed partial derivative in y and z /// @@ -682,5 +701,4 @@ Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); - #endif // __DERIVS_H__ diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx index ebab0a1c63..2b5c6746fd 100644 --- a/include/bout/difops.hxx +++ b/include/bout/difops.hxx @@ -36,10 +36,10 @@ #ifndef __DIFOPS_H__ #define __DIFOPS_H__ -#include "field3d.hxx" -#include "field2d.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" -#include "bout_types.hxx" +#include "bout/bout_types.hxx" #include "bout/solver.hxx" /*! diff --git a/include/bout/expr.hxx b/include/bout/expr.hxx index 30a9d9664c..f2de9c3b62 100644 --- a/include/bout/expr.hxx +++ b/include/bout/expr.hxx @@ -14,19 +14,20 @@ #warning expr.hxx is deprecated. Do not use! -#include -#include #include +#include +#include /// Literal class to capture BoutReal values in expressions class Literal { - public: +public: /// Type of this expression using type = Literal; Literal(BoutReal v) : val(v) {} ~Literal() {} - BoutReal operator()(int x, int y, int z) const {return val;} + BoutReal operator()(int x, int y, int z) const { return val; } + private: const BoutReal val; }; @@ -34,21 +35,28 @@ private: class Field3DExpr { public: using type = Field3D; - - Field3DExpr(const Field3D &f) : data(&f(0,0,0)) {} - const BoutReal& operator()(int x, int y, int z) const { return data[(x*bout::globals::mesh->LocalNy + y)*bout::globals::mesh->LocalNz + z]; } + + Field3DExpr(const Field3D& f) : data(&f(0, 0, 0)) {} + const BoutReal& operator()(int x, int y, int z) const { + return data[(x * bout::globals::mesh->LocalNy + y) * bout::globals::mesh->LocalNz + + z]; + } + private: - const BoutReal *data; + const BoutReal* data; }; class Field2DExpr { public: using type = Field2D; - - Field2DExpr(const Field2D &f) : data(&f(0,0)) {} - const BoutReal& operator()(int x, int y, int z) const { return data[x*bout::globals::mesh->LocalNy + y]; } + + Field2DExpr(const Field2D& f) : data(&f(0, 0)) {} + const BoutReal& operator()(int x, int y, int z) const { + return data[x * bout::globals::mesh->LocalNy + y]; + } + private: - const BoutReal *data; + const BoutReal* data; }; /// Expression traits, to convert doubles etc. to Literal @@ -79,38 +87,38 @@ struct exprTraits { template struct asExpr { using type = T; - static const T& getExpr(const T& x) {return x;} + static const T& getExpr(const T& x) { return x; } }; template <> struct asExpr { using type = Literal; - static const Literal getExpr(const int& x) {return Literal(x);} + static const Literal getExpr(const int& x) { return Literal(x); } }; template <> struct asExpr { using type = Literal; - static const Literal getExpr(const double& x) {return Literal(x);} + static const Literal getExpr(const double& x) { return Literal(x); } }; template <> struct asExpr { using type = Literal; - static const Literal getExpr(const float& x) {return Literal(x);} + static const Literal getExpr(const float& x) { return Literal(x); } }; template <> struct asExpr { using type = Field3DExpr; - static const Field3DExpr getExpr(const Field3D& x) {return Field3DExpr(x);} + static const Field3DExpr getExpr(const Field3D& x) { return Field3DExpr(x); } }; ///////////////////////////////////////////////////////////// // Type promotion. Work out the type of a calculation, // based on the type of the arguments -template // If in doubt, convert to Field3D +template // If in doubt, convert to Field3D struct PromoteType { using type = Field3D; }; @@ -118,65 +126,63 @@ struct PromoteType { ///////////////////////////////////////////////////////////// // Binary expressions -template -class BinaryExpr { +template +class BinaryExpr { public: - BinaryExpr(const ExprT1 &e1, const ExprT2 &e2) - : _expr1(e1),_expr2(e2) { - } - + BinaryExpr(const ExprT1& e1, const ExprT2& e2) : _expr1(e1), _expr2(e2) {} + // Work out the type of the inputs using ltype = typename exprTraits::expr_type; using rtype = typename exprTraits::expr_type; - + /// Type of the resulting expression using type = typename PromoteType::type; - + BoutReal operator()(int x, int y, int z) const { - return BinOp::apply((_expr1)(x,y,z),(_expr2)(x,y,z)); + return BinOp::apply((_expr1)(x, y, z), (_expr2)(x, y, z)); } - + private: ltype const _expr1; rtype const _expr2; }; -template +template struct BinaryResult { using arg1 = typename asExpr::type; using arg2 = typename asExpr::type; - using type = BinaryExpr; + using type = BinaryExpr; }; /// Binary operator classes -#define DEFINE_BINARY_OP(name,op) \ -struct name { \ - template \ - static inline T \ - apply(T a, T b) \ - { return a op b; } \ -}; +#define DEFINE_BINARY_OP(name, op) \ + struct name { \ + template \ + static inline T apply(T a, T b) { \ + return a op b; \ + } \ + }; -DEFINE_BINARY_OP(Add,+) -DEFINE_BINARY_OP(Subtract,-) -DEFINE_BINARY_OP(Multiply,*) -DEFINE_BINARY_OP(Divide,/) +DEFINE_BINARY_OP(Add, +) +DEFINE_BINARY_OP(Subtract, -) +DEFINE_BINARY_OP(Multiply, *) +DEFINE_BINARY_OP(Divide, /) struct Power { - template + template static inline T apply(T a, T b) { - return pow(a, b); + return pow(a, b); } }; /// Define functions add, mul which use operator structs -#define DEFINE_OVERLOAD_FUNC(name, func) \ - template \ - typename BinaryResult::type \ - func(const ExprT1 &e1, const ExprT2 &e2) { \ - using type = typename BinaryResult::type; \ - return type(asExpr::getExpr(e1), asExpr::getExpr(e2)); \ +#define DEFINE_OVERLOAD_FUNC(name, func) \ + template \ + typename BinaryResult::type func(const ExprT1& e1, \ + const ExprT2& e2) { \ + using type = typename BinaryResult::type; \ + return type(asExpr::getExpr(e1), asExpr::getExpr(e2)); \ } /// Addition of two Expressions @@ -185,14 +191,17 @@ DEFINE_OVERLOAD_FUNC(Add, add); DEFINE_OVERLOAD_FUNC(Multiply, mul); /// A function to evaluate expressions -template +template const Field3D eval3D(Expr e) { Field3D result; result.allocate(); - for(int i=0;iLocalNx;i++) - for(int j=0;jLocalNy;j++) - for(int k=0;kLocalNz;k++) - result(i,j,k) = e(i,j,k); + for (int i = 0; i < bout::globals::mesh->LocalNx; i++) { + for (int j = 0; j < bout::globals::mesh->LocalNy; j++) { + for (int k = 0; k < bout::globals::mesh->LocalNz; k++) { + result(i, j, k) = e(i, j, k); + } + } + } return result; } diff --git a/include/bout/fft.hxx b/include/bout/fft.hxx index e6f00c91aa..8e74321f2a 100644 --- a/include/bout/fft.hxx +++ b/include/bout/fft.hxx @@ -28,7 +28,7 @@ #ifndef __FFT_H__ #define __FFT_H__ -#include "dcomplex.hxx" +#include "bout/dcomplex.hxx" #include #include @@ -53,7 +53,7 @@ namespace fft { * \param[in] length Number of points in the input array * \param[out] out Pointer to the complex 1D array which is the FFT of in */ -void rfft(const BoutReal *in, int length, dcomplex *out); +void rfft(const BoutReal* in, int length, dcomplex* out); /*! * Take the inverse fft of signal where the outputs are only reals. @@ -71,21 +71,21 @@ void rfft(const BoutReal *in, int length, dcomplex *out); * \param[in] length Number of points in the input array * \param[out] out Pointer to the complex 1D array which is IFFTed */ -void irfft(const dcomplex *in, int length, BoutReal *out); +void irfft(const dcomplex* in, int length, BoutReal* out); /*! * Discrete Sine Transform * * \p in and \p out arrays must both be of the same \p length */ -void DST(const BoutReal *in, int length, dcomplex *out); +void DST(const BoutReal* in, int length, dcomplex* out); /*! * Inverse Discrete Sine Transform * * \p in and \p out arrays must both be of the same \p length */ -void DST_rev(dcomplex *in, int length, BoutReal *out); +void DST_rev(dcomplex* in, int length, BoutReal* out); /// Should the FFT functions find and use an optimised plan? void fft_init(bool fft_measure); @@ -116,19 +116,19 @@ Array irfft(const Array& in, int length); // Legacy non-namespaced versions -inline void rfft(const BoutReal *in, int length, dcomplex *out) { +inline void rfft(const BoutReal* in, int length, dcomplex* out) { return bout::fft::rfft(in, length, out); } -inline void irfft(const dcomplex *in, int length, BoutReal *out) { +inline void irfft(const dcomplex* in, int length, BoutReal* out) { return bout::fft::irfft(in, length, out); } -inline void DST(const BoutReal *in, int length, dcomplex *out) { +inline void DST(const BoutReal* in, int length, dcomplex* out) { return bout::fft::DST(in, length, out); } -inline void DST_rev(dcomplex *in, int length, BoutReal *out) { +inline void DST_rev(dcomplex* in, int length, BoutReal* out) { return bout::fft::DST_rev(in, length, out); } diff --git a/include/bout/field.hxx b/include/bout/field.hxx index a92f34596d..6b14d6a3a2 100644 --- a/include/bout/field.hxx +++ b/include/bout/field.hxx @@ -36,21 +36,20 @@ class Field; #include #include -#include "field_data.hxx" - -#include "bout/region.hxx" -#include "bout_types.hxx" -#include "boutcomm.hxx" -#include "boutexception.hxx" -#include -#include "msg_stack.hxx" +#include "bout/field_data.hxx" + +#include "bout/bout_types.hxx" +#include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" +#include "bout/msg_stack.hxx" +#include "bout/stencils.hxx" +#include "bout/utils.hxx" #include "bout/region.hxx" -#include "stencils.hxx" -#include "utils.hxx" -#include #include "bout/traits.hxx" +#include +#include -#include "unused.hxx" +#include "bout/unused.hxx" class Mesh; @@ -67,15 +66,9 @@ public: Field(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in); /// Getters for DIRECTION types - DirectionTypes getDirections() const { - return directions; - } - YDirectionType getDirectionY() const { - return directions.y; - } - ZDirectionType getDirectionZ() const { - return directions.z; - } + DirectionTypes getDirections() const { return directions; } + YDirectionType getDirectionY() const { return directions.y; } + ZDirectionType getDirectionZ() const { return directions.z; } /// Setters for *DirectionType virtual Field& setDirections(DirectionTypes directions_in) { @@ -95,19 +88,23 @@ public: #if CHECK > 0 // Routines to test guard/boundary cells set - + virtual bool bndryValid() { - if(!bndry_xin) + if (!bndry_xin) { throw BoutException("Inner X guard cells not set\n"); - if(!bndry_xout) + } + if (!bndry_xout) { throw BoutException("Outer X guard cells not set\n"); - if(!bndry_yup) + } + if (!bndry_yup) { throw BoutException("Upper y guard cells not set\n"); - if(!bndry_ydown) + } + if (!bndry_ydown) { throw BoutException("Lower y guard cells not set\n"); + } return true; } - + /// Status of the 4 boundaries bool bndry_xin{true}, bndry_xout{true}, bndry_yup{true}, bndry_ydown{true}; #endif @@ -139,56 +136,57 @@ private: /// Check if Fields have compatible meta-data inline bool areFieldsCompatible(const Field& field1, const Field& field2) { - return - field1.getCoordinates() == field2.getCoordinates() && - field1.getMesh() == field2.getMesh() && - field1.getLocation() == field2.getLocation() && - areDirectionsCompatible(field1.getDirections(), field2.getDirections()); + return field1.getCoordinates() == field2.getCoordinates() + && field1.getMesh() == field2.getMesh() + && field1.getLocation() == field2.getLocation() + && areDirectionsCompatible(field1.getDirections(), field2.getDirections()); } #if CHECKLEVEL >= 1 -#define ASSERT1_FIELDS_COMPATIBLE(field1, field2) \ - if ((field1).getLocation() != (field2).getLocation()){ \ - throw BoutException("Error in {:s}:{:d}\nFields at different position:" \ - "`{:s}` at {:s}, `{:s}` at {:s}",__FILE__,__LINE__, \ - #field1, toString((field1).getLocation()), \ - #field2, toString((field2).getLocation())); \ - } \ - if ((field1).getCoordinates() != (field2).getCoordinates()){ \ - throw BoutException("Error in {:s}:{:d}\nFields have different coordinates:" \ - "`{:s}` at {:p}, `{:s}` at {:p}",__FILE__,__LINE__, \ - #field1, static_cast((field1).getCoordinates()), \ - #field2, static_cast((field2).getCoordinates())); \ - } \ - if ((field1).getMesh() != (field2).getMesh()){ \ - throw BoutException("Error in {:s}:{:d}\nFields are on different Meshes:" \ - "`{:s}` at {:p}, `{:s}` at {:p}",__FILE__,__LINE__, \ - #field1, static_cast((field1).getMesh()), \ - #field2, static_cast((field2).getMesh())); \ - } \ - if (!areDirectionsCompatible((field1).getDirections(), \ - (field2).getDirections())){ \ - throw BoutException("Error in {:s}:{:d}\nFields at different directions:" \ - "`{:s}` at {:s}, `{:s}` at {:s}",__FILE__,__LINE__, \ - #field1, toString((field1).getDirections()), \ - #field2, toString((field2).getDirections())); \ +#define ASSERT1_FIELDS_COMPATIBLE(field1, field2) \ + if ((field1).getLocation() != (field2).getLocation()) { \ + throw BoutException("Error in {:s}:{:d}\nFields at different position:" \ + "`{:s}` at {:s}, `{:s}` at {:s}", \ + __FILE__, __LINE__, #field1, toString((field1).getLocation()), \ + #field2, toString((field2).getLocation())); \ + } \ + if ((field1).getCoordinates() != (field2).getCoordinates()) { \ + throw BoutException("Error in {:s}:{:d}\nFields have different coordinates:" \ + "`{:s}` at {:p}, `{:s}` at {:p}", \ + __FILE__, __LINE__, #field1, \ + static_cast((field1).getCoordinates()), #field2, \ + static_cast((field2).getCoordinates())); \ + } \ + if ((field1).getMesh() != (field2).getMesh()) { \ + throw BoutException("Error in {:s}:{:d}\nFields are on different Meshes:" \ + "`{:s}` at {:p}, `{:s}` at {:p}", \ + __FILE__, __LINE__, #field1, \ + static_cast((field1).getMesh()), #field2, \ + static_cast((field2).getMesh())); \ + } \ + if (!areDirectionsCompatible((field1).getDirections(), (field2).getDirections())) { \ + throw BoutException("Error in {:s}:{:d}\nFields at different directions:" \ + "`{:s}` at {:s}, `{:s}` at {:s}", \ + __FILE__, __LINE__, #field1, toString((field1).getDirections()), \ + #field2, toString((field2).getDirections())); \ } #else -#define ASSERT1_FIELDS_COMPATIBLE(field1, field2); +#define ASSERT1_FIELDS_COMPATIBLE(field1, field2) ; #endif /// Return an empty shell field of some type derived from Field, with metadata /// copied and a data array that is allocated but not initialised. -template +template inline T emptyFrom(const T& f) { static_assert(bout::utils::is_Field::value, "emptyFrom only works on Fields"); - return T(f.getMesh(), f.getLocation(), {f.getDirectionY(), f.getDirectionZ()}).allocate(); + return T(f.getMesh(), f.getLocation(), {f.getDirectionY(), f.getDirectionZ()}) + .allocate(); } /// Return a field of some type derived from Field, with metadata copied from /// another field and a data array allocated and initialised to zero. -template +template inline T zeroFrom(const T& f) { static_assert(bout::utils::is_Field::value, "zeroFrom only works on Fields"); T result{emptyFrom(f)}; @@ -198,7 +196,7 @@ inline T zeroFrom(const T& f) { /// Return a field of some type derived from Field, with metadata copied from /// another field and a data array allocated and filled with the given value. -template +template inline T filledFrom(const T& f, BoutReal fill_value) { static_assert(bout::utils::is_Field::value, "filledFrom only works on Fields"); T result{emptyFrom(f)}; @@ -213,7 +211,7 @@ inline T filledFrom(const T& f, BoutReal fill_value) { /// Field3D result = filledFrom(field, [&](const auto& index) { /// return ...; /// }); -/// +/// /// An optional third argument is the region string template < typename T, typename Function, @@ -221,15 +219,17 @@ template < inline T filledFrom(const T& f, Function func, std::string region_string = "RGN_ALL") { static_assert(bout::utils::is_Field::value, "filledFrom only works on Fields"); T result{emptyFrom(f)}; - BOUT_FOR(i, result.getRegion(region_string)) { + BOUT_FOR (i, result.getRegion(region_string)) { result[i] = func(i); } return result; } /// Unary + operator. This doesn't do anything -template> -T operator+(const T& f) {return f;} +template > +T operator+(const T& f) { + return f; +} namespace bout { /// Check if all values of a field \p var are finite. Loops over all points including the @@ -240,8 +240,9 @@ namespace bout { /// Note that checkFinite runs the check irrespective of CHECK level. It is intended to be /// used during initialization, where we always want to check inputs, even for optimized /// builds. -template -inline void checkFinite(const T& f, const std::string& name="field", const std::string& rgn="RGN_ALL") { +template +inline void checkFinite(const T& f, const std::string& name = "field", + const std::string& rgn = "RGN_ALL") { AUTO_TRACE(); if (!f.isAllocated()) { @@ -263,8 +264,9 @@ inline void checkFinite(const T& f, const std::string& name="field", const std:: /// Note that checkPositive runs the check irrespective of CHECK level. It is intended to /// be used during initialization, where we always want to check inputs, even for /// optimized builds. -template -inline void checkPositive(const T& f, const std::string& name="field", const std::string& rgn="RGN_ALL") { +template +inline void checkPositive(const T& f, const std::string& name = "field", + const std::string& rgn = "RGN_ALL") { AUTO_TRACE(); if (!f.isAllocated()) { @@ -452,7 +454,7 @@ inline BoutReal mean(const T& f, bool allpe = false, /// This loops over the entire domain, including guard/boundary cells by /// default (can be changed using the \p rgn argument) /// If CHECK >= 3 then the result will be checked for non-finite numbers -template> +template > T pow(const T& lhs, const T& rhs, const std::string& rgn = "RGN_ALL") { AUTO_TRACE(); @@ -460,14 +462,16 @@ T pow(const T& lhs, const T& rhs, const std::string& rgn = "RGN_ALL") { T result{emptyFrom(lhs)}; - BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); } + BOUT_FOR (i, result.getRegion(rgn)) { + result[i] = ::pow(lhs[i], rhs[i]); + } checkData(result); return result; } -template> -T pow(const T &lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") { +template > +T pow(const T& lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") { AUTO_TRACE(); // Check if the inputs are allocated @@ -476,14 +480,16 @@ T pow(const T &lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") { T result{emptyFrom(lhs)}; - BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs); } + BOUT_FOR (i, result.getRegion(rgn)) { + result[i] = ::pow(lhs[i], rhs); + } checkData(result); return result; } -template> -T pow(BoutReal lhs, const T &rhs, const std::string& rgn = "RGN_ALL") { +template > +T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") { AUTO_TRACE(); // Check if the inputs are allocated @@ -493,7 +499,9 @@ T pow(BoutReal lhs, const T &rhs, const std::string& rgn = "RGN_ALL") { // Define and allocate the output result T result{emptyFrom(rhs)}; - BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs, rhs[i]); } + BOUT_FOR (i, result.getRegion(rgn)) { + result[i] = ::pow(lhs, rhs[i]); + } checkData(result); return result; @@ -518,17 +526,19 @@ T pow(BoutReal lhs, const T &rhs, const std::string& rgn = "RGN_ALL") { #ifdef FIELD_FUNC #error This macro has already been defined #else -#define FIELD_FUNC(name, func) \ - template> \ - inline T name(const T &f, const std::string& rgn = "RGN_ALL") { \ - AUTO_TRACE(); \ - /* Check if the input is allocated */ \ - checkData(f); \ - /* Define and allocate the output result */ \ - T result{emptyFrom(f)}; \ - BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); } \ - checkData(result); \ - return result; \ +#define FIELD_FUNC(name, func) \ + template > \ + inline T name(const T& f, const std::string& rgn = "RGN_ALL") { \ + AUTO_TRACE(); \ + /* Check if the input is allocated */ \ + checkData(f); \ + /* Define and allocate the output result */ \ + T result{emptyFrom(f)}; \ + BOUT_FOR (d, result.getRegion(rgn)) { \ + result[d] = func(f[d]); \ + } \ + checkData(result); \ + return result; \ } #endif @@ -627,8 +637,8 @@ FIELD_FUNC(tanh, ::tanh) /// Check if all values of a field \p var are finite. /// Loops over all points including the boundaries by /// default (can be changed using the \p rgn argument -template> -inline bool finite(const T &f, const std::string& rgn = "RGN_ALL") { +template > +inline bool finite(const T& f, const std::string& rgn = "RGN_ALL") { AUTO_TRACE(); if (!f.isAllocated()) { @@ -646,8 +656,8 @@ inline bool finite(const T &f, const std::string& rgn = "RGN_ALL") { /// Makes a copy of a field \p f, ensuring that the underlying data is /// not shared. -template> -T copy(const T &f) { +template > +T copy(const T& f) { T result = f; result.allocate(); return result; @@ -659,12 +669,12 @@ T copy(const T &f) { /// @param[in] var Variable to apply floor to /// @param[in] f The floor value /// @param[in] rgn The region to calculate the result over -template> +template > inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") { checkData(var); T result = copy(var); - BOUT_FOR(d, var.getRegion(rgn)) { + BOUT_FOR (d, var.getRegion(rgn)) { if (result[d] < f) { result[d] = f; } diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index fc6fe37888..f00cd1ea69 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -31,17 +31,17 @@ class Field2D; #define __FIELD2D_H__ class Mesh; -#include "field.hxx" -#include "field_data.hxx" -class Field3D; //#include "field3d.hxx" -#include "fieldperp.hxx" -#include "stencils.hxx" +#include "bout/field.hxx" +#include "bout/field_data.hxx" +class Field3D; //#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" +#include "bout/stencils.hxx" -#include "utils.hxx" +#include "bout/utils.hxx" #include "bout/array.hxx" #include "bout/region.hxx" -#include "unused.hxx" +#include "bout/unused.hxx" #if BOUT_HAS_RAJA #include "RAJA/RAJA.hpp" // using RAJA lib @@ -200,24 +200,28 @@ public: */ BOUT_HOST_DEVICE inline BoutReal& operator()(int jx, int jy) { #if CHECK > 2 && !BOUT_USE_CUDA - if (!isAllocated()) + if (!isAllocated()) { throw BoutException("Field2D: () operator on empty data"); + } - if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny)) + if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny)) { throw BoutException("Field2D: ({:d}, {:d}) index out of bounds ({:d} , {:d})\n", jx, jy, nx, ny); + } #endif return data[jx * ny + jy]; } BOUT_HOST_DEVICE inline const BoutReal& operator()(int jx, int jy) const { #if CHECK > 2 && !BOUT_USE_CUDA - if (!isAllocated()) + if (!isAllocated()) { throw BoutException("Field2D: () operator on empty data"); + } - if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny)) + if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny)) { throw BoutException("Field2D: ({:d}, {:d}) index out of bounds ({:d} , {:d})\n", jx, jy, nx, ny); + } #endif return data[jx * ny + jy]; diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx index a59e426a42..d0341c95d4 100644 --- a/include/bout/field3d.hxx +++ b/include/bout/field3d.hxx @@ -26,23 +26,22 @@ class Field3D; #ifndef __FIELD3D_H__ #define __FIELD3D_H__ -class Mesh; // #include "bout/mesh.hxx" -#include "field.hxx" -#include "field2d.hxx" -#include "fieldperp.hxx" -#include "stencils.hxx" -#include "bout_types.hxx" +class Mesh; // #include "bout/mesh.hxx" +#include "bout/bout_types.hxx" +#include "bout/field.hxx" +#include "bout/field2d.hxx" +#include "bout/fieldperp.hxx" +#include "bout/stencils.hxx" #include "bout/array.hxx" #include "bout/region.hxx" #include "bout/assert.hxx" -#include "utils.hxx" +#include "bout/utils.hxx" #include - /// Class for 3D X-Y-Z scalar fields /*! This class represents a scalar field defined over the mesh. @@ -159,18 +158,18 @@ class Mesh; // #include "bout/mesh.hxx" */ class Field3D : public Field { - public: +public: using ind_type = Ind3D; - + /*! * Constructor * * Note: the global "mesh" can't be passed here because * fields may be created before the mesh is. */ - Field3D(Mesh *localmesh = nullptr, CELL_LOC location_in=CELL_CENTRE, - DirectionTypes directions_in = - {YDirectionType::Standard, ZDirectionType::Standard}); + Field3D(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE, + DirectionTypes directions_in = {YDirectionType::Standard, + ZDirectionType::Standard}); /*! * Copy constructor @@ -182,7 +181,7 @@ class Field3D : public Field { /// Constructor from 2D field Field3D(const Field2D& f); /// Constructor from value - Field3D(BoutReal val, Mesh *localmesh = nullptr); + Field3D(BoutReal val, Mesh* localmesh = nullptr); /// Constructor from Array and Mesh Field3D(Array data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE, DirectionTypes directions_in = {YDirectionType::Standard, @@ -197,12 +196,12 @@ class Field3D : public Field { * Ensures that memory is allocated and unique */ Field3D& allocate(); - + /*! * Test if data is allocated */ - bool isAllocated() const { return !data.empty(); } - + bool isAllocated() const { return !data.empty(); } + /*! * Return a pointer to the time-derivative field * @@ -214,15 +213,15 @@ class Field3D : public Field { /*! * Return the number of nx points */ - int getNx() const override {return nx;}; + int getNx() const override { return nx; }; /*! * Return the number of ny points */ - int getNy() const override {return ny;}; + int getNy() const override { return ny; }; /*! * Return the number of nz points */ - int getNz() const override {return nz;}; + int getNz() const override { return nz; }; // these methods return Field3D to allow method chaining Field3D& setLocation(CELL_LOC new_location) override { @@ -244,7 +243,7 @@ class Field3D : public Field { * Clear the parallel slices, yup and ydown */ void clearParallelSlices(); - + /// Check if this field has yup and ydown fields bool hasParallelSlices() const { #if CHECK > 2 @@ -263,24 +262,24 @@ class Field3D : public Field { /// Check if this field has yup and ydown fields /// Return reference to yup field - Field3D &yup(std::vector::size_type index = 0) { + Field3D& yup(std::vector::size_type index = 0) { ASSERT2(index < yup_fields.size()); return yup_fields[index]; } /// Return const reference to yup field - const Field3D &yup(std::vector::size_type index = 0) const { + const Field3D& yup(std::vector::size_type index = 0) const { ASSERT2(index < yup_fields.size()); return yup_fields[index]; } /// Return reference to ydown field - Field3D &ydown(std::vector::size_type index = 0) { + Field3D& ydown(std::vector::size_type index = 0) { ASSERT2(index < ydown_fields.size()); return ydown_fields[index]; } /// Return const reference to ydown field - const Field3D &ydown(std::vector::size_type index = 0) const { + const Field3D& ydown(std::vector::size_type index = 0) const { ASSERT2(index < ydown_fields.size()); return ydown_fields[index]; } @@ -302,26 +301,30 @@ class Field3D : public Field { /// /// Example /// ------- - /// + /// /// This loops over the interior points, not the boundary /// and inside the loop the index is used to calculate the difference /// between the point one index up in x (i.xp()) and one index down /// in x (i.xm()), putting the result into a different field 'g' - /// + /// /// for(const auto &i : f.getRegion(RGN_NOBNDRY)) { /// g[i] = f[i.xp()] - f[i.xm()]; /// } - /// - const Region& getRegion(REGION region) const; - const Region& getRegion(const std::string ®ion_name) const; + /// + const Region& getRegion(REGION region) const; + const Region& getRegion(const std::string& region_name) const; /// Return a Region reference to use to iterate over the x- and /// y-indices of this field const Region& getRegion2D(REGION region) const; - const Region& getRegion2D(const std::string ®ion_name) const; - - Region::RegionIndices::const_iterator begin() const {return std::begin(getRegion("RGN_ALL"));}; - Region::RegionIndices::const_iterator end() const {return std::end(getRegion("RGN_ALL"));}; + const Region& getRegion2D(const std::string& region_name) const; + + Region::RegionIndices::const_iterator begin() const { + return std::begin(getRegion("RGN_ALL")); + }; + Region::RegionIndices::const_iterator end() const { + return std::end(getRegion("RGN_ALL")); + }; BoutReal& BOUT_HOST_DEVICE operator[](const Ind3D& d) { return data[d.ind]; } const BoutReal& BOUT_HOST_DEVICE operator[](const Ind3D& d) const { @@ -345,34 +348,34 @@ class Field3D : public Field { inline BoutReal& operator()(int jx, int jy, int jz) { #if CHECK > 2 // Perform bounds checking - if(data.empty()) + if (data.empty()) { throw BoutException("Field3D: () operator on empty data"); - - if((jx < 0) || (jx >= nx) || - (jy < 0) || (jy >= ny) || - (jz < 0) || (jz >= nz)) + } + + if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny) || (jz < 0) || (jz >= nz)) { throw BoutException( "Field3D: ({:d}, {:d}, {:d}) operator out of bounds ({:d}, {:d}, {:d})", jx, jy, jz, nx, ny, nz); + } #endif - return data[(jx*ny +jy)*nz + jz]; + return data[(jx * ny + jy) * nz + jz]; } - + inline const BoutReal& operator()(int jx, int jy, int jz) const { #if CHECK > 2 - if(data.empty()) + if (data.empty()) { throw BoutException("Field3D: () operator on empty data"); - - if((jx < 0) || (jx >= nx) || - (jy < 0) || (jy >= ny) || - (jz < 0) || (jz >= nz)) + } + + if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny) || (jz < 0) || (jz >= nz)) { throw BoutException( "Field3D: ({:d}, {:d}, {:d}) operator out of bounds ({:d}, {:d}, {:d})", jx, jy, jz, nx, ny, nz); + } #endif - return data[(jx*ny +jy)*nz + jz]; + return data[(jx * ny + jy) * nz + jz]; } - + /*! * Direct access to the underlying data array * @@ -382,69 +385,71 @@ class Field3D : public Field { */ inline const BoutReal* operator()(int jx, int jy) const { #if CHECK > 2 - if(data.empty()) + if (data.empty()) { throw BoutException("Field3D: () operator on empty data"); + } - if((jx < 0) || (jx >= nx) || - (jy < 0) || (jy >= ny)) + if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny)) { throw BoutException("Field3D: ({:d}, {:d}) operator out of bounds ({:d}, {:d})", jx, jy, nx, ny); + } #endif - return &data[(jx*ny +jy)*nz]; + return &data[(jx * ny + jy) * nz]; } inline BoutReal* operator()(int jx, int jy) { #if CHECK > 2 - if(data.empty()) + if (data.empty()) { throw BoutException("Field3D: () operator on empty data"); + } - if((jx < 0) || (jx >= nx) || - (jy < 0) || (jy >= ny)) + if ((jx < 0) || (jx >= nx) || (jy < 0) || (jy >= ny)) { throw BoutException("Field3D: ({:d}, {:d}) operator out of bounds ({:d}, {:d})", jx, jy, nx, ny); + } #endif - return &data[(jx*ny +jy)*nz]; + return &data[(jx * ny + jy) * nz]; } - + ///////////////////////////////////////////////////////// // Operators - + /// Assignment operators ///@{ - Field3D & operator=(const Field3D &rhs); - Field3D & operator=(Field3D&& rhs); - Field3D & operator=(const Field2D &rhs); + Field3D& operator=(const Field3D& rhs); + Field3D& operator=(Field3D&& rhs); + Field3D& operator=(const Field2D& rhs); /// return void, as only part initialised - void operator=(const FieldPerp &rhs); - Field3D & operator=(BoutReal val); + void operator=(const FieldPerp& rhs); + Field3D& operator=(BoutReal val); ///@} /// Addition operators ///@{ - Field3D & operator+=(const Field3D &rhs); - Field3D & operator+=(const Field2D &rhs); - Field3D & operator+=(BoutReal rhs); + Field3D& operator+=(const Field3D& rhs); + Field3D& operator+=(const Field2D& rhs); + Field3D& operator+=(BoutReal rhs); ///@} - + /// Subtraction operators ///@{ - Field3D & operator-=(const Field3D &rhs); - Field3D & operator-=(const Field2D &rhs); - Field3D & operator-=(BoutReal rhs); + Field3D& operator-=(const Field3D& rhs); + Field3D& operator-=(const Field2D& rhs); + Field3D& operator-=(BoutReal rhs); ///@} /// Multiplication operators ///@{ - Field3D & operator*=(const Field3D &rhs); - Field3D & operator*=(const Field2D &rhs); - Field3D & operator*=(BoutReal rhs); + Field3D& operator*=(const Field3D& rhs); + Field3D& operator*=(const Field2D& rhs); + Field3D& operator*=(BoutReal rhs); ///@} /// Division operators ///@{ - Field3D & operator/=(const Field3D &rhs); - Field3D & operator/=(const Field2D &rhs); - Field3D & operator/=(BoutReal rhs); + Field3D& operator/=(const Field3D& rhs); + Field3D& operator/=(const Field2D& rhs); + Field3D& operator/=(BoutReal rhs); ///@} // FieldData virtual functions @@ -461,37 +466,40 @@ class Field3D : public Field { Field3D& calcParallelSlices(); - void applyBoundary(bool init=false) override; + void applyBoundary(bool init = false) override; void applyBoundary(BoutReal t); - void applyBoundary(const std::string &condition); + void applyBoundary(const std::string& condition); void applyBoundary(const char* condition) { applyBoundary(std::string(condition)); } - void applyBoundary(const std::string ®ion, const std::string &condition); + void applyBoundary(const std::string& region, const std::string& condition); void applyTDerivBoundary() override; - + /// Copy the boundary values half-way between cells /// This uses 2nd order central differences to set the value /// on the boundary to the value on the boundary in field \p f3d. /// Note: does not just copy values in boundary region. - void setBoundaryTo(const Field3D &f3d); + void setBoundaryTo(const Field3D& f3d); void applyParallelBoundary(); void applyParallelBoundary(BoutReal t); - void applyParallelBoundary(const std::string &condition); - void applyParallelBoundary(const char* condition) { applyParallelBoundary(std::string(condition)); } - void applyParallelBoundary(const std::string ®ion, const std::string &condition); - void applyParallelBoundary(const std::string ®ion, const std::string &condition, Field3D *f); + void applyParallelBoundary(const std::string& condition); + void applyParallelBoundary(const char* condition) { + applyParallelBoundary(std::string(condition)); + } + void applyParallelBoundary(const std::string& region, const std::string& condition); + void applyParallelBoundary(const std::string& region, const std::string& condition, + Field3D* f); friend void swap(Field3D& first, Field3D& second) noexcept; - + private: /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null int nx{-1}, ny{-1}, nz{-1}; /// Internal data array. Handles allocation/freeing of memory Array data; - + /// Time derivative (may be nullptr) - Field3D *deriv{nullptr}; + Field3D* deriv{nullptr}; /// Fields containing values along Y std::vector yup_fields{}, ydown_fields{}; @@ -500,36 +508,36 @@ private: // Non-member overloaded operators // Binary operators -FieldPerp operator+(const Field3D &lhs, const FieldPerp &rhs); -FieldPerp operator-(const Field3D &lhs, const FieldPerp &rhs); -FieldPerp operator*(const Field3D &lhs, const FieldPerp &rhs); -FieldPerp operator/(const Field3D &lhs, const FieldPerp &rhs); - -Field3D operator+(const Field3D &lhs, const Field3D &rhs); -Field3D operator-(const Field3D &lhs, const Field3D &rhs); -Field3D operator*(const Field3D &lhs, const Field3D &rhs); -Field3D operator/(const Field3D &lhs, const Field3D &rhs); - -Field3D operator+(const Field3D &lhs, const Field2D &rhs); -Field3D operator-(const Field3D &lhs, const Field2D &rhs); -Field3D operator*(const Field3D &lhs, const Field2D &rhs); -Field3D operator/(const Field3D &lhs, const Field2D &rhs); - -Field3D operator+(const Field3D &lhs, BoutReal rhs); -Field3D operator-(const Field3D &lhs, BoutReal rhs); -Field3D operator*(const Field3D &lhs, BoutReal rhs); -Field3D operator/(const Field3D &lhs, BoutReal rhs); - -Field3D operator+(BoutReal lhs, const Field3D &rhs); -Field3D operator-(BoutReal lhs, const Field3D &rhs); -Field3D operator*(BoutReal lhs, const Field3D &rhs); -Field3D operator/(BoutReal lhs, const Field3D &rhs); +FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs); +FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs); +FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs); +FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs); + +Field3D operator+(const Field3D& lhs, const Field3D& rhs); +Field3D operator-(const Field3D& lhs, const Field3D& rhs); +Field3D operator*(const Field3D& lhs, const Field3D& rhs); +Field3D operator/(const Field3D& lhs, const Field3D& rhs); + +Field3D operator+(const Field3D& lhs, const Field2D& rhs); +Field3D operator-(const Field3D& lhs, const Field2D& rhs); +Field3D operator*(const Field3D& lhs, const Field2D& rhs); +Field3D operator/(const Field3D& lhs, const Field2D& rhs); + +Field3D operator+(const Field3D& lhs, BoutReal rhs); +Field3D operator-(const Field3D& lhs, BoutReal rhs); +Field3D operator*(const Field3D& lhs, BoutReal rhs); +Field3D operator/(const Field3D& lhs, BoutReal rhs); + +Field3D operator+(BoutReal lhs, const Field3D& rhs); +Field3D operator-(BoutReal lhs, const Field3D& rhs); +Field3D operator*(BoutReal lhs, const Field3D& rhs); +Field3D operator/(BoutReal lhs, const Field3D& rhs); /*! * Unary minus. Returns the negative of given field, * iterates over whole domain including guard/boundary cells. */ -Field3D operator-(const Field3D &f); +Field3D operator-(const Field3D& f); // Non-member functions @@ -541,7 +549,8 @@ Field3D operator-(const Field3D &f); /// default (can be changed using the \p rgn argument). /// If CHECK >= 3 then the result will be checked for non-finite numbers Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn = "RGN_ALL"); -FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn = "RGN_ALL"); +FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, + const std::string& rgn = "RGN_ALL"); #if CHECK > 0 /// Throw an exception if \p f is not allocated or if any @@ -552,7 +561,8 @@ void checkData(const Field3D& f, const std::string& region = "RGN_NOBNDRY"); #else /// Ignored with disabled CHECK; Throw an exception if \p f is not /// allocated or if any elements are non-finite (for CHECK > 2) -inline void checkData(const Field3D& UNUSED(f), const std::string& UNUSED(region) = "RGN_NOBNDRY") {}; +inline void checkData(const Field3D& UNUSED(f), + const std::string& UNUSED(region) = "RGN_NOBNDRY"){}; #endif /// Fourier filtering, removes all except one mode @@ -570,7 +580,7 @@ Field3D filter(const Field3D& var, int N0, const std::string& rgn = "RGN_ALL"); /// @param[in] keep_zonal Keep the zonal component if true /// @param[in] rgn The region to calculate the result over Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, - const std::string& rgn = "RGN_ALL"); + const std::string& rgn = "RGN_ALL"); /// The argument \p keep_zonal used to be integer "zmin" -- this was a /// misnomer. Please use the version above which uses a bool instead [[deprecated("Please use a bool for `keep_zonal`")]] inline Field3D @@ -584,7 +594,7 @@ lowPass(const Field3D& var, int zmax, int keep_zonal, REGION rgn = RGN_ALL) { /// @param[in] var Variable to apply filter to /// @param[in] zmax Maximum mode in Z /// @param[in] rgn The region to calculate the result over -inline Field3D lowPass(const Field3D &var, int zmax, const std::string rgn = "RGN_ALL") { +inline Field3D lowPass(const Field3D& var, int zmax, const std::string rgn = "RGN_ALL") { return lowPass(var, zmax, true, rgn); } @@ -594,26 +604,26 @@ inline Field3D lowPass(const Field3D &var, int zmax, const std::string rgn = "RG /// @param[in] jx X index /// @param[in] jy Y index /// @param[in] zangle The Z angle to apply -void shiftZ(Field3D &var, int jx, int jy, double zangle); +void shiftZ(Field3D& var, int jx, int jy, double zangle); /// Apply a phase shift by a given angle \p zangle in Z to all points /// /// @param[inout] var The variable to modify in-place /// @param[in] zangle The angle to shift by in Z /// @param[in] rgn The region to calculate the result over -void shiftZ(Field3D &var, BoutReal zangle, const std::string& rgn="RGN_ALL"); +void shiftZ(Field3D& var, BoutReal zangle, const std::string& rgn = "RGN_ALL"); /// Average in the Z direction /// /// @param[in] f Variable to average /// @param[in] rgn The region to calculate the result over -Field2D DC(const Field3D &f, const std::string& rgn = "RGN_ALL"); +Field2D DC(const Field3D& f, const std::string& rgn = "RGN_ALL"); /// Force guard cells of passed field \p var to NaN #if CHECK > 2 -void invalidateGuards(Field3D &var); +void invalidateGuards(Field3D& var); #else -inline void invalidateGuards(Field3D &UNUSED(var)) {} +inline void invalidateGuards(Field3D& UNUSED(var)) {} #endif /// Returns a reference to the time-derivative of a field \p f @@ -630,9 +640,9 @@ inline std::string toString<>(const Field3D& UNUSED(val)) { /// Test if two fields are the same, by calculating /// the minimum absolute difference between them -bool operator==(const Field3D &a, const Field3D &b); +bool operator==(const Field3D& a, const Field3D& b); /// Output a string describing a Field3D to a stream -std::ostream& operator<<(std::ostream &out, const Field3D &value); +std::ostream& operator<<(std::ostream& out, const Field3D& value); #endif /* __FIELD3D_H__ */ diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx index 5747bbfc60..d6d203d7f7 100644 --- a/include/bout/field_accessor.hxx +++ b/include/bout/field_accessor.hxx @@ -7,10 +7,10 @@ #ifndef FIELD_ACCESSOR_H__ #define FIELD_ACCESSOR_H__ -#include "../bout_types.hxx" -#include "../field.hxx" -#include "../field2d.hxx" -#include "../field3d.hxx" +#include "bout/bout_types.hxx" +#include "bout/field.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" #include "build_config.hxx" #include "coordinates.hxx" #include "coordinates_accessor.hxx" diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx index 8d98709c6c..35e7dbcbac 100644 --- a/include/bout/field_data.hxx +++ b/include/bout/field_data.hxx @@ -30,8 +30,8 @@ class FieldData; #ifndef FIELD_DATA_H #define FIELD_DATA_H -#include "bout_types.hxx" -#include "unused.hxx" +#include "bout/bout_types.hxx" +#include "bout/unused.hxx" #include #include @@ -77,19 +77,20 @@ public: /// Number of BoutReals in one element virtual int elementSize() const { return 1; } - virtual void doneComms() { }; // Notifies that communications done - + virtual void doneComms(){}; // Notifies that communications done + // Boundary conditions - void setBoundary(const std::string &name); ///< Set the boundary conditions + void setBoundary(const std::string& name); ///< Set the boundary conditions - void copyBoundary(const FieldData &f); ///< Copy the boundary conditions from another field + void + copyBoundary(const FieldData& f); ///< Copy the boundary conditions from another field - virtual void applyBoundary(bool UNUSED(init)=false) {} - virtual void applyTDerivBoundary() {}; -//JMAD + virtual void applyBoundary(bool UNUSED(init) = false) {} + virtual void applyTDerivBoundary(){}; + //JMAD void addBndryFunction(FuncPtr userfunc, BndryLoc location); void addBndryGenerator(FieldGeneratorPtr gen, BndryLoc location); - + FieldGeneratorPtr getBndryGenerator(BndryLoc location); /// Returns a pointer to the `Mesh` object used by this field @@ -119,14 +120,14 @@ protected: Mesh* fieldmesh{nullptr}; private: - std::vector bndry_op; ///< Boundary conditions - bool boundaryIsCopy{false}; ///< True if bndry_op is a copy - bool boundaryIsSet{false}; ///< Set to true when setBoundary called + std::vector bndry_op; ///< Boundary conditions + bool boundaryIsCopy{false}; ///< True if bndry_op is a copy + bool boundaryIsSet{false}; ///< Set to true when setBoundary called // Parallel boundaries - std::vector bndry_op_par; ///< Boundary conditions + std::vector bndry_op_par; ///< Boundary conditions - std::map bndry_generator; + std::map bndry_generator; /// `Coordinates` used by this field, owned by `fieldmesh` mutable std::weak_ptr fieldCoordinates{}; diff --git a/include/bout/field_factory.hxx b/include/bout/field_factory.hxx index d36e30dfca..ee228d836c 100644 --- a/include/bout/field_factory.hxx +++ b/include/bout/field_factory.hxx @@ -33,11 +33,11 @@ class FieldFactory; #include "bout/sys/expressionparser.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "options.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" -#include "unused.hxx" +#include "bout/unused.hxx" #include #include @@ -72,7 +72,8 @@ public: /// using the given options \p opt, over Mesh \p m at time \p t. /// The resulting field is at cell location \p loc. FieldPerp createPerp(const std::string& value, const Options* opt = nullptr, - Mesh* m = nullptr, CELL_LOC loc = CELL_CENTRE, BoutReal t = 0.0) const; + Mesh* m = nullptr, CELL_LOC loc = CELL_CENTRE, + BoutReal t = 0.0) const; /// Parse a string into a tree of generators FieldGeneratorPtr parse(const std::string& input, const Options* opt = nullptr) const; @@ -90,7 +91,7 @@ public: /// Create a FieldPerp from a generator, over a given mesh /// at a given cell location and time. FieldPerp createPerp(FieldGeneratorPtr generator, Mesh* m = nullptr, - CELL_LOC loc = CELL_CENTRE, BoutReal t = 0.0) const; + CELL_LOC loc = CELL_CENTRE, BoutReal t = 0.0) const; /// Get the Singleton object static FieldFactory* get(); @@ -104,7 +105,8 @@ protected: FieldGeneratorPtr resolve(const std::string& name) const override; std::multiset - fuzzyFind(const std::string& name, std::string::size_type max_distance = 2) const override; + fuzzyFind(const std::string& name, + std::string::size_type max_distance = 2) const override; private: /// The default mesh for create functions. @@ -114,7 +116,7 @@ private: bool transform_from_field_aligned{true}; int max_recursion_depth{0}; - + /// The default options used in resolve(), can be *temporarily* /// overridden in parse()/create2D()/create3D() mutable const Options* options; @@ -152,9 +154,7 @@ private: class FieldNull : public FieldGenerator { public: FieldNull() = default; - BoutReal generate(const bout::generator::Context&) override { - return 0.0; - } + BoutReal generate(const bout::generator::Context&) override { return 0.0; } FieldGeneratorPtr clone(const std::list UNUSED(args)) override { return get(); } diff --git a/include/bout/fieldgroup.hxx b/include/bout/fieldgroup.hxx index e5ae52de82..c33bd63e16 100644 --- a/include/bout/fieldgroup.hxx +++ b/include/bout/fieldgroup.hxx @@ -1,11 +1,11 @@ #ifndef __FIELDGROUP_H__ #define __FIELDGROUP_H__ -#include "field_data.hxx" -#include +#include "bout/field_data.hxx" +#include -#include -#include +#include +#include #include @@ -26,10 +26,10 @@ public: FieldGroup& operator=(FieldGroup&& other) = default; /// Constructor with a single FieldData \p f - FieldGroup(FieldData &f) { fvec.push_back(&f); } + FieldGroup(FieldData& f) { fvec.push_back(&f); } /// Constructor with a single Field3D \p f - FieldGroup(Field3D &f) { + FieldGroup(Field3D& f) { fvec.push_back(&f); f3vec.push_back(&f); } @@ -37,7 +37,7 @@ public: /// Constructor with a single Vector2D \p v /// /// This is needed so that fvec only contains Field2D or Field3D - FieldGroup(Vector2D &v) { + FieldGroup(Vector2D& v) { fvec.push_back(&v.x); fvec.push_back(&v.y); fvec.push_back(&v.z); @@ -46,7 +46,7 @@ public: /// Constructor with a single Vector3D \p v /// /// This is needed so that fvec only contains Field2D or Field3D - FieldGroup(Vector3D &v) { + FieldGroup(Vector3D& v) { fvec.push_back(&v.x); fvec.push_back(&v.y); fvec.push_back(&v.z); @@ -62,18 +62,18 @@ public: /// types. In particular arguments to add() cannot be implicitly converted /// to FieldGroup, leading to an infinite loop. template - explicit FieldGroup(Ts &... ts) { + explicit FieldGroup(Ts&... ts) { add(ts...); } /// Copy contents of another FieldGroup \p other into this group. - void add(const FieldGroup &other) { - fvec.insert(fvec.end(), other.fvec.begin(), other.fvec.end() ); - f3vec.insert(f3vec.end(), other.f3vec.begin(), other.f3vec.end() ); + void add(const FieldGroup& other) { + fvec.insert(fvec.end(), other.fvec.begin(), other.fvec.end()); + f3vec.insert(f3vec.end(), other.f3vec.begin(), other.f3vec.end()); } /// Add the contents of \p other to this - FieldGroup &operator+=(const FieldGroup &other) { + FieldGroup& operator+=(const FieldGroup& other) { add(other); return *this; } @@ -83,16 +83,14 @@ public: /// A pointer to this field will be stored internally, /// so the lifetime of this variable should be longer /// than the lifetime of this group. - void add(FieldData &f) { - fvec.push_back(&f); - } + void add(FieldData& f) { fvec.push_back(&f); } // Add a 3D field \p f, which goes into both vectors. // // A pointer to this field will be stored internally, // so the lifetime of this variable should be longer // than the lifetime of this group. - void add(Field3D &f) { + void add(Field3D& f) { fvec.push_back(&f); f3vec.push_back(&f); } @@ -102,7 +100,7 @@ public: /// Pointers to this vector's components will be stored internally, /// so the lifetime of this variable should be longer than the /// lifetime of this group. - void add(Vector2D &v) { + void add(Vector2D& v) { fvec.push_back(&v.x); fvec.push_back(&v.y); fvec.push_back(&v.z); @@ -113,7 +111,7 @@ public: /// Pointers to this vector's components will be stored internally, /// so the lifetime of this variable should be longer than the /// lifetime of this group. - void add(Vector3D &v) { + void add(Vector3D& v) { fvec.push_back(&v.x); fvec.push_back(&v.y); fvec.push_back(&v.z); @@ -128,7 +126,7 @@ public: /// treated as a special case. An arbitrary number of fields can be /// added. template - void add(FieldData &t, Ts &... ts) { + void add(FieldData& t, Ts&... ts) { add(t); // Add the first using functions above add(ts...); // Add the rest } @@ -152,58 +150,44 @@ public: } /// Return number of fields - int size() const { - return static_cast(fvec.size()); - } + int size() const { return static_cast(fvec.size()); } /// Return number of Field3Ds - int size_field3d() const { - return static_cast(f3vec.size()); - } + int size_field3d() const { return static_cast(f3vec.size()); } /// Test whether this group is empty - bool empty() const { - return fvec.empty(); - } + bool empty() const { return fvec.empty(); } /// Remove all fields from this group - void clear() {fvec.clear(); f3vec.clear(); } + void clear() { + fvec.clear(); + f3vec.clear(); + } /// Iteration over all fields using iterator = std::vector::iterator; - iterator begin() { - return fvec.begin(); - } - iterator end() { - return fvec.end(); - } + iterator begin() { return fvec.begin(); } + iterator end() { return fvec.end(); } /// Const iteration over all fields using const_iterator = std::vector::const_iterator; - const_iterator begin() const { - return fvec.begin(); - } - const_iterator end() const { - return fvec.end(); - } + const_iterator begin() const { return fvec.begin(); } + const_iterator end() const { return fvec.end(); } - const std::vector& get() const { - return fvec; - } + const std::vector& get() const { return fvec; } /// Iteration over 3D fields - const std::vector& field3d() const { - return f3vec; - } + const std::vector& field3d() const { return f3vec; } /// Ensure that each field appears only once void makeUnique(); - private: - std::vector fvec; // Vector of fields - std::vector f3vec; // Vector of 3D fields + +private: + std::vector fvec; // Vector of fields + std::vector f3vec; // Vector of 3D fields }; /// Combine two FieldGroups -FieldGroup operator+(const FieldGroup &lhs, const FieldGroup &rhs); +FieldGroup operator+(const FieldGroup& lhs, const FieldGroup& rhs); #endif // __FIELDGROUP_H__ diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx index 6898c7fd41..4433463e8f 100644 --- a/include/bout/fieldperp.hxx +++ b/include/bout/fieldperp.hxx @@ -28,37 +28,37 @@ class FieldPerp; #ifndef __FIELDPERP_H__ #define __FIELDPERP_H__ -#include "field.hxx" +#include "bout/field.hxx" #include "bout/array.hxx" #include "bout/assert.hxx" #include "bout/region.hxx" -#include "unused.hxx" +#include "bout/unused.hxx" #include #include -class Field2D; // #include "field2d.hxx" -class Field3D; // #include "field3d.hxx" +class Field2D; // #include "bout/field2d.hxx" +class Field3D; // #include "bout/field3d.hxx" /*! * Represents a 2D field perpendicular to the magnetic field * at a particular index in Y, which only varies in X-Z. * * Primarily used inside field solvers - */ + */ class FieldPerp : public Field { - public: +public: using ind_type = IndPerp; - + /*! * Constructor */ - FieldPerp(Mesh * fieldmesh = nullptr, CELL_LOC location_in=CELL_CENTRE, - int yindex_in=-1, - DirectionTypes directions_in = - {YDirectionType::Standard, ZDirectionType::Standard}); + FieldPerp(Mesh* fieldmesh = nullptr, CELL_LOC location_in = CELL_CENTRE, + int yindex_in = -1, + DirectionTypes directions_in = {YDirectionType::Standard, + ZDirectionType::Standard}); /*! * Copy constructor. After this the data @@ -69,14 +69,14 @@ class FieldPerp : public Field { /*! * Move constructor */ - FieldPerp(FieldPerp &&rhs) = default; + FieldPerp(FieldPerp&& rhs) = default; /*! * Constructor. This creates a FieldPerp using the global Mesh pointer (mesh) * allocates data, and assigns the value \p val to all points including * boundary cells. - */ - FieldPerp(BoutReal val, Mesh *localmesh = nullptr); + */ + FieldPerp(BoutReal val, Mesh* localmesh = nullptr); /*! * Constructor from Array and Mesh @@ -91,29 +91,30 @@ class FieldPerp : public Field { /*! * Assignment operators */ - FieldPerp &operator=(const FieldPerp &rhs); - FieldPerp &operator=(FieldPerp &&rhs) = default; - FieldPerp &operator=(BoutReal rhs); + FieldPerp& operator=(const FieldPerp& rhs); + FieldPerp& operator=(FieldPerp&& rhs) = default; + FieldPerp& operator=(BoutReal rhs); /// Return a Region reference to use to iterate over this field - const Region& getRegion(REGION region) const; - const Region& getRegion(const std::string ®ion_name) const; - - Region::RegionIndices::const_iterator begin() const {return std::begin(getRegion("RGN_ALL"));}; - Region::RegionIndices::const_iterator end() const {return std::end(getRegion("RGN_ALL"));}; - - inline BoutReal& operator[](const IndPerp &d) { - return data[d.ind]; - } - inline const BoutReal& operator[](const IndPerp &d) const { - return data[d.ind]; - } + const Region& getRegion(REGION region) const; + const Region& getRegion(const std::string& region_name) const; + + Region::RegionIndices::const_iterator begin() const { + return std::begin(getRegion("RGN_ALL")); + }; + Region::RegionIndices::const_iterator end() const { + return std::end(getRegion("RGN_ALL")); + }; + + inline BoutReal& operator[](const IndPerp& d) { return data[d.ind]; } + inline const BoutReal& operator[](const IndPerp& d) const { return data[d.ind]; } - inline BoutReal& operator[](const Ind3D &d) { + inline BoutReal& operator[](const Ind3D& d) { ASSERT3(d.y() == yindex); - return operator()(d.x(), d.z()); //Could use mesh->ind3DtoPerp if we had access to mesh here + return operator()(d.x(), + d.z()); //Could use mesh->ind3DtoPerp if we had access to mesh here } - inline const BoutReal& operator[](const Ind3D &d) const { + inline const BoutReal& operator[](const Ind3D& d) const { ASSERT3(d.y() == yindex); return operator()(d.x(), d.z()); } @@ -164,25 +165,25 @@ class FieldPerp : public Field { * */ bool isAllocated() const { return !data.empty(); } - + // operators - + const BoutReal* operator[](int jx) const { ASSERT2(!data.empty()); - ASSERT2( (jx >= 0) && (jx < nx) ); - - return &data[jx*nz]; + ASSERT2((jx >= 0) && (jx < nx)); + + return &data[jx * nz]; } - + /*! * Returns a C-style array (pointer to first element) in Z * at a given X index. Used mainly for FFT routines */ BoutReal* operator[](int jx) { ASSERT2(!data.empty()); - ASSERT2( (jx >= 0) && (jx < nx) ); - - return &data[jx*nz]; + ASSERT2((jx >= 0) && (jx < nx)); + + return &data[jx * nz]; } /*! @@ -190,85 +191,89 @@ class FieldPerp : public Field { * * If CHECK > 2 then bounds checking is performed, otherwise * no checks are performed - */ + */ BoutReal& operator()(int jx, int jz) { #if CHECK > 2 // Bounds check both indices - if(data.empty()) + if (data.empty()) { throw BoutException("FieldPerp: () operator on empty data"); - if((jx < 0) || (jx >= nx) || - (jz < 0) || (jz >= nz)) + } + if ((jx < 0) || (jx >= nx) || (jz < 0) || (jz >= nz)) { throw BoutException("FieldPerp: ({:d}, {:d}) operator out of bounds ({:d}, {:d})", jx, jz, nx, nz); + } #endif - return data[jx*nz + jz]; + return data[jx * nz + jz]; } - + /*! * Const (read-only) access to the underlying data array. - */ + */ const BoutReal& operator()(int jx, int jz) const { #if CHECK > 2 // Bounds check both indices - if(data.empty()) + if (data.empty()) { throw BoutException("FieldPerp: () operator on empty data"); - if((jx < 0) || (jx >= nx) || - (jz < 0) || (jz >= nz)) + } + if ((jx < 0) || (jx >= nx) || (jz < 0) || (jz >= nz)) { throw BoutException("FieldPerp: ({:d}, {:d}) operator out of bounds ({:d}, {:d})", jx, jz, nx, nz); + } #endif - return data[jx*nz + jz]; + return data[jx * nz + jz]; } - + /*! * Access to the underlying data array. (X,Y,Z) indices for consistency with * other field types * - */ + */ BoutReal& operator()(int jx, int UNUSED(jy), int jz) { return (*this)(jx, jz); } - - const BoutReal& operator()(int jx, int UNUSED(jy), int jz) const { return (*this)(jx, jz); } + + const BoutReal& operator()(int jx, int UNUSED(jy), int jz) const { + return (*this)(jx, jz); + } /*! * Addition, modifying in-place. * This loops over the entire domain, including guard/boundary cells */ - FieldPerp & operator+=(const FieldPerp &rhs); - FieldPerp & operator+=(const Field3D &rhs); - FieldPerp & operator+=(const Field2D &rhs); - FieldPerp & operator+=(BoutReal rhs); + FieldPerp& operator+=(const FieldPerp& rhs); + FieldPerp& operator+=(const Field3D& rhs); + FieldPerp& operator+=(const Field2D& rhs); + FieldPerp& operator+=(BoutReal rhs); /*! * Subtraction, modifying in place. * This loops over the entire domain, including guard/boundary cells */ - FieldPerp & operator-=(const FieldPerp &rhs); - FieldPerp & operator-=(const Field3D &rhs); - FieldPerp & operator-=(const Field2D &rhs); - FieldPerp & operator-=(BoutReal rhs); + FieldPerp& operator-=(const FieldPerp& rhs); + FieldPerp& operator-=(const Field3D& rhs); + FieldPerp& operator-=(const Field2D& rhs); + FieldPerp& operator-=(BoutReal rhs); /*! * Multiplication, modifying in place. * This loops over the entire domain, including guard/boundary cells */ - FieldPerp & operator*=(const FieldPerp &rhs); - FieldPerp & operator*=(const Field3D &rhs); - FieldPerp & operator*=(const Field2D &rhs); - FieldPerp & operator*=(BoutReal rhs); + FieldPerp& operator*=(const FieldPerp& rhs); + FieldPerp& operator*=(const Field3D& rhs); + FieldPerp& operator*=(const Field2D& rhs); + FieldPerp& operator*=(BoutReal rhs); /*! * Division, modifying in place. * This loops over the entire domain, including guard/boundary cells */ - FieldPerp & operator/=(const FieldPerp &rhs); - FieldPerp & operator/=(const Field3D &rhs); - FieldPerp & operator/=(const Field2D &rhs); - FieldPerp & operator/=(BoutReal rhs); + FieldPerp& operator/=(const FieldPerp& rhs); + FieldPerp& operator/=(const Field3D& rhs); + FieldPerp& operator/=(const Field2D& rhs); + FieldPerp& operator/=(BoutReal rhs); /*! * Return the number of nx points */ - int getNx() const override {return nx;}; + int getNx() const override { return nx; }; /*! * Return the number of ny points */ @@ -276,7 +281,7 @@ class FieldPerp : public Field { /*! * Return the number of nz points */ - int getNz() const override {return nz;}; + int getNz() const override { return nz; }; bool is3D() const override { return false; } @@ -292,40 +297,40 @@ private: /// The underlying data array Array data; }; - + // Non-member functions // Non-member overloaded operators - -FieldPerp operator+(const FieldPerp &lhs, const FieldPerp &rhs); -FieldPerp operator+(const FieldPerp &lhs, const Field3D &rhs); -FieldPerp operator+(const FieldPerp &lhs, const Field2D &rhs); -FieldPerp operator+(const FieldPerp &lhs, BoutReal rhs); -FieldPerp operator+(BoutReal lhs, const FieldPerp &rhs); - -FieldPerp operator-(const FieldPerp &lhs, const FieldPerp &rhs); -FieldPerp operator-(const FieldPerp &lhs, const Field3D &rhs); -FieldPerp operator-(const FieldPerp &lhs, const Field2D &rhs); -FieldPerp operator-(const FieldPerp &lhs, BoutReal rhs); -FieldPerp operator-(BoutReal lhs, const FieldPerp &rhs); - -FieldPerp operator*(const FieldPerp &lhs, const FieldPerp &rhs); -FieldPerp operator*(const FieldPerp &lhs, const Field3D &rhs); -FieldPerp operator*(const FieldPerp &lhs, const Field2D &rhs); -FieldPerp operator*(const FieldPerp &lhs, BoutReal rhs); -FieldPerp operator*(BoutReal lhs, const FieldPerp &rhs); - -FieldPerp operator/(const FieldPerp &lhs, const FieldPerp &rhs); -FieldPerp operator/(const FieldPerp &lhs, const Field3D &rhs); -FieldPerp operator/(const FieldPerp &lhs, const Field2D &rhs); -FieldPerp operator/(const FieldPerp &lhs, BoutReal rhs); -FieldPerp operator/(BoutReal lhs, const FieldPerp &rhs); + +FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs); +FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs); +FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs); +FieldPerp operator+(const FieldPerp& lhs, BoutReal rhs); +FieldPerp operator+(BoutReal lhs, const FieldPerp& rhs); + +FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs); +FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs); +FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs); +FieldPerp operator-(const FieldPerp& lhs, BoutReal rhs); +FieldPerp operator-(BoutReal lhs, const FieldPerp& rhs); + +FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs); +FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs); +FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs); +FieldPerp operator*(const FieldPerp& lhs, BoutReal rhs); +FieldPerp operator*(BoutReal lhs, const FieldPerp& rhs); + +FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs); +FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs); +FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs); +FieldPerp operator/(const FieldPerp& lhs, BoutReal rhs); +FieldPerp operator/(BoutReal lhs, const FieldPerp& rhs); /*! * Unary minus. Returns the negative of given field, * iterates over whole domain including guard/boundary cells. */ -FieldPerp operator-(const FieldPerp &f); +FieldPerp operator-(const FieldPerp& f); /// Create a FieldPerp by slicing a 3D field at a given y const FieldPerp sliceXZ(const Field3D& f, int y); @@ -333,22 +338,25 @@ const FieldPerp sliceXZ(const Field3D& f, int y); // Specialize newEmptyField templates for FieldPerp /// Return an empty shell field of some type derived from Field, with metadata /// copied and a data array that is allocated but not initialised. -template<> +template <> inline FieldPerp emptyFrom(const FieldPerp& f) { - return FieldPerp(f.getMesh(), f.getLocation(), f.getIndex(), {f.getDirectionY(), f.getDirectionZ()}).allocate(); + return FieldPerp(f.getMesh(), f.getLocation(), f.getIndex(), + {f.getDirectionY(), f.getDirectionZ()}) + .allocate(); } #if CHECK > 0 -void checkData(const FieldPerp &f, const std::string& region = "RGN_NOX"); +void checkData(const FieldPerp& f, const std::string& region = "RGN_NOX"); #else -inline void checkData(const FieldPerp &UNUSED(f), const std::string& UNUSED(region) = "RGN_NOX") {} +inline void checkData(const FieldPerp& UNUSED(f), + const std::string& UNUSED(region) = "RGN_NOX") {} #endif /// Force guard cells of passed field \p var to NaN #if CHECK > 2 -void invalidateGuards(FieldPerp &var); +void invalidateGuards(FieldPerp& var); #else -inline void invalidateGuards(FieldPerp &UNUSED(var)) {} +inline void invalidateGuards(FieldPerp& UNUSED(var)) {} #endif /// toString template specialisation diff --git a/include/bout/format.hxx b/include/bout/format.hxx index 7b76ebe22a..846303a3fd 100644 --- a/include/bout/format.hxx +++ b/include/bout/format.hxx @@ -8,9 +8,9 @@ /// *this pointer, as the first argument, so often 2 would be the /// first argument. #if defined(__GNUC__) -# define BOUT_FORMAT_ARGS(i,j) __attribute__ ((format (printf, i, j))) +#define BOUT_FORMAT_ARGS(i, j) __attribute__((format(printf, i, j))) #else -# define BOUT_FORMAT_ARGS(i,j) +#define BOUT_FORMAT_ARGS(i, j) #endif #endif //__BOUT_FORMAT_H__ diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx index 575a7c240c..d2886775d8 100644 --- a/include/bout/fv_ops.hxx +++ b/include/bout/fv_ops.hxx @@ -5,11 +5,11 @@ #ifndef __FV_OPS_H__ #define __FV_OPS_H__ -#include "../globals.hxx" -#include "../field3d.hxx" -#include "../vector2d.hxx" +#include "bout/field3d.hxx" +#include "bout/globals.hxx" +#include "bout/vector2d.hxx" -#include "../utils.hxx" +#include "bout/utils.hxx" #include namespace FV { @@ -23,12 +23,13 @@ Div_a_Laplace_perp(const Field3D& a, const Field3D& x) { return Div_a_Grad_perp(a, x); } - /*! +/*! * Divergence of a parallel diffusion Div( k * Grad_par(f) ) */ - const Field3D Div_par_K_Grad_par(const Field3D &k, const Field3D &f, bool bndry_flux=true); +const Field3D Div_par_K_Grad_par(const Field3D& k, const Field3D& f, + bool bndry_flux = true); - /*! +/*! * 4th-order derivative in Y, using derivatives * on cell boundaries. * @@ -48,9 +49,9 @@ Div_a_Laplace_perp(const Field3D& a, const Field3D& x) { * * No fluxes through domain boundaries */ - const Field3D D4DY4(const Field3D &d, const Field3D &f); +const Field3D D4DY4(const Field3D& d, const Field3D& f); - /*! +/*! * 4th-order dissipation term * * @@ -66,74 +67,75 @@ Div_a_Laplace_perp(const Field3D& a, const Field3D& x) { * f_2 | f_1 | f_0 | * f_b */ - const Field3D D4DY4_Index(const Field3D &f, bool bndry_flux = true); - - /*! +const Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true); + +/*! * Stencil used for Finite Volume calculations * which includes cell face values L and R - */ - struct Stencil1D { - // Cell centre values - BoutReal c, m, p, mm, pp; - - // Left and right cell face values - BoutReal L, R; - }; - - /*! + */ +struct Stencil1D { + // Cell centre values + BoutReal c, m, p, mm, pp; + + // Left and right cell face values + BoutReal L, R; +}; + +/*! * First order upwind for testing - */ - struct Upwind { - void operator()(Stencil1D &n) { - n.L = n.R = n.c; - } - }; + */ +struct Upwind { + void operator()(Stencil1D& n) { n.L = n.R = n.c; } +}; - /*! +/*! * Fromm method */ - struct Fromm { - void operator()(Stencil1D &n) { - n.L = n.c - 0.25*(n.p - n.m); - n.R = n.c + 0.25*(n.p - n.m); - } - }; - - /*! +struct Fromm { + void operator()(Stencil1D& n) { + n.L = n.c - 0.25 * (n.p - n.m); + n.R = n.c + 0.25 * (n.p - n.m); + } +}; + +/*! * Second order slope limiter method * * Limits slope to minimum absolute value * of left and right gradients. If at a maximum * or minimum slope set to zero, i.e. reverts * to first order upwinding - */ - struct MinMod { - void operator()(Stencil1D &n) { - // Choose the gradient within the cell - // as the minimum (smoothest) solution - BoutReal slope = _minmod(n.p - n.c, n.c - n.m); - n.L = n.c - 0.5*slope; - n.R = n.c + 0.5*slope; - } - private: - /*! + */ +struct MinMod { + void operator()(Stencil1D& n) { + // Choose the gradient within the cell + // as the minimum (smoothest) solution + BoutReal slope = _minmod(n.p - n.c, n.c - n.m); + n.L = n.c - 0.5 * slope; + n.R = n.c + 0.5 * slope; + } + +private: + /*! * Internal helper function for minmod slope limiter * * If the inputs have different signs then * returns zero, otherwise chooses the value * with the minimum magnitude. */ - BoutReal _minmod(BoutReal a, BoutReal b) { - if( a*b <= 0.0 ) - return 0.0; - - if(fabs(a) < fabs(b)) - return a; - return b; + BoutReal _minmod(BoutReal a, BoutReal b) { + if (a * b <= 0.0) { + return 0.0; } - }; - /*! + if (fabs(a) < fabs(b)) { + return a; + } + return b; + } +}; + +/*! * Monotonised Central (MC) second order slope limiter (Van Leer) * * Limits the slope based on taking the slope with @@ -141,232 +143,234 @@ Div_a_Laplace_perp(const Field3D& a, const Field3D& x) { * 2*right. If any of these slopes have different signs * then the slope reverts to zero (i.e. 1st-order upwinding). */ - struct MC { - void operator()(Stencil1D &n) { - BoutReal slope = minmod(2. * (n.p - n.c), // 2*right difference - 0.5 * (n.p - n.m), // Central difference - 2. * (n.c - n.m) ); // 2*left difference - n.L = n.c - 0.5*slope; - n.R = n.c + 0.5*slope; - } - private: - // Return zero if any signs are different - // otherwise return the value with the minimum magnitude - BoutReal minmod(BoutReal a, BoutReal b, BoutReal c) { - // if any of the signs are different, return zero gradient - if ((a * b <= 0.0) || (a * c <= 0.0)) { - return 0.0; - } +struct MC { + void operator()(Stencil1D& n) { + BoutReal slope = minmod(2. * (n.p - n.c), // 2*right difference + 0.5 * (n.p - n.m), // Central difference + 2. * (n.c - n.m)); // 2*left difference + n.L = n.c - 0.5 * slope; + n.R = n.c + 0.5 * slope; + } - // Return the minimum absolute value - return SIGN(a) * BOUTMIN(fabs(a), fabs(b), fabs(c)); +private: + // Return zero if any signs are different + // otherwise return the value with the minimum magnitude + BoutReal minmod(BoutReal a, BoutReal b, BoutReal c) { + // if any of the signs are different, return zero gradient + if ((a * b <= 0.0) || (a * c <= 0.0)) { + return 0.0; } - }; - - /*! + + // Return the minimum absolute value + return SIGN(a) * BOUTMIN(fabs(a), fabs(b), fabs(c)); + } +}; + +/*! * Communicate fluxes between processors * Takes values in guard cells, and adds them to cells */ - void communicateFluxes(Field3D &f); - - /// Finite volume parallel divergence - /// - /// Preserves the sum of f*J*dx*dy*dz over the domain - /// - /// @param[in] f_in The field being advected. - /// This will be reconstructed at cell faces - /// using the given CellEdges method - /// @param[in] v_in The advection velocity. - /// This will be interpolated to cell boundaries - /// using linear interpolation - /// @param[in] wave_speed_in Local maximum speed of all waves in the system at each - // point in space - /// @param[in] fixflux Fix the flux at the boundary to be the value at the - /// midpoint (for boundary conditions) - /// - /// NB: Uses to/from FieldAligned coordinates - template - const Field3D Div_par(const Field3D &f_in, const Field3D &v_in, - const Field3D &wave_speed_in, bool fixflux=true) { - - ASSERT1_FIELDS_COMPATIBLE(f_in, v_in); - ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in); - - Mesh* mesh = f_in.getMesh(); - - CellEdges cellboundary; - - ASSERT2(f_in.getDirectionY() == v_in.getDirectionY()); - ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY()); - const bool are_unaligned - = ((f_in.getDirectionY() == YDirectionType::Standard) - and (v_in.getDirectionY() == YDirectionType::Standard) - and (wave_speed_in.getDirectionY() == YDirectionType::Standard)); - - Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in; - Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in; - Field3D wave_speed = are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") - : wave_speed_in; - - Coordinates *coord = f_in.getCoordinates(); - - Field3D result{zeroFrom(f)}; - - // Only need one guard cell, so no need to communicate fluxes - // Instead calculate in guard cells to preserve fluxes - int ys = mesh->ystart-1; - int ye = mesh->yend+1; - - for (int i = mesh->xstart; i <= mesh->xend; i++) { - - if (!mesh->firstY(i) || mesh->periodicY(i)) { - // Calculate in guard cell to get fluxes consistent between processors - ys = mesh->ystart - 1; - } else { - // Don't include the boundary cell. Note that this implies special - // handling of boundaries later - ys = mesh->ystart; - } +void communicateFluxes(Field3D& f); + +/// Finite volume parallel divergence +/// +/// Preserves the sum of f*J*dx*dy*dz over the domain +/// +/// @param[in] f_in The field being advected. +/// This will be reconstructed at cell faces +/// using the given CellEdges method +/// @param[in] v_in The advection velocity. +/// This will be interpolated to cell boundaries +/// using linear interpolation +/// @param[in] wave_speed_in Local maximum speed of all waves in the system at each +// point in space +/// @param[in] fixflux Fix the flux at the boundary to be the value at the +/// midpoint (for boundary conditions) +/// +/// NB: Uses to/from FieldAligned coordinates +template +const Field3D Div_par(const Field3D& f_in, const Field3D& v_in, + const Field3D& wave_speed_in, bool fixflux = true) { + + ASSERT1_FIELDS_COMPATIBLE(f_in, v_in); + ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in); + + Mesh* mesh = f_in.getMesh(); + + CellEdges cellboundary; + + ASSERT2(f_in.getDirectionY() == v_in.getDirectionY()); + ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY()); + const bool are_unaligned = + ((f_in.getDirectionY() == YDirectionType::Standard) + and (v_in.getDirectionY() == YDirectionType::Standard) + and (wave_speed_in.getDirectionY() == YDirectionType::Standard)); + + Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in; + Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in; + Field3D wave_speed = + are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") : wave_speed_in; + + Coordinates* coord = f_in.getCoordinates(); + + Field3D result{zeroFrom(f)}; + + // Only need one guard cell, so no need to communicate fluxes + // Instead calculate in guard cells to preserve fluxes + int ys = mesh->ystart - 1; + int ye = mesh->yend + 1; + + for (int i = mesh->xstart; i <= mesh->xend; i++) { + + if (!mesh->firstY(i) || mesh->periodicY(i)) { + // Calculate in guard cell to get fluxes consistent between processors + ys = mesh->ystart - 1; + } else { + // Don't include the boundary cell. Note that this implies special + // handling of boundaries later + ys = mesh->ystart; + } - if (!mesh->lastY(i) || mesh->periodicY(i)) { - // Calculate in guard cells - ye = mesh->yend + 1; - } else { - // Not in boundary cells - ye = mesh->yend; - } + if (!mesh->lastY(i) || mesh->periodicY(i)) { + // Calculate in guard cells + ye = mesh->yend + 1; + } else { + // Not in boundary cells + ye = mesh->yend; + } - for (int j = ys; j <= ye; j++) { - // Pre-calculate factors which multiply fluxes + for (int j = ys; j <= ye; j++) { + // Pre-calculate factors which multiply fluxes #if not(BOUT_USE_METRIC_3D) - // For right cell boundaries - BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1)) / - (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1))); + // For right cell boundaries + BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1)) + / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1))); - BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j)); - BoutReal flux_factor_rp = common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1)); + BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j)); + BoutReal flux_factor_rp = + common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1)); - // For left cell boundaries - common_factor = (coord->J(i, j) + coord->J(i, j - 1)) / - (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1))); + // For left cell boundaries + common_factor = (coord->J(i, j) + coord->J(i, j - 1)) + / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1))); - BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j)); - BoutReal flux_factor_lm = common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1)); + BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j)); + BoutReal flux_factor_lm = + common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1)); #endif - for (int k = 0; k < mesh->LocalNz; k++) { + for (int k = 0; k < mesh->LocalNz; k++) { #if BOUT_USE_METRIC_3D - // For right cell boundaries - BoutReal common_factor = - (coord->J(i, j, k) + coord->J(i, j + 1, k)) - / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k))); - - BoutReal flux_factor_rc = - common_factor / (coord->dy(i, j, k) * coord->J(i, j, k)); - BoutReal flux_factor_rp = - common_factor / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k)); - - // For left cell boundaries - common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k)) - / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k))); - - BoutReal flux_factor_lc = - common_factor / (coord->dy(i, j, k) * coord->J(i, j, k)); - BoutReal flux_factor_lm = - common_factor / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k)); + // For right cell boundaries + BoutReal common_factor = + (coord->J(i, j, k) + coord->J(i, j + 1, k)) + / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k))); + + BoutReal flux_factor_rc = + common_factor / (coord->dy(i, j, k) * coord->J(i, j, k)); + BoutReal flux_factor_rp = + common_factor / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k)); + + // For left cell boundaries + common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k)) + / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k))); + + BoutReal flux_factor_lc = + common_factor / (coord->dy(i, j, k) * coord->J(i, j, k)); + BoutReal flux_factor_lm = + common_factor / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k)); #endif - //////////////////////////////////////////// - // Reconstruct f at the cell faces - // This calculates s.R and s.L for the Right and Left - // face values on this cell - - // Reconstruct f at the cell faces - Stencil1D s; - s.c = f(i, j, k); - s.m = f(i, j - 1, k); - s.p = f(i, j + 1, k); - - cellboundary(s); // Calculate s.R and s.L - - //////////////////////////////////////////// - // Right boundary - - // Calculate velocity at right boundary (y+1/2) - BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k)); - BoutReal flux; - - if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) { - // Last point in domain - - BoutReal bndryval = 0.5 * (s.c + s.p); - if (fixflux) { - // Use mid-point to be consistent with boundary conditions - flux = bndryval * vpar; - } else { - // Add flux due to difference in boundary values - flux = s.R * vpar + wave_speed(i, j, k) * (s.R - bndryval); - } + //////////////////////////////////////////// + // Reconstruct f at the cell faces + // This calculates s.R and s.L for the Right and Left + // face values on this cell + + // Reconstruct f at the cell faces + Stencil1D s; + s.c = f(i, j, k); + s.m = f(i, j - 1, k); + s.p = f(i, j + 1, k); + + cellboundary(s); // Calculate s.R and s.L + + //////////////////////////////////////////// + // Right boundary + + // Calculate velocity at right boundary (y+1/2) + BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k)); + BoutReal flux; + + if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) { + // Last point in domain + + BoutReal bndryval = 0.5 * (s.c + s.p); + if (fixflux) { + // Use mid-point to be consistent with boundary conditions + flux = bndryval * vpar; } else { - - // Maximum wave speed in the two cells - BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k)); - - if (vpar > amax) { - // Supersonic flow out of this cell - flux = s.R * vpar; - } else if (vpar < -amax) { - // Supersonic flow into this cell - flux = 0.0; - } else { - // Subsonic flow, so a mix of right and left fluxes - flux = s.R * 0.5 * (vpar + amax); - } + // Add flux due to difference in boundary values + flux = s.R * vpar + wave_speed(i, j, k) * (s.R - bndryval); } - - result(i, j, k) += flux * flux_factor_rc; - result(i, j + 1, k) -= flux * flux_factor_rp; - - //////////////////////////////////////////// - // Calculate at left boundary - - vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k)); - - if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) { - // First point in domain - BoutReal bndryval = 0.5 * (s.c + s.m); - if (fixflux) { - // Use mid-point to be consistent with boundary conditions - flux = bndryval * vpar; - } else { - // Add flux due to difference in boundary values - flux = s.L * vpar - wave_speed(i, j, k) * (s.L - bndryval); - } + } else { + + // Maximum wave speed in the two cells + BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k)); + + if (vpar > amax) { + // Supersonic flow out of this cell + flux = s.R * vpar; + } else if (vpar < -amax) { + // Supersonic flow into this cell + flux = 0.0; } else { - - // Maximum wave speed in the two cells - BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k)); - - if (vpar < -amax) { - // Supersonic out of this cell - flux = s.L * vpar; - } else if (vpar > amax) { - // Supersonic into this cell - flux = 0.0; - } else { - flux = s.L * 0.5 * (vpar - amax); - } + // Subsonic flow, so a mix of right and left fluxes + flux = s.R * 0.5 * (vpar + amax); } - - result(i, j, k) -= flux * flux_factor_lc; - result(i, j - 1, k) += flux * flux_factor_lm; - } + + result(i, j, k) += flux * flux_factor_rc; + result(i, j + 1, k) -= flux * flux_factor_rp; + + //////////////////////////////////////////// + // Calculate at left boundary + + vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k)); + + if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) { + // First point in domain + BoutReal bndryval = 0.5 * (s.c + s.m); + if (fixflux) { + // Use mid-point to be consistent with boundary conditions + flux = bndryval * vpar; + } else { + // Add flux due to difference in boundary values + flux = s.L * vpar - wave_speed(i, j, k) * (s.L - bndryval); + } + } else { + + // Maximum wave speed in the two cells + BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k)); + + if (vpar < -amax) { + // Supersonic out of this cell + flux = s.L * vpar; + } else if (vpar > amax) { + // Supersonic into this cell + flux = 0.0; + } else { + flux = s.L * 0.5 * (vpar - amax); + } + } + + result(i, j, k) -= flux * flux_factor_lc; + result(i, j - 1, k) += flux * flux_factor_lm; } } - return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result; } - - /*! + return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result; +} + +/*! * Div ( n * v ) -- Magnetic drifts * * This uses the expression @@ -378,148 +382,147 @@ Div_a_Laplace_perp(const Field3D& a, const Field3D& x) { * Note: Uses to/from FieldAligned * */ - template - const Field3D Div_f_v(const Field3D &n_in, const Vector3D &v, bool bndry_flux) { - ASSERT1(n_in.getLocation() == v.getLocation()); - ASSERT1_FIELDS_COMPATIBLE(n_in, v.x); - - Mesh* mesh = n_in.getMesh(); - - CellEdges cellboundary; - - Coordinates *coord = n_in.getCoordinates(); - - if(v.covariant) { - // Got a covariant vector instead - throw BoutException("Div_f_v passed a covariant v"); - } - - Field3D result{zeroFrom(n_in)}; - - Field3D vx = v.x; - Field3D vz = v.z; - Field3D n = n_in; - - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { - // Calculate velocities - BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]); - BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]); - BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]); - BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]); - - // X direction - Stencil1D s; - s.c = n[i]; - s.m = n[i.xm()]; - s.mm = n[i.xmm()]; - s.p = n[i.xp()]; - s.pp = n[i.xpp()]; - - cellboundary(s); - - if ((i.x() == mesh->xend) && (mesh->lastX())) { - // At right boundary in X - if (bndry_flux) { - BoutReal flux; - if (vR > 0.0) { - // Flux to boundary - flux = vR * s.R; - } else { - // Flux in from boundary - flux = vR * 0.5 * (n[i.xp()] + n[i]); - } - result[i] += flux / (coord->dx[i] * coord->J[i]); - result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]); - } - } else { - // Not at a boundary +template +const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) { + ASSERT1(n_in.getLocation() == v.getLocation()); + ASSERT1_FIELDS_COMPATIBLE(n_in, v.x); + + Mesh* mesh = n_in.getMesh(); + + CellEdges cellboundary; + + Coordinates* coord = n_in.getCoordinates(); + + if (v.covariant) { + // Got a covariant vector instead + throw BoutException("Div_f_v passed a covariant v"); + } + + Field3D result{zeroFrom(n_in)}; + + Field3D vx = v.x; + Field3D vz = v.z; + Field3D n = n_in; + + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + // Calculate velocities + BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]); + BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]); + BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]); + BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]); + + // X direction + Stencil1D s; + s.c = n[i]; + s.m = n[i.xm()]; + s.mm = n[i.xmm()]; + s.p = n[i.xp()]; + s.pp = n[i.xpp()]; + + cellboundary(s); + + if ((i.x() == mesh->xend) && (mesh->lastX())) { + // At right boundary in X + if (bndry_flux) { + BoutReal flux; if (vR > 0.0) { - // Flux out into next cell - BoutReal flux = vR * s.R; - result[i] += flux / (coord->dx[i] * coord->J[i]); - result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]); + // Flux to boundary + flux = vR * s.R; + } else { + // Flux in from boundary + flux = vR * 0.5 * (n[i.xp()] + n[i]); } + result[i] += flux / (coord->dx[i] * coord->J[i]); + result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]); + } + } else { + // Not at a boundary + if (vR > 0.0) { + // Flux out into next cell + BoutReal flux = vR * s.R; + result[i] += flux / (coord->dx[i] * coord->J[i]); + result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]); } + } - // Left side + // Left side - if ((i.x() == mesh->xstart) && (mesh->firstX())) { - // At left boundary in X + if ((i.x() == mesh->xstart) && (mesh->firstX())) { + // At left boundary in X - if (bndry_flux) { - BoutReal flux; - if (vL < 0.0) { - // Flux to boundary - flux = vL * s.L; - } else { - // Flux in from boundary - flux = vL * 0.5 * (n[i.xm()] + n[i]); - } - result[i] -= flux / (coord->dx[i] * coord->J[i]); - result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]); - } - } else { - // Not at a boundary + if (bndry_flux) { + BoutReal flux; if (vL < 0.0) { - BoutReal flux = vL * s.L; - result[i] -= flux / (coord->dx[i] * coord->J[i]); - result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]); + // Flux to boundary + flux = vL * s.L; + } else { + // Flux in from boundary + flux = vL * 0.5 * (n[i.xm()] + n[i]); } + result[i] -= flux / (coord->dx[i] * coord->J[i]); + result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]); } + } else { + // Not at a boundary + if (vL < 0.0) { + BoutReal flux = vL * s.L; + result[i] -= flux / (coord->dx[i] * coord->J[i]); + result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]); + } + } - /// NOTE: Need to communicate fluxes + /// NOTE: Need to communicate fluxes - // Z direction - s.m = n[i.zm()]; - s.mm = n[i.zmm()]; - s.p = n[i.zp()]; - s.pp = n[i.zpp()]; + // Z direction + s.m = n[i.zm()]; + s.mm = n[i.zmm()]; + s.p = n[i.zp()]; + s.pp = n[i.zpp()]; - cellboundary(s); + cellboundary(s); - if (vU > 0.0) { - BoutReal flux = vU * s.R; - result[i] += flux / (coord->J[i] * coord->dz[i]); - result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]); - } - if (vD < 0.0) { - BoutReal flux = vD * s.L; - result[i] -= flux / (coord->J[i] * coord->dz[i]); - result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]); - } + if (vU > 0.0) { + BoutReal flux = vU * s.R; + result[i] += flux / (coord->J[i] * coord->dz[i]); + result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]); } - - communicateFluxes(result); - - // Y advection - // Currently just using simple centered differences - // so no fluxes need to be exchanged - - n = toFieldAligned(n_in, "RGN_NOX"); - Field3D vy = toFieldAligned(v.y, "RGN_NOX"); - - Field3D yresult = 0.0; - yresult.setDirectionY(YDirectionType::Aligned); - - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { - // Y velocities on y boundaries - BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]); - BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]); - - // n (advected quantity) on y boundaries - // Note: Use unshifted n_in variable - BoutReal nU = 0.5 * (n[i] + n[i.yp()]); - BoutReal nD = 0.5 * (n[i] + n[i.ym()]); - - yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]); + if (vD < 0.0) { + BoutReal flux = vD * s.L; + result[i] -= flux / (coord->J[i] * coord->dz[i]); + result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]); } - return result + fromFieldAligned(yresult, "RGN_NOBNDRY"); } - /*! + communicateFluxes(result); + + // Y advection + // Currently just using simple centered differences + // so no fluxes need to be exchanged + + n = toFieldAligned(n_in, "RGN_NOX"); + Field3D vy = toFieldAligned(v.y, "RGN_NOX"); + + Field3D yresult = 0.0; + yresult.setDirectionY(YDirectionType::Aligned); + + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + // Y velocities on y boundaries + BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]); + BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]); + + // n (advected quantity) on y boundaries + // Note: Use unshifted n_in variable + BoutReal nU = 0.5 * (n[i] + n[i.yp()]); + BoutReal nD = 0.5 * (n[i] + n[i.ym()]); + + yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]); + } + return result + fromFieldAligned(yresult, "RGN_NOBNDRY"); +} + +/*! * X-Z Finite Volume diffusion operator */ - Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, - CELL_LOC outloc = CELL_DEFAULT); -} // namespace FV +Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT); +} // namespace FV #endif // __FV_OPS_H__ diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx index 65f27bc4ad..3a2a63c94c 100644 --- a/include/bout/generic_factory.hxx +++ b/include/bout/generic_factory.hxx @@ -4,8 +4,8 @@ #ifndef __BOUT_GENERIC_FACTORY_H__ #define __BOUT_GENERIC_FACTORY_H__ -#include "boutexception.hxx" -#include "options.hxx" +#include "bout/boutexception.hxx" +#include "bout/options.hxx" #include @@ -136,7 +136,9 @@ public: /// /// @param[in] name The identifier for the type to be removed /// @returns true if the type was successfully removed - bool removeUnavailable(const std::string& name) { return unavailable_options.erase(name) == 1; } + bool removeUnavailable(const std::string& name) { + return unavailable_options.erase(name) == 1; + } /// Get the name of the type to create /// @@ -183,8 +185,8 @@ public: if (unavailable_index != std::end(unavailable_options)) { throw BoutException("Error when trying to create a {0:s}: '{1:s}' is not available " "because {2:s}\nAvailable {0:s}s are:\n{3:s}", - DerivedFactory::type_name, - unavailable_index->first, unavailable_index->second, available); + DerivedFactory::type_name, unavailable_index->first, + unavailable_index->second, available); } throw BoutException("Error when trying to create a {0:s}: Could not find " diff --git a/include/bout/globalfield.hxx b/include/bout/globalfield.hxx index c4fe90677e..85252f4962 100644 --- a/include/bout/globalfield.hxx +++ b/include/bout/globalfield.hxx @@ -16,54 +16,61 @@ class GlobalField2D; * which takes into account the local and global indices * * This is a base class which is inherited by GlobalField2D and GlobalField3D - */ + */ class GlobalField { public: GlobalField() = delete; virtual ~GlobalField() = default; - virtual bool valid() const = 0; ///< Is the data valid on any processor? - bool dataIsLocal() const {return valid() && (data_on_proc == mype);} ///< Data is on this processor + virtual bool valid() const = 0; ///< Is the data valid on any processor? + bool dataIsLocal() const { + return valid() && (data_on_proc == mype); + } ///< Data is on this processor /*! * Data access by index. This doesn't perform any checks, * so the user should first test if the data is available * on this processor by calling dataIsLocal() */ - BoutReal& operator()(int jx, int jy, int jz) {return data[jz + nz*jy + nz*ny*jx];} + BoutReal& operator()(int jx, int jy, int jz) { + return data[jz + nz * jy + nz * ny * jx]; + } /// Const data access by index - const BoutReal& operator()(int jx, int jy, int jz) const {return data[jz + nz*jy + nz*ny*jx];} - + const BoutReal& operator()(int jx, int jy, int jz) const { + return data[jz + nz * jy + nz * ny * jx]; + } + /// Size of the field in X - int xSize() const {return nx;} + int xSize() const { return nx; } /// Size of the field in Y - int ySize() const {return ny;} + int ySize() const { return ny; } /// Size of the field in Z - int zSize() const {return nz;} - + int zSize() const { return nz; } + /* * Direct data access * * Stored as a 1D array [x*ny*nz + y*nz + z] - */ - Array& getData() {return data;} + */ + Array& getData() { return data; } + protected: - GlobalField(Mesh *m, int proc, int xsize, int ysize, int zsize); - - Mesh *mesh; ///< The mesh we're gathering/scattering over + GlobalField(Mesh* m, int proc, int xsize, int ysize, int zsize); + + Mesh* mesh; ///< The mesh we're gathering/scattering over - int data_on_proc; ///< Which processor is this data on? - int nx, ny, nz; ///< Global field sizes + int data_on_proc; ///< Which processor is this data on? + int nx, ny, nz; ///< Global field sizes Array data; ///< The global data, if on this processor - MPI_Comm comm; ///< Communicator for all mesh + MPI_Comm comm; ///< Communicator for all mesh int npes, mype; ///< Number of MPI processes, this processor index - void proc_local_origin(int proc, int *x, int *y, int *z = nullptr) const; + void proc_local_origin(int proc, int* x, int* y, int* z = nullptr) const; /// Return the global origin of processor proc - void proc_origin(int proc, int *x, int *y, int *z = nullptr) const; + void proc_origin(int proc, int* x, int* y, int* z = nullptr) const; /// Return the array size of processor proc - void proc_size(int proc, int *lx, int *ly, int *lz = nullptr) const; + void proc_size(int proc, int* lx, int* ly, int* lz = nullptr) const; }; /*! @@ -109,7 +116,7 @@ protected: * x, y, * g2d(x, y)); * - */ + */ class GlobalField2D : public GlobalField { public: /// Can't be constructed without args @@ -118,7 +125,7 @@ public: /// /// @param[in] mesh The mesh to gather over /// @param[in] proc The processor index where everything will be gathered/scattered to/from - GlobalField2D(Mesh *mesh, int proc = 0); + GlobalField2D(Mesh* mesh, int proc = 0); /// Destructor ~GlobalField2D() override; @@ -127,29 +134,29 @@ public: bool valid() const override { return data_valid; } /// Gather all data onto one processor - void gather(const Field2D &f); + void gather(const Field2D& f); /// Scatter data back from one to many processors const Field2D scatter() const; - + /// Assignment from a 2D field. Shorthand for a gather, and must be called on all processors /// The scatter assignment operator needs to be a member of Field2D. - GlobalField2D& operator=(const Field2D &rhs) { + GlobalField2D& operator=(const Field2D& rhs) { gather(rhs); return *this; } - + /// Data access by global index - BoutReal& operator()(int jx, int jy) {return GlobalField::operator()(jx, jy, 0);} - const BoutReal& operator()(int jx, int jy) const {return GlobalField::operator()(jx, jy, 0);} - + BoutReal& operator()(int jx, int jy) { return GlobalField::operator()(jx, jy, 0); } + const BoutReal& operator()(int jx, int jy) const { + return GlobalField::operator()(jx, jy, 0); + } + protected: - private: - /// Buffer for sending and receiving. First index /// is the processor index, and second is the data BoutReal** buffer; - + /// The length of message (in BoutReals) to /// be sent to or from processor \p proc /// @@ -214,7 +221,7 @@ public: /// /// @param[in] mesh The mesh to gather over /// @param[in] proc The processor index where everything will be gathered/scattered to/from - GlobalField3D(Mesh *mesh, int proc = 0); + GlobalField3D(Mesh* mesh, int proc = 0); /// Destructor ~GlobalField3D() override; @@ -223,24 +230,22 @@ public: bool valid() const override { return data_valid; } /// Gather all data onto one processor - void gather(const Field3D &f); + void gather(const Field3D& f); /// Scatter data back from one to many processors const Field3D scatter() const; - + /// Assignment from a 2D field. Shorthand for a gather, and must be called on all processors /// The scatter assignment operator needs to be a member of Field2D. - GlobalField3D& operator=(const Field3D &rhs) { + GlobalField3D& operator=(const Field3D& rhs) { gather(rhs); return *this; } - + protected: - private: - /// Buffer for sending and receiving. First index /// is the processor index, and second is the data - BoutReal** buffer; + BoutReal** buffer; /// The length of message (in BoutReals) to /// be sent to or from processor \p proc diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index e83d13209f..a6d0c2f676 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -6,8 +6,8 @@ #include #include #include -#include -#include +#include +#include template class GlobalIndexer; @@ -183,7 +183,7 @@ private: numOffDiagonal = std::vector(size(), 0); // Set initial guess for number of on-diagonal elements - BOUT_FOR(i, regionAll) { + BOUT_FOR (i, regionAll) { numDiagonal[getGlobal(i) - globalStart] = stencils.getStencilSize(i); } diff --git a/include/bout/globals.hxx b/include/bout/globals.hxx index 3b7e3ba7ea..ae7edff298 100644 --- a/include/bout/globals.hxx +++ b/include/bout/globals.hxx @@ -1,4 +1,4 @@ -/************************************************************************//** +/************************************************************************/ /** * \brief Global variables for BOUT++ * * @@ -42,36 +42,46 @@ namespace globals { #define SETTING(name, val) name = val #endif -SETTING(Mesh *mesh, nullptr); ///< The mesh object +SETTING(Mesh* mesh, nullptr); ///< The mesh object SETTING(MpiWrapper* mpi, nullptr); ///< The MPI wrapper object /// Define for reading a variable from the grid #define GRID_LOAD1(var) mesh->get(var, #var) -#define GRID_LOAD2(var1, var2) {\ - mesh->get(var1, #var1); \ - mesh->get(var2, #var2);} -#define GRID_LOAD3(var1, var2, var3) {\ - mesh->get(var1, #var1); \ - mesh->get(var2, #var2); \ - mesh->get(var3, #var3);} -#define GRID_LOAD4(var1, var2, var3, var4) { \ - mesh->get(var1, #var1); \ - mesh->get(var2, #var2); \ - mesh->get(var3, #var3); \ - mesh->get(var4, #var4); } -#define GRID_LOAD5(var1, var2, var3, var4, var5) {\ - mesh->get(var1, #var1); \ - mesh->get(var2, #var2); \ - mesh->get(var3, #var3); \ - mesh->get(var4, #var4); \ - mesh->get(var5, #var5);} -#define GRID_LOAD6(var1, var2, var3, var4, var5, var6) {\ - mesh->get(var1, #var1); \ - mesh->get(var2, #var2); \ - mesh->get(var3, #var3); \ - mesh->get(var4, #var4); \ - mesh->get(var5, #var5); \ - mesh->get(var6, #var6);} +#define GRID_LOAD2(var1, var2) \ + { \ + mesh->get(var1, #var1); \ + mesh->get(var2, #var2); \ + } +#define GRID_LOAD3(var1, var2, var3) \ + { \ + mesh->get(var1, #var1); \ + mesh->get(var2, #var2); \ + mesh->get(var3, #var3); \ + } +#define GRID_LOAD4(var1, var2, var3, var4) \ + { \ + mesh->get(var1, #var1); \ + mesh->get(var2, #var2); \ + mesh->get(var3, #var3); \ + mesh->get(var4, #var4); \ + } +#define GRID_LOAD5(var1, var2, var3, var4, var5) \ + { \ + mesh->get(var1, #var1); \ + mesh->get(var2, #var2); \ + mesh->get(var3, #var3); \ + mesh->get(var4, #var4); \ + mesh->get(var5, #var5); \ + } +#define GRID_LOAD6(var1, var2, var3, var4, var5, var6) \ + { \ + mesh->get(var1, #var1); \ + mesh->get(var2, #var2); \ + mesh->get(var3, #var3); \ + mesh->get(var4, #var4); \ + mesh->get(var5, #var5); \ + mesh->get(var6, #var6); \ + } /// Read fields from the global mesh /// The name of the variable will be used as the name diff --git a/include/bout/griddata.hxx b/include/bout/griddata.hxx index f0889cd5e0..952d241692 100644 --- a/include/bout/griddata.hxx +++ b/include/bout/griddata.hxx @@ -28,12 +28,12 @@ class GridDataSource; #ifndef __GRIDDATA_H__ #define __GRIDDATA_H__ -#include "bout_types.hxx" +#include "bout/bout_types.hxx" #include "mesh.hxx" -#include "options.hxx" +#include "bout/options.hxx" -#include -#include +#include +#include /// Interface class to serve grid data /*! @@ -46,31 +46,34 @@ public: GridDataSource(const bool source_is_file = false) : is_file(source_is_file) {} virtual ~GridDataSource() = default; - virtual bool hasVar(const std::string &name) = 0; ///< Test if source can supply a variable + virtual bool + hasVar(const std::string& name) = 0; ///< Test if source can supply a variable /// Get a string virtual bool get(Mesh* m, std::string& sval, const std::string& name, const std::string& def = "") = 0; /// Get an integer - virtual bool get(Mesh* m, int& ival, const std::string& name, - int def = 0) = 0; + virtual bool get(Mesh* m, int& ival, const std::string& name, int def = 0) = 0; /// Get a BoutReal number virtual bool get(Mesh* m, BoutReal& rval, const std::string& name, BoutReal def = 0.0) = 0; - virtual bool get(Mesh *m, Field2D &var, const std::string &name, BoutReal def = 0.0, CELL_LOC location=CELL_DEFAULT) = 0; - virtual bool get(Mesh *m, Field3D &var, const std::string &name, BoutReal def = 0.0, CELL_LOC location=CELL_DEFAULT) = 0; - virtual bool get(Mesh *m, FieldPerp &var, const std::string &name, BoutReal def = 0.0, CELL_LOC location=CELL_DEFAULT) = 0; - - enum class Direction {X, Y, Z}; + virtual bool get(Mesh* m, Field2D& var, const std::string& name, BoutReal def = 0.0, + CELL_LOC location = CELL_DEFAULT) = 0; + virtual bool get(Mesh* m, Field3D& var, const std::string& name, BoutReal def = 0.0, + CELL_LOC location = CELL_DEFAULT) = 0; + virtual bool get(Mesh* m, FieldPerp& var, const std::string& name, BoutReal def = 0.0, + CELL_LOC location = CELL_DEFAULT) = 0; + + enum class Direction { X, Y, Z }; // Define some aliases so GridDataSource::X, GridDataSource::Y and GridDataSource::Z can // be used, for backward compatibility static constexpr Direction X = Direction::X; static constexpr Direction Y = Direction::Y; static constexpr Direction Z = Direction::Z; - virtual bool get(Mesh *m, std::vector &var, const std::string &name, int len, int offset = 0, - Direction dir = GridDataSource::X) = 0; - virtual bool get(Mesh *m, std::vector &var, const std::string &name, int len, + virtual bool get(Mesh* m, std::vector& var, const std::string& name, int len, + int offset = 0, Direction dir = GridDataSource::X) = 0; + virtual bool get(Mesh* m, std::vector& var, const std::string& name, int len, int offset = 0, Direction dir = GridDataSource::X) = 0; /// Are x-boundary guard cells read from the source? @@ -94,7 +97,7 @@ public: GridFile(std::string gridfilename); ~GridFile() = default; - bool hasVar(const std::string &name) override; + bool hasVar(const std::string& name) override; /// Get a string bool get(Mesh* m, std::string& sval, const std::string& name, @@ -103,16 +106,19 @@ public: bool get(Mesh* m, int& ival, const std::string& name, int def = 0) override; /// Get a BoutReal number bool get(Mesh* m, BoutReal& rval, const std::string& name, BoutReal def = 0.0) override; - bool get(Mesh* m, Field2D& var, const std::string& name, BoutReal def = 0.0, CELL_LOC location = CELL_DEFAULT) override; - bool get(Mesh *m, Field3D &var, const std::string &name, BoutReal def = 0.0, CELL_LOC location = CELL_DEFAULT) override; - bool get(Mesh *m, FieldPerp &var, const std::string &name, BoutReal def = 0.0, CELL_LOC location = CELL_DEFAULT) override { + bool get(Mesh* m, Field2D& var, const std::string& name, BoutReal def = 0.0, + CELL_LOC location = CELL_DEFAULT) override; + bool get(Mesh* m, Field3D& var, const std::string& name, BoutReal def = 0.0, + CELL_LOC location = CELL_DEFAULT) override; + bool get(Mesh* m, FieldPerp& var, const std::string& name, BoutReal def = 0.0, + CELL_LOC location = CELL_DEFAULT) override { return getField(m, var, name, def, location); } - bool get(Mesh *m, std::vector &var, const std::string &name, int len, int offset = 0, - GridDataSource::Direction dir = GridDataSource::X) override; - bool get(Mesh *m, std::vector &var, const std::string &name, int len, int offset = 0, - GridDataSource::Direction dir = GridDataSource::X) override; + bool get(Mesh* m, std::vector& var, const std::string& name, int len, + int offset = 0, GridDataSource::Direction dir = GridDataSource::X) override; + bool get(Mesh* m, std::vector& var, const std::string& name, int len, + int offset = 0, GridDataSource::Direction dir = GridDataSource::X) override; /// Are x-boundary guard cells read from the source? bool hasXBoundaryGuards(Mesh* m) override; @@ -126,31 +132,32 @@ private: int grid_yguards{0}; int ny_inner{0}; - bool readgrid_3dvar_fft(Mesh *m, const std::string &name, int yread, int ydest, int ysize, - int xread, int xdest, int xsize, Field3D &var); + bool readgrid_3dvar_fft(Mesh* m, const std::string& name, int yread, int ydest, + int ysize, int xread, int xdest, int xsize, Field3D& var); - bool readgrid_3dvar_real(const std::string &name, int yread, int ydest, int ysize, - int xread, int xdest, int xsize, Field3D &var); + bool readgrid_3dvar_real(const std::string& name, int yread, int ydest, int ysize, + int xread, int xdest, int xsize, Field3D& var); - bool readgrid_perpvar_fft(Mesh *m, const std::string &name, int xread, int xdest, - int xsize, FieldPerp &var); + bool readgrid_perpvar_fft(Mesh* m, const std::string& name, int xread, int xdest, + int xsize, FieldPerp& var); - bool readgrid_perpvar_real(const std::string &name, int xread, int xdest, int xsize, - FieldPerp &var); + bool readgrid_perpvar_real(const std::string& name, int xread, int xdest, int xsize, + FieldPerp& var); // convenience template method to remove code duplication between Field2D, // Field3D and FieldPerp versions of get - template - bool getField(Mesh* m, T& var, const std::string& name, BoutReal def, CELL_LOC location); + template + bool getField(Mesh* m, T& var, const std::string& name, BoutReal def, + CELL_LOC location); // utility method for Field2D to implement unshared parts of getField - void readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, - int xs, int xd, int nx_to_read, const std::vector& size, Field2D& var); + void readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, int xs, + int xd, int nx_to_read, const std::vector& size, Field2D& var); // utility method for Field3D to implement unshared parts of getField - void readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, - int xs, int xd, int nx_to_read, const std::vector& size, Field3D& var); + void readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, int xs, + int xd, int nx_to_read, const std::vector& size, Field3D& var); // utility method for FieldPerp to implement unshared parts of getField - void readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, - int xs, int xd, int nx_to_read, const std::vector& size, FieldPerp& var); + void readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, int xs, + int xd, int nx_to_read, const std::vector& size, FieldPerp& var); }; /*! @@ -166,12 +173,12 @@ public: * @param[in] opt Options section to use as input. By default the "mesh" section under * root will be used. */ - GridFromOptions(Options *opt = nullptr) : options(opt) {} + GridFromOptions(Options* opt = nullptr) : options(opt) {} /*! * Checks if the options has a given variable */ - bool hasVar(const std::string &name) override; + bool hasVar(const std::string& name) override; /*! * Reads strings from options. Uses Options::get to handle @@ -197,7 +204,7 @@ public: * * @return True if option is set, false if ival is default (0) */ - bool get(Mesh *mesh, int &ival, const std::string &name, int def = 0) override; + bool get(Mesh* mesh, int& ival, const std::string& name, int def = 0) override; /*! * Reads BoutReal from options. Uses Options::get to handle @@ -222,7 +229,7 @@ public: * @param[in] def Default value to use if option not found * @param[in] location Location at which to get the variable */ - bool get(Mesh *mesh, Field2D &var, const std::string &name, BoutReal def = 0.0, + bool get(Mesh* mesh, Field2D& var, const std::string& name, BoutReal def = 0.0, CELL_LOC location = CELL_DEFAULT) override; /*! @@ -235,7 +242,7 @@ public: * @param[in] def Default value to use if option not found * @param[in] location Location at which to get the variable */ - bool get(Mesh *mesh, Field3D &var, const std::string &name, BoutReal def = 0.0, + bool get(Mesh* mesh, Field3D& var, const std::string& name, BoutReal def = 0.0, CELL_LOC location = CELL_DEFAULT) override; /*! @@ -248,7 +255,7 @@ public: * @param[in] def Default value to use if option not found * @param[in] location Location at which to get the variable */ - bool get(Mesh *mesh, FieldPerp &var, const std::string &name, BoutReal def = 0.0, + bool get(Mesh* mesh, FieldPerp& var, const std::string& name, BoutReal def = 0.0, CELL_LOC location = CELL_DEFAULT) override; /*! @@ -262,8 +269,8 @@ public: * @param[in] offset Not currently used * @param[in] dir The direction (X,Y,Z) of the array */ - bool get(Mesh *mesh, std::vector &var, const std::string &name, int len, int offset = 0, - GridDataSource::Direction dir = GridDataSource::X) override; + bool get(Mesh* mesh, std::vector& var, const std::string& name, int len, + int offset = 0, GridDataSource::Direction dir = GridDataSource::X) override; /*! * Get an array of BoutReals. Uses FieldFactory to generate @@ -278,8 +285,8 @@ public: * dir is X. * @param[in] dir The direction (X,Y,Z) of the array */ - bool get(Mesh *mesh, std::vector &var, const std::string &name, int len, int offset = 0, - GridDataSource::Direction dir = GridDataSource::X) override; + bool get(Mesh* mesh, std::vector& var, const std::string& name, int len, + int offset = 0, GridDataSource::Direction dir = GridDataSource::X) override; /// Are x-boundary guard cells read from the source? bool hasXBoundaryGuards(Mesh* UNUSED(m)) override { return true; } @@ -289,7 +296,7 @@ public: private: /// The options section to use. Could be nullptr - Options *options; + Options* options; }; #endif // __GRIDDATA_H__ diff --git a/include/bout/gyro_average.hxx b/include/bout/gyro_average.hxx index e424a5789a..0f9f2a13f7 100644 --- a/include/bout/gyro_average.hxx +++ b/include/bout/gyro_average.hxx @@ -32,8 +32,8 @@ #ifndef __GYRO_AVERAGE_H__ #define __GYRO_AVERAGE_H__ -#include "field3d.hxx" -#include "invert_laplace.hxx" +#include "bout/field3d.hxx" +#include "bout/invert_laplace.hxx" /// INVERT_BNDRY_ONE | INVERT_IN_RHS | INVERT_OUT_RHS; uses old-style /// Laplacian inversion flags @@ -67,14 +67,13 @@ Field3D gyroPade0(const Field3D& f, const Field3D& rho, Field3D gyroPade0(const Field3D& f, const Field2D& rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); -Field3D gyroPade0(const Field3D& f, BoutReal rho, - int inner_boundary_flags = GYRO_FLAGS, +Field3D gyroPade0(const Field3D& f, BoutReal rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); /// Pade approximation \f$Gamma_1 = (1 - \frac{1}{2} \rho^2 \nabla_\perp^2)g = f\f$ /// /// Note: Have to use Z average of rho for efficient inversion -/// +/// /// @param[in] f The field to gyro-average /// @param[in] rho Gyro-radius /// @param[in] inner_boundary_flags Flags for the inner boundary to be passed @@ -87,14 +86,13 @@ Field3D gyroPade1(const Field3D& f, const Field3D& rho, Field3D gyroPade1(const Field3D& f, const Field2D& rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); -Field3D gyroPade1(const Field3D& f, BoutReal rho, - int inner_boundary_flags = GYRO_FLAGS, +Field3D gyroPade1(const Field3D& f, BoutReal rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); Field2D gyroPade1(const Field2D& f, const Field2D& rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); -/// Pade approximation +/// Pade approximation /// /// \f[ /// \Gamma_2(f) = \frac{1}{2}\rho^2 \nabla_\perp^2 ( 1 - \frac{1}{2} \rho^2 \nabla_\perp^2)^{-1}\Gamma_1(f) @@ -114,8 +112,7 @@ Field3D gyroPade2(const Field3D& f, const Field3D& rho, Field3D gyroPade2(const Field3D& f, const Field2D& rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); -Field3D gyroPade2(const Field3D& f, BoutReal rho, - int inner_boundary_flags = GYRO_FLAGS, +Field3D gyroPade2(const Field3D& f, BoutReal rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); #endif // __GYRO_AVERAGE_H__ diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx index 10daa3c4da..9e049ecdde 100644 --- a/include/bout/hypre_interface.hxx +++ b/include/bout/hypre_interface.hxx @@ -5,9 +5,9 @@ #if BOUT_HAS_HYPRE -#include "boutcomm.hxx" -#include "field.hxx" -#include "utils.hxx" +#include "bout/boutcomm.hxx" +#include "bout/field.hxx" +#include "bout/utils.hxx" #include "bout/bout_enum_class.hxx" #include "bout/caliper_wrapper.hxx" #include "bout/globalindexer.hxx" @@ -42,10 +42,10 @@ int checkHypreError(int error) { // warning, or otherwise investigate further. char error_cstr[2048]; HYPRE_DescribeError(error, &error_cstr[0]); - if (error > 1) + if (error > 1) { throw BoutException("A Hypre call failed with error code {:d}: {:s}", error, &error_cstr[0]); - else if (error == 1) { + } else if (error == 1) { output_error.write("Hypre returns {} {}\n", error, error_cstr); HYPRE_ClearAllErrors(); } @@ -256,9 +256,10 @@ public: break; } } - if (vec_i < 0) + if (vec_i < 0) { throw BoutException("Error cannot find global index in HypreVector, index = {}", index); + } value = vector->V[vec_i]; } @@ -789,9 +790,8 @@ private: decltype(HYPRE_ParCSRGMRESSetTol)* solverSetTol{nullptr}; decltype(HYPRE_ParCSRGMRESSetAbsoluteTol)* solverSetAbsoluteTol{nullptr}; decltype(HYPRE_ParCSRGMRESSetMaxIter)* solverSetMaxIter{nullptr}; - decltype( - HYPRE_ParCSRGMRESGetFinalRelativeResidualNorm)* solverGetFinalRelativeResidualNorm{ - nullptr}; + decltype(HYPRE_ParCSRGMRESGetFinalRelativeResidualNorm)* + solverGetFinalRelativeResidualNorm{nullptr}; decltype(HYPRE_ParCSRGMRESGetNumIterations)* solverGetNumIterations{nullptr}; decltype(HYPRE_ParCSRGMRESSetPrecond)* solverSetPrecond{nullptr}; decltype(HYPRE_ParCSRGMRESSetup)* solverSetup{nullptr}; diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx index 4331602d5a..7d36143732 100644 --- a/include/bout/index_derivs.hxx +++ b/include/bout/index_derivs.hxx @@ -40,12 +40,12 @@ #include #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include class Field3D; class Field2D; @@ -89,25 +89,26 @@ public: || meta.derivType == DERIV::StandardFourth) ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); - BOUT_FOR(i, var.getRegion(region)) { + BOUT_FOR (i, var.getRegion(region)) { result[i] = apply(populateStencil(var, i)); } return; } template - void upwindOrFlux(const T& vel, const T& var, T& result, const std::string& region) const { + void upwindOrFlux(const T& vel, const T& var, T& result, + const std::string& region) const { AUTO_TRACE(); ASSERT2(meta.derivType == DERIV::Upwind || meta.derivType == DERIV::Flux) ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); if (meta.derivType == DERIV::Flux || stagger != STAGGER::None) { - BOUT_FOR(i, var.getRegion(region)) { + BOUT_FOR (i, var.getRegion(region)) { result[i] = apply(populateStencil(vel, i), populateStencil(var, i)); } } else { - BOUT_FOR(i, var.getRegion(region)) { + BOUT_FOR (i, var.getRegion(region)) { result[i] = apply(vel[i], populateStencil(var, i)); } @@ -186,23 +187,23 @@ struct registerMethod { const std::function theFunc = std::bind( - // Method to store in function - &Method::template upwindOrFlux, - // Arguments -- first is hidden this of type-bound, others are placeholders - // for input field, output field, region - method, _1, _2, _3, _4); + // Method to store in function + &Method::template upwindOrFlux, + // Arguments -- first is hidden this of type-bound, others are placeholders + // for input field, output field, region + method, _1, _2, _3, _4); derivativeRegister.registerDerivative(theFunc, Direction{}, Stagger{}, method); } else { const std::function theFunc = std::bind( - // Method to store in function - &Method::template upwindOrFlux, - // Arguments -- first is hidden this of type-bound, others are placeholders - // for input field, output field, region - method, _1, _2, _3, _4); + // Method to store in function + &Method::template upwindOrFlux, + // Arguments -- first is hidden this of type-bound, others are placeholders + // for input field, output field, region + method, _1, _2, _3, _4); derivativeRegister.registerDerivative(theFunc, Direction{}, Stagger{}, method); } break; diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx index 737ecd5ef5..8866abe180 100644 --- a/include/bout/index_derivs_interface.hxx +++ b/include/bout/index_derivs_interface.hxx @@ -29,10 +29,10 @@ #ifndef __INDEX_DERIVS_INTERFACE_HXX__ #define __INDEX_DERIVS_INTERFACE_HXX__ -#include -#include -#include #include "bout/traits.hxx" +#include +#include +#include class Field3D; class Field2D; diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx index ad533536dd..debd52c046 100644 --- a/include/bout/interpolation.hxx +++ b/include/bout/interpolation.hxx @@ -81,7 +81,7 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL if (region != "RGN_NOBNDRY") { // result is requested in some boundary region(s) - result = var; // NOTE: This is just for boundaries. FIX! + result = var; // NOTE: This is just for boundaries. FIX! result.setLocation(loc); // location gets reset when assigning from var result.allocate(); } @@ -101,12 +101,12 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL ASSERT0(fieldmesh->xstart >= 2); if ((location == CELL_CENTRE) && (loc == CELL_XLOW)) { // C2L - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { // Producing a stencil centred around a lower X value result[i] = interp(populateStencil(var, i)); } } else if (location == CELL_XLOW) { // L2C - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { // Stencil centred around a cell centre result[i] = interp(populateStencil(var, i)); } @@ -121,8 +121,9 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL // We can't interpolate in y unless we're field-aligned // Field2D doesn't need to shift to/from field-aligned because it is axisymmetric, // so always set is_unaligned=false for Field2D. - const bool is_unaligned = std::is_same::value ? false - : (var.getDirectionY() == YDirectionType::Standard); + const bool is_unaligned = std::is_same::value + ? false + : (var.getDirectionY() == YDirectionType::Standard); const T var_fa = is_unaligned ? toFieldAligned(var, "RGN_NOX") : var; if (not std::is_base_of::value) { @@ -139,19 +140,19 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL // to get the boundary cells // // result is requested in some boundary region(s) - result = var_fa; // NOTE: This is just for boundaries. FIX! + result = var_fa; // NOTE: This is just for boundaries. FIX! result.setLocation(loc); // location gets reset when assigning from var result.allocate(); } if ((location == CELL_CENTRE) && (loc == CELL_YLOW)) { // C2L - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { // Producing a stencil centred around a lower X value result[i] = interp(populateStencil(var_fa, i)); } } else if (location == CELL_YLOW) { // L2C - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { // Stencil centred around a cell centre result[i] = interp(populateStencil(var_fa, i)); @@ -167,12 +168,12 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL case CELL_ZLOW: { if ((location == CELL_CENTRE) && (loc == CELL_ZLOW)) { // C2L - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { // Producing a stencil centred around a lower X value result[i] = interp(populateStencil(var, i)); } } else if (location == CELL_ZLOW) { // L2C - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { // Stencil centred around a cell centre result[i] = interp(populateStencil(var, i)); } diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 47474ad39c..b3e8ba04ca 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -24,17 +24,17 @@ #ifndef __INTERP_XZ_H__ #define __INTERP_XZ_H__ -#include "mask.hxx" +#include "bout/mask.hxx" class Options; /// Interpolate a field onto a perturbed set of points -const Field3D interpolate(const Field3D &f, const Field3D &delta_x, - const Field3D &delta_z); +const Field3D interpolate(const Field3D& f, const Field3D& delta_x, + const Field3D& delta_z); -const Field3D interpolate(const Field2D &f, const Field3D &delta_x, - const Field3D &delta_z); -const Field3D interpolate(const Field2D &f, const Field3D &delta_x); +const Field3D interpolate(const Field2D& f, const Field3D& delta_x, + const Field3D& delta_z); +const Field3D interpolate(const Field2D& f, const Field3D& delta_x); class XZInterpolation { protected: @@ -47,14 +47,13 @@ public: XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr) : localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), skip_mask(*localmesh, false), y_offset(y_offset) {} - XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) + XZInterpolation(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr) : XZInterpolation(y_offset, mesh) { skip_mask = mask; } virtual ~XZInterpolation() = default; - - void setMask(const BoutMask &mask) { skip_mask = mask; } + void setMask(const BoutMask& mask) { skip_mask = mask; } virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region = "RGN_NOBNDRY") = 0; virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z, @@ -114,10 +113,9 @@ protected: Field3D h11_z; public: - XZHermiteSpline(Mesh *mesh = nullptr) - : XZHermiteSpline(0, mesh) {} - XZHermiteSpline(int y_offset = 0, Mesh *mesh = nullptr); - XZHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) + XZHermiteSpline(Mesh* mesh = nullptr) : XZHermiteSpline(0, mesh) {} + XZHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr); + XZHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr) : XZHermiteSpline(y_offset, mesh) { skip_mask = mask; } @@ -150,11 +148,10 @@ public: /// problems most obviously occur. class XZMonotonicHermiteSpline : public XZHermiteSpline { public: - XZMonotonicHermiteSpline(Mesh *mesh = nullptr) - : XZHermiteSpline(0, mesh) {} - XZMonotonicHermiteSpline(int y_offset = 0, Mesh *mesh = nullptr) + XZMonotonicHermiteSpline(Mesh* mesh = nullptr) : XZHermiteSpline(0, mesh) {} + XZMonotonicHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr) : XZHermiteSpline(y_offset, mesh) {} - XZMonotonicHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) + XZMonotonicHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr) : XZHermiteSpline(mask, y_offset, mesh) {} using XZHermiteSpline::interpolate; @@ -172,10 +169,9 @@ class XZLagrange4pt : public XZInterpolation { Field3D t_x, t_z; public: - XZLagrange4pt(Mesh *mesh = nullptr) - : XZLagrange4pt(0, mesh) {} - XZLagrange4pt(int y_offset = 0, Mesh *mesh = nullptr); - XZLagrange4pt(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) + XZLagrange4pt(Mesh* mesh = nullptr) : XZLagrange4pt(0, mesh) {} + XZLagrange4pt(int y_offset = 0, Mesh* mesh = nullptr); + XZLagrange4pt(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr) : XZLagrange4pt(y_offset, mesh) { skip_mask = mask; } @@ -206,9 +202,9 @@ class XZBilinear : public XZInterpolation { Field3D w0, w1, w2, w3; public: - XZBilinear(Mesh *mesh = nullptr) : XZBilinear(0, mesh) {} - XZBilinear(int y_offset = 0, Mesh *mesh = nullptr); - XZBilinear(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) + XZBilinear(Mesh* mesh = nullptr) : XZBilinear(0, mesh) {} + XZBilinear(int y_offset = 0, Mesh* mesh = nullptr); + XZBilinear(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr) : XZBilinear(y_offset, mesh) { skip_mask = mask; } diff --git a/include/bout/interpolation_z.hxx b/include/bout/interpolation_z.hxx index b10f338030..596b2634fb 100644 --- a/include/bout/interpolation_z.hxx +++ b/include/bout/interpolation_z.hxx @@ -45,9 +45,7 @@ public: virtual Field3D interpolate(const Field3D& f, const Field3D& delta_z, const std::string& region_str = "DEFAULT") = 0; - void setRegion(Region new_region) { - region = new_region; - } + void setRegion(Region new_region) { region = new_region; } virtual std::vector getWeightsForYUpApproximation(int i, int j, int k) const { diff --git a/include/bout/invert/laplacexy.hxx b/include/bout/invert/laplacexy.hxx index 38b83a4794..c4c4ef4f52 100644 --- a/include/bout/invert/laplacexy.hxx +++ b/include/bout/invert/laplacexy.hxx @@ -40,7 +40,7 @@ #warning LaplaceXY requires PETSc. No LaplaceXY available -#include +#include class Field2D; class Mesh; @@ -81,11 +81,11 @@ public: #undef MPI_Waitall #undef MPI_Waitany -#include "utils.hxx" +#include "bout/utils.hxx" #include "bout/solver.hxx" #include #include -#include +#include class Options; class Solver; @@ -95,7 +95,7 @@ public: /*! * Constructor */ - LaplaceXY(Mesh *m = nullptr, Options *opt = nullptr, const CELL_LOC loc = CELL_CENTRE); + LaplaceXY(Mesh* m = nullptr, Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE); /*! * Destructor */ @@ -105,8 +105,8 @@ public: * Set coefficients (A, B) in equation: * Div( A * Grad_perp(x) ) + B*x = b */ - void setCoefs(const Field2D &A, const Field2D &B); - + void setCoefs(const Field2D& A, const Field2D& B); + /*! * Solve Laplacian in X-Y * @@ -124,7 +124,7 @@ public: * The solution as a Field2D. On failure an exception will be raised * */ - const Field2D solve(const Field2D &rhs, const Field2D &x0); + const Field2D solve(const Field2D& rhs, const Field2D& x0); /*! * Preconditioner function @@ -139,14 +139,13 @@ public: void savePerformance(Solver& solver, const std::string& name = ""); private: - - PetscLib lib; ///< Requires PETSc library - Mat MatA; ///< Matrix to be inverted - Vec xs, bs; ///< Solution and RHS vectors - KSP ksp; ///< Krylov Subspace solver - PC pc; ///< Preconditioner + PetscLib lib; ///< Requires PETSc library + Mat MatA; ///< Matrix to be inverted + Vec xs, bs; ///< Solution and RHS vectors + KSP ksp; ///< Krylov Subspace solver + PC pc; ///< Preconditioner - Mesh *localmesh; ///< The mesh this operates on, provides metrics and communication + Mesh* localmesh; ///< The mesh this operates on, provides metrics and communication /// default prefix for writing performance logging variables std::string default_prefix; @@ -162,25 +161,25 @@ private: // Y derivatives bool include_y_derivs; // Include Y derivative terms? - + // Boundary conditions - bool x_inner_dirichlet; // Dirichlet on inner X boundary? - bool x_outer_dirichlet; // Dirichlet on outer X boundary? + bool x_inner_dirichlet; // Dirichlet on inner X boundary? + bool x_outer_dirichlet; // Dirichlet on outer X boundary? std::string y_bndry{"neumann"}; // Boundary condition for y-boundary // Location of the rhs and solution CELL_LOC location; - + /*! * Number of grid points on this processor */ int localSize(); - + /*! * Return the communicator for XY */ MPI_Comm communicator(); - + /*! * Return the global index of a local (x,y) coordinate * including guard cells. @@ -191,7 +190,7 @@ private: * to an integer. Guard cells are filled by communication * so no additional logic is needed in Mesh. */ - int globalIndex(int x, int y); + int globalIndex(int x, int y); Field2D indexXY; ///< Global index (integer stored as BoutReal) // Save performance information? @@ -211,10 +210,10 @@ private: // Utility methods void setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz); void setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nnz); - void setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B); - void setMatrixElementsFiniteDifference(const Field2D &A, const Field2D &B); - void solveFiniteVolume(const Field2D &x0); - void solveFiniteDifference(const Field2D &x0); + void setMatrixElementsFiniteVolume(const Field2D& A, const Field2D& B); + void setMatrixElementsFiniteDifference(const Field2D& A, const Field2D& B); + void solveFiniteVolume(const Field2D& x0); + void solveFiniteDifference(const Field2D& x0); // Monitor class used to reset performance-monitoring variables for a new // output timestep diff --git a/include/bout/invert/laplacexy2.hxx b/include/bout/invert/laplacexy2.hxx index 75a5477fba..86df7433d3 100644 --- a/include/bout/invert/laplacexy2.hxx +++ b/include/bout/invert/laplacexy2.hxx @@ -41,8 +41,8 @@ #warning LaplaceXY2 requires PETSc and 2D metrics. No LaplaceXY2 available #include -#include -#include +#include +#include /*! * Create a dummy class so that code will compile @@ -77,11 +77,11 @@ public: #undef MPI_Waitall #undef MPI_Waitany -#include "utils.hxx" +#include "bout/utils.hxx" #include #include #include -#include +#include class LaplaceXY2 { public: diff --git a/include/bout/invert/laplacexy2_hypre.hxx b/include/bout/invert/laplacexy2_hypre.hxx index 6038db8083..ea3b6c4440 100644 --- a/include/bout/invert/laplacexy2_hypre.hxx +++ b/include/bout/invert/laplacexy2_hypre.hxx @@ -42,8 +42,8 @@ #include "bout/globalindexer.hxx" #include -#include -#include +#include +#include /*! * Create a dummy class so that code will compile @@ -66,7 +66,7 @@ public: class Mesh; -#include "utils.hxx" +#include "bout/utils.hxx" #include class LaplaceXY2Hypre { diff --git a/include/bout/invert/laplacexz.hxx b/include/bout/invert/laplacexz.hxx index 0333a9f94e..800b8cc1c4 100644 --- a/include/bout/invert/laplacexz.hxx +++ b/include/bout/invert/laplacexz.hxx @@ -31,11 +31,11 @@ #ifndef __LAPLACEXZ_H__ #define __LAPLACEXZ_H__ -#include -#include -#include -#include #include +#include +#include +#include +#include class LaplaceXZ; @@ -70,10 +70,10 @@ public: : localmesh(m == nullptr ? bout::globals::mesh : m), location(loc) {} virtual ~LaplaceXZ() = default; - virtual void setCoefs(const Field2D &A, const Field2D &B) = 0; - virtual void setCoefs(const Field3D &A, const Field3D &B) { setCoefs(DC(A), DC(B)); } + virtual void setCoefs(const Field2D& A, const Field2D& B) = 0; + virtual void setCoefs(const Field3D& A, const Field3D& B) { setCoefs(DC(A), DC(B)); } - virtual Field3D solve(const Field3D &b, const Field3D &x0) = 0; + virtual Field3D solve(const Field3D& b, const Field3D& x0) = 0; static std::unique_ptr create(Mesh* m = nullptr, Options* opt = nullptr, CELL_LOC loc = CELL_CENTRE) { @@ -81,14 +81,14 @@ public: } protected: - static const int INVERT_DC_GRAD = 1; - static const int INVERT_AC_GRAD = 2; // Use zero neumann (NOTE: AC is a misnomer) - static const int INVERT_SET = 16; // Set boundary to x0 value - static const int INVERT_RHS = 32; // Set boundary to b value - Mesh* localmesh; ///< The mesh this operates on, provides metrics and communication + static const int INVERT_DC_GRAD = 1; + static const int INVERT_AC_GRAD = 2; // Use zero neumann (NOTE: AC is a misnomer) + static const int INVERT_SET = 16; // Set boundary to x0 value + static const int INVERT_RHS = 32; // Set boundary to b value + Mesh* localmesh; ///< The mesh this operates on, provides metrics and communication CELL_LOC location; -private: +private: }; #endif // __LAPLACEXZ_H__ diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index 0d4ac69c78..be4b5b44ee 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -40,15 +40,15 @@ class Laplacian; #define PVEC_REAL_MPI_TYPE MPI_DOUBLE #endif -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" -#include "unused.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" +#include "bout/unused.hxx" #include "bout/generic_factory.hxx" #include "bout/monitor.hxx" -#include +#include -#include "dcomplex.hxx" +#include "bout/dcomplex.hxx" class Solver; class Datafile; @@ -176,84 +176,86 @@ public: virtual ~Laplacian() = default; /// Set coefficients for inversion. Re-builds matrices if necessary - virtual void setCoefA(const Field2D &val) = 0; - virtual void setCoefA(const Field3D &val) { setCoefA(DC(val)); } + virtual void setCoefA(const Field2D& val) = 0; + virtual void setCoefA(const Field3D& val) { setCoefA(DC(val)); } virtual void setCoefA(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefA(f); } - - virtual void setCoefC(const Field2D &val) = 0; - virtual void setCoefC(const Field3D &val) { setCoefC(DC(val)); } + + virtual void setCoefC(const Field2D& val) = 0; + virtual void setCoefC(const Field3D& val) { setCoefC(DC(val)); } virtual void setCoefC(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefC(f); } - - virtual void setCoefC1(const Field2D &UNUSED(val)) { + + virtual void setCoefC1(const Field2D& UNUSED(val)) { throw BoutException("setCoefC1 is not implemented for this Laplacian solver"); } - virtual void setCoefC1(const Field3D &val) { setCoefC1(DC(val)); } + virtual void setCoefC1(const Field3D& val) { setCoefC1(DC(val)); } virtual void setCoefC1(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefC1(f); } - - virtual void setCoefC2(const Field2D &UNUSED(val)) { + + virtual void setCoefC2(const Field2D& UNUSED(val)) { throw BoutException("setCoefC2 is not implemented for this Laplacian solver"); } - virtual void setCoefC2(const Field3D &val) { setCoefC2(DC(val)); } + virtual void setCoefC2(const Field3D& val) { setCoefC2(DC(val)); } virtual void setCoefC2(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefC2(f); } - - virtual void setCoefD(const Field2D &val) = 0; - virtual void setCoefD(const Field3D &val) { setCoefD(DC(val)); } + + virtual void setCoefD(const Field2D& val) = 0; + virtual void setCoefD(const Field3D& val) { setCoefD(DC(val)); } virtual void setCoefD(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefD(f); } - - virtual void setCoefEx(const Field2D &val) = 0; - virtual void setCoefEx(const Field3D &val) { setCoefEx(DC(val)); } + + virtual void setCoefEx(const Field2D& val) = 0; + virtual void setCoefEx(const Field3D& val) { setCoefEx(DC(val)); } virtual void setCoefEx(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefEx(f); } - - virtual void setCoefEz(const Field2D &val) = 0; - virtual void setCoefEz(const Field3D &val) { setCoefEz(DC(val)); } + + virtual void setCoefEz(const Field2D& val) = 0; + virtual void setCoefEz(const Field3D& val) { setCoefEz(DC(val)); } virtual void setCoefEz(BoutReal r) { Field2D f(r, localmesh); f.setLocation(location); setCoefEz(f); } - + virtual void setGlobalFlags(int f) { global_flags = f; } virtual void setInnerBoundaryFlags(int f) { inner_boundary_flags = f; } virtual void setOuterBoundaryFlags(int f) { outer_boundary_flags = f; } /// Does this solver use Field3D coefficients (true) or only their DC component (false) virtual bool uses3DCoefs() const { return false; } - - virtual FieldPerp solve(const FieldPerp &b) = 0; - virtual Field3D solve(const Field3D &b); - virtual Field2D solve(const Field2D &b); - - virtual FieldPerp solve(const FieldPerp &b, const FieldPerp &UNUSED(x0)) { return solve(b); } - virtual Field3D solve(const Field3D &b, const Field3D &x0); - virtual Field2D solve(const Field2D &b, const Field2D &x0); + + virtual FieldPerp solve(const FieldPerp& b) = 0; + virtual Field3D solve(const Field3D& b); + virtual Field2D solve(const Field2D& b); + + virtual FieldPerp solve(const FieldPerp& b, const FieldPerp& UNUSED(x0)) { + return solve(b); + } + virtual Field3D solve(const Field3D& b, const Field3D& x0); + virtual Field2D solve(const Field2D& b, const Field2D& x0); /// Coefficients in tridiagonal inversion - void tridagCoefs(int jx, int jy, int jz, dcomplex &a, dcomplex &b, dcomplex &c, - const Field2D *ccoef = nullptr, const Field2D *d = nullptr, + void tridagCoefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcomplex& c, + const Field2D* ccoef = nullptr, const Field2D* d = nullptr, CELL_LOC loc = CELL_DEFAULT); /*! @@ -297,27 +299,27 @@ public: protected: bool async_send; ///< If true, use asyncronous send in parallel algorithms - - int maxmode; ///< The maximum Z mode to solve for - - bool low_mem; ///< If true, reduce the amount of memory used - bool all_terms; ///< applies to Delp2 operator and laplacian inversion - bool nonuniform; ///< Non-uniform mesh correction - bool include_yguards; ///< solve in y-guard cells, default true. + + int maxmode; ///< The maximum Z mode to solve for + + bool low_mem; ///< If true, reduce the amount of memory used + bool all_terms; ///< applies to Delp2 operator and laplacian inversion + bool nonuniform; ///< Non-uniform mesh correction + bool include_yguards; ///< solve in y-guard cells, default true. int extra_yguards_lower; ///< exclude some number of points at the lower boundary, useful for staggered grids or when boundary conditions make inversion redundant int extra_yguards_upper; ///< exclude some number of points at the upper boundary, useful for staggered grids or when boundary conditions make inversion redundant - - int global_flags; ///< Default flags + + int global_flags; ///< Default flags int inner_boundary_flags; ///< Flags to set inner boundary condition int outer_boundary_flags; ///< Flags to set outer boundary condition - void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex &a, dcomplex &b, dcomplex &c, - const Field2D *ccoef = nullptr, const Field2D *d = nullptr, + void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, dcomplex& c, + const Field2D* ccoef = nullptr, const Field2D* d = nullptr, CELL_LOC loc = CELL_DEFAULT) { tridagCoefs(jx, jy, kwave, a, b, c, ccoef, ccoef, d, loc); } - void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex &a, dcomplex &b, dcomplex &c, - const Field2D *c1coef, const Field2D *c2coef, const Field2D *d, + void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, dcomplex& c, + const Field2D* c1coef, const Field2D* c2coef, const Field2D* d, CELL_LOC loc = CELL_DEFAULT); void tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk, int jy, @@ -369,9 +371,8 @@ protected: // Legacy interface // These will be removed at some point -void laplace_tridag_coefs(int jx, int jy, int jz, dcomplex &a, dcomplex &b, dcomplex &c, - const Field2D *ccoef = nullptr, const Field2D *d = nullptr, +void laplace_tridag_coefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcomplex& c, + const Field2D* ccoef = nullptr, const Field2D* d = nullptr, CELL_LOC loc = CELL_DEFAULT); #endif // __LAPLACE_H__ - diff --git a/include/bout/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx index 38b2505358..8273690a72 100644 --- a/include/bout/invert_parderiv.hxx +++ b/include/bout/invert_parderiv.hxx @@ -31,10 +31,10 @@ #ifndef __INV_PAR_H__ #define __INV_PAR_H__ -#include "field3d.hxx" -#include "field2d.hxx" -#include "options.hxx" -#include "unused.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" +#include "bout/unused.hxx" #include "bout/generic_factory.hxx" // Parderiv implementations @@ -83,69 +83,72 @@ using RegisterUnavailableInvertPar = InvertParFactory::RegisterUnavailableInFact */ class InvertPar { public: - /*! * Constructor. Note that this is a base class, * with pure virtual members, so can't be created directly. * To create an InvertPar object call the create() static function. - */ - InvertPar(Options *UNUSED(opt), CELL_LOC location_in, Mesh *mesh_in = nullptr) - : location(location_in), - localmesh(mesh_in==nullptr ? bout::globals::mesh : mesh_in) {} + */ + InvertPar(Options* UNUSED(opt), CELL_LOC location_in, Mesh* mesh_in = nullptr) + : location(location_in), + localmesh(mesh_in == nullptr ? bout::globals::mesh : mesh_in) {} virtual ~InvertPar() = default; /*! * Create an instance of InvertPar */ - static std::unique_ptr create(Options *opt_in = nullptr, + static std::unique_ptr create(Options* opt_in = nullptr, CELL_LOC location_in = CELL_CENTRE, - Mesh *mesh_in = nullptr) { + Mesh* mesh_in = nullptr) { return InvertParFactory::getInstance().create(opt_in, location_in, mesh_in); } - + /*! * Solve the system of equations * Warning: Default implementation very inefficient. This converts * the Field2D to a Field3D then calls solve() on the 3D variable - */ - virtual const Field2D solve(const Field2D &f); - + */ + virtual const Field2D solve(const Field2D& f); + /*! * Solve the system of equations * * This method must be implemented */ - virtual const Field3D solve(const Field3D &f) = 0; - + virtual const Field3D solve(const Field3D& f) = 0; + /*! * Solve, given an initial guess for the solution * This can help if using an iterative scheme */ - virtual const Field3D solve(const Field2D &f, const Field2D &UNUSED(start)) {return solve(f);} - virtual const Field3D solve(const Field3D &f, const Field3D &UNUSED(start)) {return solve(f);} - + virtual const Field3D solve(const Field2D& f, const Field2D& UNUSED(start)) { + return solve(f); + } + virtual const Field3D solve(const Field3D& f, const Field3D& UNUSED(start)) { + return solve(f); + } + /*! * Set the constant coefficient A */ - virtual void setCoefA(const Field2D &f) = 0; - virtual void setCoefA(const Field3D &f) {setCoefA(DC(f));} + virtual void setCoefA(const Field2D& f) = 0; + virtual void setCoefA(const Field3D& f) { setCoefA(DC(f)); } virtual void setCoefA(BoutReal f) { auto A = Field2D(f, localmesh); A.setLocation(location); setCoefA(A); } - + /*! * Set the Grad2_par2 coefficient B - */ - virtual void setCoefB(const Field2D &f) = 0; - virtual void setCoefB(const Field3D &f) {setCoefB(DC(f));} + */ + virtual void setCoefB(const Field2D& f) = 0; + virtual void setCoefB(const Field3D& f) { setCoefB(DC(f)); } virtual void setCoefB(BoutReal f) { auto B = Field2D(f, localmesh); B.setLocation(location); setCoefB(B); } - + /*! * Set the D2DYDZ coefficient C */ @@ -186,6 +189,4 @@ protected: private: }; - #endif // __INV_PAR_H__ - diff --git a/include/bout/invert_pardiv.hxx b/include/bout/invert_pardiv.hxx index 23ea59e943..74827c7303 100644 --- a/include/bout/invert_pardiv.hxx +++ b/include/bout/invert_pardiv.hxx @@ -31,10 +31,10 @@ #ifndef INV_PARDIV_H #define INV_PARDIV_H -#include "field2d.hxx" -#include "field3d.hxx" -#include "options.hxx" -#include "unused.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" +#include "bout/unused.hxx" #include "bout/generic_factory.hxx" // Pardivergence implementations diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx index 233263c5b4..10c1e813cc 100644 --- a/include/bout/invertable_operator.hxx +++ b/include/bout/invertable_operator.hxx @@ -28,7 +28,7 @@ namespace inversion { template class InvertableOperator; }; -}; +}; // namespace bout #ifndef __INVERTABLE_OPERATOR_H__ #define __INVERTABLE_OPERATOR_H__ @@ -40,12 +40,12 @@ class InvertableOperator; #include "bout/traits.hxx" #include #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include #include @@ -136,8 +136,7 @@ public: : operatorFunction(func), preconditionerFunction(func), opt(optIn == nullptr ? Options::getRoot()->getSection("invertableOperator") : optIn), - localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), - lib(opt) { + localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), lib(opt) { AUTO_TRACE(); }; @@ -207,30 +206,34 @@ public: // to only include unique points Region nocorner3D = localmesh->getRegion3D("RGN_NOBNDRY"); if (!localmesh->periodicX) { - if (localmesh->firstX()) + if (localmesh->firstX()) { nocorner3D += Region(0, localmesh->xstart - 1, localmesh->ystart, localmesh->yend, 0, localmesh->LocalNz - 1, localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize); - if (localmesh->lastX()) + } + if (localmesh->lastX()) { nocorner3D += Region( localmesh->LocalNx - localmesh->xstart, localmesh->LocalNx - 1, localmesh->ystart, localmesh->yend, 0, localmesh->LocalNz - 1, localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize); + } } if (localmesh->firstY() or localmesh->lastY()) { for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) { if (not localmesh->periodicY(ix)) { - if (localmesh->firstY()) + if (localmesh->firstY()) { nocorner3D += Region(ix, ix, 0, localmesh->ystart - 1, 0, localmesh->LocalNz - 1, localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize); - if (localmesh->lastY()) + } + if (localmesh->lastY()) { nocorner3D += Region( ix, ix, localmesh->LocalNy - localmesh->ystart, localmesh->LocalNy - 1, 0, localmesh->LocalNz - 1, localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize); + } } } } @@ -244,28 +247,32 @@ public: // This avoids all guard cells and corners but includes boundaries Region nocorner2D = localmesh->getRegion2D("RGN_NOBNDRY"); if (!localmesh->periodicX) { - if (localmesh->firstX()) + if (localmesh->firstX()) { nocorner2D += Region(0, localmesh->xstart - 1, localmesh->ystart, localmesh->yend, 0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize); - if (localmesh->lastX()) + } + if (localmesh->lastX()) { nocorner2D += Region(localmesh->LocalNx - localmesh->xstart, localmesh->LocalNx - 1, localmesh->ystart, localmesh->yend, 0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize); + } } if (localmesh->firstY() or localmesh->lastY()) { for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) { if (not localmesh->periodicY(ix)) { - if (localmesh->firstY()) + if (localmesh->firstY()) { nocorner2D += Region(ix, ix, 0, localmesh->ystart - 1, 0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize); - if (localmesh->lastY()) + } + if (localmesh->lastY()) { nocorner2D += Region(ix, ix, localmesh->LocalNy - localmesh->ystart, localmesh->LocalNy - 1, 0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize); + } } } } @@ -278,15 +285,17 @@ public: // This avoids all guard cells and corners but includes boundaries Region nocornerPerp = localmesh->getRegionPerp("RGN_NOBNDRY"); if (!localmesh->periodicX) { - if (localmesh->firstX()) + if (localmesh->firstX()) { nocornerPerp += Region(0, localmesh->xstart - 1, 0, 0, 0, localmesh->LocalNz - 1, 1, localmesh->LocalNz, localmesh->maxregionblocksize); - if (localmesh->lastX()) + } + if (localmesh->lastX()) { nocornerPerp += Region(localmesh->LocalNx - localmesh->xstart, localmesh->LocalNx - 1, 0, 0, 0, localmesh->LocalNz - 1, 1, localmesh->LocalNz, localmesh->maxregionblocksize); + } } nocornerPerp.unique(); localmesh->addRegionPerp("RGN_WITHBNDRIES", nocornerPerp); @@ -565,7 +574,7 @@ public: }; #endif // PETSC -}; -}; +}; // namespace inversion +}; // namespace bout #endif // HEADER GUARD diff --git a/include/bout/lapack_routines.hxx b/include/bout/lapack_routines.hxx index 3eaed50dce..70a3128f81 100644 --- a/include/bout/lapack_routines.hxx +++ b/include/bout/lapack_routines.hxx @@ -23,7 +23,7 @@ #ifndef __LAPACK_ROUTINES_H__ #define __LAPACK_ROUTINES_H__ -#include +#include /* Tridiagonal inversion * @@ -42,15 +42,18 @@ */ // Tri-diagonal solvers -int tridag(const dcomplex *a, const dcomplex *b, const dcomplex *c, const dcomplex *r, dcomplex *u, int n); -bool tridag(const BoutReal *a, const BoutReal *b, const BoutReal *c, const BoutReal *r, BoutReal *x, int n); +int tridag(const dcomplex* a, const dcomplex* b, const dcomplex* c, const dcomplex* r, + dcomplex* u, int n); +bool tridag(const BoutReal* a, const BoutReal* b, const BoutReal* c, const BoutReal* r, + BoutReal* x, int n); // Cyclic tridiagonal -void cyclic_tridag(BoutReal *a, BoutReal *b, BoutReal *c, BoutReal *r, BoutReal *x, int n); -void cyclic_tridag(dcomplex *a, dcomplex *b, dcomplex *c, dcomplex *r, dcomplex *x, int n); +void cyclic_tridag(BoutReal* a, BoutReal* b, BoutReal* c, BoutReal* r, BoutReal* x, + int n); +void cyclic_tridag(dcomplex* a, dcomplex* b, dcomplex* c, dcomplex* r, dcomplex* x, + int n); /// Complex band matrix solver -void cband_solve(Matrix &a, int n, int m1, int m2, Array &b); +void cband_solve(Matrix& a, int n, int m1, int m2, Array& b); #endif // __LAPACK_ROUTINES_H__ - diff --git a/include/bout/macro_for_each.hxx b/include/bout/macro_for_each.hxx index 4825776c7e..10cbd21818 100644 --- a/include/bout/macro_for_each.hxx +++ b/include/bout/macro_for_each.hxx @@ -4,12 +4,12 @@ // Provides a macro MACRO_FOR_EACH which applies a // macro to each argument in a VA_ARGS list -// +// // Based on this blog post by Daniel Hardman: // https://codecraft.co/2014/11/25/variadic-macros-tricks/ // This answer on StackOverflow: // https://stackoverflow.com/questions/11761703/overloading-macro-on-number-of-arguments/11763277 -// See also: +// See also: // https://github.com/cormacc/va_args_iterators // @@ -30,15 +30,33 @@ /// _fe_x set of macros expand a number of arguments with ';' between them #define _fe_1(_call, x) _call(x); -#define _fe_2(_call, x, ...) _call(x); BOUT_EXPAND(_fe_1(_call, __VA_ARGS__)) -#define _fe_3(_call, x, ...) _call(x); BOUT_EXPAND(_fe_2(_call, __VA_ARGS__)) -#define _fe_4(_call, x, ...) _call(x); BOUT_EXPAND(_fe_3(_call, __VA_ARGS__)) -#define _fe_5(_call, x, ...) _call(x); BOUT_EXPAND(_fe_4(_call, __VA_ARGS__)) -#define _fe_6(_call, x, ...) _call(x); BOUT_EXPAND(_fe_5(_call, __VA_ARGS__)) -#define _fe_7(_call, x, ...) _call(x); BOUT_EXPAND(_fe_6(_call, __VA_ARGS__)) -#define _fe_8(_call, x, ...) _call(x); BOUT_EXPAND(_fe_7(_call, __VA_ARGS__)) -#define _fe_9(_call, x, ...) _call(x); BOUT_EXPAND(_fe_8(_call, __VA_ARGS__)) -#define _fe_10(_call, x, ...) _call(x); BOUT_EXPAND(_fe_9(_call, __VA_ARGS__)) +#define _fe_2(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_1(_call, __VA_ARGS__)) +#define _fe_3(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_2(_call, __VA_ARGS__)) +#define _fe_4(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_3(_call, __VA_ARGS__)) +#define _fe_5(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_4(_call, __VA_ARGS__)) +#define _fe_6(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_5(_call, __VA_ARGS__)) +#define _fe_7(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_6(_call, __VA_ARGS__)) +#define _fe_8(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_7(_call, __VA_ARGS__)) +#define _fe_9(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_8(_call, __VA_ARGS__)) +#define _fe_10(_call, x, ...) \ + _call(x); \ + BOUT_EXPAND(_fe_9(_call, __VA_ARGS__)) /// _ae_x set of macros expand a number of arguments with ',' between them #define _ae_1(_call, x) _call(x) @@ -75,12 +93,11 @@ /// - No braces are put around the expansion. These /// should usually be added in the top-level macro /// to avoid surprising results. -/// -#define MACRO_FOR_EACH(mac, ...) \ - BOUT_EXPAND(_GET_FOR_EACH_EXPANSION(__VA_ARGS__, \ - _me_10, _me_9, _me_8, _me_7, _me_6, _me_5, \ - _me_4, _me_3, _me_2, _me_1) \ - (mac, __VA_ARGS__)) +/// +#define MACRO_FOR_EACH(mac, ...) \ + BOUT_EXPAND(_GET_FOR_EACH_EXPANSION(__VA_ARGS__, _me_10, _me_9, _me_8, _me_7, _me_6, \ + _me_5, _me_4, _me_3, _me_2, \ + _me_1)(mac, __VA_ARGS__)) /// Apply a function (first argument) to each /// of the following arguments. @@ -101,11 +118,10 @@ /// should usually be added in the top-level macro /// to avoid surprising results. /// -#define MACRO_FOR_EACH_FN(fn, ...) \ - BOUT_EXPAND(_GET_FOR_EACH_EXPANSION(__VA_ARGS__, \ - _fe_10, _fe_9, _fe_8, _fe_7, _fe_6, _fe_5, \ - _fe_4, _fe_3, _fe_2, _fe_1) \ - (fn, __VA_ARGS__)) +#define MACRO_FOR_EACH_FN(fn, ...) \ + BOUT_EXPAND(_GET_FOR_EACH_EXPANSION(__VA_ARGS__, _fe_10, _fe_9, _fe_8, _fe_7, _fe_6, \ + _fe_5, _fe_4, _fe_3, _fe_2, \ + _fe_1)(fn, __VA_ARGS__)) /// Apply a macro (first argument) to each /// of the following arguments, separate by commas. diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx index 8940edbb16..d36f8446c5 100644 --- a/include/bout/mask.hxx +++ b/include/bout/mask.hxx @@ -24,9 +24,9 @@ #include +#include "bout/globals.hxx" +#include "bout/msg_stack.hxx" #include "bout/mesh.hxx" -#include "globals.hxx" -#include "msg_stack.hxx" /** * 3D array of bools to mask Field3Ds @@ -48,13 +48,13 @@ class BoutMask { // Internal data Tensor mask; + public: - BoutMask(int nx, int ny, int nz, bool value=false) : - mask(nx, ny, nz) { + BoutMask(int nx, int ny, int nz, bool value = false) : mask(nx, ny, nz) { mask = value; } - explicit BoutMask(const Mesh& mesh, bool value=false) : - BoutMask(mesh.LocalNx, mesh.LocalNy, mesh.LocalNz, value) {} + explicit BoutMask(const Mesh& mesh, bool value = false) + : BoutMask(mesh.LocalNx, mesh.LocalNy, mesh.LocalNz, value) {} explicit BoutMask(const Mesh* mesh = nullptr, bool value = false) : BoutMask(mesh == nullptr ? *bout::globals::mesh : *mesh, value) {} @@ -64,12 +64,8 @@ public: return *this; } - inline bool& operator()(int jx, int jy, int jz) { - return mask(jx, jy, jz); - } - inline const bool& operator()(int jx, int jy, int jz) const { - return mask(jx, jy, jz); - } + inline bool& operator()(int jx, int jy, int jz) { return mask(jx, jy, jz); } + inline const bool& operator()(int jx, int jy, int jz) const { return mask(jx, jy, jz); } }; #endif //__MASK_H__ diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index c3126f8ce0..fd466875b2 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -49,11 +49,11 @@ class Mesh; #include #include -#include "bout_types.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "field_data.hxx" -#include "options.hxx" +#include "bout/bout_types.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/field_data.hxx" +#include "bout/options.hxx" #include "fieldgroup.hxx" @@ -64,18 +64,18 @@ class BoundaryRegionPar; #include -#include "coordinates.hxx" // Coordinates class +#include "coordinates.hxx" // Coordinates class -#include "unused.hxx" +#include "bout/unused.hxx" -#include #include "bout/generic_factory.hxx" +#include #include #include -#include #include +#include #include #include @@ -101,17 +101,15 @@ using RegisterMesh = MeshFactory::RegisterInFactory; using comm_handle = void*; class Mesh { - public: - +public: /// Constructor for a "bare", uninitialised Mesh /// Only useful for testing - Mesh() : source(nullptr), options(nullptr), - include_corner_cells(true) {} + Mesh() : source(nullptr), options(nullptr), include_corner_cells(true) {} /// Constructor /// @param[in] s The source to be used for loading variables /// @param[in] options The options section for settings - Mesh(GridDataSource *s, Options *options); + Mesh(GridDataSource* s, Options* options); /// Destructor virtual ~Mesh(); @@ -120,7 +118,7 @@ class Mesh { /// /// @param[in] source The data source to use for loading variables /// @param[in] opt The option section. By default this is "mesh" - static Mesh *create(GridDataSource *source, Options *opt = nullptr); + static Mesh* create(GridDataSource* source, Options* opt = nullptr); /// Create a Mesh object /// @@ -130,47 +128,47 @@ class Mesh { /// 3) Use options as data source /// /// @param[in] opt Input options. Default is "mesh" section - static Mesh *create(Options *opt = nullptr); + static Mesh* create(Options* opt = nullptr); /// Loads the mesh values - /// + /// /// Currently need to create and load mesh in separate calls /// because creating Fields uses the global "mesh" pointer /// which isn't created until Mesh is constructed - virtual int load() {return 1;} + virtual int load() { return 1; } /// Add output variables to \p output_options /// These are used for post-processing virtual void outputVars(MAYBE_UNUSED(Options& output_options)) {} // Get routines to request data from mesh file - + /// Get a string from the input source - /// + /// /// @param[out] sval The value will be put into this variable /// @param[in] name The name of the variable to read /// @param[in] def The default value if not found /// /// @returns zero if successful, non-zero on failure - int get(std::string& sval, const std::string& name, const std::string& def=""); + int get(std::string& sval, const std::string& name, const std::string& def = ""); /// Get an integer from the input source - /// + /// /// @param[out] ival The value will be put into this variable /// @param[in] name The name of the variable to read /// @param[in] def The default value if not found /// /// @returns zero if successful, non-zero on failure - int get(int &ival, const std::string &name, int def=0); + int get(int& ival, const std::string& name, int def = 0); /// Get a BoutReal from the input source - /// + /// /// @param[out] rval The value will be put into this variable /// @param[in] name The name of the variable to read /// @param[in] def The default value if not found /// /// @returns zero if successful, non-zero on failure - int get(BoutReal& rval, const std::string& name, BoutReal def=0.0); + int get(BoutReal& rval, const std::string& name, BoutReal def = 0.0); /// Get a bool from the input source /// @@ -179,7 +177,7 @@ class Mesh { /// @param[in] def The default value if not found /// /// @returns zero if successful, non-zero on failure - int get(bool &bval, const std::string &name, bool def=false); + int get(bool& bval, const std::string& name, bool def = false); /// Get a Field2D from the input source /// including communicating guard cells @@ -190,8 +188,8 @@ class Mesh { /// @param[in] communicate Should the field be communicated to fill guard cells? /// /// @returns zero if successful, non-zero on failure - int get(Field2D& var, const std::string& name, BoutReal def=0.0, - bool communicate = true, CELL_LOC location=CELL_DEFAULT); + int get(Field2D& var, const std::string& name, BoutReal def = 0.0, + bool communicate = true, CELL_LOC location = CELL_DEFAULT); /// Get a Field3D from the input source /// @@ -201,7 +199,8 @@ class Mesh { /// @param[in] communicate Should the field be communicated to fill guard cells? /// /// @returns zero if successful, non-zero on failure - int get(Field3D &var, const std::string &name, BoutReal def=0.0, bool communicate=true, CELL_LOC location=CELL_DEFAULT); + int get(Field3D& var, const std::string& name, BoutReal def = 0.0, + bool communicate = true, CELL_LOC location = CELL_DEFAULT); /// Get a FieldPerp from the input source /// @@ -211,7 +210,8 @@ class Mesh { /// @param[in] communicate Should the field be communicated to fill guard cells? /// /// @returns zero if successful, non-zero on failure - int get(FieldPerp &var, const std::string &name, BoutReal def=0.0, bool communicate=true, CELL_LOC location=CELL_DEFAULT); + int get(FieldPerp& var, const std::string& name, BoutReal def = 0.0, + bool communicate = true, CELL_LOC location = CELL_DEFAULT); /// Get a Vector2D from the input source. /// If \p var is covariant then this gets three @@ -251,14 +251,14 @@ class Mesh { bool isDataSourceGridFile() const; /// Wrapper for GridDataSource::hasVar - bool sourceHasVar(const std::string &name); + bool sourceHasVar(const std::string& name); /// Wrapper for GridDataSource::hasXBoundaryGuards bool sourceHasXBoundaryGuards(); /// Wrapper for GridDataSource::hasYBoundaryGuards bool sourceHasYBoundaryGuards(); - + // Communications /*! * Communicate a list of FieldData objects @@ -286,19 +286,19 @@ class Mesh { /*! * Communicate a group of fields */ - void communicate(FieldGroup &g); + void communicate(FieldGroup& g); /// Communcate guard cells in XZ only /// i.e. no Y communication /// /// @param g The group of fields to communicate. Guard cells will be modified - void communicateXZ(FieldGroup &g); + void communicateXZ(FieldGroup& g); /// Communcate guard cells in YZ only /// i.e. no X communication /// /// @param g The group of fields to communicate. Guard cells will be modified - void communicateYZ(FieldGroup &g); + void communicateYZ(FieldGroup& g); /*! * Communicate an X-Z field @@ -339,28 +339,30 @@ class Mesh { /// /// \param g Group of fields to communicate /// \returns handle to be used as input to wait() - virtual comm_handle send(FieldGroup &g) = 0; + virtual comm_handle send(FieldGroup& g) = 0; /// Send only the x-guard cells - virtual comm_handle sendX(FieldGroup &g, comm_handle handle = nullptr, + virtual comm_handle sendX(FieldGroup& g, comm_handle handle = nullptr, bool disable_corners = false) = 0; /// Send only the y-guard cells - virtual comm_handle sendY(FieldGroup &g, comm_handle handle = nullptr) = 0; + virtual comm_handle sendY(FieldGroup& g, comm_handle handle = nullptr) = 0; /// Wait for the handle, return error code virtual int wait(comm_handle handle) = 0; ///< Wait for the handle, return error code // non-local communications - virtual int getNXPE() = 0; ///< The number of processors in the X direction - virtual int getNYPE() = 0; ///< The number of processors in the Y direction + virtual int getNXPE() = 0; ///< The number of processors in the X direction + virtual int getNYPE() = 0; ///< The number of processors in the Y direction virtual int getXProcIndex() = 0; ///< This processor's index in X direction virtual int getYProcIndex() = 0; ///< This processor's index in Y direction - + // X communications - virtual bool firstX() const = 0; ///< Is this processor first in X? i.e. is there a boundary to the left in X? - virtual bool lastX() const = 0; ///< Is this processor last in X? i.e. is there a boundary to the right in X? + virtual bool firstX() + const = 0; ///< Is this processor first in X? i.e. is there a boundary to the left in X? + virtual bool lastX() + const = 0; ///< Is this processor last in X? i.e. is there a boundary to the right in X? /// Domain is periodic in X? bool periodicX{false}; @@ -372,30 +374,32 @@ class Mesh { /// @param[in] buffer The data to send. Must be at least length \p size /// @param[in] size The number of BoutReals to send /// @param[in] tag A label for the communication. Must be the same at receive - virtual int sendXOut(BoutReal *buffer, int size, int tag) = 0; + virtual int sendXOut(BoutReal* buffer, int size, int tag) = 0; /// Send a buffer of data to processor at X index -1 /// /// @param[in] buffer The data to send. Must be at least length \p size /// @param[in] size The number of BoutReals to send /// @param[in] tag A label for the communication. Must be the same at receive - virtual int sendXIn(BoutReal *buffer, int size, int tag) = 0; + virtual int sendXIn(BoutReal* buffer, int size, int tag) = 0; /// Receive a buffer of data from X index +1 /// /// @param[in] buffer A buffer to put the data in. Must already be allocated of length \p size /// @param[in] size The number of BoutReals to receive and put in \p buffer /// @param[in] tag A label for the communication. Must be the same as sent - virtual comm_handle irecvXOut(BoutReal *buffer, int size, int tag) = 0; + virtual comm_handle irecvXOut(BoutReal* buffer, int size, int tag) = 0; /// Receive a buffer of data from X index -1 /// /// @param[in] buffer A buffer to put the data in. Must already be allocated of length \p size /// @param[in] size The number of BoutReals to receive and put in \p buffer /// @param[in] tag A label for the communication. Must be the same as sent - virtual comm_handle irecvXIn(BoutReal *buffer, int size, int tag) = 0; + virtual comm_handle irecvXIn(BoutReal* buffer, int size, int tag) = 0; - MPI_Comm getXcomm() {return getXcomm(0);} ///< Return communicator containing all processors in X + MPI_Comm getXcomm() { + return getXcomm(0); + } ///< Return communicator containing all processors in X virtual MPI_Comm getXcomm(int jy) const = 0; ///< Return X communicator virtual MPI_Comm getYcomm(int jx) const = 0; ///< Return Y communicator @@ -411,7 +415,7 @@ class Mesh { /// /// \param[in] jx The local (on this processor) index in X /// \param[out] ts The Twist-Shift angle if periodic - virtual bool periodicY(int jx, BoutReal &ts) const = 0; + virtual bool periodicY(int jx, BoutReal& ts) const = 0; /// Get number of boundaries in the y-direction, i.e. locations where there are boundary /// cells in the global grid @@ -432,7 +436,7 @@ class Mesh { /// BoutReal gives the total zShift for a 2pi /// poloidal circuit if there is a branch cut virtual std::pair hasBranchCutUpper(int jx) const = 0; - + virtual int ySize(int jx) const; ///< The number of points in Y at fixed X index \p jx // Y communications @@ -494,20 +498,20 @@ class Mesh { BoundaryParType UNUSED(type)) {} /// Branch-cut special handling (experimental) - virtual Field3D smoothSeparatrix(const Field3D &f) {return f;} - - virtual BoutReal GlobalX(int jx) const = 0; ///< Continuous X index between 0 and 1 - virtual BoutReal GlobalY(int jy) const = 0; ///< Continuous Y index (0 -> 1) + virtual Field3D smoothSeparatrix(const Field3D& f) { return f; } + + virtual BoutReal GlobalX(int jx) const = 0; ///< Continuous X index between 0 and 1 + virtual BoutReal GlobalY(int jy) const = 0; ///< Continuous Y index (0 -> 1) virtual BoutReal GlobalX(BoutReal jx) const = 0; ///< Continuous X index between 0 and 1 virtual BoutReal GlobalY(BoutReal jy) const = 0; ///< Continuous Y index (0 -> 1) - + ////////////////////////////////////////////////////////// - + int GlobalNx, GlobalNy, GlobalNz; ///< Size of the global arrays. Note: can have holes /// Size of the global arrays excluding boundary points. int GlobalNxNoBoundaries, GlobalNyNoBoundaries, GlobalNzNoBoundaries; - int OffsetX, OffsetY, OffsetZ; ///< Offset of this mesh within the global array - ///< so startx on this processor is OffsetX in global + int OffsetX, OffsetY, OffsetZ; ///< Offset of this mesh within the global array + ///< so startx on this processor is OffsetX in global /// Returns the number of unique cells (i.e., ones not used for /// communication) on this processor for 3D fields. Boundaries @@ -579,17 +583,17 @@ class Mesh { /// Size of the mesh on this processor including guard/boundary cells int LocalNx, LocalNy, LocalNz; - + /// Local ranges of data (inclusive), excluding guard cells int xstart, xend, ystart, yend, zstart, zend; - + /// Include integrated shear (if shifting X) bool IncIntShear{false}; int numberOfXPoints{0}; /// Coordinate system - Coordinates *getCoordinates(const CELL_LOC location = CELL_CENTRE) { + Coordinates* getCoordinates(const CELL_LOC location = CELL_CENTRE) { return getCoordinatesSmart(location).get(); }; @@ -675,7 +679,7 @@ class Mesh { /////////////////////////////////////////////////////////// ////// Utilties and parameters - + /// Fraction of modes to filter. This is set in derivs_init from option "ddz:fft_filter" BoutReal fft_derivs_filter{0.0}; @@ -700,14 +704,14 @@ class Mesh { /// /// Throws if region_name not found template - const Region& getRegion(const std::string ®ion_name) const; + const Region& getRegion(const std::string& region_name) const; - const Region<> &getRegion(const std::string ®ion_name) const{ + const Region<>& getRegion(const std::string& region_name) const { return getRegion3D(region_name); } - const Region &getRegion3D(const std::string ®ion_name) const; - const Region &getRegion2D(const std::string ®ion_name) const; - const Region &getRegionPerp(const std::string ®ion_name) const; + const Region& getRegion3D(const std::string& region_name) const; + const Region& getRegion2D(const std::string& region_name) const; + const Region& getRegionPerp(const std::string& region_name) const; /// Indicate if named region has already been defined bool hasRegion3D(const std::string& region_name) const; @@ -717,34 +721,38 @@ class Mesh { /// Add a new region to the region_map for the data iterator /// /// Outputs an error message if region_name already exists - void addRegion(const std::string ®ion_name, const Region<> ®ion) { + void addRegion(const std::string& region_name, const Region<>& region) { return addRegion3D(region_name, region); } - void addRegion(const std::string ®ion_name, const Region ®ion) { + void addRegion(const std::string& region_name, const Region& region) { return addRegion2D(region_name, region); } - void addRegion(const std::string ®ion_name, const Region ®ion) { + void addRegion(const std::string& region_name, const Region& region) { return addRegionPerp(region_name, region); } - void addRegion3D(const std::string ®ion_name, const Region ®ion); - void addRegion2D(const std::string ®ion_name, const Region ®ion); - void addRegionPerp(const std::string ®ion_name, const Region ®ion); + void addRegion3D(const std::string& region_name, const Region& region); + void addRegion2D(const std::string& region_name, const Region& region); + void addRegionPerp(const std::string& region_name, const Region& region); /// Converts an Ind2D to an Ind3D using calculation - Ind3D ind2Dto3D(const Ind2D &ind2D, int jz = 0) { return {ind2D.ind * LocalNz + jz, LocalNy, LocalNz}; } + Ind3D ind2Dto3D(const Ind2D& ind2D, int jz = 0) { + return {ind2D.ind * LocalNz + jz, LocalNy, LocalNz}; + } /// Converts an Ind3D to an Ind2D using calculation - Ind2D ind3Dto2D(const Ind3D &ind3D) { return {ind3D.ind / LocalNz, LocalNy, 1}; } + Ind2D ind3Dto2D(const Ind3D& ind3D) { return {ind3D.ind / LocalNz, LocalNy, 1}; } /// Converts an Ind3D to an IndPerp using calculation - IndPerp ind3DtoPerp(const Ind3D &ind3D) { return {ind3D.x() * LocalNz + ind3D.z(), 1, LocalNz}; } + IndPerp ind3DtoPerp(const Ind3D& ind3D) { + return {ind3D.x() * LocalNz + ind3D.z(), 1, LocalNz}; + } /// Converts an IndPerp to an Ind3D using calculation - Ind3D indPerpto3D(const IndPerp &indPerp, int jy = 0) { + Ind3D indPerpto3D(const IndPerp& indPerp, int jy = 0) { int jz = indPerp.z(); - return { (indPerp.ind - jz) * LocalNy + LocalNz * jy + jz , LocalNy, LocalNz}; + return {(indPerp.ind - jz) * LocalNy + LocalNz * jy + jz, LocalNy, LocalNz}; } - + /// Converts an Ind3D to an Ind2D representing a 2D index using a lookup -- to be used with care BOUT_HOST_DEVICE Ind2D map3Dto2D(const Ind3D& ind3D) { return {indexLookup3Dto2D[ind3D.ind], LocalNy, 1}; @@ -754,9 +762,8 @@ class Mesh { /// /// Creates RGN_{ALL,NOBNDRY,NOX,NOY} void createDefaultRegions(); - -protected: +protected: /// Source for grid data GridDataSource* source{nullptr}; @@ -764,17 +771,18 @@ protected: std::map> coords_map; /// Mesh options section - Options *options{nullptr}; + Options* options{nullptr}; /// Set whether to call calcParallelSlices on all communicated fields (true) or not (false) bool calcParallelSlices_on_communicate{true}; /// Read a 1D array of integers - const std::vector readInts(const std::string &name, int n); - + const std::vector readInts(const std::string& name, int n); + /// Calculates the size of a message for a given x and y range - int msg_len(const std::vector &var_list, int xge, int xlt, int yge, int ylt); - + int msg_len(const std::vector& var_list, int xge, int xlt, int yge, + int ylt); + /// Initialise derivatives void derivs_init(Options* options); @@ -795,15 +803,15 @@ public: const bool include_corner_cells; private: - /// Allocates default Coordinates objects /// By default attempts to read staggered Coordinates from grid data source, /// interpolating from CELL_CENTRE if not present. Set /// force_interpolate_from_centre argument to true to always interpolate /// (useful if CELL_CENTRE Coordinates have been changed, so reading from file /// would not be correct). - std::shared_ptr createDefaultCoordinates(const CELL_LOC location, - bool force_interpolate_from_centre=false); + std::shared_ptr + createDefaultCoordinates(const CELL_LOC location, + bool force_interpolate_from_centre = false); //Internal region related information std::map> regionMap3D; @@ -815,15 +823,18 @@ private: }; template <> -inline const Region& Mesh::getRegion(const std::string& region_name) const { +inline const Region& +Mesh::getRegion(const std::string& region_name) const { return getRegion3D(region_name); } template <> -inline const Region& Mesh::getRegion(const std::string& region_name) const { +inline const Region& +Mesh::getRegion(const std::string& region_name) const { return getRegion2D(region_name); } template <> -inline const Region& Mesh::getRegion(const std::string& region_name) const { +inline const Region& +Mesh::getRegion(const std::string& region_name) const { return getRegionPerp(region_name); } diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx index 2f98c41ff7..339aae031e 100644 --- a/include/bout/monitor.hxx +++ b/include/bout/monitor.hxx @@ -1,9 +1,9 @@ #ifndef __MONITOR_H__ #define __MONITOR_H__ -#include "bout_types.hxx" +#include "bout/bout_types.hxx" +#include "bout/utils.hxx" #include "bout/assert.hxx" -#include "utils.hxx" #include @@ -17,23 +17,23 @@ inline bool isMultiple(BoutReal a, BoutReal b) { ASSERT2(a > 0); ASSERT2(b > 0); - auto min = a>b?b:a; - auto max = a>b?a:b; - auto ratio = std::round(max/min); - auto error = ratio*min - max; - return (std::abs(error/max) < 1e-12); + auto min = a > b ? b : a; + auto max = a > b ? a : b; + auto ratio = std::round(max / min); + auto error = ratio * min - max; + return (std::abs(error / max) < 1e-12); } /// Monitor baseclass for the Solver /// /// Can be called ether with a specified frequency, or with the /// frequency of the BOUT++ output monitor. -class Monitor{ +class Monitor { friend class Solver; ///< needs access to timestep and freq public: /// A \p timestep_ of -1 defaults to the the frequency of the BOUT++ /// output monitor - Monitor(BoutReal timestep_ = -1) : timestep(timestep_) {}; + Monitor(BoutReal timestep_ = -1) : timestep(timestep_){}; virtual ~Monitor() = default; @@ -78,7 +78,7 @@ private: }; struct RunMetrics { - public: +public: /// cumulative wall clock time in seconds BoutReal t_elapsed = 0; /// time step's wall clock time in seconds @@ -123,8 +123,6 @@ struct RunMetrics { * Write job progress to screen */ void writeProgress(BoutReal simtime, bool output_split); - }; - #endif // __MONITOR_H__ diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx index 0b309c9585..fc0f98c952 100644 --- a/include/bout/msg_stack.hxx +++ b/include/bout/msg_stack.hxx @@ -31,13 +31,13 @@ class MsgStack; #include "bout/build_config.hxx" -#include "unused.hxx" +#include "bout/unused.hxx" #include "bout/format.hxx" #include "fmt/core.h" -#include #include +#include #include #include @@ -48,7 +48,7 @@ class MsgStack; /// we need to say if we support this or not by defining BOUT_HAS_PRETTY_FUNCTION (to be /// implemented in configure) #if BOUT_HAS_PRETTY_FUNCTION -#define __thefunc__ __PRETTY_FUNCTION__ +#define __thefunc__ __PRETTY_FUNCTION__ #else #define __thefunc__ __func__ #endif @@ -103,7 +103,7 @@ public: #endif private: - std::vector stack; ///< Message stack; + std::vector stack; ///< Message stack; std::vector::size_type position{0}; ///< Position in stack }; @@ -200,7 +200,7 @@ private: original MsgStackItem constructor so that the message is the last of the required arguments and the optional arguments follow from there. */ -#define TRACE(...) \ +#define TRACE(...) \ MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__) #else #define TRACE(...) diff --git a/include/bout/multiostream.hxx b/include/bout/multiostream.hxx index bdd8ba210b..b90ccf9419 100644 --- a/include/bout/multiostream.hxx +++ b/include/bout/multiostream.hxx @@ -1,22 +1,22 @@ #ifndef __MULTIOSTREAM_H__ #define __MULTIOSTREAM_H__ +#include #include #include -#include /// Template class to split streams /*! from http://accu.org/index.php/journals/260 */ -template > +template > class multioutbuf : public std::basic_streambuf { private: - using stream_container = std::vector *>; + using stream_container = std::vector*>; stream_container streams_; public: - void add(std::basic_ostream &str) { + void add(std::basic_ostream& str) { auto pos = std::find(streams_.begin(), streams_.end(), &str); // Already been added @@ -27,7 +27,7 @@ public: streams_.push_back(&str); } - void remove(std::basic_ostream &str) { + void remove(std::basic_ostream& str) { auto pos = std::find(streams_.begin(), streams_.end(), &str); if (pos != streams_.end()) { @@ -36,9 +36,9 @@ public: } protected: - std::streamsize xsputn(const char_type *sequence, std::streamsize num) override { + std::streamsize xsputn(const char_type* sequence, std::streamsize num) override { - for (auto ¤t : streams_) { + for (auto& current : streams_) { current->write(sequence, num); current->flush(); } @@ -48,7 +48,7 @@ protected: int overflow(int c) override { - for (auto ¤t : streams_) { + for (auto& current : streams_) { current->put(static_cast(c)); current->flush(); } @@ -57,37 +57,31 @@ protected: } }; -template +template class multioutbuf_init { private: multioutbuf buf_; public: - multioutbuf* buf() { - return &buf_; - } + multioutbuf* buf() { return &buf_; } }; -template > -class multiostream : private - multioutbuf_init, - public - std::basic_ostream { - private: +template > +class multiostream : private multioutbuf_init, + public std::basic_ostream { +private: using multioutbuf_init = ::multioutbuf_init; - public: - multiostream() : multioutbuf_init(), std::basic_ostream(multioutbuf_init::buf()) {} +public: + multiostream() + : multioutbuf_init(), std::basic_ostream( + multioutbuf_init::buf()) {} - void add(std::basic_ostream& str) { + void add(std::basic_ostream& str) { multioutbuf_init::buf()->add(str); } - void remove(std::basic_ostream& str) { + void remove(std::basic_ostream& str) { multioutbuf_init::buf()->remove(str); } }; @@ -96,4 +90,3 @@ using cmultiostream = multiostream; using wmultiostream = multiostream; #endif // __MULTIOSTREAM_H__ - diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index abb725f15a..032705e61a 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -1,4 +1,4 @@ -/************************************************************************//** +/************************************************************************/ /** * \brief Openmp utilitiy wrappers * * @@ -47,4 +47,3 @@ // #undef INDIRECT1 // #undef INDIRECT2 #endif - diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 90c036abb2..39e870ea2e 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -39,27 +39,27 @@ class Options; #ifndef __OPTIONS_H__ #define __OPTIONS_H__ -#include "bout_types.hxx" -#include "unused.hxx" -#include "output.hxx" -#include "utils.hxx" -#include "bout/sys/variant.hxx" +#include "bout/bout_types.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/sys/type_name.hxx" +#include "bout/sys/variant.hxx" #include "bout/traits.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" #include +#include +#include #include #include #include -#include #include -#include +#include #include -#include /// Class to represent hierarchy of options /*! @@ -161,12 +161,12 @@ class Options { public: /// Constructor. This is called to create the root object Options() = default; - + /// Constructor used to create non-root objects /// /// @param[in] parent Parent object /// @param[in] sectionName Name of the section, including path from the root - Options(Options *parent_instance, std::string full_name) + Options(Options* parent_instance, std::string full_name) : parent_instance(parent_instance), full_name(std::move(full_name)){}; /// Initialise with a value @@ -175,21 +175,21 @@ public: Options(T value) { assign(value); } - + /// Construct with a nested initializer list /// This allows Options trees to be constructed, using a mix of types. /// /// Example: { {"key1", 42}, {"key2", field} } Options(std::initializer_list> values); - + /// Copy constructor Options(const Options& other); ~Options() = default; /// Get a reference to the only root instance - static Options &root(); - + static Options& root(); + /// Free all memory static void cleanup(); @@ -205,7 +205,7 @@ public: /// Note: Due to default initialisation rules, if an attribute /// is used without being set, it will be false, 0, 0.0 and /// throw std::bad_cast if cast to std::string - /// + /// class AttributeType : public bout::utils::variant { public: using Base = bout::utils::variant; @@ -242,7 +242,10 @@ public: /// Cast operator, which allows this class to be /// assigned to type T /// This will throw std::bad_cast if it can't be done - template operator T() const { return as(); } + template + operator T() const { + return as(); + } /// Get the value as a specified type /// This will throw std::bad_cast if it can't be done @@ -254,7 +257,7 @@ public: /// The value stored ValueType value; - + /// A collection of attributes belonging to the value /// Special attributes: /// - time_dimension [string] If this is set then changes to the value @@ -264,10 +267,10 @@ public: /// /// - source [string] Describes where the value came from /// e.g. a file name, or "default". - /// + /// /// - type [string] The type the Option is converted to /// when used. - /// + /// /// - doc [string] Documentation, describing what the variable does /// std::map attributes; @@ -312,15 +315,15 @@ public: /// auto child = parent["child"]; /// /// parent is now a section. - Options& operator[](const std::string &name); + Options& operator[](const std::string& name); // Prevent ambiguous overload resolution due to operator T() below - Options& operator[](const char *name) { return (*this)[std::string(name)]; } + Options& operator[](const char* name) { return (*this)[std::string(name)]; } /// Get a sub-section or value /// If this object is not a section, or if name /// is not a child, then a BoutException will be thrown - const Options& operator[](const std::string &name) const; - const Options& operator[](const char *name) const { return (*this)[std::string(name)]; } + const Options& operator[](const std::string& name) const; + const Options& operator[](const char* name) const { return (*this)[std::string(name)]; } /// Return type of `Options::fuzzyFind` struct FuzzyMatch { @@ -367,7 +370,7 @@ public: /// the value member directly e.g. option2.value = option1.value; /// Options& operator=(const Options& other); - + /// Assign a value to the option. /// This will throw an exception if already has a value /// @@ -377,16 +380,16 @@ public: /// option["test"].assign(42, "some source"); /// /// Note: Specialised versions for types stored in ValueType - template - void assign(T val, std::string source="") { + template + void assign(T val, std::string source = "") { std::stringstream ss; ss << val; _set(ss.str(), std::move(source), false); } - + /// Force to a value /// Overwrites any existing setting - template + template void force(T val, const std::string source = "") { is_section = true; // Invalidates any existing setting assign(val, source); @@ -451,27 +454,27 @@ public: } T val; - + // Try casting. This will throw std::bad_cast if it can't be done try { val = bout::utils::variantStaticCastOrThrow(value); - } catch (const std::bad_cast &e) { + } catch (const std::bad_cast& e) { // If the variant is a string then we may be able to parse it - + if (bout::utils::holds_alternative(value)) { std::stringstream ss(bout::utils::get(value)); ss >> val; - + // Check if the parse failed if (ss.fail()) { throw BoutException("Option {:s} could not be parsed ('{:s}')", full_name, bout::utils::variantToString(value)); } - + // Check if there are characters remaining std::string remainder; std::getline(ss, remainder); - for (const char &ch : remainder) { + for (const char& ch : remainder) { if (!std::isspace(static_cast(ch))) { // Meaningful character not parsed throw BoutException("Option {:s} could not be parsed", full_name); @@ -483,11 +486,11 @@ public: typeid(T).name()); } } - + // Mark this option as used value_used = true; // Note this is mutable - output_info << "\tOption " << full_name << " = " << val; + output_info << "\tOption " << full_name << " = " << val; if (attributes.count("source")) { // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; @@ -499,11 +502,12 @@ public: /// Get the value of this option. If not found, /// set to the default value - template T withDefault(T def) { + template + T withDefault(T def) { // Set the type attributes["type"] = bout::utils::typeName(); - + if (is_section) { // Option not found assign(def, DEFAULT_SOURCE); @@ -531,7 +535,7 @@ public: std::string withDefault(const char* def) { return withDefault(std::string(def)); } - + /// Overloaded version to copy from another option Options& withDefault(const Options& def) { // if def is a section, then it does not make sense to try to use it as a default for @@ -562,7 +566,8 @@ public: /// Get the value of this option. If not found, /// return the default value but do not set - template T withDefault(T def) const { + template + T withDefault(T def) const { if (is_section) { // Option not found output_info << _("\tOption ") << full_name << " = " << def << " (" << DEFAULT_SOURCE @@ -584,7 +589,8 @@ public: /// Allow the user to override defaults set later, also used by the /// BOUT_OVERRIDE_DEFAULT_OPTION. - template T overrideDefault(T def) { + template + T overrideDefault(T def) { // Set the type attributes["type"] = bout::utils::typeName(); @@ -606,7 +612,7 @@ public: } /// Get the parent Options object - Options &parent() { + Options& parent() { if (parent_instance == nullptr) { throw BoutException("Option {:s} has no parent", full_name); } @@ -616,79 +622,83 @@ public: /// Equality operator /// Converts to the same type and compares /// This conversion may fail, throwing std::bad_cast - template + template bool operator==(const T& other) const { return as() == other; } /// Overloaded equality operator for literal strings bool operator==(const char* other) const; - + /// Comparison operator - template + template bool operator<(const T& other) const { return as() < other; } /// Overloaded comparison operator for literal strings bool operator<(const char* other) const; - + ////////////////////////////////////// // Backward-compatible interface - + /// Get a pointer to the only root instance (singleton) static Options* getRoot() { return &root(); } - template - void set(const std::string &key, T val, const std::string &source = "", bool force = false) { + template + void set(const std::string& key, T val, const std::string& source = "", + bool force = false) { if (force) { (*this)[key].force(val, source); } else { (*this)[key].assign(val, source); } } - + // Setting options - template void forceSet(const std::string &key, T t, const std::string &source=""){ - (*this)[key].force(t,source); + template + void forceSet(const std::string& key, T t, const std::string& source = "") { + (*this)[key].force(t, source); } - + /*! * Test if a key is set by the user. * Values set via default values are ignored. */ - bool isSet(const std::string &key) const { + bool isSet(const std::string& key) const { // Note using operator[] here would result in exception if key does not exist - if (!is_section) + if (!is_section) { return false; + } auto it = children.find(key); - if (it == children.end()) + if (it == children.end()) { return false; + } return it->second.isSet(); } /// Get options, passing in a reference to a variable /// which will be set to the requested value. - template - void get(const std::string &key, T &val, U def, bool UNUSED(log)=false) { + template + void get(const std::string& key, T& val, U def, bool UNUSED(log) = false) { val = (*this)[key].withDefault(def); } - template - void get(const std::string &key, T &val, U def, bool UNUSED(log)=false) const { + template + void get(const std::string& key, T& val, U def, bool UNUSED(log) = false) const { val = (*this)[key].withDefault(def); } /// Creates new section if doesn't exist - Options* getSection(const std::string &name) { return &(*this)[name]; } - const Options* getSection(const std::string &name) const { return &(*this)[name]; } - Options* getParent() const {return parent_instance;} - + Options* getSection(const std::string& name) { return &(*this)[name]; } + const Options* getSection(const std::string& name) const { return &(*this)[name]; } + Options* getParent() const { return parent_instance; } + ////////////////////////////////////// - + /*! * Print string representation of this object and all sections in a tree structure */ - std::string str() const {return full_name;} + std::string str() const { return full_name; } /// Print just the name of this object without parent sections std::string name() const { @@ -720,15 +730,15 @@ public: /// clean the cache of parsed options static void cleanCache(); - + /*! * Class used to store values, together with * information about their origin and usage */ struct OptionValue { std::string value; - std::string source; // Source of the setting - mutable bool used = false; // Set to true when used + std::string source; // Source of the setting + mutable bool used = false; // Set to true when used /// This constructor needed for map::emplace /// Can be removed in C++17 with map::insert and brace initialisation @@ -740,9 +750,7 @@ public: /// to allow iteration over the tree std::map subsections() const; - const std::map& getChildren() const { - return children; - } + const std::map& getChildren() const { return children; } /// Return a vector of all the full names of all the keys below this /// in the tree (not gauranteed to be sorted) @@ -762,7 +770,7 @@ public: attributes["doc"] = docstring; return *this; } - + friend bool operator==(const Options& lhs, const Options& rhs) { if (lhs.isValue() and rhs.isValue()) { return lhs.value == rhs.value; @@ -775,21 +783,23 @@ public: private: /// The source label given to default values static const std::string DEFAULT_SOURCE; - - static Options *root_instance; ///< Only instance of the root section - Options *parent_instance {nullptr}; + static Options* root_instance; ///< Only instance of the root section + + Options* parent_instance{nullptr}; std::string full_name; // full path name for logging only // An Option object can either be a section or a value, defaulting to a section - bool is_section = true; ///< Is this Options object a section? + bool is_section = true; ///< Is this Options object a section? std::map children; ///< If a section then has children - mutable bool value_used = false; ///< Record whether this value is used - + mutable bool value_used = false; ///< Record whether this value is used + template void _set_no_check(T val, std::string source) { if (not children.empty()) { - throw BoutException("Trying to assign value to Option '{}', but it's a non-empty section", full_name); + throw BoutException( + "Trying to assign value to Option '{}', but it's a non-empty section", + full_name); } value = std::move(val); @@ -824,18 +834,36 @@ private: _set_no_check(std::move(val), std::move(source)); } - - /// Tests if two values are similar. - template bool similar(T a, T b) const { return a == b; } + + /// Tests if two values are similar. + template + bool similar(T a, T b) const { + return a == b; + } }; // Specialised assign methods for types stored in ValueType -template<> inline void Options::assign<>(bool val, std::string source) { _set(val, std::move(source), false); } -template<> inline void Options::assign<>(int val, std::string source) { _set(val, std::move(source), false); } -template<> inline void Options::assign<>(BoutReal val, std::string source) { _set(val, std::move(source), false); } -template<> inline void Options::assign<>(std::string val, std::string source) { _set(std::move(val), std::move(source), false); } +template <> +inline void Options::assign<>(bool val, std::string source) { + _set(val, std::move(source), false); +} +template <> +inline void Options::assign<>(int val, std::string source) { + _set(val, std::move(source), false); +} +template <> +inline void Options::assign<>(BoutReal val, std::string source) { + _set(val, std::move(source), false); +} +template <> +inline void Options::assign<>(std::string val, std::string source) { + _set(std::move(val), std::move(source), false); +} // Note: const char* version needed to avoid conversion to bool -template<> inline void Options::assign<>(const char *val, std::string source) { _set(std::string(val), source, false);} +template <> +inline void Options::assign<>(const char* val, std::string source) { + _set(std::string(val), source, false); +} // Note: Field assignments don't check for previous assignment (always force) template <> void Options::assign<>(Field2D val, std::string source); @@ -851,16 +879,26 @@ template <> void Options::assign<>(Tensor val, std::string source); /// Specialised similar comparison methods -template <> inline bool Options::similar(BoutReal a, BoutReal b) const { return fabs(a - b) < 1e-10; } +template <> +inline bool Options::similar(BoutReal a, BoutReal b) const { + return fabs(a - b) < 1e-10; +} /// Specialised as routines -template <> std::string Options::as(const std::string& similar_to) const; -template <> int Options::as(const int& similar_to) const; -template <> BoutReal Options::as(const BoutReal& similar_to) const; -template <> bool Options::as(const bool& similar_to) const; -template <> Field2D Options::as(const Field2D& similar_to) const; -template <> Field3D Options::as(const Field3D& similar_to) const; -template <> FieldPerp Options::as(const FieldPerp& similar_to) const; +template <> +std::string Options::as(const std::string& similar_to) const; +template <> +int Options::as(const int& similar_to) const; +template <> +BoutReal Options::as(const BoutReal& similar_to) const; +template <> +bool Options::as(const bool& similar_to) const; +template <> +Field2D Options::as(const Field2D& similar_to) const; +template <> +Field3D Options::as(const Field3D& similar_to) const; +template <> +FieldPerp Options::as(const FieldPerp& similar_to) const; template <> Array Options::as>(const Array& similar_to) const; template <> @@ -894,7 +932,7 @@ void checkForUnusedOptions(); /// used to customise the error message for the actual input file used void checkForUnusedOptions(const Options& options, const std::string& data_dir, const std::string& option_file); -} +} // namespace bout namespace bout { namespace details { @@ -902,8 +940,7 @@ namespace details { /// so that we can put the function definitions in the .cxx file, /// avoiding lengthy recompilation if we change it struct OptionsFormatterBase { - auto parse(fmt::format_parse_context& ctx) - -> fmt::format_parse_context::iterator; + auto parse(fmt::format_parse_context& ctx) -> fmt::format_parse_context::iterator; auto format(const Options& options, fmt::format_context& ctx) -> fmt::format_context::iterator; @@ -936,51 +973,63 @@ template <> struct fmt::formatter : public bout::details::OptionsFormatterBase {}; /// Define for reading options which passes the variable name -#define OPTION(options, var, def) \ - pointer(options)->get(#var, var, def) +#define OPTION(options, var, def) pointer(options)->get(#var, var, def) -#define OPTION2(options, var1, var2, def){ \ - pointer(options)->get(#var1, var1, def); \ - pointer(options)->get(#var2, var2, def);} +#define OPTION2(options, var1, var2, def) \ + { \ + pointer(options)->get(#var1, var1, def); \ + pointer(options)->get(#var2, var2, def); \ + } -#define OPTION3(options, var1, var2, var3, def){ \ - pointer(options)->get(#var1, var1, def); \ - pointer(options)->get(#var2, var2, def); \ - pointer(options)->get(#var3, var3, def);} +#define OPTION3(options, var1, var2, var3, def) \ + { \ + pointer(options)->get(#var1, var1, def); \ + pointer(options)->get(#var2, var2, def); \ + pointer(options)->get(#var3, var3, def); \ + } + +#define OPTION4(options, var1, var2, var3, var4, def) \ + { \ + pointer(options)->get(#var1, var1, def); \ + pointer(options)->get(#var2, var2, def); \ + pointer(options)->get(#var3, var3, def); \ + pointer(options)->get(#var4, var4, def); \ + } -#define OPTION4(options, var1, var2, var3, var4, def){ \ - pointer(options)->get(#var1, var1, def); \ - pointer(options)->get(#var2, var2, def); \ - pointer(options)->get(#var3, var3, def); \ - pointer(options)->get(#var4, var4, def);} +#define OPTION5(options, var1, var2, var3, var4, var5, def) \ + { \ + pointer(options)->get(#var1, var1, def); \ + pointer(options)->get(#var2, var2, def); \ + pointer(options)->get(#var3, var3, def); \ + pointer(options)->get(#var4, var4, def); \ + pointer(options)->get(#var5, var5, def); \ + } -#define OPTION5(options, var1, var2, var3, var4, var5, def){ \ +#define OPTION6(options, var1, var2, var3, var4, var5, var6, def) \ + { \ pointer(options)->get(#var1, var1, def); \ pointer(options)->get(#var2, var2, def); \ pointer(options)->get(#var3, var3, def); \ pointer(options)->get(#var4, var4, def); \ - pointer(options)->get(#var5, var5, def);} - -#define OPTION6(options, var1, var2, var3, var4, var5, var6, def){ \ - pointer(options)->get(#var1, var1, def); \ - pointer(options)->get(#var2, var2, def); \ - pointer(options)->get(#var3, var3, def); \ - pointer(options)->get(#var4, var4, def); \ - pointer(options)->get(#var5, var5, def); \ - pointer(options)->get(#var6, var6, def);} - -#define VAROPTION(options, var, def) { \ - if (pointer(options)->isSet(#var)){ \ - pointer(options)->get(#var, var, def); \ - } else { \ - Options::getRoot()->getSection("all")->get(#var, var, def); \ - }} \ + pointer(options)->get(#var5, var5, def); \ + pointer(options)->get(#var6, var6, def); \ + } + +#define VAROPTION(options, var, def) \ + { \ + if (pointer(options)->isSet(#var)) { \ + pointer(options)->get(#var, var, def); \ + } else { \ + Options::getRoot()->getSection("all")->get(#var, var, def); \ + } \ + } /// Define for over-riding library defaults for options, should be called in global /// namespace so that the new default is set before main() is called. -#define BOUT_OVERRIDE_DEFAULT_OPTION(name, value) \ - namespace { \ - const auto BOUT_CONCAT(user_default,__LINE__) = \ - Options::root()[name].overrideDefault(value); } \ +#define BOUT_OVERRIDE_DEFAULT_OPTION(name, value) \ + namespace { \ + const auto BOUT_CONCAT(user_default, \ + __LINE__) = Options::root()[name].overrideDefault(value); \ + } #endif // __OPTIONS_H__ diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index f9c58a8d78..2fdb71c6d4 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -10,31 +10,29 @@ #include -#include "boutexception.hxx" -#include "options.hxx" +#include "bout/boutexception.hxx" +#include "bout/options.hxx" namespace bout { class OptionsNetCDF { public: enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing + replace, ///< Overwrite file when writing + append ///< Append to file when writing }; - - OptionsNetCDF(const std::string &filename, FileMode mode = FileMode::replace) {} + + OptionsNetCDF(const std::string& filename, FileMode mode = FileMode::replace) {} OptionsNetCDF(const OptionsNetCDF&) = default; OptionsNetCDF(OptionsNetCDF&&) = default; OptionsNetCDF& operator=(const OptionsNetCDF&) = default; OptionsNetCDF& operator=(OptionsNetCDF&&) = default; /// Read options from file - Options read() { - throw BoutException("OptionsNetCDF not available\n"); - } + Options read() { throw BoutException("OptionsNetCDF not available\n"); } /// Write options to file - void write(const Options &options) { + void write(const Options& options) { throw BoutException("OptionsNetCDF not available\n"); } }; @@ -46,7 +44,7 @@ public: #include #include -#include "options.hxx" +#include "bout/options.hxx" /// Forward declare netCDF file type so we don't need to depend /// directly on netCDF @@ -59,8 +57,8 @@ namespace bout { class OptionsNetCDF { public: enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing + replace, ///< Overwrite file when writing + append ///< Append to file when writing }; // Constructors need to be defined in implementation due to forward diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx index f37a743238..900c3aedaa 100644 --- a/include/bout/optionsreader.hxx +++ b/include/bout/optionsreader.hxx @@ -34,7 +34,7 @@ class OptionsReader; #ifndef __OPTIONSREADER_H__ #define __OPTIONSREADER_H__ -#include "options.hxx" +#include "bout/options.hxx" #include "bout/format.hxx" #include "fmt/core.h" @@ -53,12 +53,13 @@ class OptionsReader; /// opt now contains a tree of sections and options from the input file "somefile.inp" /// class OptionsReader { - public: +public: /// Return a pointer to the instance singleton - static OptionsReader *getInstance(); + static OptionsReader* getInstance(); /// Delete the instance - static void cleanup() {delete instance; + static void cleanup() { + delete instance; instance = nullptr; } @@ -67,7 +68,7 @@ class OptionsReader { /// /// @param[inout] options The options section to insert values and subsections into /// @param[in] file The name of the file. printf style arguments can be used to create the file name. - void read(Options *options, const std::string& filename); + void read(Options* options, const std::string& filename); template void read(Options* options, const S& format, const Args&... args) { @@ -78,7 +79,7 @@ class OptionsReader { /// /// @param[in] options The options tree to be written /// @param[in] file The name of the file to (over)write - void write(Options *options, const std::string& filename); + void write(Options* options, const std::string& filename); template void write(Options* options, const S& format, const Args&... args) { @@ -100,14 +101,12 @@ class OptionsReader { /// ... /// return 0; /// } - void parseCommandLine(Options *options, int argc, char **argv); - void parseCommandLine(Options *options, const std::vector& argv); - - private: + void parseCommandLine(Options* options, int argc, char** argv); + void parseCommandLine(Options* options, const std::vector& argv); + +private: /// The instance of this singleton - static OptionsReader *instance; - + static OptionsReader* instance; }; #endif // __OPTIONSREADER_H__ - diff --git a/include/bout/output.hxx b/include/bout/output.hxx index a690e8d7ea..986fd94537 100644 --- a/include/bout/output.hxx +++ b/include/bout/output.hxx @@ -29,17 +29,17 @@ class Output; #ifndef __OUTPUT_H__ #define __OUTPUT_H__ -#include "multiostream.hxx" -#include +#include "bout/multiostream.hxx" #include #include +#include #include +#include "bout/boutexception.hxx" +#include "bout/unused.hxx" #include "bout/assert.hxx" -#include "boutexception.hxx" -#include "unused.hxx" #include "bout/format.hxx" -#include "bout/sys/gettext.hxx" // for gettext _() macro +#include "bout/sys/gettext.hxx" // for gettext _() macro #include "fmt/core.h" @@ -79,9 +79,7 @@ public: template Output(const S& format, const Args&... args) : Output(fmt::format(format, args...)) {} - ~Output() override { - close(); - } + ~Output() override { close(); } virtual void enable(); ///< Enables writing to stdout (default) virtual void disable(); ///< Disables stdout @@ -113,35 +111,35 @@ public: } /// Add an output stream. All output will be sent to all streams - void add(std::basic_ostream &str) { multioutbuf_init::buf()->add(str); } + void add(std::basic_ostream& str) { multioutbuf_init::buf()->add(str); } /// Remove an output stream - void remove(std::basic_ostream &str) { + void remove(std::basic_ostream& str) { multioutbuf_init::buf()->remove(str); } - static Output *getInstance(); ///< Return pointer to instance + static Output* getInstance(); ///< Return pointer to instance protected: friend class ConditionalOutput; - virtual Output *getBase() { return this; } + virtual Output* getBase() { return this; } virtual bool isEnabled() { return true; } private: - std::ofstream file; ///< Log file stream - bool enabled; ///< Whether output to stdout is enabled + std::ofstream file; ///< Log file stream + bool enabled; ///< Whether output to stdout is enabled }; /// Class which behaves like Output, but has no effect. /// This is to allow debug outputs to be disabled at compile time -/// -/// +/// +/// class DummyOutput : public Output { public: template - void write(const S&, const Args&...) {}; + void write(const S&, const Args&...){}; template - void print(const S&, const Args&...) {}; + void print(const S&, const Args&...){}; void enable() override{}; void disable() override{}; void enable(MAYBE_UNUSED(bool enable)){}; @@ -157,14 +155,13 @@ class ConditionalOutput : public Output { public: /// @param[in] base The Output object which will be written to if enabled /// @param[in] enabled Should this be enabled by default? - ConditionalOutput(Output *base, bool enabled = true) : base(base), enabled(enabled) {}; + ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled){}; /// Constuctor taking ConditionalOutput. This allows several layers of conditions - /// + /// /// @param[in] base A ConditionalOutput which will be written to if enabled - /// - ConditionalOutput(ConditionalOutput *base) - : base(base), enabled(base->enabled) {}; + /// + ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled){}; /// If enabled, writes a string using fmt formatting /// by calling base->write @@ -192,7 +189,7 @@ public: } /// Get the lowest-level Output object which is the base of this ConditionalOutput - Output *getBase() override { + Output* getBase() override { ASSERT1(base != nullptr); return base->getBase(); }; @@ -216,7 +213,7 @@ public: private: /// The lower-level Output to send output to - Output *base; + Output* base; protected: friend class WithQuietOutput; @@ -228,36 +225,40 @@ protected: /// statements like /// output_debug << "debug message"; /// compile but have no effect if BOUT_USE_OUTPUT_DEBUG is false -template DummyOutput &operator<<(DummyOutput &out, T const &UNUSED(t)) { +template +DummyOutput& operator<<(DummyOutput& out, T const& UNUSED(t)) { return out; } -template DummyOutput &operator<<(DummyOutput &out, const T *UNUSED(t)) { +template +DummyOutput& operator<<(DummyOutput& out, const T* UNUSED(t)) { return out; } // Function pointer so we can apply unused macro to pf in function below -using stream_manipulator = std::ostream &(*)(std::ostream &); +using stream_manipulator = std::ostream& (*)(std::ostream&); -inline DummyOutput &operator<<(DummyOutput &out, stream_manipulator UNUSED(pf)) { +inline DummyOutput& operator<<(DummyOutput& out, stream_manipulator UNUSED(pf)) { return out; } -inline ConditionalOutput &operator<<(ConditionalOutput &out, stream_manipulator pf) { +inline ConditionalOutput& operator<<(ConditionalOutput& out, stream_manipulator pf) { if (out.isEnabled()) { *out.getBase() << pf; } return out; } -template ConditionalOutput &operator<<(ConditionalOutput &out, T const &t) { +template +ConditionalOutput& operator<<(ConditionalOutput& out, T const& t) { if (out.isEnabled()) { *out.getBase() << t; } return out; } -template ConditionalOutput &operator<<(ConditionalOutput &out, const T *t) { +template +ConditionalOutput& operator<<(ConditionalOutput& out, const T* t) { if (out.isEnabled()) { *out.getBase() << t; } @@ -293,11 +294,11 @@ extern ConditionalOutput output_debug; #else extern DummyOutput output_debug; #endif -extern ConditionalOutput output_warn; ///< warnings -extern ConditionalOutput output_progress; ///< progress -extern ConditionalOutput output_info; ///< information -extern ConditionalOutput output_error; ///< errors -extern ConditionalOutput output_verbose; ///< less interesting messages +extern ConditionalOutput output_warn; ///< warnings +extern ConditionalOutput output_progress; ///< progress +extern ConditionalOutput output_info; ///< information +extern ConditionalOutput output_error; ///< errors +extern ConditionalOutput output_verbose; ///< less interesting messages /// Generic output, given the same level as output_progress extern ConditionalOutput output; diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx index a4fde136e1..6b1829b088 100644 --- a/include/bout/output_bout_types.hxx +++ b/include/bout/output_bout_types.hxx @@ -7,7 +7,7 @@ #include -#include "output.hxx" +#include "bout/output.hxx" #include "bout/region.hxx" template diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx index 08e157e9d5..8b1fc8098f 100644 --- a/include/bout/parallel_boundary_op.hxx +++ b/include/bout/parallel_boundary_op.hxx @@ -1,11 +1,11 @@ #ifndef __PAR_BNDRY_OP_H__ #define __PAR_BNDRY_OP_H__ -#include "boundary_op.hxx" -#include "bout_types.hxx" -#include "parallel_boundary_region.hxx" -#include "utils.hxx" -#include "unused.hxx" +#include "bout/boundary_op.hxx" +#include "bout/bout_types.hxx" +#include "bout/parallel_boundary_region.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include @@ -15,21 +15,22 @@ class BoundaryOpPar : public BoundaryOpBase { public: BoundaryOpPar() = default; - BoundaryOpPar(BoundaryRegionPar *region, std::shared_ptr value) + BoundaryOpPar(BoundaryRegionPar* region, std::shared_ptr value) : bndry(region), gen_values(std::move(value)), value_type(ValueType::GEN) {} - BoundaryOpPar(BoundaryRegionPar *region, Field3D* value) : - bndry(region), - field_values(value), - value_type(ValueType::FIELD) {} - BoundaryOpPar(BoundaryRegionPar *region, BoutReal value) : - bndry(region), - real_value(value), - value_type(ValueType::REAL) {} + BoundaryOpPar(BoundaryRegionPar* region, Field3D* value) + : bndry(region), field_values(value), value_type(ValueType::FIELD) {} + BoundaryOpPar(BoundaryRegionPar* region, BoutReal value) + : bndry(region), real_value(value), value_type(ValueType::REAL) {} ~BoundaryOpPar() override = default; // Note: All methods must implement clone, except for modifiers (see below) - virtual BoundaryOpPar* clone(BoundaryRegionPar *UNUSED(region), const std::list &UNUSED(args)) {return nullptr; } - virtual BoundaryOpPar* clone(BoundaryRegionPar *UNUSED(region), Field3D *UNUSED(f)) {return nullptr; } + virtual BoundaryOpPar* clone(BoundaryRegionPar* UNUSED(region), + const std::list& UNUSED(args)) { + return nullptr; + } + virtual BoundaryOpPar* clone(BoundaryRegionPar* UNUSED(region), Field3D* UNUSED(f)) { + return nullptr; + } virtual BoundaryOpPar* clone(BoundaryRegionPar* region, const std::list& args, @@ -39,29 +40,27 @@ public: } using BoundaryOpBase::apply; - void apply(Field2D &UNUSED(f)) override { + void apply(Field2D& UNUSED(f)) override { throw BoutException("Can't apply parallel boundary conditions to Field2D!"); } - void apply(Field2D &UNUSED(f), BoutReal UNUSED(t)) override { + void apply(Field2D& UNUSED(f), BoutReal UNUSED(t)) override { throw BoutException("Can't apply parallel boundary conditions to Field2D!"); } BoundaryRegionPar* bndry{nullptr}; protected: - /// Possible ways to get boundary values - std::shared_ptr gen_values; + std::shared_ptr gen_values; Field3D* field_values; BoutReal real_value{0.}; /// Where to take boundary values from - the generator, field or BoutReal - enum class ValueType {GEN, FIELD, REAL}; + enum class ValueType { GEN, FIELD, REAL }; const ValueType value_type{ValueType::REAL}; BoutReal getValue(int x, int y, int z, BoutReal t); - BoutReal getValue(const BoundaryRegionPar &bndry, BoutReal t); - + BoutReal getValue(const BoundaryRegionPar& bndry, BoutReal t); }; ////////////////////////////////////////////////// @@ -70,89 +69,88 @@ protected: class BoundaryOpPar_dirichlet : public BoundaryOpPar { public: BoundaryOpPar_dirichlet() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet(BoundaryRegionPar* region) : BoundaryOpPar(region, 0.) {} + BoundaryOpPar_dirichlet(BoundaryRegionPar* region, + std::shared_ptr value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet(BoundaryRegionPar* region, Field3D* value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet(BoundaryRegionPar* region, BoutReal value) + : BoundaryOpPar(region, value) {} using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, + const std::list& args) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override; using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; - + void apply(Field3D& f) override { return apply(f, 0); } + void apply(Field3D& f, BoutReal t) override; }; class BoundaryOpPar_dirichlet_O3 : public BoundaryOpPar { public: BoundaryOpPar_dirichlet_O3() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_O3(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet_O3(BoundaryRegionPar* region) : BoundaryOpPar(region, 0.) {} + BoundaryOpPar_dirichlet_O3(BoundaryRegionPar* region, + std::shared_ptr value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet_O3(BoundaryRegionPar* region, Field3D* value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet_O3(BoundaryRegionPar* region, BoutReal value) + : BoundaryOpPar(region, value) {} using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, + const std::list& args) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override; using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; - + void apply(Field3D& f) override { return apply(f, 0); } + void apply(Field3D& f, BoutReal t) override; }; class BoundaryOpPar_dirichlet_interp : public BoundaryOpPar { public: BoundaryOpPar_dirichlet_interp() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_dirichlet_interp(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet_interp(BoundaryRegionPar* region) : BoundaryOpPar(region, 0.) {} + BoundaryOpPar_dirichlet_interp(BoundaryRegionPar* region, + std::shared_ptr value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet_interp(BoundaryRegionPar* region, Field3D* value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_dirichlet_interp(BoundaryRegionPar* region, BoutReal value) + : BoundaryOpPar(region, value) {} using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, + const std::list& args) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override; using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; - + void apply(Field3D& f) override { return apply(f, 0); } + void apply(Field3D& f, BoutReal t) override; }; class BoundaryOpPar_neumann : public BoundaryOpPar { public: BoundaryOpPar_neumann() : BoundaryOpPar(nullptr, 0.) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region) : - BoundaryOpPar(region, 0.) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region, std::shared_ptr value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region, Field3D* value) : - BoundaryOpPar(region, value) {} - BoundaryOpPar_neumann(BoundaryRegionPar *region, BoutReal value) : - BoundaryOpPar(region, value) {} + BoundaryOpPar_neumann(BoundaryRegionPar* region) : BoundaryOpPar(region, 0.) {} + BoundaryOpPar_neumann(BoundaryRegionPar* region, std::shared_ptr value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_neumann(BoundaryRegionPar* region, Field3D* value) + : BoundaryOpPar(region, value) {} + BoundaryOpPar_neumann(BoundaryRegionPar* region, BoutReal value) + : BoundaryOpPar(region, value) {} using BoundaryOpPar::clone; - BoundaryOpPar* clone(BoundaryRegionPar *region, const std::list &args) override; - BoundaryOpPar* clone(BoundaryRegionPar *region, Field3D *f) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, + const std::list& args) override; + BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override; using BoundaryOpPar::apply; - void apply(Field3D &f) override {return apply(f, 0);} - void apply(Field3D &f, BoutReal t) override; - + void apply(Field3D& f) override { return apply(f, 0); } + void apply(Field3D& f, BoutReal t) override; }; #endif // __PAR_BNDRY_OP_H__ diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx index d9ea22814d..3d5525a303 100644 --- a/include/bout/parallel_boundary_region.hxx +++ b/include/bout/parallel_boundary_region.hxx @@ -1,8 +1,8 @@ #ifndef __PAR_BNDRY_H__ #define __PAR_BNDRY_H__ -#include "boundary_region.hxx" -#include "bout_types.hxx" +#include "bout/boundary_region.hxx" +#include "bout/bout_types.hxx" #include /** @@ -44,17 +44,18 @@ class BoundaryRegionPar : public BoundaryRegionBase { IndicesIter bndry_position; public: - BoundaryRegionPar(const std::string &name, int dir, Mesh* passmesh) : - BoundaryRegionBase(name, passmesh), dir(dir) { - BoundaryRegionBase::isParallel = true;} - BoundaryRegionPar(const std::string &name, BndryLoc loc,int dir, Mesh* passmesh) : - BoundaryRegionBase(name, loc, passmesh), dir(dir) { - BoundaryRegionBase::isParallel = true;} + BoundaryRegionPar(const std::string& name, int dir, Mesh* passmesh) + : BoundaryRegionBase(name, passmesh), dir(dir) { + BoundaryRegionBase::isParallel = true; + } + BoundaryRegionPar(const std::string& name, BndryLoc loc, int dir, Mesh* passmesh) + : BoundaryRegionBase(name, loc, passmesh), dir(dir) { + BoundaryRegionBase::isParallel = true; + } /// Add a point to the boundary - void add_point(int jx,int jy,int jz, - BoutReal x,BoutReal y,BoutReal z, - BoutReal length,BoutReal angle); + void add_point(int jx, int jy, int jz, BoutReal x, BoutReal y, BoutReal z, + BoutReal length, BoutReal angle); void first() override; void next() override; diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx index a52d5a3a26..2f6d343bd0 100644 --- a/include/bout/paralleltransform.hxx +++ b/include/bout/paralleltransform.hxx @@ -6,10 +6,10 @@ #ifndef __PARALLELTRANSFORM_H__ #define __PARALLELTRANSFORM_H__ -#include "bout_types.hxx" -#include "field3d.hxx" -#include "options.hxx" -#include "unused.hxx" +#include "bout/bout_types.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" +#include "bout/unused.hxx" class Mesh; @@ -24,18 +24,16 @@ class Mesh; class ParallelTransform { public: ParallelTransform(Mesh& mesh_in, Options* opt = nullptr) - : mesh(mesh_in), - options(opt == nullptr ? Options::root()["mesh:paralleltransform"] : *opt) {} + : mesh(mesh_in), + options(opt == nullptr ? Options::root()["mesh:paralleltransform"] : *opt) {} virtual ~ParallelTransform() = default; /// Given a 3D field, calculate and set the Y up down fields - virtual void calcParallelSlices(Field3D &f) = 0; + virtual void calcParallelSlices(Field3D& f) = 0; /// Calculate Yup and Ydown fields by integrating over mapped points /// This should be used for parallel divergence operators - virtual void integrateParallelSlices(Field3D &f) { - return calcParallelSlices(f); - } + virtual void integrateParallelSlices(Field3D& f) { return calcParallelSlices(f); } /// Convert a field into field-aligned coordinates /// so that the y index is along the magnetic field @@ -96,8 +94,8 @@ protected: /// has a 'parallel_transform' variable, it has the correct value virtual void checkInputGrid() = 0; - Mesh &mesh; ///< The mesh this paralleltransform is part of - Options &options; ///< Options for this ParallelTransform + Mesh& mesh; ///< The mesh this paralleltransform is part of + Options& options; ///< Options for this ParallelTransform }; /*! @@ -154,15 +152,15 @@ public: return result.setDirectionY(YDirectionType::Standard); } - virtual std::vector getWeightsForYApproximation(int i, - int j, int k, int yoffset) override { + virtual std::vector + getWeightsForYApproximation(int i, int j, int k, int yoffset) override { return {{i, j + yoffset, k, 1.0}}; } - bool canToFromFieldAligned() override { return true; } - bool requiresTwistShift(bool twist_shift_enabled, YDirectionType UNUSED(ytype)) override { + bool requiresTwistShift(bool twist_shift_enabled, + YDirectionType UNUSED(ytype)) override { // All Field3Ds require twist-shift, because all are effectively field-aligned, but // allow twist-shift to be turned off by twist_shift_enabled return twist_shift_enabled; @@ -230,7 +228,7 @@ public: // Twist-shift only if field-aligned if (ytype == YDirectionType::Aligned and not twist_shift_enabled) { throw BoutException("'twistshift = true' is required to communicate field-aligned " - "Field3Ds when using ShiftedMetric."); + "Field3Ds when using ShiftedMetric."); } return ytype == YDirectionType::Aligned; } diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index da87d6cb07..01af336d75 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -44,8 +44,8 @@ #include #include #include -#include -#include +#include +#include #if BOUT_HAS_PETSC @@ -166,7 +166,8 @@ public: Element(const Element& other) = default; Element(Vec* vector, int index) : petscVector(vector), petscIndex(index) { int status; - BOUT_OMP(critical) status = VecGetValues(*petscVector, 1, &petscIndex, &value); + BOUT_OMP(critical) + status = VecGetValues(*petscVector, 1, &petscIndex, &value); if (status != 0) { value = 0.; } @@ -235,7 +236,8 @@ public: #endif BoutReal value; int status; - BOUT_OMP(critical) status = VecGetValues(*get(), 1, &global, &value); + BOUT_OMP(critical) + status = VecGetValues(*get(), 1, &global, &value); if (status != 0) { throw BoutException("Error when getting element of a PETSc vector."); } @@ -329,8 +331,9 @@ public: // preallocating memory if requeted and possible. PetscMatrix(IndexerPtr indConverter, bool preallocate = true) : matrix(new Mat(), MatrixDeleter()), indexConverter(indConverter) { - const MPI_Comm comm = - std::is_same::value ? indConverter->getMesh()->getXcomm() : BoutComm::get(); + const MPI_Comm comm = std::is_same::value + ? indConverter->getMesh()->getXcomm() + : BoutComm::get(); pt = &indConverter->getMesh()->getCoordinates()->getParallelTransform(); const int size = indexConverter->size(); diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index 2e9019fafb..c3f63663a5 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -59,26 +59,29 @@ class Options; * The first instance which is created initialises PETSc * Keeps a count of the number of how many instances exist * When the last instance is destroyed it finalises PETSc. - */ + */ class PetscLib { public: /*! * Ensure that PETSc has been initialised */ explicit PetscLib(Options* opt = nullptr); - + /*! * Calls PetscFinalize when all PetscLib instances are destroyed - */ + */ ~PetscLib(); - + /*! * This is called once to set the command-line options. * Should be done early in the program, before any instances of * PetscLib are created. * The arguments will be passed to PetscInitialize() - */ - static void setArgs(int &c, char** &v) { pargc = &c; pargv = &v;} + */ + static void setArgs(int& c, char**& v) { + pargc = &c; + pargv = &v; + } /// Set options for a KSP linear solver that uses the options specific to this PetscLib, /// by setting an options prefix for the KSP, and adding that prefix to all the options @@ -95,16 +98,17 @@ public: /*! * Force cleanup. This will call PetscFinalize, printing a warning * if any instances of PetscLib still exist - */ - static void cleanup(); + */ + static void cleanup(); + private: - static int count; ///< How many instances? + static int count; ///< How many instances? static char help[]; ///< Help string - + // Command-line arguments static int* pargc; static char*** pargv; - + // Prefix for object-specific options std::string options_prefix; @@ -117,16 +121,18 @@ private: // Newer versions of PETSc define these symbols for testing library version // This is a re-implementation of the PETSc BSD-licensed code -#define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ - ( (PETSC_VERSION_MAJOR > MAJOR) || \ - ( (PETSC_VERSION_MAJOR == MAJOR) && ( (PETSC_VERSION_MINOR > MINOR) || \ - ( (PETSC_VERSION_MINOR == MINOR) && (PETSC_VERSION_SUBMINOR >= SUBMINOR))))) +#define PETSC_VERSION_GE(MAJOR, MINOR, SUBMINOR) \ + ((PETSC_VERSION_MAJOR > MAJOR) \ + || ((PETSC_VERSION_MAJOR == MAJOR) \ + && ((PETSC_VERSION_MINOR > MINOR) \ + || ((PETSC_VERSION_MINOR == MINOR) \ + && (PETSC_VERSION_SUBMINOR >= SUBMINOR))))) #endif // PETSC_VERSION_GE #else // BOUT_HAS_PETSC -#include "unused.hxx" +#include "bout/unused.hxx" // PETSc not available, so KSP not already defined. KSP should never be called, so forward // declaration OK here. @@ -137,9 +143,9 @@ class PetscLib { public: explicit PetscLib(Options* UNUSED(opt) = nullptr) {} ~PetscLib() {} - - static void setArgs(int &UNUSED(c), char** &UNUSED(v)) {} - + + static void setArgs(int& UNUSED(c), char**& UNUSED(v)) {} + void setOptionsFromInputFile(KSP& UNUSED(ksp)) {} void setOptionsFromInputFile(SNES& UNUSED(snes)) {} @@ -148,5 +154,4 @@ public: #endif // BOUT_HAS_PETSC - #endif // __PETSCLIB_H__ diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index b0ec535008..f17282b38b 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -37,13 +37,13 @@ class PhysicsModel; #ifndef __PHYSICS_MODEL_H__ #define __PHYSICS_MODEL_H__ -#include "bout.hxx" -#include "msg_stack.hxx" -#include "options.hxx" -#include "options_netcdf.hxx" +#include "bout/bout.hxx" +#include "bout/msg_stack.hxx" +#include "bout/options.hxx" +#include "bout/options_netcdf.hxx" #include "solver.hxx" -#include "unused.hxx" -#include "utils.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/macro_for_each.hxx" #include "bout/sys/variant.hxx" @@ -138,7 +138,7 @@ public: : mesh(mesh_), output_enabled(output_enabled_), restart_enabled(restart_enabled_) {} virtual ~PhysicsModel() = default; - + Mesh* mesh{nullptr}; bout::DataFileFacade dump{}; bout::DataFileFacade restart{}; @@ -169,12 +169,12 @@ public: * Returns a flag: 0 indicates success, non-zero an error flag */ int runRHS(BoutReal time, bool linear = false); - + /*! * True if this model uses split operators - */ + */ bool splitOperator(); - + /*! * Run the convective (usually explicit) part of the model * @@ -183,7 +183,7 @@ public: * */ int runConvective(BoutReal time, bool linear = false); - + /*! * Run the diffusive (usually implicit) part of the model * @@ -192,12 +192,12 @@ public: * */ int runDiffusive(BoutReal time, bool linear = false); - + /*! * True if a preconditioner has been defined - */ + */ bool hasPrecon(); - + /*! * Run the preconditioner. The system state should be in the * evolving variables, and the vector to be solved in the ddt() variables. @@ -207,20 +207,22 @@ public: * */ int runPrecon(BoutReal t, BoutReal gamma, BoutReal delta); - + /*! * True if a Jacobian function has been defined */ bool hasJacobian(); - + /*! * Run the Jacobian-vector multiplication function * * Note: this is usually only called by the Solver - */ + */ int runJacobian(BoutReal t); - int runTimestepMonitor(BoutReal simtime, BoutReal dt) {return timestepMonitor(simtime, dt);} + int runTimestepMonitor(BoutReal simtime, BoutReal dt) { + return timestepMonitor(simtime, dt); + } /// Write \p options to `output_file` void writeOutputFile(const Options& options); @@ -232,7 +234,6 @@ public: void finishOutputTimestep() const; protected: - // The init and rhs functions are implemented by user code to specify problem /*! * @brief This function is called once by the solver at the start of a simulation. @@ -243,13 +244,13 @@ protected: * be evolved should be specified. */ virtual int init(bool restarting) = 0; - + /// Post-initialise. This reads the restart file /// /// @param[in] restarting If true, will load state from restart file /// virtual int postInit(bool restarting); - + /*! * @brief This function is called by the time integration solver * at least once per time step @@ -265,8 +266,8 @@ protected: * which is set to true when the rhs() function can be * linearised. This is used in e.g. linear iterative solves. */ - virtual int rhs(BoutReal UNUSED(t)) {return 1;} - virtual int rhs(BoutReal t, bool UNUSED(linear)) {return rhs(t);} + virtual int rhs(BoutReal UNUSED(t)) { return 1; } + virtual int rhs(BoutReal t, bool UNUSED(linear)) { return rhs(t); } /// Output additional variables other than the evolving variables virtual void outputVars(Options& options); @@ -283,30 +284,29 @@ protected: and the sum used to evolve the system: rhs() = convective() + diffusive() */ - virtual int convective(BoutReal UNUSED(t)) {return 1;} + virtual int convective(BoutReal UNUSED(t)) { return 1; } virtual int convective(BoutReal t, bool UNUSED(linear)) { return convective(t); } - virtual int diffusive(BoutReal UNUSED(t)) {return 1;} + virtual int diffusive(BoutReal UNUSED(t)) { return 1; } virtual int diffusive(BoutReal t, bool UNUSED(linear)) { return diffusive(t); } - + /*! * Implemented by user code to monitor solution at output times */ - virtual int outputMonitor(BoutReal UNUSED(simtime), int UNUSED(iter), int UNUSED(NOUT)) { + virtual int outputMonitor(BoutReal UNUSED(simtime), int UNUSED(iter), + int UNUSED(NOUT)) { return 0; } - + /*! * Timestep monitor. If enabled by setting solver:monitor_timestep=true * then this function is called every internal timestep. */ - virtual int timestepMonitor(BoutReal UNUSED(simtime), BoutReal UNUSED(dt)) {return 0;} - - + virtual int timestepMonitor(BoutReal UNUSED(simtime), BoutReal UNUSED(dt)) { return 0; } // Functions called by the user to set callback functions /// Specify that this model is split into a convective and diffusive part - void setSplitOperator(bool split=true) {splitop = split;} + void setSplitOperator(bool split = true) { splitop = split; } /// Specify a preconditioner function void setPrecon(preconfunc pset) { userprecon = pset; } @@ -337,10 +337,10 @@ protected: * To evolve the state, the solver will set \p var, and the user-supplied * rhs() function should calculate ddt(var). */ - void bout_solve(Field2D &var, const char *name, const std::string& description=""); - void bout_solve(Field3D &var, const char *name, const std::string& description=""); - void bout_solve(Vector2D &var, const char *name, const std::string& description=""); - void bout_solve(Vector3D &var, const char *name, const std::string& description=""); + void bout_solve(Field2D& var, const char* name, const std::string& description = ""); + void bout_solve(Field3D& var, const char* name, const std::string& description = ""); + void bout_solve(Vector2D& var, const char* name, const std::string& description = ""); + void bout_solve(Vector3D& var, const char* name, const std::string& description = ""); /// Helper function for reading from restart_options Options& readFromRestartFile(const std::string& name) { return restart_options[name]; } @@ -359,8 +359,8 @@ protected: * @param[in] F_var The control variable, which the user will set * @param[in] name The name to use for initialisation and output * - */ - bool bout_constrain(Field3D &var, Field3D &F_var, const char *name); + */ + bool bout_constrain(Field3D& var, Field3D& F_var, const char* name); /*! * Monitor class for PhysicsModel @@ -368,11 +368,11 @@ protected: class PhysicsModelMonitor : public Monitor { public: PhysicsModelMonitor() = delete; - PhysicsModelMonitor(PhysicsModel *model) : model(model) {} + PhysicsModelMonitor(PhysicsModel* model) : model(model) {} int call(Solver* solver, BoutReal simtime, int iter, int nout) override; private: - PhysicsModel *model; + PhysicsModel* model; }; private: @@ -442,35 +442,45 @@ private: /// Macro to replace solver->add, passing variable name #define SOLVE_FOR1(var) solver->add(var, #var); -#define SOLVE_FOR2(var1, var2) { \ - solver->add(var1, #var1); \ - solver->add(var2, #var2);} -#define SOLVE_FOR3(var1, var2, var3) { \ - solver->add(var1, #var1); \ - solver->add(var2, #var2); \ - solver->add(var3, #var3);} -#define SOLVE_FOR4(var1, var2, var3, var4) { \ - solver->add(var1, #var1); \ - solver->add(var2, #var2); \ - solver->add(var3, #var3); \ - solver->add(var4, #var4);} -#define SOLVE_FOR5(var1, var2, var3, var4, var5) { \ - solver->add(var1, #var1); \ - solver->add(var2, #var2); \ - solver->add(var3, #var3); \ - solver->add(var4, #var4); \ - solver->add(var5, #var5);} -#define SOLVE_FOR6(var1, var2, var3, var4, var5, var6) { \ - solver->add(var1, #var1); \ - solver->add(var2, #var2); \ - solver->add(var3, #var3); \ - solver->add(var4, #var4); \ - solver->add(var5, #var5); \ - solver->add(var6, #var6);} +#define SOLVE_FOR2(var1, var2) \ + { \ + solver->add(var1, #var1); \ + solver->add(var2, #var2); \ + } +#define SOLVE_FOR3(var1, var2, var3) \ + { \ + solver->add(var1, #var1); \ + solver->add(var2, #var2); \ + solver->add(var3, #var3); \ + } +#define SOLVE_FOR4(var1, var2, var3, var4) \ + { \ + solver->add(var1, #var1); \ + solver->add(var2, #var2); \ + solver->add(var3, #var3); \ + solver->add(var4, #var4); \ + } +#define SOLVE_FOR5(var1, var2, var3, var4, var5) \ + { \ + solver->add(var1, #var1); \ + solver->add(var2, #var2); \ + solver->add(var3, #var3); \ + solver->add(var4, #var4); \ + solver->add(var5, #var5); \ + } +#define SOLVE_FOR6(var1, var2, var3, var4, var5, var6) \ + { \ + solver->add(var1, #var1); \ + solver->add(var2, #var2); \ + solver->add(var3, #var3); \ + solver->add(var4, #var4); \ + solver->add(var5, #var5); \ + solver->add(var6, #var6); \ + } /// Add fields to the solver. /// This should accept up to ten arguments -#define SOLVE_FOR(...) \ +#define SOLVE_FOR(...) \ { MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__) } /// Write this variable once to the grid file @@ -556,4 +566,3 @@ private: { MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__) } #endif // __PHYSICS_MODEL_H__ - diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx index b9f6913459..db19573f02 100644 --- a/include/bout/rajalib.hxx +++ b/include/bout/rajalib.hxx @@ -136,7 +136,7 @@ private: /// If no RAJA, BOUT_FOR_RAJA reverts to BOUT_FOR /// Note: Redundant ';' after closing brace should be ignored by compiler /// Ignores any additional arguments -#define BOUT_FOR_RAJA(index, region, ...) BOUT_FOR(index, region) +#define BOUT_FOR_RAJA(index, region, ...) BOUT_FOR (index, region) /// If not using RAJA, CAPTURE doesn't do anything #define CAPTURE(...) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index f84c058814..1ff118bd56 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -48,7 +48,7 @@ #include #include -#include "bout_types.hxx" +#include "bout/bout_types.hxx" #include "bout/assert.hxx" #include "bout/openmpwrap.hxx" @@ -109,16 +109,16 @@ /// } // -#define BOUT_FOR_SERIAL(index, region) \ - for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend(); \ - block < end; ++block) \ +#define BOUT_FOR_SERIAL(index, region) \ + for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend(); \ + block < end; ++block) \ for (auto index = block->first; index < block->second; ++index) #if BOUT_USE_OPENMP -#define BOUT_FOR_OMP(index, region, omp_pragmas) \ - BOUT_OMP(omp_pragmas) \ - for (auto block = region.getBlocks().cbegin(); block < region.getBlocks().cend(); \ - ++block) \ +#define BOUT_FOR_OMP(index, region, omp_pragmas) \ + BOUT_OMP(omp_pragmas) \ + for (auto block = region.getBlocks().cbegin(); block < region.getBlocks().cend(); \ + ++block) \ for (auto index = block->first; index < block->second; ++index) #else // No OpenMP, so fall back to slightly more efficient serial form @@ -163,13 +163,13 @@ struct SpecificInd { SpecificInd() = default; SpecificInd(int i, int ny, int nz) : ind(i), ny(ny), nz(nz){}; - explicit SpecificInd(int i) : ind(i) {}; + explicit SpecificInd(int i) : ind(i){}; /// Allow explicit conversion to an int explicit operator int() const { return ind; } /// Pre-increment operator - SpecificInd &operator++() { + SpecificInd& operator++() { ++ind; return *this; } @@ -182,7 +182,7 @@ struct SpecificInd { } /// Pre-decrement operator - SpecificInd &operator--() { + SpecificInd& operator--() { --ind; return *this; } @@ -195,23 +195,23 @@ struct SpecificInd { } /// In-place addition - SpecificInd &operator+=(SpecificInd n) { + SpecificInd& operator+=(SpecificInd n) { ind += n.ind; return *this; } - SpecificInd &operator+=(int n) { + SpecificInd& operator+=(int n) { ind += n; return *this; } /// In-place subtraction - SpecificInd &operator-=(SpecificInd n) { + SpecificInd& operator-=(SpecificInd n) { ind -= n.ind; return *this; } - SpecificInd &operator-=(int n) { + SpecificInd& operator-=(int n) { ind -= n; return *this; } @@ -230,19 +230,19 @@ struct SpecificInd { /// Templated routine to return index.?p(offset), where `?` is one of {x,y,z} /// and is determined by the `dir` template argument. The offset corresponds /// to the `dd` template argument. - template - const inline SpecificInd plus() const{ + template + const inline SpecificInd plus() const { static_assert(dir == DIRECTION::X || dir == DIRECTION::Y || dir == DIRECTION::Z || dir == DIRECTION::YAligned || dir == DIRECTION::YOrthogonal, "Unhandled DIRECTION in SpecificInd::plus"); - switch(dir) { - case(DIRECTION::X): + switch (dir) { + case (DIRECTION::X): return xp(dd); - case(DIRECTION::Y): - case(DIRECTION::YAligned): - case(DIRECTION::YOrthogonal): + case (DIRECTION::Y): + case (DIRECTION::YAligned): + case (DIRECTION::YOrthogonal): return yp(dd); - case(DIRECTION::Z): + case (DIRECTION::Z): return zp(dd); } } @@ -250,19 +250,19 @@ struct SpecificInd { /// Templated routine to return index.?m(offset), where `?` is one of {x,y,z} /// and is determined by the `dir` template argument. The offset corresponds /// to the `dd` template argument. - template - const inline SpecificInd minus() const{ + template + const inline SpecificInd minus() const { static_assert(dir == DIRECTION::X || dir == DIRECTION::Y || dir == DIRECTION::Z || dir == DIRECTION::YAligned || dir == DIRECTION::YOrthogonal, "Unhandled DIRECTION in SpecificInd::minus"); - switch(dir) { - case(DIRECTION::X): + switch (dir) { + case (DIRECTION::X): return xm(dd); - case(DIRECTION::Y): - case(DIRECTION::YAligned): - case(DIRECTION::YOrthogonal): + case (DIRECTION::Y): + case (DIRECTION::YAligned): + case (DIRECTION::YOrthogonal): return ym(dd); - case(DIRECTION::Z): + case (DIRECTION::Z): return zm(dd); } } @@ -285,7 +285,7 @@ struct SpecificInd { /// The index one point +1 in z. Wraps around zend to zstart /// An alternative, non-branching calculation is : /// ind + dz - nz * ((ind + dz) / nz - ind / nz) - /// but this appears no faster (and perhaps slower). + /// but this appears no faster (and perhaps slower). const inline SpecificInd zp(int dz = 1) const { ASSERT3(dz >= 0); dz = dz <= nz ? dz : dz % nz; //Fix in case dz > nz, if not force it to be in range @@ -317,97 +317,108 @@ struct SpecificInd { }; /// Relational operators -template -inline bool operator==(const SpecificInd &lhs, const SpecificInd &rhs) { +template +inline bool operator==(const SpecificInd& lhs, const SpecificInd& rhs) { return lhs.ind == rhs.ind; } -template -inline bool operator!=(const SpecificInd &lhs, const SpecificInd &rhs) { +template +inline bool operator!=(const SpecificInd& lhs, const SpecificInd& rhs) { return !operator==(lhs, rhs); } -template -inline bool operator<(const SpecificInd &lhs, const SpecificInd &rhs) { +template +inline bool operator<(const SpecificInd& lhs, const SpecificInd& rhs) { return lhs.ind < rhs.ind; } -template -inline bool operator>(const SpecificInd &lhs, const SpecificInd &rhs) { +template +inline bool operator>(const SpecificInd& lhs, const SpecificInd& rhs) { return operator<(rhs, lhs); } -template -inline bool operator>=(const SpecificInd &lhs, const SpecificInd &rhs) { +template +inline bool operator>=(const SpecificInd& lhs, const SpecificInd& rhs) { return !operator<(lhs, rhs); } -template -inline bool operator<=(const SpecificInd &lhs, const SpecificInd &rhs) { +template +inline bool operator<=(const SpecificInd& lhs, const SpecificInd& rhs) { return !operator>(lhs, rhs); } /// Arithmetic operators with integers -template -inline SpecificInd operator+(SpecificInd lhs, const SpecificInd &rhs) { return lhs += rhs; } +template +inline SpecificInd operator+(SpecificInd lhs, const SpecificInd& rhs) { + return lhs += rhs; +} -template -inline SpecificInd operator+(SpecificInd lhs, int n) { return lhs += SpecificInd(n); } +template +inline SpecificInd operator+(SpecificInd lhs, int n) { + return lhs += SpecificInd(n); +} -template -inline SpecificInd operator+(int n, SpecificInd rhs) { return rhs += SpecificInd(n); } +template +inline SpecificInd operator+(int n, SpecificInd rhs) { + return rhs += SpecificInd(n); +} -template -inline SpecificInd operator-(SpecificInd lhs, int n) { return lhs -= SpecificInd(n); } +template +inline SpecificInd operator-(SpecificInd lhs, int n) { + return lhs -= SpecificInd(n); +} -template -inline SpecificInd operator-(SpecificInd lhs, const SpecificInd &rhs) { return lhs -= rhs; } +template +inline SpecificInd operator-(SpecificInd lhs, const SpecificInd& rhs) { + return lhs -= rhs; +} -/// Define aliases for global indices in 3D and 2D +/// Define aliases for global indices in 3D and 2D using Ind3D = SpecificInd; using Ind2D = SpecificInd; using IndPerp = SpecificInd; /// Get string representation of Ind3D inline const std::string toString(const Ind3D& i) { - return "(" + std::to_string(i.x()) + ", " - + std::to_string(i.y()) + ", " - + std::to_string(i.z()) + ")"; + return "(" + std::to_string(i.x()) + ", " + std::to_string(i.y()) + ", " + + std::to_string(i.z()) + ")"; } /// Get string representation of Ind2D inline const std::string toString(const Ind2D& i) { - return "(" + std::to_string(i.x()) + ", " - + std::to_string(i.y()) + ")"; + return "(" + std::to_string(i.x()) + ", " + std::to_string(i.y()) + ")"; } /// Get string representation of IndPerp inline const std::string toString(const IndPerp& i) { - return "(" + std::to_string(i.x()) + ", " - + std::to_string(i.z()) + ")"; + return "(" + std::to_string(i.x()) + ", " + std::to_string(i.z()) + ")"; } /// Structure to hold various derived "statistics" from a particular region struct RegionStats { - int numBlocks = 0; ///< How many blocks - int minBlockSize = 0; ///< Size of smallest block - int numMinBlocks = 0; ///< Number of blocks with min size - int maxBlockSize = 0; ///< Size of largest block - int numMaxBlocks = 0; ///< Number of blocks with max size - int numSmallBlocks = 0; ///< Number of "small" blocks, for definition see Region::getStats - BoutReal maxImbalance = 0; ///< Ratio of largest block to smallest + int numBlocks = 0; ///< How many blocks + int minBlockSize = 0; ///< Size of smallest block + int numMinBlocks = 0; ///< Number of blocks with min size + int maxBlockSize = 0; ///< Size of largest block + int numMaxBlocks = 0; ///< Number of blocks with max size + int numSmallBlocks = + 0; ///< Number of "small" blocks, for definition see Region::getStats + BoutReal maxImbalance = 0; ///< Ratio of largest block to smallest }; /// Provide an easy way to report a Region's statistics -inline std::ostream &operator<<(std::ostream &out, const RegionStats &stats){ - if ( stats.numBlocks == 0 ) { +inline std::ostream& operator<<(std::ostream& out, const RegionStats& stats) { + if (stats.numBlocks == 0) { out << "Empty"; return out; } - out << "Total blocks : "<< stats.numBlocks; - out << ", " << "min(count)/max(count) :"; + out << "Total blocks : " << stats.numBlocks; + out << ", " + << "min(count)/max(count) :"; out << " " << stats.minBlockSize << " (" << stats.numMinBlocks << ")/"; out << " " << stats.maxBlockSize << " (" << stats.numMaxBlocks << ")"; - out << ", " << "Max imbalance : " << stats.maxImbalance; - out << ", " << "Small block count : " << stats.numSmallBlocks; + out << ", " + << "Max imbalance : " << stats.maxImbalance; + out << ", " + << "Small block count : " << stats.numSmallBlocks; return out; } @@ -466,10 +477,12 @@ inline std::ostream &operator<<(std::ostream &out, const RegionStats &stats){ /// BOUT_FOR_SERIAL(i, region) { /// max = f[i] > max ? f[i] : max; /// } -template class Region { +template +class Region { // Following prevents a Region being created with anything other // than Ind2D, Ind3D or IndPerp as template type - static_assert(std::is_base_of::value || std::is_base_of::value || std::is_base_of::value, + static_assert(std::is_base_of::value || std::is_base_of::value + || std::is_base_of::value, "Region must be templated with one of IndPerp, Ind2D or Ind3D"); public: @@ -508,44 +521,49 @@ public: : ny(ny), nz(nz) { #if CHECK > 1 if (std::is_base_of::value) { - if (nz != 1) + if (nz != 1) { throw BoutException( "Trying to make Region with nz = {:d}, but expected nz = 1", nz); - if (zstart != 0) + } + if (zstart != 0) { throw BoutException( "Trying to make Region with zstart = {:d}, but expected zstart = 0", zstart); - if (zstart != 0) + } + if (zstart != 0) { throw BoutException( "Trying to make Region with zend = {:d}, but expected zend = 0", zend); + } } if (std::is_base_of::value) { - if (ny != 1) + if (ny != 1) { throw BoutException( "Trying to make Region with ny = {:d}, but expected ny = 1", ny); - if (ystart != 0) + } + if (ystart != 0) { throw BoutException( "Trying to make Region with ystart = {:d}, but expected ystart = 0", ystart); - if (ystart != 0) + } + if (ystart != 0) { throw BoutException( "Trying to make Region with yend = {:d}, but expected yend = 0", yend); + } } #endif - + indices = createRegionIndices(xstart, xend, ystart, yend, zstart, zend, ny, nz); blocks = getContiguousBlocks(maxregionblocksize); }; - Region(RegionIndices &indices, int maxregionblocksize = MAXREGIONBLOCKSIZE) : indices(indices) { + Region(RegionIndices& indices, int maxregionblocksize = MAXREGIONBLOCKSIZE) + : indices(indices) { blocks = getContiguousBlocks(maxregionblocksize); }; - Region(ContiguousBlocks &blocks) : blocks(blocks) { - indices = getRegionIndices(); - }; + Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; /// Destructor ~Region() = default; @@ -562,24 +580,24 @@ public: typename RegionIndices::const_iterator end() const { return std::end(indices); }; typename RegionIndices::const_iterator cend() const { return indices.cend(); }; - const ContiguousBlocks &getBlocks() const { return blocks; }; - const RegionIndices &getIndices() const { return indices; }; + const ContiguousBlocks& getBlocks() const { return blocks; }; + const RegionIndices& getIndices() const { return indices; }; /// Set the indices and ensure blocks updated - void setIndices (RegionIndices &indicesIn, int maxregionblocksize = MAXREGIONBLOCKSIZE) { + void setIndices(RegionIndices& indicesIn, int maxregionblocksize = MAXREGIONBLOCKSIZE) { indices = indicesIn; blocks = getContiguousBlocks(maxregionblocksize); }; /// Set the blocks and ensure indices updated - void setBlocks (ContiguousBlocks &blocksIn) { + void setBlocks(ContiguousBlocks& blocksIn) { blocks = blocksIn; indices = getRegionIndices(); }; /// Return a new Region that has the same indices as this one but /// ensures the indices are sorted. - Region asSorted(){ + Region asSorted() { auto sortedIndices = getIndices(); std::sort(std::begin(sortedIndices), std::end(sortedIndices)); return Region(sortedIndices); @@ -615,7 +633,7 @@ public: /// Return a new region equivalent to *this but with indices contained /// in mask Region removed - Region mask(const Region & maskRegion){ + Region mask(const Region& maskRegion) { // Get mask indices and sort as we're going to be searching through // this vector so if it's sorted we can be more efficient auto maskIndices = maskRegion.getIndices(); @@ -627,16 +645,14 @@ public: // Lambda that returns true/false depending if the passed value is in maskIndices // With C++14 T can be auto instead - auto isInVector = [&](T val){ + auto isInVector = [&](T val) { return std::binary_search(std::begin(maskIndices), std::end(maskIndices), val); }; // Erase elements of currentIndices that are in maskIndices currentIndices.erase( - std::remove_if(std::begin(currentIndices), std::end(currentIndices), - isInVector), - std::end(currentIndices) - ); + std::remove_if(std::begin(currentIndices), std::end(currentIndices), isInVector), + std::end(currentIndices)); // Update indices setIndices(currentIndices); @@ -674,13 +690,13 @@ public: } /// Accumulate operator - Region & operator+=(const Region &rhs){ + Region& operator+=(const Region& rhs) { (*this) = (*this) + rhs; return *this; } /// Offset all indices by fixed value - Region &offset(int offset) { + Region& offset(int offset) { // Exit early if possible if (offset == 0) { return *this; @@ -704,14 +720,14 @@ public: /// directions (e.g. z). For example for shift = 1, period = mesh->LocalNz /// we would find the zplus indices. For shift = mesh->LocalNy*mesh->LocalNz, /// period = mesh->LocalNx*mesh->LocalNy*mesh->LocalNz we find xplus indices. - Region & periodicShift(int shift, int period){ + Region& periodicShift(int shift, int period) { // Exit early if possible - if ( shift == 0 || period == 1 ){ + if (shift == 0 || period == 1) { return *this; } // Handle -ve shifts as a +ve shift - if ( shift < 0 ){ - return periodicShift(period+shift, period); + if (shift < 0) { + return periodicShift(period + shift, period); } auto newInd = getIndices(); @@ -719,7 +735,7 @@ public: // localPos = index + shift % period; // Find the shifted position within the period // globalPos = (index/period) * period; // Find which period block we're in // newIndex = globalPos + localPos; - for (unsigned int i = 0; i < newInd.size(); i++){ + for (unsigned int i = 0; i < newInd.size(); i++) { int index = newInd[i].ind; int whichBlock = index / period; newInd[i].ind = ((index + shift) % period) + period * whichBlock; @@ -731,41 +747,45 @@ public: } /// Number of indices (possibly repeated) - unsigned int size() const { - return indices.size(); - } + unsigned int size() const { return indices.size(); } /// Returns a RegionStats struct desribing the region RegionStats getStats() const { RegionStats result; result.numBlocks = blocks.size(); - if ( result.numBlocks == 0 ) return result; - + if (result.numBlocks == 0) { + return result; + } + std::vector blockSizes(result.numBlocks); - + // Get the size of each block using lambda to calculate size std::transform(std::begin(blocks), std::end(blocks), std::begin(blockSizes), - [](const ContiguousBlock &a) { return a.second.ind - a.first.ind;}); + [](const ContiguousBlock& a) { return a.second.ind - a.first.ind; }); auto minMaxSize = std::minmax_element(std::begin(blockSizes), std::end(blockSizes)); - result.minBlockSize = *(minMaxSize.first); //Note have to derefence to get actual value - result.numMinBlocks = std::count(std::begin(blockSizes), std::end(blockSizes), result.minBlockSize); + result.minBlockSize = + *(minMaxSize.first); //Note have to derefence to get actual value + result.numMinBlocks = + std::count(std::begin(blockSizes), std::end(blockSizes), result.minBlockSize); - result.maxBlockSize = *(minMaxSize.second); //Note have to derefence to get actual value - result.numMaxBlocks = std::count(std::begin(blockSizes), std::end(blockSizes), result.maxBlockSize); + result.maxBlockSize = + *(minMaxSize.second); //Note have to derefence to get actual value + result.numMaxBlocks = + std::count(std::begin(blockSizes), std::end(blockSizes), result.maxBlockSize); - - result.maxImbalance = static_cast(result.maxBlockSize)/static_cast(result.minBlockSize); + result.maxImbalance = static_cast(result.maxBlockSize) + / static_cast(result.minBlockSize); // Count the number of small blocks, defined as blocks less than smallSizeFrac of maxBlockSize const BoutReal smallSizeFrac = 0.5; result.numSmallBlocks = - std::count_if(std::begin(blockSizes), std::end(blockSizes), - [&result, smallSizeFrac](int theSize) { - return theSize < smallSizeFrac * result.maxBlockSize; - }); + std::count_if(std::begin(blockSizes), std::end(blockSizes), + [&result, smallSizeFrac](int theSize) { + return theSize < smallSizeFrac * result.maxBlockSize; + }); return result; } @@ -787,9 +807,7 @@ private: inline RegionIndices createRegionIndices(int xstart, int xend, int ystart, int yend, int zstart, int zend, int ny, int nz) { - if ((xend + 1 <= xstart) || - (yend + 1 <= ystart) || - (zend + 1 <= zstart)) { + if ((xend + 1 <= xstart) || (yend + 1 <= ystart) || (zend + 1 <= zstart)) { // Empty region return {}; } @@ -800,7 +818,9 @@ private: int len = (xend - xstart + 1) * (yend - ystart + 1) * (zend - zstart + 1); ASSERT1(len > 0); // Guard against invalid length ranges - if (len <= 0 ) return {}; + if (len <= 0) { + return {}; + } RegionIndices region(len, {-1, ny, nz}); @@ -829,13 +849,12 @@ private: return region; } - /// Returns a vector of all contiguous blocks contained in the passed region. /// Limits the maximum size of any contiguous block to maxBlockSize. /// A contiguous block is described by the inclusive start and the exclusive end /// of the contiguous block. ContiguousBlocks getContiguousBlocks(int maxregionblocksize) const { - ASSERT1(maxregionblocksize>0); + ASSERT1(maxregionblocksize > 0); const int npoints = indices.size(); ContiguousBlocks result; int index = 0; // Index within vector of indices @@ -858,7 +877,7 @@ private: } // This contains the inclusive end currently - T lastIndex = indices[index-1]; + T lastIndex = indices[index - 1]; // Increase the index stored by one to get exclusive end lastIndex++; // Add pair to output, denotes inclusive start and exclusive end @@ -868,34 +887,31 @@ private: return result; } - /// Constructs the vector of indices from the stored blocks information RegionIndices getRegionIndices() { RegionIndices result; // This has to be serial unless we can make result large enough in advance // otherwise there will be a race between threads to extend the vector - BOUT_FOR_SERIAL(curInd, (*this)) { - result.push_back(curInd); - } + BOUT_FOR_SERIAL(curInd, (*this)) { result.push_back(curInd); } return result; } }; /// Return a new region with sorted indices -template -Region sort(Region ®ion) { +template +Region sort(Region& region) { return region.asSorted(); } /// Return a new region with unique indices -template -Region unique(Region ®ion) { +template +Region unique(Region& region) { return region.asUnique(); } /// Return a masked version of a region -template -Region mask(const Region ®ion, const Region &mask) { +template +Region mask(const Region& region, const Region& mask) { auto result = region; return result.mask(mask); } @@ -911,14 +927,14 @@ Region getIntersection(const Region& region, const Region& otherRegion) /// This doesn't attempt to avoid duplicate elements or enforce /// any sorting etc. but could be done if desired. /// - -/// Addition is currently simple and just extends. Probably mostly ok +/// Addition is currently simple and just extends. Probably mostly ok /// but we could seek to remove duplicate points. Note we do /// want to allow duplicate points (one reason we use vector and /// not set) but what if we add a region that has some duplicates? /// We could retain them but common usage would probably not want /// the duplicates. -template -Region operator+(const Region &lhs, const Region &rhs){ +template +Region operator+(const Region& lhs, const Region& rhs) { auto indices = lhs.getIndices(); // Indices is a copy of the indices auto indicesRhs = rhs.getIndices(); indices.insert(std::end(indices), std::begin(indicesRhs), std::end(indicesRhs)); @@ -927,15 +943,15 @@ Region operator+(const Region &lhs, const Region &rhs){ /// Returns a new region based on input but with indices offset by /// a constant -template -Region offset(const Region ®ion, int offset){ +template +Region offset(const Region& region, int offset) { auto result = region; return result.offset(offset); } /// Return the number of indices in a Region -template -unsigned int size(const Region ®ion){ +template +unsigned int size(const Region& region) { return region.size(); } diff --git a/include/bout/rkscheme.hxx b/include/bout/rkscheme.hxx index 822e67fc10..f4e5959aff 100644 --- a/include/bout/rkscheme.hxx +++ b/include/bout/rkscheme.hxx @@ -35,9 +35,9 @@ class RKScheme; #ifndef __RKSCHEME_H__ #define __RKSCHEME_H__ -#include -#include #include "bout/generic_factory.hxx" +#include +#include #include #include @@ -75,26 +75,27 @@ public: void init(int nlocalIn, int neqIn, bool adaptiveIn, BoutReal atolIn, BoutReal rtolIn); /// Get the time at given stage - BoutReal setCurTime(BoutReal timeIn,BoutReal dt,int curStage); + BoutReal setCurTime(BoutReal timeIn, BoutReal dt, int curStage); /// Get the state vector at given stage - virtual void setCurState(const Array &start, Array &out,int curStage, - BoutReal dt); + virtual void setCurState(const Array& start, Array& out, + int curStage, BoutReal dt); /// Calculate the output state and return the error estimate (if adaptive) - virtual BoutReal setOutputStates(const Array &start,BoutReal dt, Array &resultFollow); + virtual BoutReal setOutputStates(const Array& start, BoutReal dt, + Array& resultFollow); /// Update the timestep - virtual BoutReal updateTimestep(BoutReal dt,BoutReal err); + virtual BoutReal updateTimestep(BoutReal dt, BoutReal err); /// Returns the string name for the given scheme - virtual std::string getType(){return label;}; + virtual std::string getType() { return label; }; /// Returns the number of stages for the current scheme - int getStageCount(){return numStages;}; + int getStageCount() { return numStages; }; /// Returns the number of orders for the current scheme - int getNumOrders(){return numOrders;}; + int getNumOrders() { return numOrders; }; /// The intermediate stages Matrix steps; diff --git a/include/bout/rvec.hxx b/include/bout/rvec.hxx index 5723c7372e..0b611d64bf 100644 --- a/include/bout/rvec.hxx +++ b/include/bout/rvec.hxx @@ -3,7 +3,7 @@ #ifndef __RVEC_H__ #define __RVEC_H__ -#include +#include #include using rvec = std::vector; diff --git a/include/bout/scorepwrapper.hxx b/include/bout/scorepwrapper.hxx index db83ff3901..210d48e49f 100644 --- a/include/bout/scorepwrapper.hxx +++ b/include/bout/scorepwrapper.hxx @@ -3,8 +3,8 @@ #include "bout/build_config.hxx" -#include -#include "msg_stack.hxx" +#include "bout/msg_stack.hxx" +#include #if BOUT_HAS_SCOREP #include @@ -19,7 +19,7 @@ /// The scorep call is identical for all levels, so just define it here. /// If we don't have scorep support then just define a null function #if BOUT_HAS_SCOREP -#define SCOREP_BASE_CALL(...) \ +#define SCOREP_BASE_CALL(...) \ SCOREP_USER_REGION(__thefunc__, SCOREP_USER_REGION_TYPE_FUNCTION) #else #define SCOREP_BASE_CALL(...) @@ -52,7 +52,7 @@ /// Instrument a region with scorep #if BOUT_HAS_SCOREP -#define BOUT_SCOREP_REGION(...) \ +#define BOUT_SCOREP_REGION(...) \ SCOREP_USER_REGION(__VA_ARGS__, SCOREP_USER_REGION_TYPE_COMMON) #else #define BOUT_SCOREP_REGION(...) diff --git a/include/bout/slepclib.hxx b/include/bout/slepclib.hxx index ea8bd645cf..f6df9ce98c 100644 --- a/include/bout/slepclib.hxx +++ b/include/bout/slepclib.hxx @@ -55,36 +55,38 @@ class SlepcLib { public: SlepcLib(); ~SlepcLib(); - - static void setArgs(int &c, char** &v) { pargc = &c; pargv = &v;} - + + static void setArgs(int& c, char**& v) { + pargc = &c; + pargv = &v; + } + static void cleanup(); // Force cleanup private: - static int count; // How many instances? + static int count; // How many instances? static char help[]; // Help string - + // Command-line arguments static int* pargc; static char*** pargv; - + static PetscLogEvent USER_EVENT; }; #else // BOUT_HAS_SLEPC -#include "unused.hxx" +#include "bout/unused.hxx" class SlepcLib { public: SlepcLib() {} ~SlepcLib() {} - - static void setArgs(int &UNUSED(c), char** &UNUSED(v)) {} - + + static void setArgs(int& UNUSED(c), char**& UNUSED(v)) {} + static void cleanup() {} }; #endif // BOUT_HAS_SLEPC - #endif // __SLEPCLIB_H__ diff --git a/include/bout/smoothing.hxx b/include/bout/smoothing.hxx index 3d7d0abd3a..8a0d6e81b8 100644 --- a/include/bout/smoothing.hxx +++ b/include/bout/smoothing.hxx @@ -28,16 +28,16 @@ #ifndef __SMOOTHING_H__ #define __SMOOTHING_H__ -#include "field3d.hxx" +#include "bout/field3d.hxx" /// Smooth in X using simple 1-2-1 filter -const Field3D smooth_x(const Field3D &f); +const Field3D smooth_x(const Field3D& f); /// Smooth in Y using 1-2-1 filter -const Field3D smooth_y(const Field3D &f); +const Field3D smooth_y(const Field3D& f); /// Smooth using a stencil in X and Y -const Field3D smoothXY(const Field3D &f); +const Field3D smoothXY(const Field3D& f); /*! * Average over Y @@ -50,7 +50,7 @@ const Field3D smoothXY(const Field3D &f); * Assumes every processor has the same domain shape * */ -const Field2D averageY(const Field2D &f); +const Field2D averageY(const Field2D& f); /*! * Average in Y @@ -67,11 +67,11 @@ const Field2D averageY(const Field2D &f); * Assumes every processor has the same domain shape * */ -const Field3D averageY(const Field3D &f); +const Field3D averageY(const Field3D& f); /// Average over X -const Field2D averageX(const Field2D &f); -const Field3D averageX(const Field3D &f); +const Field2D averageX(const Field2D& f); +const Field3D averageX(const Field3D& f); /*! Volume integral of Field2D variable @@ -85,11 +85,11 @@ const Field3D averageX(const Field3D &f); Will only work if X communicator is constant in Y so no processor/branch cuts in X */ -BoutReal Average_XY(const Field2D &var); +BoutReal Average_XY(const Field2D& var); /// Volume integral of Field2D variable /// which uses Average_XY -BoutReal Vol_Integral(const Field2D &var); +BoutReal Vol_Integral(const Field2D& var); /// Nonlinear filtering to remove grid-scale noise in X /*! @@ -100,7 +100,7 @@ BoutReal Vol_Integral(const Field2D &var); "On the Suppression of Numerical Oscillations Using a Non-Linear Filter" */ -const Field3D nl_filter_x(const Field3D &f, BoutReal w=1.0); +const Field3D nl_filter_x(const Field3D& f, BoutReal w = 1.0); /// Nonlinear filtering to remove grid-scale noise in Y /*! @@ -111,7 +111,7 @@ const Field3D nl_filter_x(const Field3D &f, BoutReal w=1.0); "On the Suppression of Numerical Oscillations Using a Non-Linear Filter" */ -const Field3D nl_filter_y(const Field3D &f, BoutReal w=1.0); +const Field3D nl_filter_y(const Field3D& f, BoutReal w = 1.0); /// Nonlinear filtering to remove grid-scale noise in Z /*! @@ -122,7 +122,7 @@ const Field3D nl_filter_y(const Field3D &f, BoutReal w=1.0); "On the Suppression of Numerical Oscillations Using a Non-Linear Filter" */ -const Field3D nl_filter_z(const Field3D &f, BoutReal w=1.0); +const Field3D nl_filter_z(const Field3D& f, BoutReal w = 1.0); /// Nonlinear filtering to remove grid-scale noise in X,Y and Z /*! @@ -133,6 +133,6 @@ const Field3D nl_filter_z(const Field3D &f, BoutReal w=1.0); "On the Suppression of Numerical Oscillations Using a Non-Linear Filter" */ -const Field3D nl_filter(const Field3D &f, BoutReal w=1.0); +const Field3D nl_filter(const Field3D& f, BoutReal w = 1.0); #endif // __SMOOTHING_H__ diff --git a/include/bout/snb.hxx b/include/bout/snb.hxx index d58beb72b0..880477c09c 100644 --- a/include/bout/snb.hxx +++ b/include/bout/snb.hxx @@ -1,4 +1,4 @@ -#include "options.hxx" +#include "bout/options.hxx" #include "bout/invert_pardiv.hxx" #include diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index 42c04638eb..3862a24309 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -38,10 +38,10 @@ #include "bout/build_config.hxx" -#include "bout_types.hxx" -#include "boutexception.hxx" -#include "options.hxx" -#include "unused.hxx" +#include "bout/bout_types.hxx" +#include "bout/boutexception.hxx" +#include "bout/options.hxx" +#include "bout/unused.hxx" #include "bout/monitor.hxx" #include @@ -63,11 +63,11 @@ using Jacobian = int (*)(BoutReal t); /// Solution monitor, called each timestep using TimestepMonitorFunc = int (*)(Solver* solver, BoutReal simtime, BoutReal lastdt); -//#include "globals.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "vector2d.hxx" -#include "vector3d.hxx" +//#include "bout/globals.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" #include "bout/generic_factory.hxx" #define BOUT_NO_USING_NAMESPACE_BOUTGLOBALS @@ -92,10 +92,10 @@ constexpr auto SOLVERIMEXBDF2 = "imexbdf2"; constexpr auto SOLVERSNES = "snes"; constexpr auto SOLVERRKGENERIC = "rkgeneric"; -enum class SOLVER_VAR_OP {LOAD_VARS, LOAD_DERIVS, SET_ID, SAVE_VARS, SAVE_DERIVS}; +enum class SOLVER_VAR_OP { LOAD_VARS, LOAD_DERIVS, SET_ID, SAVE_VARS, SAVE_DERIVS }; /// A type to set where in the list monitors are added -enum class MonitorPosition {BACK, FRONT}; +enum class MonitorPosition { BACK, FRONT }; class SolverFactory : public Factory { public: @@ -250,10 +250,14 @@ public: /// Add a variable to be solved. This must be done in the /// initialisation stage, before the simulation starts. - virtual void add(Field2D& v, const std::string& name, const std::string& description = ""); - virtual void add(Field3D& v, const std::string& name, const std::string& description = ""); - virtual void add(Vector2D& v, const std::string& name, const std::string& description = ""); - virtual void add(Vector3D& v, const std::string& name, const std::string& description = ""); + virtual void add(Field2D& v, const std::string& name, + const std::string& description = ""); + virtual void add(Field3D& v, const std::string& name, + const std::string& description = ""); + virtual void add(Vector2D& v, const std::string& name, + const std::string& description = ""); + virtual void add(Vector3D& v, const std::string& name, + const std::string& description = ""); /// Returns true if constraints available virtual bool constraints() { return has_constraints; } @@ -377,13 +381,13 @@ protected: }; /// Does \p var represent field \p name? - template + template friend bool operator==(const VarStr& var, const std::string& name) { return var.name == name; } /// Does \p vars contain a field with \p name? - template + template bool contains(const std::vector>& vars, const std::string& name) { const auto in_vars = std::find(begin(vars), end(vars), name); return in_vars != end(vars); @@ -408,16 +412,16 @@ protected: /// Vectors of diagnostic variables to save std::vector> diagnostic_int; std::vector> diagnostic_BoutReal; - void add_int_diagnostic(int &i, const std::string &name, - const std::string &description = "") { + void add_int_diagnostic(int& i, const std::string& name, + const std::string& description = "") { VarStr v; v.var = &i; v.name = name; v.description = description; diagnostic_int.emplace_back(std::move(v)); }; - void add_BoutReal_diagnostic(BoutReal &r, const std::string &name, - const std::string &description = "") { + void add_BoutReal_diagnostic(BoutReal& r, const std::string& name, + const std::string& description = "") { VarStr v; v.var = &r; v.name = name; @@ -542,7 +546,7 @@ private: /// Should non-split physics models be treated as diffusive? bool is_nonsplit_model_diffusive{true}; - + /// Enable sources and solutions for Method of Manufactured Solutions bool mms{false}; /// Initialise variables to the manufactured solution diff --git a/include/bout/solverfactory.hxx b/include/bout/solverfactory.hxx index 56c7c12057..a628aed0c1 100644 --- a/include/bout/solverfactory.hxx +++ b/include/bout/solverfactory.hxx @@ -2,9 +2,9 @@ #define __SOLVER_FACTORY_H__ #ifndef _MSC_VER -# warning("Deprecated header: use #include instead") +#warning("Deprecated header: use #include instead") #else -# pragma message("Warning: deprecated header: use #include instead") +#pragma message("Warning: deprecated header: use #include instead") #endif #include diff --git a/include/bout/sourcex.hxx b/include/bout/sourcex.hxx index a08bf3457e..6727c8bcc9 100644 --- a/include/bout/sourcex.hxx +++ b/include/bout/sourcex.hxx @@ -5,17 +5,20 @@ #ifndef __MASKX_H__ #define __MASKX_H__ -#include "field3d.hxx" +#include "bout/field3d.hxx" // create a radial buffer zone to set jpar zero near radial boundary -const Field3D mask_x(const Field3D &f, bool BoutRealspace = true); -const Field2D source_tanhx(const Field2D &f,BoutReal swidth,BoutReal slength); -const Field2D source_expx2(const Field2D &f,BoutReal swidth,BoutReal slength); -const Field3D sink_tanhx(const Field2D &f0, const Field3D &f,BoutReal swidth,BoutReal slength, bool BoutRealspace = true); +const Field3D mask_x(const Field3D& f, bool BoutRealspace = true); +const Field2D source_tanhx(const Field2D& f, BoutReal swidth, BoutReal slength); +const Field2D source_expx2(const Field2D& f, BoutReal swidth, BoutReal slength); +const Field3D sink_tanhx(const Field2D& f0, const Field3D& f, BoutReal swidth, + BoutReal slength, bool BoutRealspace = true); -const Field3D sink_tanhxl(const Field2D &f0, const Field3D &f,BoutReal swidth,BoutReal slength, bool BoutRealspace = true); -const Field3D sink_tanhxr(const Field2D &f0, const Field3D &f,BoutReal swidth,BoutReal slength, bool BoutRealspace = true); +const Field3D sink_tanhxl(const Field2D& f0, const Field3D& f, BoutReal swidth, + BoutReal slength, bool BoutRealspace = true); +const Field3D sink_tanhxr(const Field2D& f0, const Field3D& f, BoutReal swidth, + BoutReal slength, bool BoutRealspace = true); -const Field3D buff_x(const Field3D &f, bool BoutRealspace = true); +const Field3D buff_x(const Field3D& f, bool BoutRealspace = true); #endif // __MASKX_H__ diff --git a/include/bout/stencils.hxx b/include/bout/stencils.hxx index fe3b8b1160..fa55e7dd2d 100644 --- a/include/bout/stencils.hxx +++ b/include/bout/stencils.hxx @@ -28,24 +28,24 @@ #ifndef __STENCILS_H__ #define __STENCILS_H__ -#include "bout_types.hxx" +#include "bout/bout_types.hxx" /// Defines a set of values in 1D in the neighbourhood of an index /// Used for calculating derivatives struct stencil { /// stencil 2 each side of the centre -- in effect means M?G > 2 is not supported - BoutReal mm = BoutNaN, m = BoutNaN, c = BoutNaN, p = BoutNaN, pp = BoutNaN; + BoutReal mm = BoutNaN, m = BoutNaN, c = BoutNaN, p = BoutNaN, pp = BoutNaN; }; - -template -void inline populateStencil(stencil &s, const FieldType& f, const typename FieldType::ind_type i){ +template +void inline populateStencil(stencil& s, const FieldType& f, + const typename FieldType::ind_type i) { static_assert(nGuard == 1 || nGuard == 2, - "populateStencil currently only supports one or two guard cells" - ); - - switch(stagger) { - case(STAGGER::None): + "populateStencil currently only supports one or two guard cells"); + + switch (stagger) { + case (STAGGER::None): if (nGuard == 2) { if (direction == DIRECTION::YOrthogonal) { s.mm = f.ynext(-2)[i.template minus<2, direction>()]; @@ -72,7 +72,7 @@ void inline populateStencil(stencil &s, const FieldType& f, const typename Field } } break; - case(STAGGER::C2L): + case (STAGGER::C2L): if (nGuard == 2) { if (direction == DIRECTION::YOrthogonal) { s.mm = f.ynext(-2)[i.template minus<2, direction>()]; @@ -93,7 +93,7 @@ void inline populateStencil(stencil &s, const FieldType& f, const typename Field s.pp = f[i.template plus<1, direction>()]; } break; - case(STAGGER::L2C): + case (STAGGER::L2C): if (direction == DIRECTION::YOrthogonal) { s.mm = f.ynext(-1)[i.template minus<1, direction>()]; } else { @@ -118,8 +118,9 @@ void inline populateStencil(stencil &s, const FieldType& f, const typename Field return; } -template -stencil inline populateStencil(const FieldType& f, const typename FieldType::ind_type i){ +template +stencil inline populateStencil(const FieldType& f, const typename FieldType::ind_type i) { stencil s; populateStencil(s, f, i); return s; diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index f077ce4532..9c96de1935 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -23,7 +23,7 @@ #include #endif -#include "unused.hxx" +#include "bout/unused.hxx" #if SUNDIALS_VERSION_MAJOR < 3 using SUNLinearSolver = int*; diff --git a/include/bout/surfaceiter.hxx b/include/bout/surfaceiter.hxx index b94b4e8d2e..ebe33b9864 100644 --- a/include/bout/surfaceiter.hxx +++ b/include/bout/surfaceiter.hxx @@ -1,6 +1,6 @@ /// \file surfaceiter.hxx /// Defines a class for iterating over flux surfaces (surfaces of constant x) -/// +/// class SurfaceIter; @@ -29,36 +29,36 @@ class SurfaceIter; /// // Boundary at upper Y on this processor /// } /// } -/// } +/// } class SurfaceIter { - public: +public: /// Constructor, needs a mesh to iterate over /// @param[in] mesh The mesh to iterate over - SurfaceIter(Mesh *mesh, bool include_guards=false) - : m(mesh), firstpos(include_guards ? 0 : mesh->xstart), - lastpos(include_guards ? mesh->LocalNx - 1 : mesh->xend) {} - + SurfaceIter(Mesh* mesh, bool include_guards = false) + : m(mesh), firstpos(include_guards ? 0 : mesh->xstart), + lastpos(include_guards ? mesh->LocalNx - 1 : mesh->xend) {} + int xpos; ///< X position where iteration is currently at int ySize(); ///< Return the length of the current surface in Y - + bool closed(); ///< Test if the current surface is closed /// Test if the current surface (x = xpos) is closed /// @param[out] ts The twist-shift angle by which points are shifted in Z between the end and beginning of Y - bool closed(BoutReal &ts); - + bool closed(BoutReal& ts); + MPI_Comm communicator(); ///< Communicator for this surface - + int yGlobal(int yloc); ///< Return global y index of given local index \p yloc bool firstY(); ///< Is this processor at the lower end? bool lastY(); ///< Is this processor at the upper end? - void first(); ///< Begin iteration - void next(); ///< Move to next flux surface + void first(); ///< Begin iteration + void next(); ///< Move to next flux surface bool isDone(); ///< Are we done iterating? private: - Mesh *m; ///< The mesh being iterated over + Mesh* m; ///< The mesh being iterated over const int firstpos; const int lastpos; }; diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx index 5e8e0a879b..25ad3abe1e 100644 --- a/include/bout/sys/expressionparser.hxx +++ b/include/bout/sys/expressionparser.hxx @@ -27,8 +27,8 @@ #ifndef __EXPRESSION_PARSER_H__ #define __EXPRESSION_PARSER_H__ +#include "bout/unused.hxx" #include "bout/format.hxx" -#include "unused.hxx" #include "fmt/core.h" @@ -125,7 +125,9 @@ public: protected: /// This will be called to resolve any unknown symbols - virtual FieldGeneratorPtr resolve(const std::string& UNUSED(name)) const { return nullptr; } + virtual FieldGeneratorPtr resolve(const std::string& UNUSED(name)) const { + return nullptr; + } /// A result that's almost what we were looking for. Return type of /// `ExpressionParser::fuzzyFind` @@ -187,7 +189,7 @@ private: /// Matches /// [ symbol = expression , symbol = expression ... ] ( expression ) FieldGeneratorPtr parseContextExpr(LexInfo& lex) const; - + /// Parse a primary expression, one of: /// - number /// - identifier @@ -229,9 +231,7 @@ public: return std::make_shared(value); } - double generate(const bout::generator::Context&) override { - return value; - } + double generate(const bout::generator::Context&) override { return value; } std::string str() const override { std::stringstream ss; ss << value; diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx index 6be5c8df96..3f912ec1da 100644 --- a/include/bout/sys/generator_context.hxx +++ b/include/bout/sys/generator_context.hxx @@ -1,7 +1,7 @@ #pragma once -#include "bout/region.hxx" #include "bout/assert.hxx" +#include "bout/region.hxx" class BoundaryRegion; class Mesh; @@ -11,20 +11,20 @@ class Mesh; namespace bout { namespace generator { - + class Context { public: /// Set using an index. Can be Ind2D, Ind3D or IndPerp. - template + template Context(const SpecificInd& i, CELL_LOC loc, Mesh* msh, BoutReal t) : Context(i.x(), i.y(), i.z(), loc, msh, t) {} // If Ind2D, z should be 0.0 even if ZLOW (Is this sensible?) Context(const Ind2D& i, CELL_LOC loc, Mesh* msh, BoutReal t) - : Context(i.x(), i.y(), 0, (loc == CELL_ZLOW) ? CELL_CENTRE : loc, msh, t) {} - + : Context(i.x(), i.y(), 0, (loc == CELL_ZLOW) ? CELL_CENTRE : loc, msh, t) {} + /// Specify a cell index, together with the cell location, mesh and time - /// + /// Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t); /// If constructed without parameters, contains no values (null). @@ -38,12 +38,12 @@ public: Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, Mesh* msh); Context(const BoundaryRegion* bndry, CELL_LOC loc, BoutReal t, Mesh* msh) : Context(bndry, 0, loc, t, msh){}; - - BoutReal x() const {return get("x");} - BoutReal y() const {return get("y");} - BoutReal z() const {return get("z");} - BoutReal t() const {return get("t");} - + + BoutReal x() const { return get("x"); } + BoutReal y() const { return get("y"); } + BoutReal z() const { return get("z"); } + BoutReal t() const { return get("t"); } + /// Set the value of a parameter with given name Context& set(const std::string& name, BoutReal value) { parameters[name] = value; @@ -53,16 +53,14 @@ public: /// Set multiple values, by passing alternating strings and values /// /// eg. set("x", 1, "y", 2) - template + template Context& set(const std::string& name, BoutReal value, Args... args) { set(name, value); return set(args...); } - + /// Retrieve a value previously set - BoutReal get(const std::string& name) const { - return parameters.at(name); - } + BoutReal get(const std::string& name) const { return parameters.at(name); } /// Get the mesh for this context (position) /// If the mesh is null this will throw a BoutException (if CHECK >= 1) @@ -72,8 +70,8 @@ public: } private: - Mesh *localmesh{nullptr}; ///< The mesh on which the position is defined - + Mesh* localmesh{nullptr}; ///< The mesh on which the position is defined + /// Contains user-set values which can be set and retrieved std::map parameters{ {"x", 0.0}, {"y", 0.0}, {"z", 0.0}, {"t", 0.0}}; diff --git a/include/bout/sys/range.hxx b/include/bout/sys/range.hxx index 70d33ab741..a210983f25 100644 --- a/include/bout/sys/range.hxx +++ b/include/bout/sys/range.hxx @@ -28,9 +28,9 @@ class RangeIterator { public: /// Can be given a single range RangeIterator() = default; - RangeIterator(int start, int end, RangeIterator *join = nullptr); - RangeIterator(int start, int end, const RangeIterator &join); - RangeIterator(const RangeIterator &r); + RangeIterator(int start, int end, RangeIterator* join = nullptr); + RangeIterator(int start, int end, const RangeIterator& join); + RangeIterator(const RangeIterator& r); ~RangeIterator(); void first(); @@ -38,7 +38,7 @@ public: bool isDone() const; int operator*() { return ind; } - RangeIterator &operator++() { + RangeIterator& operator++() { next(); return *this; } @@ -48,15 +48,15 @@ public: return original; } - bool operator==(const RangeIterator &x) const { return cur == x.cur; } - bool operator!=(const RangeIterator &x) const { return cur != x.cur; } + bool operator==(const RangeIterator& x) const { return cur == x.cur; } + bool operator!=(const RangeIterator& x) const { return cur != x.cur; } - bool intersects(const RangeIterator &other, bool all = true) const; + bool intersects(const RangeIterator& other, bool all = true) const; bool intersects(int ind, bool all = true) const; - RangeIterator &operator=(const RangeIterator &r); - RangeIterator &operator+=(const RangeIterator &r); // Add ranges - RangeIterator &operator-=(const RangeIterator &r); // Remove ranges + RangeIterator& operator=(const RangeIterator& r); + RangeIterator& operator+=(const RangeIterator& r); // Add ranges + RangeIterator& operator-=(const RangeIterator& r); // Remove ranges static RangeIterator end() { return RangeIterator(1, 0); } @@ -64,14 +64,14 @@ public: int min() const { return is; } int max() const { return ie; } - RangeIterator *nextRange() const { return n; }; + RangeIterator* nextRange() const { return n; }; private: int is{1}, ie{0}; RangeIterator* n{nullptr}; // Next range. Doesn't change after creation RangeIterator* cur{nullptr}; // Currently iterating. Changes during iteration - int curend; // End of current range - bool delete_next = false; // Flag to delete this->n if we created it + int curend; // End of current range + bool delete_next = false; // Flag to delete this->n if we created it }; #endif // __RANGE_H__ diff --git a/include/bout/sys/timer.hxx b/include/bout/sys/timer.hxx index 6310266fa6..6f04630c9d 100644 --- a/include/bout/sys/timer.hxx +++ b/include/bout/sys/timer.hxx @@ -6,8 +6,8 @@ #include #include -#include "output.hxx" -#include "msg_stack.hxx" +#include "bout/msg_stack.hxx" +#include "bout/output.hxx" /*! * Timing class for performance benchmarking and diagnosis @@ -77,7 +77,9 @@ public: static double getTime(const std::string& label) { return getTime(getInfo(label)); } /// Total time elapsed since the very first initialisation - static double getTotalTime(const std::string& label) { return getTotalTime(getInfo(label)); } + static double getTotalTime(const std::string& label) { + return getTotalTime(getInfo(label)); + } /*! * The total time in seconds, resets the timer to zero @@ -131,5 +133,5 @@ public: static void printTimeReport(); }; -#define AUTO_TIME() Timer CONCATENATE(time_,__LINE__)(__thefunc__) +#define AUTO_TIME() Timer CONCATENATE(time_, __LINE__)(__thefunc__) #endif // __TIMER_H__ diff --git a/include/bout/sys/type_name.hxx b/include/bout/sys/type_name.hxx index 046ffa467f..be4d096b4d 100644 --- a/include/bout/sys/type_name.hxx +++ b/include/bout/sys/type_name.hxx @@ -4,9 +4,9 @@ #ifndef TYPE_NAME_HXX #define TYPE_NAME_HXX -#include +#include "bout/bout_types.hxx" #include -#include "bout_types.hxx" +#include class Field2D; class Field3D; @@ -14,34 +14,34 @@ class FieldPerp; namespace bout { namespace utils { - - template - std::string typeName() { - return typeid(T).name(); - } - - template <> - std::string typeName(); - - template <> - std::string typeName(); - - template <> - std::string typeName(); - - // Specialised for BOUT++ types to ensure that the result is human-readable - template <> - std::string typeName(); - - template <> - std::string typeName(); - - template <> - std::string typeName(); - - template <> - std::string typeName(); -} + +template +std::string typeName() { + return typeid(T).name(); } +template <> +std::string typeName(); + +template <> +std::string typeName(); + +template <> +std::string typeName(); + +// Specialised for BOUT++ types to ensure that the result is human-readable +template <> +std::string typeName(); + +template <> +std::string typeName(); + +template <> +std::string typeName(); + +template <> +std::string typeName(); +} // namespace utils +} // namespace bout + #endif //TYPE_NAME_HXX diff --git a/include/bout/sys/uncopyable.hxx b/include/bout/sys/uncopyable.hxx index a03cbca663..76606620ed 100644 --- a/include/bout/sys/uncopyable.hxx +++ b/include/bout/sys/uncopyable.hxx @@ -10,8 +10,8 @@ protected: ~Uncopyable() = default; public: - Uncopyable(const Uncopyable &) = delete; - Uncopyable &operator=(const Uncopyable &) = delete; + Uncopyable(const Uncopyable&) = delete; + Uncopyable& operator=(const Uncopyable&) = delete; }; #endif // __UNCOPYABLE_H__ diff --git a/include/bout/sys/variant.hxx b/include/bout/sys/variant.hxx index 1461b9fe4a..f47d67e229 100644 --- a/include/bout/sys/variant.hxx +++ b/include/bout/sys/variant.hxx @@ -23,7 +23,7 @@ #include "mpark/variant.hpp" -#include "utils.hxx" +#include "bout/utils.hxx" namespace bout { namespace utils { @@ -36,11 +36,11 @@ namespace utils { // using std::holds_alternative; // using std::get; +using mpark::get; +using mpark::holds_alternative; using mpark::variant; using mpark::visit; -using mpark::holds_alternative; -using mpark::get; - + //////////////////////////////////////////////////////////// // Variant comparison @@ -136,23 +136,25 @@ struct StaticCastOrThrow { /// Note: \p T can be a type which variant \p v cannot hold /// in which case std::bad_cast will be thrown at runtime template -T variantStaticCastOrThrow(const Variant &v) { - return bout::utils::visit( details::StaticCastOrThrow(), v ); +T variantStaticCastOrThrow(const Variant& v) { + return bout::utils::visit(details::StaticCastOrThrow(), v); } namespace details { - + struct ToString { template std::string operator()(T&& val) { return toString(std::forward(val)); } }; - + } // namespace details template -std::string variantToString(const Variant& v) { return bout::utils::visit(details::ToString(), v); } +std::string variantToString(const Variant& v) { + return bout::utils::visit(details::ToString(), v); +} } // namespace utils } // namespace bout diff --git a/include/bout/template_combinations.hxx b/include/bout/template_combinations.hxx index e416ba278d..81848cf252 100644 --- a/include/bout/template_combinations.hxx +++ b/include/bout/template_combinations.hxx @@ -30,7 +30,7 @@ #ifndef __TEMPLATE_COMBINATIONS_H__ #define __TEMPLATE_COMBINATIONS_H__ -#include +#include /// Here we define an empty templated struct that can represent /// a collection of arbitrary types. This is useful for passing @@ -142,7 +142,7 @@ void addItemToDeferredFunction(theFunction func, item, nextSet, otherSets...) { /// Terminal routine -- the current Set is empty /// so nothing left to do. template -void processSet(theFunction UNUSED(func), Set<>, Sets...){} +void processSet(theFunction UNUSED(func), Set<>, Sets...) {} /// Here we use type inference to allow us to refer to the firstItem in the first Set /// and the otherItems in this Set. We use this to pass the firstItem off to the routines diff --git a/include/bout/traits.hxx b/include/bout/traits.hxx index b7eec0b5c8..ecfdec8a40 100644 --- a/include/bout/traits.hxx +++ b/include/bout/traits.hxx @@ -104,28 +104,28 @@ using is_Options = std::is_base_of; /// `Field2D` if `V` is `Field2D`, and `Field3D` if `V` is `Field3D`. template using EnableIfField = - typename std::enable_if::value ...), + typename std::enable_if::value...), typename std::common_type::type>::type; /// Enable a function if all the Ts are subclasses of `Field2D`, and /// returns the common type template using EnableIfField2D = - typename std::enable_if::value ...), + typename std::enable_if::value...), typename std::common_type::type>::type; /// Enable a function if all the Ts are subclasses of `Field3D`, and /// returns the common type template using EnableIfField3D = - typename std::enable_if::value ...), + typename std::enable_if::value...), typename std::common_type::type>::type; /// Enable a function if all the Ts are subclasses of `FieldPerp`, and /// returns the common type template using EnableIfFieldPerp = - typename std::enable_if::value ...), + typename std::enable_if::value...), typename std::common_type::type>::type; /// Enable a function if T is a subclass of Options diff --git a/include/bout/unused.hxx b/include/bout/unused.hxx index eab3562552..6e7a46c7c0 100644 --- a/include/bout/unused.hxx +++ b/include/bout/unused.hxx @@ -26,15 +26,15 @@ /// /// void someFunction(int UNUSED(x)) {}; #if defined(__GNUC__) -# define UNUSED(x) UNUSED_ ## x __attribute__((unused)) +#define UNUSED(x) UNUSED_##x __attribute__((unused)) #elif defined(_MSC_VER) -#define UNUSED(x) __pragma(warning(suppress : 4100)) UNUSED_ ## x +#define UNUSED(x) __pragma(warning(suppress : 4100)) UNUSED_##x #elif defined(__LCLINT__) -# define UNUSED(x) /*@unused@*/ x +#define UNUSED(x) /*@unused@*/ x #elif defined(__cplusplus) -# define UNUSED(x) +#define UNUSED(x) #else -# define UNUSED(x) x +#define UNUSED(x) x #endif /// Mark a function parameter as possibly unused in the function body @@ -44,16 +44,16 @@ /// MAYBE_UNUSED(int foo); #ifdef __has_cpp_attribute #if __has_cpp_attribute(maybe_unused) -# define MAYBE_UNUSED(x) [[maybe_unused]] x +#define MAYBE_UNUSED(x) [[maybe_unused]] x #endif #endif #ifndef MAYBE_UNUSED #if defined(__GNUC__) -# define MAYBE_UNUSED(x) [[gnu::unused]] x +#define MAYBE_UNUSED(x) [[gnu::unused]] x #elif defined(_MSC_VER) -# define MAYBE_UNUSED(x) __pragma(warning(suppress : 4100)) x +#define MAYBE_UNUSED(x) __pragma(warning(suppress : 4100)) x #else -# define MAYBE_UNUSED(x) x +#define MAYBE_UNUSED(x) x #endif #endif diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 9de4628358..960a45849c 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -29,12 +29,12 @@ #ifndef __UTILS_H__ #define __UTILS_H__ -#include "bout_types.hxx" -#include "dcomplex.hxx" -#include "boutexception.hxx" +#include "bout/bout_types.hxx" +#include "bout/boutexception.hxx" +#include "bout/dcomplex.hxx" -#include "msg_stack.hxx" -#include "unused.hxx" +#include "bout/msg_stack.hxx" +#include "bout/unused.hxx" #include "bout/array.hxx" #include "bout/assert.hxx" #include "bout/build_config.hxx" @@ -210,7 +210,7 @@ public: data.reallocate(n1 * n2); } - Matrix(const Matrix &other) : n1(other.n1), n2(other.n2), data(other.data) { + Matrix(const Matrix& other) : n1(other.n1), n2(other.n2), data(other.data) { // Prevent copy on write for Matrix data.ensureUnique(); } @@ -227,7 +227,7 @@ public: data.reallocate(new_size_1 * new_size_2); } - Matrix& operator=(const Matrix &other) { + Matrix& operator=(const Matrix& other) { n1 = other.n1; n2 = other.n2; data = other.data; @@ -235,29 +235,29 @@ public: data.ensureUnique(); return *this; } - + inline T& operator()(size_type i1, size_type i2) { - ASSERT2(0<=i1 && i1 shape() const { return std::make_tuple(n1, n2); }; @@ -268,10 +268,8 @@ public: * This should be called before performing any write operations * on the data. */ - void ensureUnique() { - data.ensureUnique(); - } - + void ensureUnique() { data.ensureUnique(); } + /// Access the underlying storage Array& getData() { return data; } const Array& getData() const { return data; } @@ -306,7 +304,8 @@ public: ASSERT2(n3 >= 0); data.reallocate(n1 * n2 * n3); } - Tensor(const Tensor &other) : n1(other.n1), n2(other.n2), n3(other.n3), data(other.data) { + Tensor(const Tensor& other) + : n1(other.n1), n2(other.n2), n3(other.n3), data(other.data) { // Prevent copy on write for Tensor data.ensureUnique(); } @@ -325,7 +324,7 @@ public: data.reallocate(new_size_1 * new_size_2 * new_size_3); } - Tensor& operator=(const Tensor &other) { + Tensor& operator=(const Tensor& other) { n1 = other.n1; n2 = other.n2; n3 = other.n3; @@ -336,29 +335,29 @@ public: } T& operator()(size_type i1, size_type i2, size_type i3) { - ASSERT2(0<=i1 && i1 shape() const { return std::make_tuple(n1, n2, n3); @@ -371,9 +370,7 @@ public: * This should be called before performing any write operations * on the data. */ - void ensureUnique() { - data.ensureUnique(); - } + void ensureUnique() { data.ensureUnique(); } /// Access the underlying storage Array& getData() { return data; } @@ -399,7 +396,8 @@ bool operator==(const Tensor& lhs, const Tensor& rhs) { /// us to throw due to the matrix being singular (ill conditioned); /// If small is less than zero then instead of throwing we return 1. /// This is ugly but can be used to support some use cases. -template int invert3x3(Matrix &a, BoutReal small = 1.0e-15) { +template +int invert3x3(Matrix& a, BoutReal small = 1.0e-15) { TRACE("invert3x3"); // Calculate the first co-factors @@ -411,11 +409,11 @@ template int invert3x3(Matrix &a, BoutReal small = 1.0e-15) { T det = a(0, 0) * A + a(0, 1) * B + a(0, 2) * C; if (std::abs(det) < std::abs(small)) { - if (small >=0 ){ + if (small >= 0) { throw BoutException("Determinant of matrix < {:e} --> Poorly conditioned", small); } else { return 1; - } + } } // Calculate the rest of the co-factors @@ -455,13 +453,13 @@ inline BoutReal randomu() { */ template BOUT_HOST_DEVICE inline T SQ(const T& t) { - return t*t; + return t * t; } /*! * Round \p x to the nearest integer */ -inline int ROUND(BoutReal x){ +inline int ROUND(BoutReal x) { return (x > 0.0) ? static_cast(x + 0.5) : static_cast(x - 0.5); } @@ -491,10 +489,8 @@ T BOUTMIN(T a, T b, Args... args) { /*! * Check if a number is a power of 2 - */ -inline bool is_pow2(int x) { - return x && !((x-1) & x); -} + */ +inline bool is_pow2(int x) { return x && !((x - 1) & x); } /*! * Return the sign of a number \p a @@ -513,7 +509,7 @@ T SIGN(T a) { // Return +1 or -1 (0 -> +1) * if |a| < |b| then return a, otherwise return b */ inline BoutReal MINMOD(BoutReal a, BoutReal b) { - return 0.5*(SIGN(a) + SIGN(b)) * BOUTMIN(std::abs(a), std::abs(b)); + return 0.5 * (SIGN(a) + SIGN(b)) * BOUTMIN(std::abs(a), std::abs(b)); } #if CHECK > 0 @@ -530,10 +526,9 @@ inline void checkData(BoutReal UNUSED(f)){}; /*! * Allocate memory and copy string \p s - */ + */ char* copy_string(const char* s); - /// Convert a value to a string /// by writing to a stringstream template @@ -546,9 +541,7 @@ std::string toString(const T& val) { /// Simple case where input is already a string /// This is so that toString can be used in templates /// where the type may be std::string. -inline std::string toString(const std::string& val) { - return val; -} +inline std::string toString(const std::string& val) { return val; } template <> inline std::string toString<>(const Array& UNUSED(val)) { @@ -574,7 +567,7 @@ inline std::string toString(const bool& val) { } inline std::string toString(const DirectionTypes& dir) { - return "{"+toString(dir.y)+", "+toString(dir.z)+"}"; + return "{" + toString(dir.y) + ", " + toString(dir.z) + "}"; } /// Convert a time stamp to a string @@ -584,30 +577,30 @@ std::string toString(const time_t& time); /*! * Convert a string to lower case */ -const std::string lowercase(const std::string &str); +const std::string lowercase(const std::string& str); /*! * Convert a string to upper case */ -const std::string uppercase(const std::string &str); +const std::string uppercase(const std::string& str); /*! * Convert to lower case, except inside quotes (" or ') */ -const std::string lowercasequote(const std::string &str); +const std::string lowercasequote(const std::string& str); /*! * Convert a string to a BoutReal * Throws BoutException if can't be done - */ -BoutReal stringToReal(const std::string &s); + */ +BoutReal stringToReal(const std::string& s); /*! * Convert a string to an int * * Throws BoutException if can't be done */ -int stringToInt(const std::string &s); +int stringToInt(const std::string& s); /*! * Split a string on a given delimiter @@ -616,7 +609,8 @@ int stringToInt(const std::string &s); * @param[in] delim The delimiter to split on (single char) * @param[in, out] elems A list to which the pieces will be appended using push_back */ -std::list &strsplit(const std::string &s, char delim, std::list &elems); +std::list& strsplit(const std::string& s, char delim, + std::list& elems); /*! * Split a string on a given delimiter @@ -624,7 +618,7 @@ std::list &strsplit(const std::string &s, char delim, std::list strsplit(const std::string &s, char delim); +std::list strsplit(const std::string& s, char delim); /*! * Strips leading and trailing spaces from a string @@ -632,7 +626,7 @@ std::list strsplit(const std::string &s, char delim); * @param[in] s The string to trim (not modified) * @param[in] c Collection of characters to remove */ -std::string trim(const std::string &s, const std::string &c=" \t\r"); +std::string trim(const std::string& s, const std::string& c = " \t\r"); /*! * Strips leading spaces from a string @@ -640,7 +634,7 @@ std::string trim(const std::string &s, const std::string &c=" \t\r"); * @param[in] s The string to trim (not modified) * @param[in] c Collection of characters to remove */ -std::string trimLeft(const std::string &s, const std::string &c=" \t"); +std::string trimLeft(const std::string& s, const std::string& c = " \t"); /*! * Strips leading spaces from a string @@ -648,7 +642,7 @@ std::string trimLeft(const std::string &s, const std::string &c=" \t"); * @param[in] s The string to trim (not modified) * @param[in] c Collection of characters to remove */ -std::string trimRight(const std::string &s, const std::string &c=" \t\r"); +std::string trimRight(const std::string& s, const std::string& c = " \t\r"); /*! * Strips the comments from a string @@ -656,7 +650,7 @@ std::string trimRight(const std::string &s, const std::string &c=" \t\r"); * @param[in] s The string to trim (not modified) * @param[in] c Collection of characters to remove */ -std::string trimComments(const std::string &s, const std::string &c="#;"); +std::string trimComments(const std::string& s, const std::string& c = "#;"); /// Returns the "edit distance" between two strings: how many /// insertions, deletions, substitutions and transpositions are needed @@ -675,32 +669,39 @@ std::string::size_type editDistance(const std::string& str1, const std::string& /// fmt: the const char * descriping the format. /// note that fmt should be the first argument of the function of type /// const char * and has to be directly followed by the variable arguments. -#define bout_vsnprintf(buf,len,fmt) { \ - va_list va; \ - va_start(va, fmt); \ - int _vsnprintflen=vsnprintf(buf,len,fmt,va); \ - va_end(va); \ - if ( _vsnprintflen + 1 > int(len)) { \ - _vsnprintflen+=1; \ - delete[] buf; \ - buf = new char[_vsnprintflen]; \ - len = _vsnprintflen; \ - va_start(va,fmt); \ - vsnprintf(buf,len,fmt,va); \ - va_end(va); \ - } \ +#define bout_vsnprintf(buf, len, fmt) \ + { \ + va_list va; \ + va_start(va, fmt); \ + int _vsnprintflen = vsnprintf(buf, len, fmt, va); \ + va_end(va); \ + if (_vsnprintflen + 1 > int(len)) { \ + _vsnprintflen += 1; \ + delete[] buf; \ + buf = new char[_vsnprintflen]; \ + len = _vsnprintflen; \ + va_start(va, fmt); \ + vsnprintf(buf, len, fmt, va); \ + va_end(va); \ + } \ } /// Convert pointer or reference to pointer /// This allows consistent handling of both in macros, templates -template T *pointer(T *val) { return val; } -template T *pointer(T &val) { return &val; } +template +T* pointer(T* val) { + return val; +} +template +T* pointer(T& val) { + return &val; +} #ifndef BOUT_CONCAT /// Utility to evaluate and concatenate macro symbols /// Note that ## operator doesn't evaluate symols A or B -#define BOUT_CONCAT_(A,B) A##B -#define BOUT_CONCAT(A,B) BOUT_CONCAT_(A,B) +#define BOUT_CONCAT_(A, B) A##B +#define BOUT_CONCAT(A, B) BOUT_CONCAT_(A, B) #endif #endif // __UTILS_H__ diff --git a/include/bout/vecops.hxx b/include/bout/vecops.hxx index 6c15b95f05..8dc16d26f4 100644 --- a/include/bout/vecops.hxx +++ b/include/bout/vecops.hxx @@ -29,12 +29,12 @@ #ifndef __VECOPS_H__ #define __VECOPS_H__ -#include "bout_types.hxx" +#include "bout/bout_types.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" #include "bout/coordinates.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "vector2d.hxx" -#include "vector3d.hxx" /// Gradient of scalar field \p f, returning a covariant vector /// diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx index d86268c4e8..9ff4a69ba8 100644 --- a/include/bout/vector2d.hxx +++ b/include/bout/vector2d.hxx @@ -39,17 +39,17 @@ class Vector2D; class Field2D; class Field3D; -class Vector3D; //#include "vector3d.hxx" +class Vector3D; //#include "bout/vector3d.hxx" #include /*! * A vector with three components (x,y,z) which only vary in 2D * (x and y). Implemented as a collection of three Field2D objects. - */ + */ class Vector2D : public FieldData { public: - Vector2D(const Vector2D &f); + Vector2D(const Vector2D& f); /// Many-argument constructor for fully specifying the initialisation of a Vector3D Vector2D(Mesh* localmesh = nullptr, bool covariant = true, @@ -71,7 +71,7 @@ public: Vector2D* timeDeriv(); /// Assignment - Vector2D & operator=(const Vector2D &rhs); + Vector2D& operator=(const Vector2D& rhs); /*! * Assign a BoutReal value. This sets all components @@ -88,48 +88,52 @@ public: * * The only real use for this is setting vector to zero. */ - Vector2D & operator=(BoutReal val); + Vector2D& operator=(BoutReal val); // operators - Vector2D & operator+=(const Vector2D &rhs); + Vector2D& operator+=(const Vector2D& rhs); /// Unary minus, changes sign of all components const Vector2D operator-() const; /// Subtract another vector - Vector2D & operator-=(const Vector2D &rhs); + Vector2D& operator-=(const Vector2D& rhs); /// Multiply all components by \p rhs - Vector2D & operator*=(BoutReal rhs); + Vector2D& operator*=(BoutReal rhs); /// Multiply all components by \p rhs - Vector2D & operator*=(const Field2D &rhs); + Vector2D& operator*=(const Field2D& rhs); /// Divide all components by \p rhs - Vector2D & operator/=(BoutReal rhs); + Vector2D& operator/=(BoutReal rhs); /// Divide all components by \p rhs - Vector2D & operator/=(const Field2D &rhs); + Vector2D& operator/=(const Field2D& rhs); // Binary operators - - const Vector2D operator+(const Vector2D &rhs) const; ///< Addition - const Vector3D operator+(const Vector3D &rhs) const; ///< Addition - const Vector2D operator-(const Vector2D &rhs) const; ///< Subtract vector \p rhs - const Vector3D operator-(const Vector3D &rhs) const; ///< Subtract vector \p rhs + const Vector2D operator+(const Vector2D& rhs) const; ///< Addition + const Vector3D operator+(const Vector3D& rhs) const; ///< Addition + + const Vector2D operator-(const Vector2D& rhs) const; ///< Subtract vector \p rhs + const Vector3D operator-(const Vector3D& rhs) const; ///< Subtract vector \p rhs const Vector2D operator*(BoutReal rhs) const; ///< Multiply all components by \p rhs - const Vector2D operator*(const Field2D &rhs) const; ///< Multiply all components by \p rhs - const Vector3D operator*(const Field3D &rhs) const; ///< Multiply all components by \p rhs + const Vector2D + operator*(const Field2D& rhs) const; ///< Multiply all components by \p rhs + const Vector3D + operator*(const Field3D& rhs) const; ///< Multiply all components by \p rhs const Vector2D operator/(BoutReal rhs) const; ///< Divides all components by \p rhs - const Vector2D operator/(const Field2D &rhs) const; ///< Divides all components by \p rhs - const Vector3D operator/(const Field3D &rhs) const; ///< Divides all components by \p rhs + const Vector2D + operator/(const Field2D& rhs) const; ///< Divides all components by \p rhs + const Vector3D + operator/(const Field3D& rhs) const; ///< Divides all components by \p rhs const Coordinates::FieldMetric operator*(const Vector2D& rhs) const; ///< Dot product - const Field3D operator*(const Vector3D &rhs) const; ///< Dot product + const Field3D operator*(const Vector3D& rhs) const; ///< Dot product /// Set component locations consistently Vector2D& setLocation(CELL_LOC loc) override; @@ -142,14 +146,15 @@ public: int elementSize() const override { return 3; } /// Apply boundary condition to all fields - void applyBoundary(bool init=false) override; - void applyBoundary(const std::string &condition) { + void applyBoundary(bool init = false) override; + void applyBoundary(const std::string& condition) { x.applyBoundary(condition); y.applyBoundary(condition); z.applyBoundary(condition); } void applyBoundary(const char* condition) { applyBoundary(std::string(condition)); } void applyTDerivBoundary() override; + private: Vector2D* deriv{nullptr}; ///< Time-derivative, can be NULL CELL_LOC location{CELL_CENTRE}; ///< Location of the variable in the cell @@ -157,15 +162,14 @@ private: // Non-member overloaded operators -const Vector2D operator*(BoutReal lhs, const Vector2D &rhs); -const Vector2D operator*(const Field2D &lhs, const Vector2D &rhs); -const Vector3D operator*(const Field3D &lhs, const Vector2D &rhs); - +const Vector2D operator*(BoutReal lhs, const Vector2D& rhs); +const Vector2D operator*(const Field2D& lhs, const Vector2D& rhs); +const Vector3D operator*(const Field3D& lhs, const Vector2D& rhs); /// Cross product -const Vector2D cross(const Vector2D & lhs, const Vector2D &rhs); +const Vector2D cross(const Vector2D& lhs, const Vector2D& rhs); /// Cross product -const Vector3D cross(const Vector2D & lhs, const Vector3D &rhs); +const Vector3D cross(const Vector2D& lhs, const Vector3D& rhs); /*! * Absolute value (Modulus) of given vector \p v @@ -175,12 +179,14 @@ const Vector3D cross(const Vector2D & lhs, const Vector3D &rhs); Coordinates::FieldMetric abs(const Vector2D& v, const std::string& region = "RGN_ALL"); /// Transform to and from field-aligned coordinates -inline Vector2D toFieldAligned(Vector2D v, const std::string& UNUSED(region) = "RGN_ALL") { +inline Vector2D toFieldAligned(Vector2D v, + const std::string& UNUSED(region) = "RGN_ALL") { // toFieldAligned is a null operation for the Field2D components of v, so return a copy // of the argument (hence pass-by-value instead of pass-by-reference) return v; } -inline Vector2D fromFieldAligned(Vector2D v, const std::string& UNUSED(region) = "RGN_ALL") { +inline Vector2D fromFieldAligned(Vector2D v, + const std::string& UNUSED(region) = "RGN_ALL") { // fromFieldAligned is a null operation for the Field2D components of v, so return a copy // of the argument (hence pass-by-value instead of pass-by-reference) return v; @@ -209,8 +215,6 @@ inline Vector2D zeroFrom(const Vector2D& v) { /*! * @brief Time derivative of 2D vector field */ -inline Vector2D& ddt(Vector2D &f) { - return *(f.timeDeriv()); -} +inline Vector2D& ddt(Vector2D& f) { return *(f.timeDeriv()); } #endif // __VECTOR2D_H__ diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx index d68393316a..f3adf41ae8 100644 --- a/include/bout/vector3d.hxx +++ b/include/bout/vector3d.hxx @@ -33,10 +33,10 @@ class Vector3D; #ifndef __VECTOR3D_H__ #define __VECTOR3D_H__ -class Field2D; //#include "field2d.hxx" -#include "field3d.hxx" +class Field2D; //#include "bout/field2d.hxx" +#include "bout/field3d.hxx" -class Vector2D; //#include "vector2d.hxx" +class Vector2D; //#include "bout/vector2d.hxx" /*! * Represents a 3D vector, with x,y,z components @@ -50,14 +50,14 @@ class Vector2D; //#include "vector2d.hxx" * a.x; // Error! a.x not allocated * * - */ + */ class Vector3D : public FieldData { - public: +public: /*! * Copy constructor. After this the components (x,y,z) * will refer to the same data as f.(x,y,z) */ - Vector3D(const Vector3D &f); + Vector3D(const Vector3D& f); /// Many-argument constructor for fully specifying the initialisation of a Vector3D Vector3D(Mesh* localmesh = nullptr, bool covariant = true, @@ -74,7 +74,7 @@ class Vector3D : public FieldData { * The components of the vector. These can be * either co- or contra-variant, depending on * the boolean flag "covariant" - */ + */ Field3D x, y, z; /*! @@ -99,7 +99,7 @@ class Vector3D : public FieldData { * If contravariant, multiplies by metric tensor g_{ij} */ void toCovariant(); - + /*! * In-place conversion to contravariant form * @@ -108,7 +108,7 @@ class Vector3D : public FieldData { * */ void toContravariant(); - + /*! * Return a pointer to the time-derivative field * @@ -127,44 +127,44 @@ class Vector3D : public FieldData { Vector3D* timeDeriv(); // Assignment - Vector3D & operator=(const Vector3D &rhs); - Vector3D & operator=(const Vector2D &rhs); - Vector3D & operator=(BoutReal val); - + Vector3D& operator=(const Vector3D& rhs); + Vector3D& operator=(const Vector2D& rhs); + Vector3D& operator=(BoutReal val); + // Operators - Vector3D & operator+=(const Vector3D &rhs); - Vector3D & operator+=(const Vector2D &rhs); + Vector3D& operator+=(const Vector3D& rhs); + Vector3D& operator+=(const Vector2D& rhs); const Vector3D operator-() const; - Vector3D & operator-=(const Vector3D &rhs); - Vector3D & operator-=(const Vector2D &rhs); - - Vector3D & operator*=(BoutReal rhs); - Vector3D & operator*=(const Field2D &rhs); - Vector3D & operator*=(const Field3D &rhs); - - Vector3D & operator/=(BoutReal rhs); - Vector3D & operator/=(const Field2D &rhs); - Vector3D & operator/=(const Field3D &rhs); - + Vector3D& operator-=(const Vector3D& rhs); + Vector3D& operator-=(const Vector2D& rhs); + + Vector3D& operator*=(BoutReal rhs); + Vector3D& operator*=(const Field2D& rhs); + Vector3D& operator*=(const Field3D& rhs); + + Vector3D& operator/=(BoutReal rhs); + Vector3D& operator/=(const Field2D& rhs); + Vector3D& operator/=(const Field3D& rhs); + // Binary operators - const Vector3D operator+(const Vector3D &rhs) const; - const Vector3D operator+(const Vector2D &rhs) const; + const Vector3D operator+(const Vector3D& rhs) const; + const Vector3D operator+(const Vector2D& rhs) const; - const Vector3D operator-(const Vector3D &rhs) const; - const Vector3D operator-(const Vector2D &rhs) const; + const Vector3D operator-(const Vector3D& rhs) const; + const Vector3D operator-(const Vector2D& rhs) const; const Vector3D operator*(BoutReal rhs) const; - const Vector3D operator*(const Field2D &rhs) const; - const Vector3D operator*(const Field3D &rhs) const; + const Vector3D operator*(const Field2D& rhs) const; + const Vector3D operator*(const Field3D& rhs) const; const Vector3D operator/(BoutReal rhs) const; - const Vector3D operator/(const Field2D &rhs) const; - const Vector3D operator/(const Field3D &rhs) const; + const Vector3D operator/(const Field2D& rhs) const; + const Vector3D operator/(const Field3D& rhs) const; - const Field3D operator*(const Vector3D &rhs) const; // Dot product - const Field3D operator*(const Vector2D &rhs) const; + const Field3D operator*(const Vector3D& rhs) const; // Dot product + const Field3D operator*(const Vector2D& rhs) const; /// Set component locations consistently Vector3D& setLocation(CELL_LOC loc) override; @@ -176,37 +176,37 @@ class Vector3D : public FieldData { bool is3D() const override { return true; } int elementSize() const override { return 3; } - void applyBoundary(bool init=false) override; - void applyBoundary(const std::string &condition) { + void applyBoundary(bool init = false) override; + void applyBoundary(const std::string& condition) { x.applyBoundary(condition); y.applyBoundary(condition); z.applyBoundary(condition); } void applyBoundary(const char* condition) { applyBoundary(std::string(condition)); } void applyTDerivBoundary() override; - private: - Vector3D* deriv{nullptr}; ///< Time-derivative, can be NULL - CELL_LOC location{CELL_CENTRE}; ///< Location of the variable in the cell + +private: + Vector3D* deriv{nullptr}; ///< Time-derivative, can be NULL + CELL_LOC location{CELL_CENTRE}; ///< Location of the variable in the cell }; // Non-member overloaded operators -const Vector3D operator*(BoutReal lhs, const Vector3D &rhs); -const Vector3D operator*(const Field2D &lhs, const Vector3D &rhs); -const Vector3D operator*(const Field3D &lhs, const Vector3D &rhs); +const Vector3D operator*(BoutReal lhs, const Vector3D& rhs); +const Vector3D operator*(const Field2D& lhs, const Vector3D& rhs); +const Vector3D operator*(const Field3D& lhs, const Vector3D& rhs); /// Cross-product of two vectors -const Vector3D cross(const Vector3D & lhs, const Vector3D &rhs); +const Vector3D cross(const Vector3D& lhs, const Vector3D& rhs); /// Cross-product of two vectors -const Vector3D cross(const Vector3D & lhs, const Vector2D &rhs); - +const Vector3D cross(const Vector3D& lhs, const Vector2D& rhs); /*! * Absolute magnitude (modulus) of a vector |v| * * sqrt( v.x^2 + v.y^2 + v.z^2 ) - */ + */ const Field3D abs(const Vector3D& v, const std::string& region = "RGN_ALL"); /// Transform to and from field-aligned coordinates @@ -236,9 +236,6 @@ inline Vector3D zeroFrom(const Vector3D& v) { /*! * @brief Time derivative of 3D vector field */ -inline Vector3D& ddt(Vector3D &f) { - return *(f.timeDeriv()); -} +inline Vector3D& ddt(Vector3D& f) { return *(f.timeDeriv()); } #endif // __VECTOR3D_H__ - diff --git a/include/bout/where.hxx b/include/bout/where.hxx index a024f67dc1..4b1d8090d0 100644 --- a/include/bout/where.hxx +++ b/include/bout/where.hxx @@ -28,9 +28,9 @@ #ifndef __WHERE_H__ #define __WHERE_H__ -#include "field.hxx" -#include "field2d.hxx" -#include "field3d.hxx" +#include "bout/field.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" /// For each point, choose between two inputs based on a third input /// @@ -45,7 +45,7 @@ auto where(const T& test, const U& gt0, const V& le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { result[i] = (test[i] > 0.0) ? gt0[i] : le0[i]; } return result; @@ -57,7 +57,7 @@ auto where(const T& test, const U& gt0, BoutReal le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { // clang-format: ignore + BOUT_FOR (i, result.getRegion("RGN_ALL")) { // clang-format: ignore result[i] = (test[i] > 0.0) ? gt0[i] : le0; } return result; @@ -69,7 +69,7 @@ auto where(const T& test, BoutReal gt0, const V& le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { // clang-format: ignore + BOUT_FOR (i, result.getRegion("RGN_ALL")) { // clang-format: ignore result[i] = (test[i] > 0.0) ? gt0 : le0[i]; } return result; @@ -79,7 +79,7 @@ template auto where(const T& test, BoutReal gt0, BoutReal le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { // clang-format: ignore + BOUT_FOR (i, result.getRegion("RGN_ALL")) { // clang-format: ignore result[i] = (test[i] > 0.0) ? gt0 : le0; } return result; diff --git a/src/bout++-time.cxx b/src/bout++-time.cxx index d9fb269b41..1d9d7e0732 100644 --- a/src/bout++-time.cxx +++ b/src/bout++-time.cxx @@ -1,2 +1,2 @@ -const char * boutcompiledate{__DATE__}; -const char * boutcompiletime{__TIME__}; +const char* boutcompiledate{__DATE__}; +const char* boutcompiletime{__TIME__}; diff --git a/src/bout++-time.hxx b/src/bout++-time.hxx index 14173cc62a..78f21a350f 100644 --- a/src/bout++-time.hxx +++ b/src/bout++-time.hxx @@ -1,2 +1,2 @@ -extern const char * boutcompiledate; -extern const char * boutcompiletime; +extern const char* boutcompiledate; +extern const char* boutcompiletime; diff --git a/src/bout++.cxx b/src/bout++.cxx index 98911741a3..4659194f9b 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -31,17 +31,17 @@ const char DEFAULT_DIR[] = "data"; #define GLOBALORIGIN -#include "boundary_factory.hxx" +#include "bout/boundary_factory.hxx" #include "bout++-time.hxx" -#include "boutcomm.hxx" -#include "boutexception.hxx" -#include "interpolation_xz.hxx" -#include "interpolation_z.hxx" -#include "invert_laplace.hxx" -#include "invert_parderiv.hxx" -#include "msg_stack.hxx" -#include "optionsreader.hxx" -#include "output.hxx" +#include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" +#include "bout/interpolation_xz.hxx" +#include "bout/interpolation_z.hxx" +#include "bout/invert_laplace.hxx" +#include "bout/invert_parderiv.hxx" +#include "bout/msg_stack.hxx" +#include "bout/optionsreader.hxx" +#include "bout/output.hxx" #include "bout/coordinates_accessor.hxx" #include "bout/hyprelib.hxx" #include "bout/invert/laplacexz.hxx" @@ -56,7 +56,7 @@ const char DEFAULT_DIR[] = "data"; #include "bout/version.hxx" #define BOUT_NO_USING_NAMESPACE_BOUTGLOBALS -#include "bout.hxx" +#include "bout/bout.hxx" #undef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS #include @@ -382,9 +382,11 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs { " --list-solvers\t\tList the available time solvers\n" " --help-solver \tPrint help for the given time solver\n" " --list-laplacians\t\tList the available Laplacian inversion solvers\n" - " --help-laplacian \tPrint help for the given Laplacian inversion solver\n" + " --help-laplacian \tPrint help for the given Laplacian " + "inversion solver\n" " --list-laplacexz\t\tList the available LaplaceXZ inversion solvers\n" - " --help-laplacexz \tPrint help for the given LaplaceXZ inversion solver\n" + " --help-laplacexz \tPrint help for the given LaplaceXZ " + "inversion solver\n" " --list-invertpars\t\tList the available InvertPar solvers\n" " --help-invertpar \tPrint help for the given InvertPar solver\n" " --list-rkschemes\t\tList the available Runge-Kutta schemes\n" @@ -392,9 +394,11 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs { " --list-meshes\t\t\tList the available Meshes\n" " --help-mesh \t\tPrint help for the given Mesh\n" " --list-xzinterpolations\tList the available XZInterpolations\n" - " --help-xzinterpolation \tPrint help for the given XZInterpolation\n" + " --help-xzinterpolation \tPrint help for the given " + "XZInterpolation\n" " --list-zinterpolations\tList the available ZInterpolations\n" - " --help-zinterpolation \tPrint help for the given ZInterpolation\n" + " --help-zinterpolation \tPrint help for the given " + "ZInterpolation\n" " -h, --help\t\t\tThis message\n" " restart [append]\t\tRestart the simulation. If append is specified, " "append to the existing output files, otherwise overwrite them\n" @@ -525,7 +529,8 @@ void printStartupHeader(int MYPE, int NPES) { #ifdef MD5SUM output_progress.write("MD5 checksum: {:s}\n", BUILDFLAG(MD5SUM)); #endif - output_progress.write(_("Code compiled on {:s} at {:s}\n\n"), boutcompiledate, boutcompiletime); + output_progress.write(_("Code compiled on {:s} at {:s}\n\n"), boutcompiledate, + boutcompiletime); output_info.write("B.Dudson (University of York), M.Umansky (LLNL) 2007\n"); output_info.write("Based on BOUT by Xueqiao Xu, 1999\n\n"); @@ -1010,21 +1015,22 @@ void RunMetrics::calculateDerivedMetrics() { void RunMetrics::writeProgress(BoutReal simtime, bool output_split) { if (!output_split) { output_progress.write( - "{:.3e} {:5d} {:.2e} {:5.1f} {:5.1f} {:5.1f} {:5.1f} {:5.1f}\n", simtime, ncalls, - wtime, 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime, + "{:.3e} {:5d} {:.2e} {:5.1f} {:5.1f} {:5.1f} {:5.1f} {:5.1f}\n", + simtime, ncalls, wtime, 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime, 100. * wtime_invert / wtime, // Inversions 100. * wtime_comms / wtime, // Communications 100. * wtime_io / wtime, // I/O 100. * (wtime - wtime_io - wtime_rhs) / wtime); // Everything else } else { - output_progress.write( - "{:.3e} {:5d} {:5d} {:.2e} {:5.1f} {:5.1f} {:5.1f} {:5.1f} {:5.1f}\n", - simtime, ncalls_e, ncalls_i, wtime, - 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime, - 100. * wtime_invert / wtime, // Inversions - 100. * wtime_comms / wtime, // Communications - 100. * wtime_io / wtime, // I/O - 100. * (wtime - wtime_io - wtime_rhs) / wtime); // Everything else + output_progress.write("{:.3e} {:5d} {:5d} {:.2e} {:5.1f} " + "{:5.1f} {:5.1f} {:5.1f} {:5.1f}\n", + simtime, ncalls_e, ncalls_i, wtime, + 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime, + 100. * wtime_invert / wtime, // Inversions + 100. * wtime_comms / wtime, // Communications + 100. * wtime_io / wtime, // I/O + 100. * (wtime - wtime_io - wtime_rhs) + / wtime); // Everything else } } diff --git a/src/field/field.cxx b/src/field/field.cxx index 91b8d72b0b..34be778d8f 100644 --- a/src/field/field.cxx +++ b/src/field/field.cxx @@ -23,27 +23,21 @@ * **************************************************************************/ -//#include +//#include #include #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include Field::Field(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in) : FieldData(localmesh, location_in), directions(directions_in) {} -int Field::getNx() const{ - return getMesh()->LocalNx; -} +int Field::getNx() const { return getMesh()->LocalNx; } -int Field::getNy() const{ - return getMesh()->LocalNy; -} +int Field::getNy() const { return getMesh()->LocalNy; } -int Field::getNz() const{ - return getMesh()->LocalNz; -} +int Field::getNz() const { return getMesh()->LocalNz; } diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx index 219e564693..953d27953b 100644 --- a/src/field/field2d.cxx +++ b/src/field/field2d.cxx @@ -27,24 +27,24 @@ #include "bout/build_config.hxx" -#include #include +#include -#include // for mesh +#include // for mesh -#include +#include -#include +#include -#include -#include +#include +#include -#include -#include #include +#include +#include #include -#include +#include #include @@ -74,9 +74,7 @@ Field2D::Field2D(const Field2D& f) : Field(f), data(f.data) { } } -Field2D::Field2D(BoutReal val, Mesh* localmesh) : Field2D(localmesh) { - *this = val; -} +Field2D::Field2D(BoutReal val, Mesh* localmesh) : Field2D(localmesh) { *this = val; } Field2D::Field2D(Array data_in, Mesh* localmesh, CELL_LOC datalocation, DirectionTypes directions_in) @@ -95,36 +93,38 @@ Field2D::Field2D(Array data_in, Mesh* localmesh, CELL_LOC datalocation Field2D::~Field2D() { delete deriv; } Field2D& Field2D::allocate() { - if(data.empty()) { - if(!fieldmesh) { + if (data.empty()) { + if (!fieldmesh) { // fieldmesh was not initialized when this field was initialized, so use // the global mesh and set some members to default values fieldmesh = bout::globals::mesh; nx = fieldmesh->LocalNx; ny = fieldmesh->LocalNy; } - data.reallocate(nx*ny); + data.reallocate(nx * ny); #if CHECK > 2 invalidateGuards(*this); #endif - }else + } else { data.ensureUnique(); + } return *this; } BOUT_HOST_DEVICE Field2D* Field2D::timeDeriv() { - if(deriv == nullptr) + if (deriv == nullptr) { deriv = new Field2D{emptyFrom(*this)}; + } return deriv; } ////////////// Indexing /////////////////// -const Region &Field2D::getRegion(REGION region) const { +const Region& Field2D::getRegion(REGION region) const { return fieldmesh->getRegion2D(toString(region)); } -const Region &Field2D::getRegion(const std::string ®ion_name) const { +const Region& Field2D::getRegion(const std::string& region_name) const { return fieldmesh->getRegion2D(region_name); } @@ -139,10 +139,11 @@ BOUT_HOST_DEVICE const BoutReal& Field2D::operator[](const Ind3D& d) const { ///////////// OPERATORS //////////////// -Field2D &Field2D::operator=(const Field2D &rhs) { +Field2D& Field2D::operator=(const Field2D& rhs) { // Check for self-assignment - if (this == &rhs) + if (this == &rhs) { return (*this); // skip this assignment + } TRACE("Field2D: Assignment from Field2D"); @@ -179,7 +180,7 @@ Field2D& Field2D::operator=(Field2D&& rhs) noexcept { return *this; } -Field2D &Field2D::operator=(const BoutReal rhs) { +Field2D& Field2D::operator=(const BoutReal rhs) { #if BOUT_USE_TRACK name = ""; #endif @@ -187,7 +188,9 @@ Field2D &Field2D::operator=(const BoutReal rhs) { TRACE("Field2D = BoutReal"); allocate(); - BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = rhs; } + BOUT_FOR (i, getRegion("RGN_ALL")) { + (*this)[i] = rhs; + } return *this; } @@ -232,50 +235,50 @@ void Field2D::applyBoundary(BoutReal time) { } } -void Field2D::applyBoundary(const std::string &condition) { +void Field2D::applyBoundary(const std::string& condition) { TRACE("Field2D::applyBoundary(condition)"); checkData(*this); /// Get the boundary factory (singleton) - BoundaryFactory *bfact = BoundaryFactory::getInstance(); + BoundaryFactory* bfact = BoundaryFactory::getInstance(); /// Loop over the mesh boundary regions - for(const auto& reg : fieldmesh->getBoundaries()) { + for (const auto& reg : fieldmesh->getBoundaries()) { auto op = std::unique_ptr{ dynamic_cast(bfact->create(condition, reg))}; op->apply(*this); } // Set the corners to zero - for(int jx=0;jxxstart;jx++) { - for(int jy=0;jyystart;jy++) { - operator()(jx,jy) = 0.; + for (int jx = 0; jx < fieldmesh->xstart; jx++) { + for (int jy = 0; jy < fieldmesh->ystart; jy++) { + operator()(jx, jy) = 0.; } - for(int jy=fieldmesh->yend+1;jyLocalNy;jy++) { - operator()(jx,jy) = 0.; + for (int jy = fieldmesh->yend + 1; jy < fieldmesh->LocalNy; jy++) { + operator()(jx, jy) = 0.; } } - for(int jx=fieldmesh->xend+1;jxLocalNx;jx++) { - for(int jy=0;jyystart;jy++) { - operator()(jx,jy) = 0.; + for (int jx = fieldmesh->xend + 1; jx < fieldmesh->LocalNx; jx++) { + for (int jy = 0; jy < fieldmesh->ystart; jy++) { + operator()(jx, jy) = 0.; } - for(int jy=fieldmesh->yend+1;jyLocalNy;jy++) { - operator()(jx,jy) = 0.; + for (int jy = fieldmesh->yend + 1; jy < fieldmesh->LocalNy; jy++) { + operator()(jx, jy) = 0.; } } } -void Field2D::applyBoundary(const std::string ®ion, const std::string &condition) { +void Field2D::applyBoundary(const std::string& region, const std::string& condition) { TRACE("Field2D::applyBoundary(string, string)"); checkData(*this); /// Get the boundary factory (singleton) - BoundaryFactory *bfact = BoundaryFactory::getInstance(); + BoundaryFactory* bfact = BoundaryFactory::getInstance(); bool region_found = false; /// Loop over the mesh boundary regions - for (const auto ® : fieldmesh->getBoundaries()) { + for (const auto& reg : fieldmesh->getBoundaries()) { if (reg->label == region) { region_found = true; auto op = std::unique_ptr{ @@ -290,20 +293,20 @@ void Field2D::applyBoundary(const std::string ®ion, const std::string &condit } // Set the corners to zero - for(int jx=0;jxxstart;jx++) { - for(int jy=0;jyystart;jy++) { - operator()(jx,jy) = 0.; + for (int jx = 0; jx < fieldmesh->xstart; jx++) { + for (int jy = 0; jy < fieldmesh->ystart; jy++) { + operator()(jx, jy) = 0.; } - for(int jy=fieldmesh->yend+1;jyLocalNy;jy++) { - operator()(jx,jy) = 0.; + for (int jy = fieldmesh->yend + 1; jy < fieldmesh->LocalNy; jy++) { + operator()(jx, jy) = 0.; } } - for(int jx=fieldmesh->xend+1;jxLocalNx;jx++) { - for(int jy=0;jyystart;jy++) { - operator()(jx,jy) = 0.; + for (int jx = fieldmesh->xend + 1; jx < fieldmesh->LocalNx; jx++) { + for (int jy = 0; jy < fieldmesh->ystart; jy++) { + operator()(jx, jy) = 0.; } - for(int jy=fieldmesh->yend+1;jyLocalNy;jy++) { - operator()(jx,jy) = 0.; + for (int jy = fieldmesh->yend + 1; jy < fieldmesh->LocalNy; jy++) { + operator()(jx, jy) = 0.; } } } @@ -320,7 +323,7 @@ void Field2D::applyTDerivBoundary() { } } -void Field2D::setBoundaryTo(const Field2D &f2d) { +void Field2D::setBoundaryTo(const Field2D& f2d) { TRACE("Field2D::setBoundary(const Field2D&)"); checkData(f2d); @@ -328,13 +331,14 @@ void Field2D::setBoundaryTo(const Field2D &f2d) { allocate(); // Make sure data allocated /// Loop over boundary regions - for(const auto& reg : fieldmesh->getBoundaries()) { + for (const auto& reg : fieldmesh->getBoundaries()) { /// Loop within each region - for(reg->first(); !reg->isDone(); reg->next()) { + for (reg->first(); !reg->isDone(); reg->next()) { // Get value half-way between cells - BoutReal val = 0.5*(f2d(reg->x,reg->y) + f2d(reg->x-reg->bx, reg->y-reg->by)); + BoutReal val = + 0.5 * (f2d(reg->x, reg->y) + f2d(reg->x - reg->bx, reg->y - reg->by)); // Set to this value - (*this)(reg->x,reg->y) = 2.*val - (*this)(reg->x-reg->bx, reg->y-reg->by); + (*this)(reg->x, reg->y) = 2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by); } } } @@ -342,13 +346,13 @@ void Field2D::setBoundaryTo(const Field2D &f2d) { ////////////// NON-MEMBER OVERLOADED OPERATORS ////////////// // Unary minus -Field2D operator-(const Field2D &f) { return -1.0 * f; } +Field2D operator-(const Field2D& f) { return -1.0 * f; } //////////////// NON-MEMBER FUNCTIONS ////////////////// namespace { - // Internal routine to avoid ugliness with interactions between CHECK - // levels and UNUSED parameters +// Internal routine to avoid ugliness with interactions between CHECK +// levels and UNUSED parameters #if CHECK > 2 void checkDataIsFiniteOnRegion(const Field2D& f, const std::string& region) { // Do full checks @@ -361,13 +365,14 @@ void checkDataIsFiniteOnRegion(const Field2D& f, const std::string& region) { } #elif CHECK > 0 // No-op for no checking -void checkDataIsFiniteOnRegion(const Field2D &UNUSED(f), const std::string& UNUSED(region)) {} +void checkDataIsFiniteOnRegion(const Field2D& UNUSED(f), + const std::string& UNUSED(region)) {} #endif -} +} // namespace #if CHECK > 0 /// Check if the data is valid -void checkData(const Field2D &f, const std::string& region) { +void checkData(const Field2D& f, const std::string& region) { if (!f.isAllocated()) { throw BoutException("Field2D: Operation on empty data\n"); } @@ -377,19 +382,21 @@ void checkData(const Field2D &f, const std::string& region) { #endif #if CHECK > 2 -void invalidateGuards(Field2D &var) { - BOUT_FOR(i, var.getRegion("RGN_GUARDS")) { var[i] = BoutNaN; } +void invalidateGuards(Field2D& var) { + BOUT_FOR (i, var.getRegion("RGN_GUARDS")) { + var[i] = BoutNaN; + } } #endif -bool operator==(const Field2D &a, const Field2D &b) { +bool operator==(const Field2D& a, const Field2D& b) { if (!a.isAllocated() || !b.isAllocated()) { return false; } return min(abs(a - b)) < 1e-10; } -std::ostream& operator<<(std::ostream &out, const Field2D &value) { +std::ostream& operator<<(std::ostream& out, const Field2D& value) { out << toString(value); return out; } diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 7d48b3914d..4347c7942d 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -27,29 +27,28 @@ #include "bout/build_config.hxx" -#include -#include +#include +#include #include -#include "parallel_boundary_op.hxx" -#include "parallel_boundary_region.hxx" +#include "bout/parallel_boundary_op.hxx" +#include "bout/parallel_boundary_region.hxx" #include #include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include /// Constructor -Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, - DirectionTypes directions_in) +Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in) : Field(localmesh, location_in, directions_in) { #if BOUT_USE_TRACK name = ""; @@ -109,8 +108,8 @@ Field3D::Field3D(Array data_in, Mesh* localmesh, CELL_LOC datalocation Field3D::~Field3D() { delete deriv; } Field3D& Field3D::allocate() { - if(data.empty()) { - if(!fieldmesh) { + if (data.empty()) { + if (!fieldmesh) { // fieldmesh was not initialized when this field was initialized, so use // the global mesh and set some members to default values fieldmesh = bout::globals::mesh; @@ -122,14 +121,15 @@ Field3D& Field3D::allocate() { #if CHECK > 2 invalidateGuards(*this); #endif - } else + } else { data.ensureUnique(); + } return *this; } BOUT_HOST_DEVICE Field3D* Field3D::timeDeriv() { - if(deriv == nullptr) { + if (deriv == nullptr) { deriv = new Field3D{emptyFrom(*this)}; } return deriv; @@ -181,7 +181,7 @@ const Field3D& Field3D::ynext(int dir) const { } } -Field3D &Field3D::ynext(int dir) { +Field3D& Field3D::ynext(int dir) { // Call the `const` version: need to add `const` to `this` to call // it, then throw it away after. This is ok because `this` wasn't // `const` to begin with. @@ -198,37 +198,37 @@ bool Field3D::requiresTwistShift(bool twist_shift_enabled) { return false; } return getCoordinates()->getParallelTransform().requiresTwistShift(twist_shift_enabled, - getDirectionY()); + getDirectionY()); } // Not in header because we need to access fieldmesh -BoutReal &Field3D::operator()(const IndPerp &d, int jy) { +BoutReal& Field3D::operator()(const IndPerp& d, int jy) { return operator[](fieldmesh->indPerpto3D(d, jy)); } -const BoutReal &Field3D::operator()(const IndPerp &d, int jy) const { +const BoutReal& Field3D::operator()(const IndPerp& d, int jy) const { return operator[](fieldmesh->indPerpto3D(d, jy)); } -BoutReal &Field3D::operator()(const Ind2D &d, int jz) { +BoutReal& Field3D::operator()(const Ind2D& d, int jz) { return operator[](fieldmesh->ind2Dto3D(d, jz)); } -const BoutReal &Field3D::operator()(const Ind2D &d, int jz) const { +const BoutReal& Field3D::operator()(const Ind2D& d, int jz) const { return operator[](fieldmesh->ind2Dto3D(d, jz)); } -const Region &Field3D::getRegion(REGION region) const { +const Region& Field3D::getRegion(REGION region) const { return fieldmesh->getRegion3D(toString(region)); } -const Region &Field3D::getRegion(const std::string ®ion_name) const { +const Region& Field3D::getRegion(const std::string& region_name) const { return fieldmesh->getRegion3D(region_name); } -const Region &Field3D::getRegion2D(REGION region) const { +const Region& Field3D::getRegion2D(REGION region) const { return fieldmesh->getRegion2D(toString(region)); } -const Region &Field3D::getRegion2D(const std::string ®ion_name) const { +const Region& Field3D::getRegion2D(const std::string& region_name) const { return fieldmesh->getRegion2D(region_name); } @@ -238,10 +238,11 @@ const Region &Field3D::getRegion2D(const std::string ®ion_name) const /////////////////// ASSIGNMENT //////////////////// -Field3D & Field3D::operator=(const Field3D &rhs) { +Field3D& Field3D::operator=(const Field3D& rhs) { /// Check for self-assignment - if(this == &rhs) - return(*this); // skip this assignment + if (this == &rhs) { + return (*this); // skip this assignment + } TRACE("Field3D: Assignment from Field3D"); @@ -282,7 +283,7 @@ Field3D& Field3D::operator=(Field3D&& rhs) { return *this; } -Field3D & Field3D::operator=(const Field2D &rhs) { +Field3D& Field3D::operator=(const Field2D& rhs) { TRACE("Field3D = Field2D"); /// Check that the data is allocated @@ -299,7 +300,7 @@ Field3D & Field3D::operator=(const Field2D &rhs) { ASSERT1_FIELDS_COMPATIBLE(*this, rhs); /// Copy data - BOUT_FOR(i, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (i, rhs.getRegion("RGN_ALL")) { for (int iz = 0; iz < nz; iz++) { (*this)(i, iz) = rhs[i]; } @@ -308,7 +309,7 @@ Field3D & Field3D::operator=(const Field2D &rhs) { return *this; } -void Field3D::operator=(const FieldPerp &rhs) { +void Field3D::operator=(const FieldPerp& rhs) { TRACE("Field3D = FieldPerp"); ASSERT1_FIELDS_COMPATIBLE(*this, rhs); @@ -323,10 +324,12 @@ void Field3D::operator=(const FieldPerp &rhs) { allocate(); /// Copy data - BOUT_FOR(i, rhs.getRegion("RGN_ALL")) { (*this)(i, rhs.getIndex()) = rhs[i]; } + BOUT_FOR (i, rhs.getRegion("RGN_ALL")) { + (*this)(i, rhs.getIndex()) = rhs[i]; + } } -Field3D & Field3D::operator=(const BoutReal val) { +Field3D& Field3D::operator=(const BoutReal val) { TRACE("Field3D = BoutReal"); // Delete existing parallel slices. We don't copy parallel slices, so any @@ -335,7 +338,9 @@ Field3D & Field3D::operator=(const BoutReal val) { allocate(); - BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = val; } + BOUT_FOR (i, getRegion("RGN_ALL")) { + (*this)[i] = val; + } return *this; } @@ -387,16 +392,16 @@ void Field3D::applyBoundary(BoutReal t) { } } -void Field3D::applyBoundary(const std::string &condition) { +void Field3D::applyBoundary(const std::string& condition) { TRACE("Field3D::applyBoundary(condition)"); - + checkData(*this); /// Get the boundary factory (singleton) - BoundaryFactory *bfact = BoundaryFactory::getInstance(); - + BoundaryFactory* bfact = BoundaryFactory::getInstance(); + /// Loop over the mesh boundary regions - for(const auto& reg : fieldmesh->getBoundaries()) { + for (const auto& reg : fieldmesh->getBoundaries()) { auto op = std::unique_ptr{ dynamic_cast(bfact->create(condition, reg))}; op->apply(*this); @@ -405,16 +410,16 @@ void Field3D::applyBoundary(const std::string &condition) { //Field2D sets the corners to zero here, should we do the same here? } -void Field3D::applyBoundary(const std::string ®ion, const std::string &condition) { +void Field3D::applyBoundary(const std::string& region, const std::string& condition) { TRACE("Field3D::applyBoundary(string, string)"); checkData(*this); /// Get the boundary factory (singleton) - BoundaryFactory *bfact = BoundaryFactory::getInstance(); + BoundaryFactory* bfact = BoundaryFactory::getInstance(); bool region_found = false; /// Loop over the mesh boundary regions - for (const auto ® : fieldmesh->getBoundaries()) { + for (const auto& reg : fieldmesh->getBoundaries()) { if (reg->label == region) { region_found = true; auto op = std::unique_ptr{ @@ -443,22 +448,24 @@ void Field3D::applyTDerivBoundary() { } } -void Field3D::setBoundaryTo(const Field3D &f3d) { +void Field3D::setBoundaryTo(const Field3D& f3d) { TRACE("Field3D::setBoundary(const Field3D&)"); - + checkData(f3d); allocate(); // Make sure data allocated /// Loop over boundary regions - for(const auto& reg : fieldmesh->getBoundaries()) { + for (const auto& reg : fieldmesh->getBoundaries()) { /// Loop within each region - for(reg->first(); !reg->isDone(); reg->next()) { - for(int z=0;zfirst(); !reg->isDone(); reg->next()) { + for (int z = 0; z < nz; z++) { // Get value half-way between cells - BoutReal val = 0.5*(f3d(reg->x,reg->y,z) + f3d(reg->x-reg->bx, reg->y-reg->by, z)); + BoutReal val = + 0.5 * (f3d(reg->x, reg->y, z) + f3d(reg->x - reg->bx, reg->y - reg->by, z)); // Set to this value - (*this)(reg->x,reg->y,z) = 2.*val - (*this)(reg->x-reg->bx, reg->y-reg->by, z); + (*this)(reg->x, reg->y, z) = + 2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by, z); } } } @@ -490,7 +497,7 @@ void Field3D::applyParallelBoundary(BoutReal t) { } } -void Field3D::applyParallelBoundary(const std::string &condition) { +void Field3D::applyParallelBoundary(const std::string& condition) { TRACE("Field3D::applyParallelBoundary(condition)"); @@ -508,7 +515,8 @@ void Field3D::applyParallelBoundary(const std::string &condition) { } } -void Field3D::applyParallelBoundary(const std::string ®ion, const std::string &condition) { +void Field3D::applyParallelBoundary(const std::string& region, + const std::string& condition) { TRACE("Field3D::applyParallelBoundary(region, condition)"); @@ -529,7 +537,8 @@ void Field3D::applyParallelBoundary(const std::string ®ion, const std::string } } -void Field3D::applyParallelBoundary(const std::string ®ion, const std::string &condition, Field3D *f) { +void Field3D::applyParallelBoundary(const std::string& region, + const std::string& condition, Field3D* f) { TRACE("Field3D::applyParallelBoundary(region, condition, f)"); @@ -554,16 +563,15 @@ void Field3D::applyParallelBoundary(const std::string ®ion, const std::string } } - /*************************************************************** * NON-MEMBER OVERLOADED OPERATORS ***************************************************************/ -Field3D operator-(const Field3D &f) { return -1.0 * f; } +Field3D operator-(const Field3D& f) { return -1.0 * f; } //////////////// NON-MEMBER FUNCTIONS ////////////////// -Field3D pow(const Field3D &lhs, const Field2D &rhs, const std::string& rgn) { +Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn) { TRACE("pow(Field3D, Field2D)"); // Check if the inputs are allocated checkData(lhs); @@ -573,13 +581,15 @@ Field3D pow(const Field3D &lhs, const Field2D &rhs, const std::string& rgn) { // Define and allocate the output result Field3D result{emptyFrom(lhs)}; - BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); } + BOUT_FOR (i, result.getRegion(rgn)) { + result[i] = ::pow(lhs[i], rhs[i]); + } checkData(result); return result; } -FieldPerp pow(const Field3D &lhs, const FieldPerp &rhs, const std::string& rgn) { +FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn) { TRACE("pow(Field3D, FieldPerp)"); checkData(lhs); @@ -587,8 +597,8 @@ FieldPerp pow(const Field3D &lhs, const FieldPerp &rhs, const std::string& rgn) ASSERT1_FIELDS_COMPATIBLE(lhs, rhs); FieldPerp result{emptyFrom(rhs)}; - - BOUT_FOR(i, result.getRegion(rgn)) { + + BOUT_FOR (i, result.getRegion(rgn)) { result[i] = ::pow(lhs(i, rhs.getIndex()), rhs[i]); } @@ -599,9 +609,9 @@ FieldPerp pow(const Field3D &lhs, const FieldPerp &rhs, const std::string& rgn) ///////////////////////////////////////////////////////////////////// // Friend functions -Field3D filter(const Field3D &var, int N0, const std::string& rgn) { +Field3D filter(const Field3D& var, int N0, const std::string& rgn) { TRACE("filter(Field3D, int)"); - + checkData(var); int ncz = var.getNz(); @@ -611,13 +621,12 @@ Field3D filter(const Field3D &var, int N0, const std::string& rgn) { const auto region_str = toString(rgn); // Only allow a whitelist of regions for now - ASSERT2(region_str == "RGN_ALL" || region_str == "RGN_NOBNDRY" || - region_str == "RGN_NOX" || region_str == "RGN_NOY"); + ASSERT2(region_str == "RGN_ALL" || region_str == "RGN_NOBNDRY" + || region_str == "RGN_NOX" || region_str == "RGN_NOY"); - const Region ®ion = var.getRegion2D(region_str); + const Region& region = var.getRegion2D(region_str); - BOUT_OMP(parallel) - { + BOUT_OMP(parallel) { Array f(ncz / 2 + 1); BOUT_FOR_INNER(i, region) { @@ -645,7 +654,7 @@ Field3D filter(const Field3D &var, int N0, const std::string& rgn) { } // Fourier filter in z with zmin -Field3D lowPass(const Field3D &var, int zmax, bool keep_zonal, const std::string& rgn) { +Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string& rgn) { TRACE("lowPass(Field3D, {}, {})", zmax, keep_zonal); checkData(var); @@ -661,10 +670,10 @@ Field3D lowPass(const Field3D &var, int zmax, bool keep_zonal, const std::string const auto region_str = toString(rgn); // Only allow a whitelist of regions for now - ASSERT2(region_str == "RGN_ALL" || region_str == "RGN_NOBNDRY" || - region_str == "RGN_NOX" || region_str == "RGN_NOY"); + ASSERT2(region_str == "RGN_ALL" || region_str == "RGN_NOBNDRY" + || region_str == "RGN_NOX" || region_str == "RGN_NOY"); - const Region ®ion = var.getRegion2D(region_str); + const Region& region = var.getRegion2D(region_str); BOUT_OMP(parallel) { Array f(ncz / 2 + 1); @@ -674,8 +683,9 @@ Field3D lowPass(const Field3D &var, int zmax, bool keep_zonal, const std::string rfft(var(i.x(), i.y()), ncz, f.begin()); // Filter in z - for (int jz = zmax + 1; jz <= ncz / 2; jz++) + for (int jz = zmax + 1; jz <= ncz / 2; jz++) { f[jz] = 0.0; + } // Filter zonal mode if (!keep_zonal) { @@ -693,49 +703,48 @@ Field3D lowPass(const Field3D &var, int zmax, bool keep_zonal, const std::string /* * Use FFT to shift by an angle in the Z direction */ -void shiftZ(Field3D &var, int jx, int jy, double zangle) { +void shiftZ(Field3D& var, int jx, int jy, double zangle) { TRACE("shiftZ"); checkData(var); var.allocate(); // Ensure that var is unique - Mesh *localmesh = var.getMesh(); + Mesh* localmesh = var.getMesh(); int ncz = localmesh->LocalNz; - if(ncz == 1) + if (ncz == 1) { return; // Shifting doesn't do anything - - Array v(ncz/2 + 1); - - rfft(&(var(jx,jy,0)), ncz, v.begin()); // Forward FFT + } + + Array v(ncz / 2 + 1); + + rfft(&(var(jx, jy, 0)), ncz, v.begin()); // Forward FFT BoutReal zlength = var.getCoordinates()->zlength()(jx, jy); // Apply phase shift - for(int jz=1;jz<=ncz/2;jz++) { - BoutReal kwave=jz*2.0*PI/zlength; // wave number is 1/[rad] - v[jz] *= dcomplex(cos(kwave*zangle) , -sin(kwave*zangle)); + for (int jz = 1; jz <= ncz / 2; jz++) { + BoutReal kwave = jz * 2.0 * PI / zlength; // wave number is 1/[rad] + v[jz] *= dcomplex(cos(kwave * zangle), -sin(kwave * zangle)); } - irfft(v.begin(), ncz, &(var(jx,jy,0))); // Reverse FFT + irfft(v.begin(), ncz, &(var(jx, jy, 0))); // Reverse FFT } -void shiftZ(Field3D &var, double zangle, const std::string& rgn) { +void shiftZ(Field3D& var, double zangle, const std::string& rgn) { const auto region_str = toString(rgn); // Only allow a whitelist of regions for now - ASSERT2(region_str == "RGN_ALL" || region_str == "RGN_NOBNDRY" || - region_str == "RGN_NOX" || region_str == "RGN_NOY"); + ASSERT2(region_str == "RGN_ALL" || region_str == "RGN_NOBNDRY" + || region_str == "RGN_NOX" || region_str == "RGN_NOY"); - const Region ®ion = var.getRegion2D(region_str); + const Region& region = var.getRegion2D(region_str); // Could be OpenMP if shiftZ(Field3D, int, int, double) didn't throw - BOUT_FOR_SERIAL(i, region) { - shiftZ(var, i.x(), i.y(), zangle); - } + BOUT_FOR_SERIAL(i, region) { shiftZ(var, i.x(), i.y(), zangle); } } namespace { - // Internal routine to avoid ugliness with interactions between CHECK - // levels and UNUSED parameters +// Internal routine to avoid ugliness with interactions between CHECK +// levels and UNUSED parameters #if CHECK > 2 void checkDataIsFiniteOnRegion(const Field3D& f, const std::string& region) { // Do full checks @@ -748,29 +757,31 @@ void checkDataIsFiniteOnRegion(const Field3D& f, const std::string& region) { } #elif CHECK > 0 // No-op for no checking -void checkDataIsFiniteOnRegion(const Field3D &UNUSED(f), const std::string& UNUSED(region)) {} +void checkDataIsFiniteOnRegion(const Field3D& UNUSED(f), + const std::string& UNUSED(region)) {} #endif -} +} // namespace #if CHECK > 0 -void checkData(const Field3D &f, const std::string& region) { - if (!f.isAllocated()) +void checkData(const Field3D& f, const std::string& region) { + if (!f.isAllocated()) { throw BoutException("Field3D: Operation on empty data\n"); + } checkDataIsFiniteOnRegion(f, region); } #endif -Field2D DC(const Field3D &f, const std::string& rgn) { +Field2D DC(const Field3D& f, const std::string& rgn) { TRACE("DC(Field3D)"); checkData(f); - Mesh *localmesh = f.getMesh(); + Mesh* localmesh = f.getMesh(); Field2D result(localmesh, f.getLocation()); result.allocate(); - BOUT_FOR(i, result.getRegion(rgn)) { + BOUT_FOR (i, result.getRegion(rgn)) { result[i] = 0.0; for (int k = 0; k < localmesh->LocalNz; k++) { result[i] += f[localmesh->ind2Dto3D(i, k)]; @@ -783,19 +794,21 @@ Field2D DC(const Field3D &f, const std::string& rgn) { } #if CHECK > 2 -void invalidateGuards(Field3D &var) { - BOUT_FOR(i, var.getRegion("RGN_GUARDS")) { var[i] = BoutNaN; } +void invalidateGuards(Field3D& var) { + BOUT_FOR (i, var.getRegion("RGN_GUARDS")) { + var[i] = BoutNaN; + } } #endif -bool operator==(const Field3D &a, const Field3D &b) { +bool operator==(const Field3D& a, const Field3D& b) { if (!a.isAllocated() || !b.isAllocated()) { return false; } return min(abs(a - b)) < 1e-10; } -std::ostream& operator<<(std::ostream &out, const Field3D &value) { +std::ostream& operator<<(std::ostream& out, const Field3D& value) { out << toString(value); return out; } diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx index 2c7ba6b1fb..689f2549c3 100644 --- a/src/field/field_data.cxx +++ b/src/field/field_data.cxx @@ -1,13 +1,13 @@ -#include "parallel_boundary_op.hxx" -#include "parallel_boundary_region.hxx" -#include "unused.hxx" +#include "bout/parallel_boundary_op.hxx" +#include "bout/parallel_boundary_region.hxx" +#include "bout/unused.hxx" #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include namespace bout { /// Make sure \p location is a sensible value for \p mesh @@ -69,10 +69,11 @@ FieldData::FieldData(const FieldData& other) { } FieldData::~FieldData() { - if(!boundaryIsCopy) { + if (!boundaryIsCopy) { // Delete the boundary operations - for(const auto& bndry : bndry_op) + for (const auto& bndry : bndry_op) { delete bndry; + } } } @@ -145,8 +146,9 @@ void FieldData::setBoundary(const std::string& name) { /// Loop over the mesh boundary regions for (const auto& reg : mesh->getBoundaries()) { auto* op = dynamic_cast(bfact->createFromOptions(name, reg)); - if (op != nullptr) + if (op != nullptr) { bndry_op.push_back(op); + } output_info << endl; } @@ -155,8 +157,9 @@ void FieldData::setBoundary(const std::string& name) { /// Loop over the mesh parallel boundary regions for (const auto& reg : mesh->getBoundariesPar()) { auto* op = dynamic_cast(bfact->createFromOptions(name, reg)); - if (op != nullptr) + if (op != nullptr) { bndry_op_par.push_back(op); + } output_info << endl; } @@ -164,7 +167,7 @@ void FieldData::setBoundary(const std::string& name) { boundaryIsCopy = false; } -void FieldData::copyBoundary(const FieldData &f) { +void FieldData::copyBoundary(const FieldData& f) { bndry_op = f.bndry_op; bndry_op_par = f.bndry_op_par; boundaryIsCopy = true; @@ -172,7 +175,7 @@ void FieldData::copyBoundary(const FieldData &f) { } //JMAD -void FieldData::addBndryFunction(FuncPtr userfunc, BndryLoc location){ +void FieldData::addBndryFunction(FuncPtr userfunc, BndryLoc location) { addBndryGenerator(std::make_shared(userfunc), location); } @@ -194,8 +197,9 @@ void FieldData::addBndryGenerator(FieldGeneratorPtr gen, BndryLoc location) { FieldGeneratorPtr FieldData::getBndryGenerator(BndryLoc location) { auto it = bndry_generator.find(location); - if(it == bndry_generator.end()) + if (it == bndry_generator.end()) { return nullptr; + } return it->second; } diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx index 9c1f0304a5..685a1a9727 100644 --- a/src/field/field_factory.cxx +++ b/src/field/field_factory.cxx @@ -19,15 +19,15 @@ * along with BOUT++. If not, see . * **************************************************************************/ -#include +#include -#include +#include #include #include -#include -#include +#include +#include #include "bout/constants.hxx" @@ -46,37 +46,41 @@ FieldGeneratorPtr generator(BoutReal* ptr) { } namespace { - /// Provides a placeholder whose target can be changed after creation. - /// This enables recursive FieldGenerator expressions to be generated - class FieldIndirect : public FieldGenerator { - public: - /// depth_limit sets the maximum iteration depth. Set to < 0 for no limit - FieldIndirect(std::string name, int depth_limit = 0) : name(name), depth_limit(depth_limit) {} - - /// Set the target, to be called when generator is called - void setTarget(FieldGeneratorPtr fieldgen) { target = fieldgen; } - - double generate(const Context& ctx) override { - if (depth_counter == depth_limit) { - throw BoutException("Calling {:s} to recursion depth {:d} exceeds maximum {:d}\n", - name, depth_counter, depth_limit); - } - ++depth_counter; - BoutReal result = target->generate(ctx); - --depth_counter; - return result; +/// Provides a placeholder whose target can be changed after creation. +/// This enables recursive FieldGenerator expressions to be generated +class FieldIndirect : public FieldGenerator { +public: + /// depth_limit sets the maximum iteration depth. Set to < 0 for no limit + FieldIndirect(std::string name, int depth_limit = 0) + : name(name), depth_limit(depth_limit) {} + + /// Set the target, to be called when generator is called + void setTarget(FieldGeneratorPtr fieldgen) { target = fieldgen; } + + double generate(const Context& ctx) override { + if (depth_counter == depth_limit) { + throw BoutException("Calling {:s} to recursion depth {:d} exceeds maximum {:d}\n", + name, depth_counter, depth_limit); } + ++depth_counter; + BoutReal result = target->generate(ctx); + --depth_counter; + return result; + } - /// Note: returns the name rather than target->str, to avoid infinite recursion - std::string str() const override { return name; } - private: - std::string name; ///< Name of the expression being pointed to - int depth_counter {0}; ///< Counts the iteration depth, to provide a maximum number of iterations - int depth_limit{0}; ///< Maximum call depth. If 0 then no recursion allowed (generate fails first time). - - FieldGeneratorPtr target; - }; -} + /// Note: returns the name rather than target->str, to avoid infinite recursion + std::string str() const override { return name; } + +private: + std::string name; ///< Name of the expression being pointed to + int depth_counter{ + 0}; ///< Counts the iteration depth, to provide a maximum number of iterations + int depth_limit{ + 0}; ///< Maximum call depth. If 0 then no recursion allowed (generate fails first time). + + FieldGeneratorPtr target; +}; +} // namespace ////////////////////////////////////////////////////////// // FieldFactory public functions @@ -89,21 +93,23 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt) // Note: don't use 'options' here because 'options' is a 'const Options*' // pointer, so this would fail if the "input" section is not present. Options& nonconst_options{opt == nullptr ? Options::root() : *opt}; - transform_from_field_aligned - = nonconst_options["input"]["transform_from_field_aligned"].withDefault(true); + transform_from_field_aligned = + nonconst_options["input"]["transform_from_field_aligned"].withDefault(true); // Convert using stoi rather than Options, or a FieldFactory is used to parse // the string, leading to infinite loop. try { - max_recursion_depth = std::stoi(nonconst_options["input"]["max_recursion_depth"] - .doc("Maximum recursion depth allowed in expressions. 0 = no " - "recursion; -1 = unlimited") - .withDefault("0")); + max_recursion_depth = + std::stoi(nonconst_options["input"]["max_recursion_depth"] + .doc("Maximum recursion depth allowed in expressions. 0 = no " + "recursion; -1 = unlimited") + .withDefault("0")); } catch (const std::exception&) { - throw ParseException("Invalid integer given as input:max_recursion_depth: '{:s}'", + throw ParseException( + "Invalid integer given as input:max_recursion_depth: '{:s}'", nonconst_options["input"]["max_recursion_depth"].as()); } - + // Useful values addGenerator("pi", std::make_shared(PI)); addGenerator("π", std::make_shared(PI)); @@ -177,7 +183,7 @@ Field2D FieldFactory::create2D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC result.allocate(); result.setLocation(loc); - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { result[i] = gen->generate(Context(i, loc, localmesh, t)); }; @@ -209,7 +215,7 @@ Field3D FieldFactory::create3D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC auto result = Field3D(localmesh).setLocation(loc).setDirectionY(y_direction).allocate(); - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { result[i] = gen->generate(Context(i, loc, localmesh, t)); }; @@ -236,7 +242,7 @@ Field3D FieldFactory::create3D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC } FieldPerp FieldFactory::createPerp(const std::string& value, const Options* opt, - Mesh* localmesh, CELL_LOC loc, BoutReal t) const { + Mesh* localmesh, CELL_LOC loc, BoutReal t) const { return createPerp(parse(value, opt), localmesh, loc, t); } @@ -258,9 +264,10 @@ FieldPerp FieldFactory::createPerp(FieldGeneratorPtr gen, Mesh* localmesh, CELL_ const auto y_direction = transform_from_field_aligned ? YDirectionType::Aligned : YDirectionType::Standard; - auto result = FieldPerp(localmesh).setLocation(loc).setDirectionY(y_direction).allocate(); + auto result = + FieldPerp(localmesh).setLocation(loc).setDirectionY(y_direction).allocate(); - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { result[i] = gen->generate(Context(i, loc, localmesh, t)); }; @@ -295,8 +302,9 @@ const Options* FieldFactory::findOption(const Options* opt, const std::string& n while (!result->isSet(name)) { result = result->getParent(); - if (result == nullptr) + if (result == nullptr) { throw ParseException("Cannot find variable '{:s}'", name); + } } result->get(name, val, ""); @@ -372,21 +380,22 @@ FieldGeneratorPtr FieldFactory::resolve(const std::string& name) const { if (max_recursion_depth != 0) { // Recursion allowed. If < 0 then no limit, if > 0 then recursion limited - + // Create an object which can be used in FieldGenerator trees. // The target does not yet exist, but will be set after parsing is complete auto indirection = std::make_shared(name, max_recursion_depth); - + cache[key] = indirection; FieldGeneratorPtr g = parse(value, section); - indirection->setTarget(g); // set so that calls to self will point to the right place + indirection->setTarget( + g); // set so that calls to self will point to the right place cache[key] = g; return g; } // Recursion not allowed. Keep track of keys being resolved // This is done so that an error can be printed at parse time rather // than run time (generate call). - + lookup.push_back(key); FieldGeneratorPtr g = parse(value, section); @@ -402,7 +411,8 @@ FieldGeneratorPtr FieldFactory::resolve(const std::string& name) const { } std::multiset -FieldFactory::fuzzyFind(const std::string& name, std::string::size_type max_distance) const { +FieldFactory::fuzzyFind(const std::string& name, + std::string::size_type max_distance) const { // First use parent fuzzyFind to check the list of generators auto matches = ExpressionParser::fuzzyFind(name, max_distance); @@ -418,7 +428,8 @@ FieldFactory::fuzzyFind(const std::string& name, std::string::size_type max_dist return matches; } -FieldGeneratorPtr FieldFactory::parse(const std::string& input, const Options* opt) const { +FieldGeneratorPtr FieldFactory::parse(const std::string& input, + const Options* opt) const { // Check if in the cache std::string key = "#" + input; diff --git a/src/field/fieldgenerators.cxx b/src/field/fieldgenerators.cxx index bd369d1ab2..1f21f5c262 100644 --- a/src/field/fieldgenerators.cxx +++ b/src/field/fieldgenerators.cxx @@ -2,7 +2,7 @@ #include "fieldgenerators.hxx" #include -#include +#include using bout::generator::Context; @@ -28,7 +28,7 @@ FieldGeneratorPtr FieldGaussian::clone(const std::list args) BoutReal FieldGaussian::generate(const Context& ctx) { BoutReal sigma = s->generate(ctx); - return exp(-SQ(X->generate(ctx)/sigma)/2.) / (sqrt(TWOPI) * sigma); + return exp(-SQ(X->generate(ctx) / sigma) / 2.) / (sqrt(TWOPI) * sigma); } FieldGeneratorPtr FieldHeaviside::clone(const std::list args) { @@ -51,11 +51,11 @@ BoutReal FieldHeaviside::generate(const Context& ctx) { FieldGeneratorPtr FieldBallooning::clone(const std::list args) { int n = ball_n; - switch(args.size()) { + switch (args.size()) { case 2: { // Second optional argument is ball_n, an integer // This should probably warn if arg isn't constant - n = ROUND( args.back()->generate(Context()) ); + n = ROUND(args.back()->generate(Context())); } // Fall through case 1: { return std::make_shared(mesh, args.front(), n); @@ -66,19 +66,22 @@ FieldGeneratorPtr FieldBallooning::clone(const std::list args } BoutReal FieldBallooning::generate(const Context& ctx) { - Mesh *localmesh = ctx.getMesh(); - if (!localmesh) + Mesh* localmesh = ctx.getMesh(); + if (!localmesh) { throw BoutException("ballooning function needs a valid mesh"); - if (ball_n < 1) + } + if (ball_n < 1) { throw BoutException("ballooning function ball_n less than 1"); + } BoutReal ts; // Twist-shift angle Coordinates* coords = localmesh->getCoordinates(); // Need to find the nearest flux surface (x index) // This assumes that localmesh->GlobalX is linear in x index - BoutReal dx = (localmesh->GlobalX(localmesh->xend) - localmesh->GlobalX(localmesh->xstart)) - / (localmesh->xend - localmesh->xstart); + BoutReal dx = + (localmesh->GlobalX(localmesh->xend) - localmesh->GlobalX(localmesh->xstart)) + / (localmesh->xend - localmesh->xstart); int jx = ROUND((ctx.x() - localmesh->GlobalX(0)) / dx); const BoutReal zlength = getUniform(coords->zlength()); @@ -110,13 +113,14 @@ FieldMixmode::FieldMixmode(FieldGeneratorPtr a, BoutReal seed) : arg(std::move(a // Calculate the phases -PI to +PI // using genRand [0,1] - for (int i = 0; i < 14; i++) + for (int i = 0; i < 14; i++) { phase[i] = PI * (2. * genRand(seed + i) - 1.); + } } FieldGeneratorPtr FieldMixmode::clone(const std::list args) { BoutReal seed = 0.5; - switch(args.size()) { + switch (args.size()) { case 2: { // Second optional argument is the seed, which should be a constant seed = args.back()->generate(Context()); @@ -133,10 +137,9 @@ BoutReal FieldMixmode::generate(const Context& ctx) { BoutReal result = 0.0; // A mixture of mode numbers - for(int i=0;i<14;i++) { + for (int i = 0; i < 14; i++) { // This produces a spectrum which is peaked around mode number 4 - result += ( 1./SQ(1. + std::abs(i - 4)) ) * - cos(i * arg->generate(ctx) + phase[i]); + result += (1. / SQ(1. + std::abs(i - 4))) * cos(i * arg->generate(ctx) + phase[i]); } return result; @@ -144,19 +147,21 @@ BoutReal FieldMixmode::generate(const Context& ctx) { BoutReal FieldMixmode::genRand(BoutReal seed) { // Make sure seed is - if(seed < 0.0) + if (seed < 0.0) { seed *= -1; + } // Round the seed to get the number of iterations int niter = 11 + (23 + ROUND(seed)) % 79; // Start x between 0 and 1 (exclusive) const BoutReal A = 0.01, B = 1.23456789; - BoutReal x = (A + fmod(seed,B)) / (B + 2.*A); + BoutReal x = (A + fmod(seed, B)) / (B + 2. * A); // Iterate logistic map - for(int i=0;i!=niter;++i) + for (int i = 0; i != niter; ++i) { x = 3.99 * x * (1. - x); + } return x; } @@ -190,11 +195,10 @@ FieldGeneratorPtr FieldTanhHat::clone(const std::list args) { BoutReal FieldTanhHat::generate(const Context& ctx) { // The following are constants - BoutReal w = width ->generate(Context()); - BoutReal c = center ->generate(Context()); + BoutReal w = width->generate(Context()); + BoutReal c = center->generate(Context()); BoutReal s = steepness->generate(Context()); - return 0.5*( - tanh( s*(X->generate(ctx) - (c - 0.5*w)) ) - - tanh( s*(X->generate(ctx) - (c + 0.5*w)) ) - ); + return 0.5 + * (tanh(s * (X->generate(ctx) - (c - 0.5 * w))) + - tanh(s * (X->generate(ctx) - (c + 0.5 * w)))); } diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx index 156a48784e..66ef11a855 100644 --- a/src/field/fieldgenerators.hxx +++ b/src/field/fieldgenerators.hxx @@ -7,9 +7,9 @@ #ifndef __FIELDGENERATORS_H__ #define __FIELDGENERATORS_H__ -#include -#include -#include +#include +#include +#include #include @@ -24,9 +24,7 @@ public: FieldGeneratorPtr clone(const std::list UNUSED(args)) override { return std::make_shared(ptr); } - BoutReal generate(const bout::generator::Context&) override { - return *ptr; - } + BoutReal generate(const bout::generator::Context&) override { return *ptr; } private: BoutReal* ptr; @@ -37,10 +35,11 @@ private: /// Template class to define generators around a C function using single_arg_op = BoutReal (*)(BoutReal); -template +template class FieldGenOneArg : public FieldGenerator { ///< Template for single-argument function public: - FieldGenOneArg(FieldGeneratorPtr g, const std::string& name = "function") : gen(g), name(name) {} + FieldGenOneArg(FieldGeneratorPtr g, const std::string& name = "function") + : gen(g), name(name) {} FieldGeneratorPtr clone(const std::list args) override { if (args.size() != 1) { throw ParseException("Incorrect number of arguments to {:s}. Expecting 1, got {:d}", @@ -65,7 +64,9 @@ using double_arg_op = BoutReal (*)(BoutReal, BoutReal); template class FieldGenTwoArg : public FieldGenerator { ///< Template for two-argument function public: - FieldGenTwoArg(FieldGeneratorPtr a, FieldGeneratorPtr b, const std::string& name = "function") : A(a), B(b), name(name) {} + FieldGenTwoArg(FieldGeneratorPtr a, FieldGeneratorPtr b, + const std::string& name = "function") + : A(a), B(b), name(name) {} FieldGeneratorPtr clone(const std::list args) override { if (args.size() != 2) { throw ParseException("Incorrect number of arguments to {:s}. Expecting 2, got {:d}", @@ -100,8 +101,9 @@ public: args.size()); } BoutReal generate(const bout::generator::Context& pos) override { - if (B == nullptr) + if (B == nullptr) { return atan(A->generate(pos)); + } return atan2(A->generate(pos), B->generate(pos)); } @@ -152,8 +154,9 @@ public: BoutReal result = (*it)->generate(pos); for (; it != input.end(); it++) { BoutReal val = (*it)->generate(pos); - if (val < result) + if (val < result) { result = val; + } } return result; } @@ -178,8 +181,9 @@ public: BoutReal result = (*it)->generate(pos); for (; it != input.end(); it++) { BoutReal val = (*it)->generate(pos); - if (val > result) + if (val > result) { result = val; + } } return result; } @@ -227,7 +231,7 @@ public: } private: - FieldGeneratorPtr value; ///< The value to be clamped + FieldGeneratorPtr value; ///< The value to be clamped FieldGeneratorPtr low, high; ///< The range within which the result will be }; @@ -303,7 +307,7 @@ public: // Constructor FieldTanhHat(FieldGeneratorPtr xin, FieldGeneratorPtr widthin, FieldGeneratorPtr centerin, FieldGeneratorPtr steepnessin) - : X(xin), width(widthin), center(centerin), steepness(steepnessin) {}; + : X(xin), width(widthin), center(centerin), steepness(steepnessin){}; // Clone containing the list of arguments FieldGeneratorPtr clone(const std::list args) override; BoutReal generate(const bout::generator::Context& pos) override; @@ -348,5 +352,4 @@ private: FieldGeneratorPtr test, gt0, lt0; }; - #endif // __FIELDGENERATORS_H__ diff --git a/src/field/fieldgroup.cxx b/src/field/fieldgroup.cxx index 4874825cb0..f85cbb6843 100644 --- a/src/field/fieldgroup.cxx +++ b/src/field/fieldgroup.cxx @@ -1,7 +1,7 @@ #include -FieldGroup operator+(const FieldGroup &lhs, const FieldGroup &rhs) { +FieldGroup operator+(const FieldGroup& lhs, const FieldGroup& rhs) { return FieldGroup(lhs) += rhs; } diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx index 16335f6d6d..23c47e762c 100644 --- a/src/field/fieldperp.cxx +++ b/src/field/fieldperp.cxx @@ -23,28 +23,27 @@ * **************************************************************************/ -#include -#include +#include +#include #include #include -#include -#include -#include -#include - -FieldPerp::FieldPerp(Mesh *localmesh, CELL_LOC location_in, int yindex_in, - DirectionTypes directions) - : Field(localmesh, location_in, directions), - yindex(yindex_in) { +#include +#include +#include +#include + +FieldPerp::FieldPerp(Mesh* localmesh, CELL_LOC location_in, int yindex_in, + DirectionTypes directions) + : Field(localmesh, location_in, directions), yindex(yindex_in) { if (fieldmesh) { nx = fieldmesh->LocalNx; nz = fieldmesh->LocalNz; } } -FieldPerp::FieldPerp(BoutReal val, Mesh *localmesh) : FieldPerp(localmesh) { +FieldPerp::FieldPerp(BoutReal val, Mesh* localmesh) : FieldPerp(localmesh) { *this = val; } @@ -70,8 +69,9 @@ FieldPerp& FieldPerp::allocate() { #if CHECK > 2 invalidateGuards(*this); #endif - } else + } else { data.ensureUnique(); + } return *this; } @@ -96,20 +96,22 @@ FieldPerp& FieldPerp::operator=(const FieldPerp& rhs) { return *this; } -FieldPerp & FieldPerp::operator=(const BoutReal rhs) { +FieldPerp& FieldPerp::operator=(const BoutReal rhs) { TRACE("FieldPerp = BoutReal"); allocate(); - BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = rhs; } + BOUT_FOR (i, getRegion("RGN_ALL")) { + (*this)[i] = rhs; + } return *this; } -const Region &FieldPerp::getRegion(REGION region) const { +const Region& FieldPerp::getRegion(REGION region) const { return fieldmesh->getRegionPerp(toString(region)); } -const Region &FieldPerp::getRegion(const std::string ®ion_name) const { +const Region& FieldPerp::getRegion(const std::string& region_name) const { return fieldmesh->getRegionPerp(region_name); } @@ -151,7 +153,7 @@ FieldPerp fromFieldAligned(const FieldPerp& f, const std::string& region) { ////////////// NON-MEMBER OVERLOADED OPERATORS ////////////// // Unary minus -FieldPerp operator-(const FieldPerp &f) { return -1.0 * f; } +FieldPerp operator-(const FieldPerp& f) { return -1.0 * f; } ///////////////////////////////////////////////// // functions @@ -165,14 +167,16 @@ const FieldPerp sliceXZ(const Field3D& f, int y) { // Allocate memory result.allocate(); - BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = f(i, y); } + BOUT_FOR (i, result.getRegion("RGN_ALL")) { + result[i] = f(i, y); + } checkData(result); return result; } #if CHECK > 2 -void checkDataIsFiniteOnRegion(const FieldPerp &f, const std::string& region) { +void checkDataIsFiniteOnRegion(const FieldPerp& f, const std::string& region) { // Do full checks BOUT_FOR_SERIAL(i, f.getRegion(region)) { if (!::finite(f[i])) { @@ -182,13 +186,13 @@ void checkDataIsFiniteOnRegion(const FieldPerp &f, const std::string& region) { } } #else -void checkDataIsFiniteOnRegion(const FieldPerp &UNUSED(f), const std::string& UNUSED(region)) {} +void checkDataIsFiniteOnRegion(const FieldPerp& UNUSED(f), + const std::string& UNUSED(region)) {} #endif - #if CHECK > 0 /// Check if the data is valid -void checkData(const FieldPerp &f, const std::string& region) { +void checkData(const FieldPerp& f, const std::string& region) { if (!f.isAllocated()) { throw BoutException("FieldPerp: Operation on empty data\n"); } @@ -200,8 +204,10 @@ void checkData(const FieldPerp &f, const std::string& region) { #endif #if CHECK > 2 -void invalidateGuards(FieldPerp &var) { - BOUT_FOR(i, var.getRegion("RGN_GUARDS")) { var[i] = BoutNaN; } +void invalidateGuards(FieldPerp& var) { + BOUT_FOR (i, var.getRegion("RGN_GUARDS")) { + var[i] = BoutNaN; + } } #endif diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx index 91fe31f3d1..b2b3e32ef9 100644 --- a/src/field/generated_fieldops.cxx +++ b/src/field/generated_fieldops.cxx @@ -1,10 +1,10 @@ // This file is autogenerated - see gen_fieldops.py #include #include -#include -#include -#include -#include +#include +#include +#include +#include // Provide the C++ wrapper for multiplication of Field3D and Field3D Field3D operator*(const Field3D& lhs, const Field3D& rhs) { @@ -14,7 +14,7 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -36,7 +36,9 @@ Field3D& Field3D::operator*=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= rhs[index]; + } checkData(*this); @@ -54,7 +56,7 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -76,7 +78,9 @@ Field3D& Field3D::operator/=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] /= rhs[index]; + } checkData(*this); @@ -94,7 +98,7 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -116,7 +120,9 @@ Field3D& Field3D::operator+=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] += rhs[index]; + } checkData(*this); @@ -134,7 +140,7 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -156,7 +162,9 @@ Field3D& Field3D::operator-=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] -= rhs[index]; + } checkData(*this); @@ -176,7 +184,7 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[base_ind + jz] * rhs[index]; @@ -201,7 +209,7 @@ Field3D& Field3D::operator*=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { (*this)[base_ind + jz] *= rhs[index]; @@ -226,7 +234,7 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); const auto tmp = 1.0 / rhs[index]; for (int jz = 0; jz < localmesh->LocalNz; ++jz) { @@ -252,7 +260,7 @@ Field3D& Field3D::operator/=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); const auto tmp = 1.0 / rhs[index]; for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { @@ -278,7 +286,7 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[base_ind + jz] + rhs[index]; @@ -303,7 +311,7 @@ Field3D& Field3D::operator+=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { (*this)[base_ind + jz] += rhs[index]; @@ -328,7 +336,7 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[base_ind + jz] - rhs[index]; @@ -353,7 +361,7 @@ Field3D& Field3D::operator-=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { (*this)[base_ind + jz] -= rhs[index]; @@ -378,7 +386,7 @@ FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] * rhs[index]; @@ -398,7 +406,7 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] / rhs[index]; @@ -418,7 +426,7 @@ FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] + rhs[index]; @@ -438,7 +446,7 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] - rhs[index]; @@ -455,7 +463,9 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] * rhs; + } checkData(result); return result; @@ -474,7 +484,9 @@ Field3D& Field3D::operator*=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= rhs; + } checkData(*this); @@ -492,7 +504,9 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] * tmp; + } checkData(result); return result; @@ -512,7 +526,9 @@ Field3D& Field3D::operator/=(const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= tmp; + } checkData(*this); @@ -529,7 +545,9 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] + rhs; + } checkData(result); return result; @@ -548,7 +566,9 @@ Field3D& Field3D::operator+=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] += rhs; + } checkData(*this); @@ -565,7 +585,9 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] - rhs; + } checkData(result); return result; @@ -584,7 +606,9 @@ Field3D& Field3D::operator-=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] -= rhs; + } checkData(*this); @@ -604,7 +628,7 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] * rhs[base_ind + jz]; @@ -625,7 +649,7 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] / rhs[base_ind + jz]; @@ -646,7 +670,7 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] + rhs[base_ind + jz]; @@ -667,7 +691,7 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] - rhs[base_ind + jz]; @@ -686,7 +710,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -704,7 +728,9 @@ Field2D& Field2D::operator*=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= rhs[index]; + } checkData(*this); @@ -722,7 +748,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -740,7 +766,9 @@ Field2D& Field2D::operator/=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] /= rhs[index]; + } checkData(*this); @@ -758,7 +786,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -776,7 +804,9 @@ Field2D& Field2D::operator+=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] += rhs[index]; + } checkData(*this); @@ -794,7 +824,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -812,7 +842,9 @@ Field2D& Field2D::operator-=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] -= rhs[index]; + } checkData(*this); @@ -832,7 +864,7 @@ FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] * rhs[index]; @@ -852,7 +884,7 @@ FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] / rhs[index]; @@ -872,7 +904,7 @@ FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] + rhs[index]; @@ -892,7 +924,7 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] - rhs[index]; @@ -909,7 +941,9 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] * rhs; + } checkData(result); return result; @@ -924,7 +958,9 @@ Field2D& Field2D::operator*=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= rhs; + } checkData(*this); @@ -942,7 +978,9 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] * tmp; + } checkData(result); return result; @@ -958,7 +996,9 @@ Field2D& Field2D::operator/=(const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= tmp; + } checkData(*this); @@ -975,7 +1015,9 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] + rhs; + } checkData(result); return result; @@ -990,7 +1032,9 @@ Field2D& Field2D::operator+=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] += rhs; + } checkData(*this); @@ -1007,7 +1051,9 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] - rhs; + } checkData(result); return result; @@ -1022,7 +1068,9 @@ Field2D& Field2D::operator-=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] -= rhs; + } checkData(*this); @@ -1042,7 +1090,7 @@ FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] * rhs[base_ind]; @@ -1064,7 +1112,7 @@ FieldPerp& FieldPerp::operator*=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] *= rhs[base_ind]; @@ -1088,7 +1136,7 @@ FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] / rhs[base_ind]; @@ -1110,7 +1158,7 @@ FieldPerp& FieldPerp::operator/=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] /= rhs[base_ind]; @@ -1134,7 +1182,7 @@ FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] + rhs[base_ind]; @@ -1156,7 +1204,7 @@ FieldPerp& FieldPerp::operator+=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] += rhs[base_ind]; @@ -1180,7 +1228,7 @@ FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] - rhs[base_ind]; @@ -1202,7 +1250,7 @@ FieldPerp& FieldPerp::operator-=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] -= rhs[base_ind]; @@ -1226,7 +1274,7 @@ FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] * rhs[base_ind]; @@ -1248,7 +1296,7 @@ FieldPerp& FieldPerp::operator*=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] *= rhs[base_ind]; @@ -1272,7 +1320,7 @@ FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] / rhs[base_ind]; @@ -1294,7 +1342,7 @@ FieldPerp& FieldPerp::operator/=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] /= rhs[base_ind]; @@ -1318,7 +1366,7 @@ FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] + rhs[base_ind]; @@ -1340,7 +1388,7 @@ FieldPerp& FieldPerp::operator+=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] += rhs[base_ind]; @@ -1364,7 +1412,7 @@ FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] - rhs[base_ind]; @@ -1386,7 +1434,7 @@ FieldPerp& FieldPerp::operator-=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { + BOUT_FOR (index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] -= rhs[base_ind]; @@ -1408,7 +1456,7 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -1426,7 +1474,9 @@ FieldPerp& FieldPerp::operator*=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= rhs[index]; + } checkData(*this); @@ -1444,7 +1494,7 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -1462,7 +1512,9 @@ FieldPerp& FieldPerp::operator/=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] /= rhs[index]; + } checkData(*this); @@ -1480,7 +1532,7 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -1498,7 +1550,9 @@ FieldPerp& FieldPerp::operator+=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] += rhs[index]; + } checkData(*this); @@ -1516,7 +1570,7 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { + BOUT_FOR (index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -1534,7 +1588,9 @@ FieldPerp& FieldPerp::operator-=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] -= rhs[index]; + } checkData(*this); @@ -1551,7 +1607,9 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] * rhs; + } checkData(result); return result; @@ -1566,7 +1624,9 @@ FieldPerp& FieldPerp::operator*=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] *= rhs; + } checkData(*this); @@ -1584,7 +1644,9 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] * tmp; + } checkData(result); return result; @@ -1599,7 +1661,9 @@ FieldPerp& FieldPerp::operator/=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] /= rhs; + } checkData(*this); @@ -1616,7 +1680,9 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] + rhs; + } checkData(result); return result; @@ -1631,7 +1697,9 @@ FieldPerp& FieldPerp::operator+=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] += rhs; + } checkData(*this); @@ -1648,7 +1716,9 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs[index] - rhs; + } checkData(result); return result; @@ -1663,7 +1733,9 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; } + BOUT_FOR (index, this->getRegion("RGN_ALL")) { + (*this)[index] -= rhs; + } checkData(*this); @@ -1680,7 +1752,9 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs * rhs[index]; + } checkData(result); return result; @@ -1693,7 +1767,9 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs / rhs[index]; + } checkData(result); return result; @@ -1706,7 +1782,9 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs + rhs[index]; + } checkData(result); return result; @@ -1719,7 +1797,9 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs - rhs[index]; + } checkData(result); return result; @@ -1732,7 +1812,9 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs * rhs[index]; + } checkData(result); return result; @@ -1745,7 +1827,9 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs / rhs[index]; + } checkData(result); return result; @@ -1758,7 +1842,9 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs + rhs[index]; + } checkData(result); return result; @@ -1771,7 +1857,9 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs - rhs[index]; + } checkData(result); return result; @@ -1784,7 +1872,9 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs * rhs[index]; + } checkData(result); return result; @@ -1797,7 +1887,9 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs / rhs[index]; + } checkData(result); return result; @@ -1810,7 +1902,9 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs + rhs[index]; + } checkData(result); return result; @@ -1823,7 +1917,9 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } + BOUT_FOR (index, result.getRegion("RGN_ALL")) { + result[index] = lhs - rhs[index]; + } checkData(result); return result; diff --git a/src/field/globalfield.cxx b/src/field/globalfield.cxx index 5428869dcd..d98a0660e1 100644 --- a/src/field/globalfield.cxx +++ b/src/field/globalfield.cxx @@ -1,48 +1,51 @@ #include -#include -#include +#include +#include + +GlobalField::GlobalField(Mesh* m, int proc, int xsize, int ysize, int zsize) + : mesh(m), data_on_proc(proc), nx(xsize), ny(ysize), nz(zsize) { -GlobalField::GlobalField(Mesh *m, int proc, int xsize, int ysize, int zsize) - : mesh(m), data_on_proc(proc), nx(xsize), ny(ysize), nz(zsize) { - comm = BoutComm::get(); // This should come from Mesh - + MPI_Comm_size(comm, &npes); MPI_Comm_rank(comm, &mype); - - if(nx*ny*nz <= 0) + + if (nx * ny * nz <= 0) { throw BoutException("GlobalField data must have non-zero size"); + } - if(mype == proc) { + if (mype == proc) { // Allocate memory data.reallocate(nx * ny * nz); } } -void GlobalField::proc_local_origin(int proc, int *x, int *y, int *z) const { - +void GlobalField::proc_local_origin(int proc, int* x, int* y, int* z) const { + int nxpe = mesh->getNXPE(); - if(proc % nxpe == 0) { + if (proc % nxpe == 0) { *x = 0; - }else + } else { *x = mesh->xstart; - + } + *y = mesh->ystart; - if (z != nullptr) + if (z != nullptr) { *z = 0; + } } -void GlobalField::proc_origin(int proc, int *x, int *y, int *z) const { +void GlobalField::proc_origin(int proc, int* x, int* y, int* z) const { // This is a hack, and should be improved with a better Mesh interface - + // Get the number of processors in X and Y int nxpe = mesh->getNXPE(); - + // Get the X and Y indices int pex = proc % nxpe; int pey = proc / nxpe; - + // Get the size of the processor domain int nx = mesh->xend - mesh->xstart + 1; int ny = mesh->yend - mesh->ystart + 1; @@ -50,80 +53,89 @@ void GlobalField::proc_origin(int proc, int *x, int *y, int *z) const { // Set the origin values *x = pex * nx; *y = pey * ny; - if (z != nullptr) + if (z != nullptr) { *z = 0; + } - if(pex != 0) + if (pex != 0) { *x += mesh->xstart; + } } -void GlobalField::proc_size(int proc, int *lx, int *ly, int *lz) const { - // Get the size of the processor domain. +void GlobalField::proc_size(int proc, int* lx, int* ly, int* lz) const { + // Get the size of the processor domain. // Assumes every processor has the same size domain - + *lx = mesh->xend - mesh->xstart + 1; *ly = mesh->yend - mesh->ystart + 1; - if (lz != nullptr) + if (lz != nullptr) { *lz = mesh->LocalNz; - + } + int nxpe = mesh->getNXPE(); int pex = proc % nxpe; - if(pex == 0) + if (pex == 0) { *lx += mesh->xstart; - if(pex == (nxpe-1)) + } + if (pex == (nxpe - 1)) { *lx += mesh->xstart; + } } /////////////////////////////////////////////////////////////////////////////////////////// -GlobalField2D::GlobalField2D(Mesh *m, int proc) - : GlobalField(m, proc, m->GlobalNx, - m->GlobalNy-m->numberOfYBoundaries()*2*m->ystart, 1), - data_valid(false) { - - if((proc < 0) || (proc >= npes)) +GlobalField2D::GlobalField2D(Mesh* m, int proc) + : GlobalField(m, proc, m->GlobalNx, + m->GlobalNy - m->numberOfYBoundaries() * 2 * m->ystart, 1), + data_valid(false) { + + if ((proc < 0) || (proc >= npes)) { throw BoutException("Processor out of range"); - - if(mype == data_on_proc) { + } + + if (mype == data_on_proc) { // Gathering onto this processor buffer = new BoutReal*[npes]; - for(int p=0;p req(npes); // Post receives - for(int p = 0; p < npes; p++) { - if( p != mype ) { + for (int p = 0; p < npes; p++) { + if (p != mype) { // Check size of the array bout::globals::mpi->MPI_Irecv(buffer[p], msg_len(p), MPI_DOUBLE, p, 3141, comm, &req[p]); } } - + req[mype] = MPI_REQUEST_NULL; // Mark as not used - + // Copy data from this processor int local_xorig, local_yorig; proc_local_origin(mype, &local_xorig, &local_yorig); @@ -131,47 +143,51 @@ void GlobalField2D::gather(const Field2D &f) { proc_origin(mype, &xorig, &yorig); int xsize, ysize; proc_size(mype, &xsize, &ysize); - - for(int x=0;x 1) { + } + + if (npes > 1) { // Wait for receives, process as they arrive int pe; MPI_Status status; do { bout::globals::mpi->MPI_Waitany(npes, req.data(), &pe, &status); - if(pe != MPI_UNDEFINED) { + if (pe != MPI_UNDEFINED) { // Unpack data from processor 'pe' int remote_xorig, remote_yorig; proc_origin(pe, &remote_xorig, &remote_yorig); int remote_xsize, remote_ysize; proc_size(pe, &remote_xsize, &remote_ysize); - - for(int x=0;xMPI_Send(buffer[0], msg_len(mype), MPI_DOUBLE, data_on_proc, 3141, comm); @@ -182,24 +198,27 @@ void GlobalField2D::gather(const Field2D &f) { const Field2D GlobalField2D::scatter() const { Field2D result(mesh); result.allocate(); - + MPI_Status status; - if(mype == data_on_proc) { + if (mype == data_on_proc) { // Data is on this processor. Send to other processors - - for(int p = 0; p < npes; p++) { - if(p == mype) continue; - + + for (int p = 0; p < npes; p++) { + if (p == mype) { + continue; + } + int xorig, yorig; proc_origin(p, &xorig, &yorig); int xsize, ysize; proc_size(p, &xsize, &ysize); - + // Send to processor p - for(int x=0;xMPI_Send(buffer[p], xsize * ysize, MPI_DOUBLE, p, 1413, comm); } @@ -210,13 +229,14 @@ const Field2D GlobalField2D::scatter() const { proc_origin(mype, &xorig, &yorig); int xsize, ysize; proc_size(mype, &xsize, &ysize); - + // Copy to result - for(int x=0;xMPI_Recv(buffer[0], msg_len(mype), MPI_DOUBLE, data_on_proc, 1413, comm, &status); @@ -227,11 +247,12 @@ const Field2D GlobalField2D::scatter() const { proc_origin(mype, &xorig, &yorig); int xsize, ysize; proc_size(mype, &xsize, &ysize); - - for(int x=0;xGlobalNx, - m->GlobalNy-m->numberOfYBoundaries()*2*m->ystart, m->LocalNz), - data_valid(false) { - - if((proc < 0) || (proc >= npes)) +GlobalField3D::GlobalField3D(Mesh* m, int proc) + : GlobalField(m, proc, m->GlobalNx, + m->GlobalNy - m->numberOfYBoundaries() * 2 * m->ystart, m->LocalNz), + data_valid(false) { + + if ((proc < 0) || (proc >= npes)) { throw BoutException("Processor out of range"); - - if(mype == data_on_proc) { + } + + if (mype == data_on_proc) { // Gathering onto this processor buffer = new BoutReal*[npes]; - for(int p=0;p req(npes); // Post receives - for(int p = 0; p < npes; p++) { - if( p != mype ) { + for (int p = 0; p < npes; p++) { + if (p != mype) { // Check size of the array bout::globals::mpi->MPI_Irecv(buffer[p], msg_len(p), MPI_DOUBLE, p, 3141, comm, &req[p]); } } - + req[mype] = MPI_REQUEST_NULL; // Mark as not used - + // Copy data from this processor int local_xorig, local_yorig; proc_local_origin(mype, &local_xorig, &local_yorig); @@ -299,52 +324,60 @@ void GlobalField3D::gather(const Field3D &f) { proc_origin(mype, &xorig, &yorig); int xsize, ysize; proc_size(mype, &xsize, &ysize); - - for(int x=0;xLocalNz;z++) { - (*this)(x+xorig,y+yorig,z) = f(local_xorig+x, local_yorig+y, z); + + for (int x = 0; x < xsize; x++) { + for (int y = 0; y < ysize; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + (*this)(x + xorig, y + yorig, z) = f(local_xorig + x, local_yorig + y, z); } - - if(npes > 1) { + } + } + + if (npes > 1) { // Wait for receives, process as they arrive int pe; MPI_Status status; do { bout::globals::mpi->MPI_Waitany(npes, req.data(), &pe, &status); - if(pe != MPI_UNDEFINED) { + if (pe != MPI_UNDEFINED) { // Unpack data from processor 'pe' int remote_xorig, remote_yorig; proc_origin(pe, &remote_xorig, &remote_yorig); int remote_xsize, remote_ysize; proc_size(pe, &remote_xsize, &remote_ysize); int zsize = mesh->LocalNz; - - for(int x=0;xLocalNz;z++) { - (*this)(x+remote_xorig,y+remote_yorig,z) = buffer[pe][x*remote_ysize*zsize + y*zsize + z]; + + for (int x = 0; x < remote_xsize; x++) { + for (int y = 0; y < remote_ysize; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + (*this)(x + remote_xorig, y + remote_yorig, z) = + buffer[pe][x * remote_ysize * zsize + y * zsize + z]; } - + } + } + req[pe] = MPI_REQUEST_NULL; } - }while(pe != MPI_UNDEFINED); + } while (pe != MPI_UNDEFINED); } - }else { + } else { // Sending data to proc - + int local_xorig, local_yorig; proc_local_origin(mype, &local_xorig, &local_yorig); int xsize, ysize; proc_size(mype, &xsize, &ysize); int zsize = mesh->LocalNz; - - for(int x=0;xLocalNz;z++) { - buffer[0][x*ysize*zsize + y*zsize + z] = f(local_xorig+x, local_yorig+y, z); + + for (int x = 0; x < xsize; x++) { + for (int y = 0; y < ysize; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + buffer[0][x * ysize * zsize + y * zsize + z] = + f(local_xorig + x, local_yorig + y, z); } + } + } bout::globals::mpi->MPI_Send(buffer[0], msg_len(mype), MPI_DOUBLE, data_on_proc, 3141, comm); @@ -355,26 +388,31 @@ void GlobalField3D::gather(const Field3D &f) { const Field3D GlobalField3D::scatter() const { Field3D result(mesh); result.allocate(); - + MPI_Status status; - if(mype == data_on_proc) { + if (mype == data_on_proc) { // Data is on this processor. Send to other processors - - for(int p = 0; p < npes; p++) { - if(p == mype) continue; - + + for (int p = 0; p < npes; p++) { + if (p == mype) { + continue; + } + int xorig, yorig; proc_origin(p, &xorig, &yorig); int xsize, ysize; proc_size(p, &xsize, &ysize); int zsize = mesh->LocalNz; - + // Send to processor p - for(int x=0;xMPI_Send(buffer[p], xsize * ysize * zsize, MPI_DOUBLE, p, 1413, comm); @@ -387,14 +425,16 @@ const Field3D GlobalField3D::scatter() const { int xsize, ysize; proc_size(mype, &xsize, &ysize); int zsize = mesh->LocalNz; - + // Copy to result - for(int x=0;xMPI_Recv(buffer[0], msg_len(mype), MPI_DOUBLE, data_on_proc, 1413, comm, &status); @@ -406,12 +446,15 @@ const Field3D GlobalField3D::scatter() const { int xsize, ysize; proc_size(mype, &xsize, &ysize); int zsize = mesh->LocalNz; - - for(int x=0;x -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include void initial_profile(const std::string& name, Field3D& var) { AUTO_TRACE(); diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx index e1499084b8..c4cfefa829 100644 --- a/src/field/vecops.cxx +++ b/src/field/vecops.cxx @@ -27,12 +27,12 @@ #include #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include /************************************************************************** * Gradient operators @@ -101,7 +101,7 @@ Vector3D Grad_perp(const Field3D& f, CELL_LOC outloc, const std::string& method) SCOREP0(); ASSERT1(outloc == CELL_DEFAULT || outloc == f.getLocation()); - Coordinates *metric = f.getCoordinates(outloc); + Coordinates* metric = f.getCoordinates(outloc); Vector3D result(f.getMesh()); @@ -123,14 +123,14 @@ Vector2D Grad_perp(const Field2D& f, CELL_LOC outloc, const std::string& method) SCOREP0(); ASSERT1(outloc == CELL_DEFAULT || outloc == f.getLocation()); - Coordinates *metric = f.getCoordinates(outloc); + Coordinates* metric = f.getCoordinates(outloc); Vector2D result(f.getMesh()); result.x = DDX(f, outloc, method) - metric->g_12 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy); result.y = 0.0; - result.z = - metric->g_23 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy); + result.z = -metric->g_23 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy); result.setLocation(result.x.getLocation()); @@ -155,15 +155,15 @@ Coordinates::FieldMetric Div(const Vector2D& v, CELL_LOC outloc, Mesh* localmesh = v.getMesh(); - Coordinates *metric = localmesh->getCoordinates(outloc); + Coordinates* metric = localmesh->getCoordinates(outloc); // get contravariant components of v Vector2D vcn = v; vcn.toContravariant(); Coordinates::FieldMetric result = DDX(metric->J * vcn.x, outloc, method); - result += DDY(metric->J*vcn.y, outloc, method); - result += DDZ(metric->J*vcn.z, outloc, method); + result += DDY(metric->J * vcn.y, outloc, method); + result += DDZ(metric->J * vcn.z, outloc, method); result /= metric->J; return result; @@ -181,7 +181,7 @@ Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) { Mesh* localmesh = v.getMesh(); - Coordinates *metric = localmesh->getCoordinates(outloc); + Coordinates* metric = localmesh->getCoordinates(outloc); // get contravariant components of v Vector3D vcn = v; @@ -217,9 +217,9 @@ Coordinates::FieldMetric Div(const Vector2D& v, const Field2D& f, CELL_LOC outlo ASSERT1(outloc != CELL_VSHIFT); - Mesh *localmesh = f.getMesh(); + Mesh* localmesh = f.getMesh(); - Coordinates *metric = localmesh->getCoordinates(outloc); + Coordinates* metric = localmesh->getCoordinates(outloc); // get contravariant components of v Vector2D vcn = v; @@ -243,9 +243,9 @@ Field3D Div(const Vector3D& v, const Field3D& f, CELL_LOC outloc, } ASSERT1(outloc != CELL_VSHIFT); - Mesh *localmesh = f.getMesh(); + Mesh* localmesh = f.getMesh(); - Coordinates *metric = localmesh->getCoordinates(outloc); + Coordinates* metric = localmesh->getCoordinates(outloc); // get contravariant components of v Vector3D vcn = v; @@ -329,7 +329,7 @@ Coordinates::FieldMetric V_dot_Grad(const Vector2D& v, const Field2D& f) { // Get contravariant components of v auto vcn = v; vcn.toContravariant(); - + return VDDX(vcn.x, f) + VDDY(vcn.y, f) + VDDZ(vcn.z, f); } @@ -340,7 +340,7 @@ Field3D V_dot_Grad(const Vector2D& v, const Field3D& f) { // Get contravariant components of v auto vcn = v; vcn.toContravariant(); - + return VDDX(vcn.x, f) + VDDY(vcn.y, f) + VDDZ(vcn.z, f); } @@ -351,7 +351,7 @@ Field3D V_dot_Grad(const Vector3D& v, const Field2D& f) { // Get contravariant components of v auto vcn = v; vcn.toContravariant(); - + return VDDX(vcn.x, f) + VDDY(vcn.y, f) + VDDZ(vcn.z, f); } @@ -362,14 +362,14 @@ Field3D V_dot_Grad(const Vector3D& v, const Field3D& f) { // Get contravariant components of v auto vcn = v; vcn.toContravariant(); - + return VDDX(vcn.x, f) + VDDY(vcn.y, f) + VDDZ(vcn.z, f); } // Here R is the deduced return type based on a promoting // operation (addition) between the two input types. -template -R V_dot_Grad(const T &v, const F &a) { +template +R V_dot_Grad(const T& v, const F& a) { AUTO_TRACE(); SCOREP0(); ASSERT1(v.getLocation() == a.getLocation()); @@ -386,57 +386,92 @@ R V_dot_Grad(const T &v, const F &a) { auto vcn = v; vcn.toContravariant(); - if (a.covariant) { + if (a.covariant) { result.x = VDDX(vcn.x, a.x) + VDDY(vcn.y, a.x) + VDDZ(vcn.z, a.x); - BOUT_FOR(i, result.x.getRegion("RGN_ALL")) { - result.x[i] -= vcn.x[i] * (metric->G1_11[i] * a.x[i] + metric->G2_11[i] * a.y[i] + metric->G3_11[i] * a.z[i]); - result.x[i] -= vcn.y[i] * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i] + metric->G3_12[i] * a.z[i]); - result.x[i] -= vcn.z[i] * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i] + metric->G3_13[i] * a.z[i]); + BOUT_FOR (i, result.x.getRegion("RGN_ALL")) { + result.x[i] -= vcn.x[i] + * (metric->G1_11[i] * a.x[i] + metric->G2_11[i] * a.y[i] + + metric->G3_11[i] * a.z[i]); + result.x[i] -= vcn.y[i] + * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i] + + metric->G3_12[i] * a.z[i]); + result.x[i] -= vcn.z[i] + * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i] + + metric->G3_13[i] * a.z[i]); } - + result.y = VDDX(vcn.x, a.y) + VDDY(vcn.y, a.y) + VDDZ(vcn.z, a.y); - BOUT_FOR(i, result.y.getRegion("RGN_ALL")) { - result.y[i] -= vcn.x[i] * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i] + metric->G3_12[i] * a.z[i]); - result.y[i] -= vcn.y[i] * (metric->G1_22[i] * a.x[i] + metric->G2_22[i] * a.y[i] + metric->G3_22[i] * a.z[i]); - result.y[i] -= vcn.z[i] * (metric->G1_23[i] * a.x[i] + metric->G2_23[i] * a.y[i] + metric->G3_23[i] * a.z[i]); + BOUT_FOR (i, result.y.getRegion("RGN_ALL")) { + result.y[i] -= vcn.x[i] + * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i] + + metric->G3_12[i] * a.z[i]); + result.y[i] -= vcn.y[i] + * (metric->G1_22[i] * a.x[i] + metric->G2_22[i] * a.y[i] + + metric->G3_22[i] * a.z[i]); + result.y[i] -= vcn.z[i] + * (metric->G1_23[i] * a.x[i] + metric->G2_23[i] * a.y[i] + + metric->G3_23[i] * a.z[i]); } - + result.z = VDDX(vcn.x, a.z) + VDDY(vcn.y, a.z) + VDDZ(vcn.z, a.z); - BOUT_FOR(i, result.z.getRegion("RGN_ALL")) { - result.z[i] -= vcn.x[i] * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i] + metric->G3_13[i] * a.z[i]); - result.z[i] -= vcn.y[i] * (metric->G1_23[i] * a.x[i] + metric->G2_23[i] * a.y[i] + metric->G3_23[i] * a.z[i]); - result.z[i] -= vcn.z[i] * (metric->G1_33[i] * a.x[i] + metric->G2_33[i] * a.y[i] + metric->G3_33[i] * a.z[i]); + BOUT_FOR (i, result.z.getRegion("RGN_ALL")) { + result.z[i] -= vcn.x[i] + * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i] + + metric->G3_13[i] * a.z[i]); + result.z[i] -= vcn.y[i] + * (metric->G1_23[i] * a.x[i] + metric->G2_23[i] * a.y[i] + + metric->G3_23[i] * a.z[i]); + result.z[i] -= vcn.z[i] + * (metric->G1_33[i] * a.x[i] + metric->G2_33[i] * a.y[i] + + metric->G3_33[i] * a.z[i]); } result.covariant = true; } else { result.x = VDDX(vcn.x, a.x) + VDDY(vcn.y, a.x) + VDDZ(vcn.z, a.x); - BOUT_FOR(i, result.x.getRegion("RGN_ALL")) { - result.x[i] += vcn.x[i] * (metric->G1_11[i] * a.x[i] + metric->G1_12[i] * a.y[i] + metric->G1_13[i] * a.z[i]); - result.x[i] += vcn.y[i] * (metric->G1_12[i] * a.x[i] + metric->G1_22[i] * a.y[i] + metric->G1_23[i] * a.z[i]); - result.x[i] += vcn.z[i] * (metric->G1_13[i] * a.x[i] + metric->G1_23[i] * a.y[i] + metric->G1_33[i] * a.z[i]); + BOUT_FOR (i, result.x.getRegion("RGN_ALL")) { + result.x[i] += vcn.x[i] + * (metric->G1_11[i] * a.x[i] + metric->G1_12[i] * a.y[i] + + metric->G1_13[i] * a.z[i]); + result.x[i] += vcn.y[i] + * (metric->G1_12[i] * a.x[i] + metric->G1_22[i] * a.y[i] + + metric->G1_23[i] * a.z[i]); + result.x[i] += vcn.z[i] + * (metric->G1_13[i] * a.x[i] + metric->G1_23[i] * a.y[i] + + metric->G1_33[i] * a.z[i]); } - + result.y = VDDX(vcn.x, a.y) + VDDY(vcn.y, a.y) + VDDZ(vcn.z, a.y); - BOUT_FOR(i, result.y.getRegion("RGN_ALL")) { - result.y[i] += vcn.x[i] * (metric->G2_11[i] * a.x[i] + metric->G2_12[i] * a.y[i] + metric->G2_13[i] * a.z[i]); - result.y[i] += vcn.y[i] * (metric->G2_12[i] * a.x[i] + metric->G2_22[i] * a.y[i] + metric->G2_23[i] * a.z[i]); - result.y[i] += vcn.z[i] * (metric->G2_13[i] * a.x[i] + metric->G2_23[i] * a.y[i] + metric->G2_33[i] * a.z[i]); + BOUT_FOR (i, result.y.getRegion("RGN_ALL")) { + result.y[i] += vcn.x[i] + * (metric->G2_11[i] * a.x[i] + metric->G2_12[i] * a.y[i] + + metric->G2_13[i] * a.z[i]); + result.y[i] += vcn.y[i] + * (metric->G2_12[i] * a.x[i] + metric->G2_22[i] * a.y[i] + + metric->G2_23[i] * a.z[i]); + result.y[i] += vcn.z[i] + * (metric->G2_13[i] * a.x[i] + metric->G2_23[i] * a.y[i] + + metric->G2_33[i] * a.z[i]); } - + result.z = VDDX(vcn.x, a.z) + VDDY(vcn.y, a.z) + VDDZ(vcn.z, a.z); - BOUT_FOR(i, result.z.getRegion("RGN_ALL")) { - result.z[i] += vcn.x[i] * (metric->G3_11[i] * a.x[i] + metric->G3_12[i] * a.y[i] + metric->G3_13[i] * a.z[i]); - result.z[i] += vcn.y[i] * (metric->G3_12[i] * a.x[i] + metric->G3_22[i] * a.y[i] + metric->G3_23[i] * a.z[i]); - result.z[i] += vcn.z[i] * (metric->G3_13[i] * a.x[i] + metric->G3_23[i] * a.y[i] + metric->G3_33[i] * a.z[i]); + BOUT_FOR (i, result.z.getRegion("RGN_ALL")) { + result.z[i] += vcn.x[i] + * (metric->G3_11[i] * a.x[i] + metric->G3_12[i] * a.y[i] + + metric->G3_13[i] * a.z[i]); + result.z[i] += vcn.y[i] + * (metric->G3_12[i] * a.x[i] + metric->G3_22[i] * a.y[i] + + metric->G3_23[i] * a.z[i]); + result.z[i] += vcn.z[i] + * (metric->G3_13[i] * a.x[i] + metric->G3_23[i] * a.y[i] + + metric->G3_33[i] * a.z[i]); } - + result.covariant = false; } result.setLocation(v.getLocation()); return result; - } // Implement vector-vector operation in terms of templated routine above diff --git a/src/field/vector2d.cxx b/src/field/vector2d.cxx index 362c003baf..2be11e4117 100644 --- a/src/field/vector2d.cxx +++ b/src/field/vector2d.cxx @@ -28,13 +28,13 @@ * **************************************************************************/ -#include +#include -#include -#include -#include #include -#include +#include +#include +#include +#include Vector2D::Vector2D(const Vector2D& f) : FieldData(f), x(f.x), y(f.y), z(f.z), covariant(f.covariant), deriv(nullptr), @@ -62,8 +62,8 @@ Vector2D::~Vector2D() { } void Vector2D::toCovariant() { - SCOREP0(); - if(!covariant) { + SCOREP0(); + if (!covariant) { Mesh* localmesh = getMesh(); if (location == CELL_VSHIFT) { @@ -85,10 +85,13 @@ void Vector2D::toCovariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR(i, x.getRegion("RGN_ALL")) { - x[i] = metric_x->g_11[i]*x[i] + metric_x->g_12[i]*y_at_x[i] + metric_x->g_13[i]*z_at_x[i]; - y[i] = metric_y->g_22[i]*y[i] + metric_y->g_12[i]*x_at_y[i] + metric_y->g_23[i]*z_at_y[i]; - z[i] = metric_z->g_33[i]*z[i] + metric_z->g_13[i]*x_at_z[i] + metric_z->g_23[i]*y_at_z[i]; + BOUT_FOR (i, x.getRegion("RGN_ALL")) { + x[i] = metric_x->g_11[i] * x[i] + metric_x->g_12[i] * y_at_x[i] + + metric_x->g_13[i] * z_at_x[i]; + y[i] = metric_y->g_22[i] * y[i] + metric_y->g_12[i] * x_at_y[i] + + metric_y->g_23[i] * z_at_y[i]; + z[i] = metric_z->g_33[i] * z[i] + metric_z->g_13[i] * x_at_z[i] + + metric_z->g_23[i] * y_at_z[i]; }; } else { const auto metric = localmesh->getCoordinates(location); @@ -96,10 +99,10 @@ void Vector2D::toCovariant() { // Need to use temporary arrays to store result Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR(i, x.getRegion("RGN_ALL")) { - gx[i] = metric->g_11[i]*x[i] + metric->g_12[i]*y[i] + metric->g_13[i]*z[i]; - gy[i] = metric->g_22[i]*y[i] + metric->g_12[i]*x[i] + metric->g_23[i]*z[i]; - gz[i] = metric->g_33[i]*z[i] + metric->g_13[i]*x[i] + metric->g_23[i]*y[i]; + BOUT_FOR (i, x.getRegion("RGN_ALL")) { + gx[i] = metric->g_11[i] * x[i] + metric->g_12[i] * y[i] + metric->g_13[i] * z[i]; + gy[i] = metric->g_22[i] * y[i] + metric->g_12[i] * x[i] + metric->g_23[i] * z[i]; + gz[i] = metric->g_33[i] * z[i] + metric->g_13[i] * x[i] + metric->g_23[i] * y[i]; }; x = gx; @@ -110,15 +113,15 @@ void Vector2D::toCovariant() { covariant = true; } } -void Vector2D::toContravariant() { +void Vector2D::toContravariant() { SCOREP0(); - if(covariant) { + if (covariant) { // multiply by g^{ij} Mesh* localmesh = getMesh(); if (location == CELL_VSHIFT) { Coordinates *metric_x, *metric_y, *metric_z; - + metric_x = localmesh->getCoordinates(CELL_XLOW); metric_y = localmesh->getCoordinates(CELL_YLOW); metric_z = localmesh->getCoordinates(CELL_ZLOW); @@ -136,10 +139,13 @@ void Vector2D::toContravariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR(i, x.getRegion("RGN_ALL")) { - x[i] = metric_x->g11[i]*x[i] + metric_x->g12[i]*y_at_x[i] + metric_x->g13[i]*z_at_x[i]; - y[i] = metric_y->g22[i]*y[i] + metric_y->g12[i]*x_at_y[i] + metric_y->g23[i]*z_at_y[i]; - z[i] = metric_z->g33[i]*z[i] + metric_z->g13[i]*x_at_z[i] + metric_z->g23[i]*y_at_z[i]; + BOUT_FOR (i, x.getRegion("RGN_ALL")) { + x[i] = metric_x->g11[i] * x[i] + metric_x->g12[i] * y_at_x[i] + + metric_x->g13[i] * z_at_x[i]; + y[i] = metric_y->g22[i] * y[i] + metric_y->g12[i] * x_at_y[i] + + metric_y->g23[i] * z_at_y[i]; + z[i] = metric_z->g33[i] * z[i] + metric_z->g13[i] * x_at_z[i] + + metric_z->g23[i] * y_at_z[i]; }; } else { @@ -148,17 +154,17 @@ void Vector2D::toContravariant() { // Need to use temporary arrays to store result Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR(i, x.getRegion("RGN_ALL")) { - gx[i] = metric->g11[i]*x[i] + metric->g12[i]*y[i] + metric->g13[i]*z[i]; - gy[i] = metric->g22[i]*y[i] + metric->g12[i]*x[i] + metric->g23[i]*z[i]; - gz[i] = metric->g33[i]*z[i] + metric->g13[i]*x[i] + metric->g23[i]*y[i]; + BOUT_FOR (i, x.getRegion("RGN_ALL")) { + gx[i] = metric->g11[i] * x[i] + metric->g12[i] * y[i] + metric->g13[i] * z[i]; + gy[i] = metric->g22[i] * y[i] + metric->g12[i] * x[i] + metric->g23[i] * z[i]; + gz[i] = metric->g33[i] * z[i] + metric->g13[i] * x[i] + metric->g23[i] * y[i]; }; x = gx; y = gy; z = gz; } - + covariant = false; } } @@ -196,7 +202,7 @@ Vector2D* Vector2D::timeDeriv() { /////////////////// ASSIGNMENT //////////////////// -Vector2D & Vector2D::operator=(const Vector2D &rhs) { +Vector2D& Vector2D::operator=(const Vector2D& rhs) { SCOREP0(); x = rhs.x; y = rhs.y; @@ -209,7 +215,7 @@ Vector2D & Vector2D::operator=(const Vector2D &rhs) { return *this; } -Vector2D & Vector2D::operator=(const BoutReal val) { +Vector2D& Vector2D::operator=(const BoutReal val) { SCOREP0(); x = val; y = val; @@ -220,13 +226,13 @@ Vector2D & Vector2D::operator=(const BoutReal val) { ////////////////// ADDITION ////////////////////// -Vector2D & Vector2D::operator+=(const Vector2D &rhs) { - if(rhs.covariant) { +Vector2D& Vector2D::operator+=(const Vector2D& rhs) { + if (rhs.covariant) { toCovariant(); - }else { + } else { toContravariant(); } - + x += rhs.x; y += rhs.y; z += rhs.z; @@ -246,13 +252,13 @@ const Vector2D Vector2D::operator-() const { return result; } -Vector2D & Vector2D::operator-=(const Vector2D &rhs) { - if(rhs.covariant) { +Vector2D& Vector2D::operator-=(const Vector2D& rhs) { + if (rhs.covariant) { toCovariant(); - }else { + } else { toContravariant(); } - + x -= rhs.x; y -= rhs.y; z -= rhs.z; @@ -262,33 +268,33 @@ Vector2D & Vector2D::operator-=(const Vector2D &rhs) { //////////////// MULTIPLICATION ////////////////// -Vector2D & Vector2D::operator*=(const BoutReal rhs) { +Vector2D& Vector2D::operator*=(const BoutReal rhs) { x *= rhs; y *= rhs; z *= rhs; - + return *this; } -Vector2D & Vector2D::operator*=(const Field2D &rhs) { +Vector2D& Vector2D::operator*=(const Field2D& rhs) { x *= rhs; y *= rhs; z *= rhs; - + return *this; } /////////////////// DIVISION ///////////////////// -Vector2D & Vector2D::operator/=(const BoutReal rhs) { +Vector2D& Vector2D::operator/=(const BoutReal rhs) { x /= rhs; y /= rhs; z /= rhs; - + return *this; } -Vector2D & Vector2D::operator/=(const Field2D &rhs) { +Vector2D& Vector2D::operator/=(const Field2D& rhs) { x /= rhs; y /= rhs; z /= rhs; @@ -302,25 +308,23 @@ Vector2D & Vector2D::operator/=(const Field2D &rhs) { ////////////////// ADDITION ////////////////////// -const Vector2D Vector2D::operator+(const Vector2D &rhs) const { +const Vector2D Vector2D::operator+(const Vector2D& rhs) const { Vector2D result = *this; result += rhs; return result; } -const Vector3D Vector2D::operator+(const Vector3D &rhs) const { - return rhs+(*this); -} +const Vector3D Vector2D::operator+(const Vector3D& rhs) const { return rhs + (*this); } ///////////////// SUBTRACTION //////////////////// -const Vector2D Vector2D::operator-(const Vector2D &rhs) const { +const Vector2D Vector2D::operator-(const Vector2D& rhs) const { Vector2D result = *this; result -= rhs; return result; } -const Vector3D Vector2D::operator-(const Vector3D &rhs) const { +const Vector3D Vector2D::operator-(const Vector3D& rhs) const { Vector3D result(getMesh()); result = *this; result -= rhs; @@ -335,13 +339,13 @@ const Vector2D Vector2D::operator*(const BoutReal rhs) const { return result; } -const Vector2D Vector2D::operator*(const Field2D &rhs) const { +const Vector2D Vector2D::operator*(const Field2D& rhs) const { Vector2D result = *this; result *= rhs; return result; } -const Vector3D Vector2D::operator*(const Field3D &rhs) const { +const Vector3D Vector2D::operator*(const Field3D& rhs) const { Vector3D result(getMesh()); result = *this; result *= rhs; @@ -356,13 +360,13 @@ const Vector2D Vector2D::operator/(const BoutReal rhs) const { return result; } -const Vector2D Vector2D::operator/(const Field2D &rhs) const { +const Vector2D Vector2D::operator/(const Field2D& rhs) const { Vector2D result = *this; result /= rhs; return result; } -const Vector3D Vector2D::operator/(const Field3D &rhs) const { +const Vector3D Vector2D::operator/(const Field3D& rhs) const { Vector3D result(getMesh()); result = *this; result /= rhs; @@ -377,34 +381,34 @@ const Coordinates::FieldMetric Vector2D::operator*(const Vector2D& rhs) const { Mesh* localmesh = getMesh(); Coordinates::FieldMetric result{emptyFrom(x)}; - if(rhs.covariant ^ covariant) { + if (rhs.covariant ^ covariant) { // Both different - just multiply components - result = x*rhs.x + y*rhs.y + z*rhs.z; - }else { + result = x * rhs.x + y * rhs.y + z * rhs.z; + } else { // Both are covariant or contravariant - Coordinates *metric = localmesh->getCoordinates(location); + Coordinates* metric = localmesh->getCoordinates(location); - if(covariant) { + if (covariant) { // Both covariant - result = x*rhs.x*metric->g11 + y*rhs.y*metric->g22 + z*rhs.z*metric->g33; - result += (x*rhs.y + y*rhs.x)*metric->g12 - + (x*rhs.z + z*rhs.x)*metric->g13 - + (y*rhs.z + z*rhs.y)*metric->g23; - }else { + result = + x * rhs.x * metric->g11 + y * rhs.y * metric->g22 + z * rhs.z * metric->g33; + result += (x * rhs.y + y * rhs.x) * metric->g12 + + (x * rhs.z + z * rhs.x) * metric->g13 + + (y * rhs.z + z * rhs.y) * metric->g23; + } else { // Both contravariant - result = x*rhs.x*metric->g_11 + y*rhs.y*metric->g_22 + z*rhs.z*metric->g_33; - result += (x*rhs.y + y*rhs.x)*metric->g_12 - + (x*rhs.z + z*rhs.x)*metric->g_13 - + (y*rhs.z + z*rhs.y)*metric->g_23; + result = + x * rhs.x * metric->g_11 + y * rhs.y * metric->g_22 + z * rhs.z * metric->g_33; + result += (x * rhs.y + y * rhs.x) * metric->g_12 + + (x * rhs.z + z * rhs.x) * metric->g_13 + + (y * rhs.z + z * rhs.y) * metric->g_23; } } return result; } -const Field3D Vector2D::operator*(const Vector3D &rhs) const { - return rhs*(*this); -} +const Field3D Vector2D::operator*(const Vector3D& rhs) const { return rhs * (*this); } /*************************************************************** * Get/set variable location for staggered meshes @@ -413,18 +417,18 @@ const Field3D Vector2D::operator*(const Vector3D &rhs) const { CELL_LOC Vector2D::getLocation() const { if (location == CELL_VSHIFT) { - ASSERT1((x.getLocation() == CELL_XLOW) && (y.getLocation() == CELL_YLOW) && - (z.getLocation() == CELL_ZLOW)); + ASSERT1((x.getLocation() == CELL_XLOW) && (y.getLocation() == CELL_YLOW) + && (z.getLocation() == CELL_ZLOW)); } else { - ASSERT1((location == x.getLocation()) && (location == y.getLocation()) && - (location == z.getLocation())); + ASSERT1((location == x.getLocation()) && (location == y.getLocation()) + && (location == z.getLocation())); } return location; } Vector2D& Vector2D::setLocation(CELL_LOC loc) { - SCOREP0(); + SCOREP0(); TRACE("Vector2D::setLocation"); if (loc == CELL_DEFAULT) { loc = CELL_CENTRE; @@ -459,17 +463,11 @@ Vector2D& Vector2D::setLocation(CELL_LOC loc) { * NON-MEMBER OVERLOADED OPERATORS ***************************************************************/ -const Vector2D operator*(const BoutReal lhs, const Vector2D &rhs) { - return rhs*lhs; -} +const Vector2D operator*(const BoutReal lhs, const Vector2D& rhs) { return rhs * lhs; } -const Vector2D operator*(const Field2D &lhs, const Vector2D &rhs) { - return rhs*lhs; -} +const Vector2D operator*(const Field2D& lhs, const Vector2D& rhs) { return rhs * lhs; } -const Vector3D operator*(const Field3D &lhs, const Vector2D &rhs) { - return rhs*lhs; -} +const Vector3D operator*(const Field3D& lhs, const Vector2D& rhs) { return rhs * lhs; } /*************************************************************** * NON-MEMBER FUNCTIONS @@ -477,7 +475,7 @@ const Vector3D operator*(const Field3D &lhs, const Vector2D &rhs) { // Return the magnitude of a vector Coordinates::FieldMetric abs(const Vector2D& v, const std::string& region) { - return sqrt(v*v, region); + return sqrt(v * v, region); } ///////////////////// BOUNDARY CONDITIONS ////////////////// diff --git a/src/field/vector3d.cxx b/src/field/vector3d.cxx index e43bd86463..2a9ac86066 100644 --- a/src/field/vector3d.cxx +++ b/src/field/vector3d.cxx @@ -28,14 +28,14 @@ * **************************************************************************/ -#include +#include -#include -#include -#include #include #include -#include +#include +#include +#include +#include Vector3D::Vector3D(const Vector3D& f) : FieldData(f), x(f.x), y(f.y), z(f.z), covariant(f.covariant), deriv(nullptr), @@ -63,8 +63,8 @@ Vector3D::~Vector3D() { } void Vector3D::toCovariant() { - SCOREP0(); - if(!covariant) { + SCOREP0(); + if (!covariant) { Mesh* localmesh = getMesh(); if (location == CELL_VSHIFT) { @@ -86,10 +86,13 @@ void Vector3D::toCovariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")){ - x[i] = metric_x->g_11[i]*x[i] + metric_x->g_12[i]*y_at_x[i] + metric_x->g_13[i]*z_at_x[i]; - y[i] = metric_y->g_22[i]*y[i] + metric_y->g_12[i]*x_at_y[i] + metric_y->g_23[i]*z_at_y[i]; - z[i] = metric_z->g_33[i]*z[i] + metric_z->g_13[i]*x_at_z[i] + metric_z->g_23[i]*y_at_z[i]; + BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + x[i] = metric_x->g_11[i] * x[i] + metric_x->g_12[i] * y_at_x[i] + + metric_x->g_13[i] * z_at_x[i]; + y[i] = metric_y->g_22[i] * y[i] + metric_y->g_12[i] * x_at_y[i] + + metric_y->g_23[i] * z_at_y[i]; + z[i] = metric_z->g_33[i] * z[i] + metric_z->g_13[i] * x_at_z[i] + + metric_z->g_23[i] * y_at_z[i]; }; } else { const auto metric = localmesh->getCoordinates(location); @@ -97,10 +100,10 @@ void Vector3D::toCovariant() { // Need to use temporary arrays to store result Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")){ - gx[i] = metric->g_11[i]*x[i] + metric->g_12[i]*y[i] + metric->g_13[i]*z[i]; - gy[i] = metric->g_22[i]*y[i] + metric->g_12[i]*x[i] + metric->g_23[i]*z[i]; - gz[i] = metric->g_33[i]*z[i] + metric->g_13[i]*x[i] + metric->g_23[i]*y[i]; + BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + gx[i] = metric->g_11[i] * x[i] + metric->g_12[i] * y[i] + metric->g_13[i] * z[i]; + gy[i] = metric->g_22[i] * y[i] + metric->g_12[i] * x[i] + metric->g_23[i] * z[i]; + gz[i] = metric->g_33[i] * z[i] + metric->g_13[i] * x[i] + metric->g_23[i] * y[i]; }; x = gx; @@ -111,15 +114,15 @@ void Vector3D::toCovariant() { covariant = true; } } -void Vector3D::toContravariant() { +void Vector3D::toContravariant() { SCOREP0(); - if(covariant) { + if (covariant) { // multiply by g^{ij} Mesh* localmesh = getMesh(); if (location == CELL_VSHIFT) { Coordinates *metric_x, *metric_y, *metric_z; - + metric_x = localmesh->getCoordinates(CELL_XLOW); metric_y = localmesh->getCoordinates(CELL_YLOW); metric_z = localmesh->getCoordinates(CELL_ZLOW); @@ -137,10 +140,13 @@ void Vector3D::toContravariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")){ - x[i] = metric_x->g11[i]*x[i] + metric_x->g12[i]*y_at_x[i] + metric_x->g13[i]*z_at_x[i]; - y[i] = metric_y->g22[i]*y[i] + metric_y->g12[i]*x_at_y[i] + metric_y->g23[i]*z_at_y[i]; - z[i] = metric_z->g33[i]*z[i] + metric_z->g13[i]*x_at_z[i] + metric_z->g23[i]*y_at_z[i]; + BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + x[i] = metric_x->g11[i] * x[i] + metric_x->g12[i] * y_at_x[i] + + metric_x->g13[i] * z_at_x[i]; + y[i] = metric_y->g22[i] * y[i] + metric_y->g12[i] * x_at_y[i] + + metric_y->g23[i] * z_at_y[i]; + z[i] = metric_z->g33[i] * z[i] + metric_z->g13[i] * x_at_z[i] + + metric_z->g23[i] * y_at_z[i]; }; } else { @@ -149,17 +155,17 @@ void Vector3D::toContravariant() { // Need to use temporary arrays to store result Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")){ - gx[i] = metric->g11[i]*x[i] + metric->g12[i]*y[i] + metric->g13[i]*z[i]; - gy[i] = metric->g22[i]*y[i] + metric->g12[i]*x[i] + metric->g23[i]*z[i]; - gz[i] = metric->g33[i]*z[i] + metric->g13[i]*x[i] + metric->g23[i]*y[i]; + BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + gx[i] = metric->g11[i] * x[i] + metric->g12[i] * y[i] + metric->g13[i] * z[i]; + gy[i] = metric->g22[i] * y[i] + metric->g12[i] * x[i] + metric->g23[i] * z[i]; + gz[i] = metric->g33[i] * z[i] + metric->g13[i] * x[i] + metric->g23[i] * y[i]; }; x = gx; y = gy; z = gz; } - + covariant = false; } } @@ -198,7 +204,7 @@ Vector3D* Vector3D::timeDeriv() { /////////////////// ASSIGNMENT //////////////////// -Vector3D & Vector3D::operator=(const Vector3D &rhs) { +Vector3D& Vector3D::operator=(const Vector3D& rhs) { SCOREP0(); x = rhs.x; y = rhs.y; @@ -210,12 +216,12 @@ Vector3D & Vector3D::operator=(const Vector3D &rhs) { return *this; } -Vector3D & Vector3D::operator=(const Vector2D &rhs) { - SCOREP0(); +Vector3D& Vector3D::operator=(const Vector2D& rhs) { + SCOREP0(); x = rhs.x; y = rhs.y; z = rhs.z; - + covariant = rhs.covariant; setLocation(rhs.getLocation()); @@ -223,24 +229,22 @@ Vector3D & Vector3D::operator=(const Vector2D &rhs) { return *this; } -Vector3D & Vector3D::operator=(const BoutReal val) -{ +Vector3D& Vector3D::operator=(const BoutReal val) { SCOREP0(); x = val; y = val; z = val; - + return *this; } ////////////////// ADDITION ////////////////////// -Vector3D & Vector3D::operator+=(const Vector3D &rhs) -{ +Vector3D& Vector3D::operator+=(const Vector3D& rhs) { // Make sure they're of the same type (co/contra-variant) - if(rhs.covariant) { + if (rhs.covariant) { toCovariant(); - }else { + } else { toContravariant(); } @@ -251,11 +255,10 @@ Vector3D & Vector3D::operator+=(const Vector3D &rhs) return *this; } -Vector3D & Vector3D::operator+=(const Vector2D &rhs) -{ - if(rhs.covariant) { +Vector3D& Vector3D::operator+=(const Vector2D& rhs) { + if (rhs.covariant) { toCovariant(); - }else { + } else { toContravariant(); } @@ -268,8 +271,7 @@ Vector3D & Vector3D::operator+=(const Vector2D &rhs) ///////////////// SUBTRACTION //////////////////// -const Vector3D Vector3D::operator-() const -{ +const Vector3D Vector3D::operator-() const { Vector3D result = *this; result.x *= -1.0; @@ -279,14 +281,13 @@ const Vector3D Vector3D::operator-() const return result; } -Vector3D & Vector3D::operator-=(const Vector3D &rhs) -{ - if(rhs.covariant) { +Vector3D& Vector3D::operator-=(const Vector3D& rhs) { + if (rhs.covariant) { toCovariant(); - }else { + } else { toContravariant(); } - + x -= rhs.x; y -= rhs.y; z -= rhs.z; @@ -294,14 +295,13 @@ Vector3D & Vector3D::operator-=(const Vector3D &rhs) return *this; } -Vector3D & Vector3D::operator-=(const Vector2D &rhs) -{ - if(rhs.covariant) { +Vector3D& Vector3D::operator-=(const Vector2D& rhs) { + if (rhs.covariant) { toCovariant(); - }else { + } else { toContravariant(); } - + x -= rhs.x; y -= rhs.y; z -= rhs.z; @@ -311,26 +311,23 @@ Vector3D & Vector3D::operator-=(const Vector2D &rhs) //////////////// MULTIPLICATION ////////////////// -Vector3D & Vector3D::operator*=(const BoutReal rhs) -{ +Vector3D& Vector3D::operator*=(const BoutReal rhs) { x *= rhs; y *= rhs; z *= rhs; - + return *this; } -Vector3D & Vector3D::operator*=(const Field2D &rhs) -{ +Vector3D& Vector3D::operator*=(const Field2D& rhs) { x *= rhs; y *= rhs; z *= rhs; - + return *this; } -Vector3D & Vector3D::operator*=(const Field3D &rhs) -{ +Vector3D& Vector3D::operator*=(const Field3D& rhs) { x *= rhs; y *= rhs; z *= rhs; @@ -340,17 +337,15 @@ Vector3D & Vector3D::operator*=(const Field3D &rhs) /////////////////// DIVISION ///////////////////// -Vector3D & Vector3D::operator/=(const BoutReal rhs) -{ +Vector3D& Vector3D::operator/=(const BoutReal rhs) { x /= rhs; y /= rhs; z /= rhs; - + return *this; } -Vector3D & Vector3D::operator/=(const Field2D &rhs) -{ +Vector3D& Vector3D::operator/=(const Field2D& rhs) { x /= rhs; y /= rhs; z /= rhs; @@ -358,8 +353,7 @@ Vector3D & Vector3D::operator/=(const Field2D &rhs) return *this; } -Vector3D & Vector3D::operator/=(const Field3D &rhs) -{ +Vector3D& Vector3D::operator/=(const Field3D& rhs) { x /= rhs; y /= rhs; z /= rhs; @@ -404,13 +398,13 @@ CROSS(Vector2D, Vector2D, Vector2D) ////////////////// ADDITION ////////////////////// -const Vector3D Vector3D::operator+(const Vector3D &rhs) const { +const Vector3D Vector3D::operator+(const Vector3D& rhs) const { Vector3D result = *this; result += rhs; return result; } -const Vector3D Vector3D::operator+(const Vector2D &rhs) const { +const Vector3D Vector3D::operator+(const Vector2D& rhs) const { Vector3D result = *this; result += rhs; return result; @@ -418,13 +412,13 @@ const Vector3D Vector3D::operator+(const Vector2D &rhs) const { ///////////////// SUBTRACTION //////////////////// -const Vector3D Vector3D::operator-(const Vector3D &rhs) const { +const Vector3D Vector3D::operator-(const Vector3D& rhs) const { Vector3D result = *this; result -= rhs; return result; } -const Vector3D Vector3D::operator-(const Vector2D &rhs) const { +const Vector3D Vector3D::operator-(const Vector2D& rhs) const { Vector3D result = *this; result -= rhs; return result; @@ -438,13 +432,13 @@ const Vector3D Vector3D::operator*(const BoutReal rhs) const { return result; } -const Vector3D Vector3D::operator*(const Field2D &rhs) const { +const Vector3D Vector3D::operator*(const Field2D& rhs) const { Vector3D result = *this; result *= rhs; return result; } -const Vector3D Vector3D::operator*(const Field3D &rhs) const { +const Vector3D Vector3D::operator*(const Field3D& rhs) const { Vector3D result = *this; result *= rhs; return result; @@ -458,13 +452,13 @@ const Vector3D Vector3D::operator/(const BoutReal rhs) const { return result; } -const Vector3D Vector3D::operator/(const Field2D &rhs) const { +const Vector3D Vector3D::operator/(const Field2D& rhs) const { Vector3D result = *this; result /= rhs; return result; } -const Vector3D Vector3D::operator/(const Field3D &rhs) const { +const Vector3D Vector3D::operator/(const Field3D& rhs) const { Vector3D result = *this; result /= rhs; return result; @@ -472,69 +466,72 @@ const Vector3D Vector3D::operator/(const Field3D &rhs) const { ////////////////// DOT PRODUCT /////////////////// -const Field3D Vector3D::operator*(const Vector3D &rhs) const { +const Field3D Vector3D::operator*(const Vector3D& rhs) const { Mesh* mesh = getMesh(); Field3D result{emptyFrom(x)}; ASSERT2(location == rhs.getLocation()) - if(rhs.covariant ^ covariant) { + if (rhs.covariant ^ covariant) { // Both different - just multiply components - result = x*rhs.x + y*rhs.y + z*rhs.z; - }else { + result = x * rhs.x + y * rhs.y + z * rhs.z; + } else { // Both are covariant or contravariant - Coordinates *metric = mesh->getCoordinates(location); - - if(covariant) { + Coordinates* metric = mesh->getCoordinates(location); + + if (covariant) { // Both covariant - result = x*rhs.x*metric->g11 + y*rhs.y*metric->g22 + z*rhs.z*metric->g33; - result += (x*rhs.y + y*rhs.x)*metric->g12 - + (x*rhs.z + z*rhs.x)*metric->g13 - + (y*rhs.z + z*rhs.y)*metric->g23; - }else { + result = + x * rhs.x * metric->g11 + y * rhs.y * metric->g22 + z * rhs.z * metric->g33; + result += (x * rhs.y + y * rhs.x) * metric->g12 + + (x * rhs.z + z * rhs.x) * metric->g13 + + (y * rhs.z + z * rhs.y) * metric->g23; + } else { // Both contravariant - result = x*rhs.x*metric->g_11 + y*rhs.y*metric->g_22 + z*rhs.z*metric->g_33; - result += (x*rhs.y + y*rhs.x)*metric->g_12 - + (x*rhs.z + z*rhs.x)*metric->g_13 - + (y*rhs.z + z*rhs.y)*metric->g_23; + result = + x * rhs.x * metric->g_11 + y * rhs.y * metric->g_22 + z * rhs.z * metric->g_33; + result += (x * rhs.y + y * rhs.x) * metric->g_12 + + (x * rhs.z + z * rhs.x) * metric->g_13 + + (y * rhs.z + z * rhs.y) * metric->g_23; } } - + return result; } -const Field3D Vector3D::operator*(const Vector2D &rhs) const -{ +const Field3D Vector3D::operator*(const Vector2D& rhs) const { ASSERT2(location == rhs.getLocation()); Field3D result{emptyFrom(x)}; - if(rhs.covariant ^ covariant) { + if (rhs.covariant ^ covariant) { // Both different - just multiply components - result = x*rhs.x + y*rhs.y + z*rhs.z; - }else { + result = x * rhs.x + y * rhs.y + z * rhs.z; + } else { // Both are covariant or contravariant - Coordinates *metric = x.getCoordinates(location); - if(covariant) { + Coordinates* metric = x.getCoordinates(location); + if (covariant) { // Both covariant - result = x*rhs.x*metric->g11 + y*rhs.y*metric->g22 + z*rhs.z*metric->g33; - result += (x*rhs.y + y*rhs.x)*metric->g12 - + (x*rhs.z + z*rhs.x)*metric->g13 - + (y*rhs.z + z*rhs.y)*metric->g23; - }else { + result = + x * rhs.x * metric->g11 + y * rhs.y * metric->g22 + z * rhs.z * metric->g33; + result += (x * rhs.y + y * rhs.x) * metric->g12 + + (x * rhs.z + z * rhs.x) * metric->g13 + + (y * rhs.z + z * rhs.y) * metric->g23; + } else { // Both contravariant - result = x*rhs.x*metric->g_11 + y*rhs.y*metric->g_22 + z*rhs.z*metric->g_33; - result += (x*rhs.y + y*rhs.x)*metric->g_12 - + (x*rhs.z + z*rhs.x)*metric->g_13 - + (y*rhs.z + z*rhs.y)*metric->g_23; + result = + x * rhs.x * metric->g_11 + y * rhs.y * metric->g_22 + z * rhs.z * metric->g_33; + result += (x * rhs.y + y * rhs.x) * metric->g_12 + + (x * rhs.z + z * rhs.x) * metric->g_13 + + (y * rhs.z + z * rhs.y) * metric->g_23; } } return result; } - + /*************************************************************** * Get/set variable location for staggered meshes ***************************************************************/ @@ -542,18 +539,18 @@ const Field3D Vector3D::operator*(const Vector2D &rhs) const CELL_LOC Vector3D::getLocation() const { if (location == CELL_VSHIFT) { - ASSERT1((x.getLocation() == CELL_XLOW) && (y.getLocation() == CELL_YLOW) && - (z.getLocation() == CELL_ZLOW)); + ASSERT1((x.getLocation() == CELL_XLOW) && (y.getLocation() == CELL_YLOW) + && (z.getLocation() == CELL_ZLOW)); } else { - ASSERT1((location == x.getLocation()) && (location == y.getLocation()) && - (location == z.getLocation())); + ASSERT1((location == x.getLocation()) && (location == y.getLocation()) + && (location == z.getLocation())); } return location; } Vector3D& Vector3D::setLocation(CELL_LOC loc) { - SCOREP0(); + SCOREP0(); TRACE("Vector3D::setLocation"); if (loc == CELL_DEFAULT) { loc = CELL_CENTRE; @@ -588,26 +585,19 @@ Vector3D& Vector3D::setLocation(CELL_LOC loc) { * NON-MEMBER OVERLOADED OPERATORS ***************************************************************/ -const Vector3D operator*(const BoutReal lhs, const Vector3D &rhs) { - return(rhs * lhs); -} +const Vector3D operator*(const BoutReal lhs, const Vector3D& rhs) { return (rhs * lhs); } -const Vector3D operator*(const Field2D &lhs, const Vector3D &rhs) { - return(rhs * lhs); -} +const Vector3D operator*(const Field2D& lhs, const Vector3D& rhs) { return (rhs * lhs); } -const Vector3D operator*(const Field3D &lhs, const Vector3D &rhs) -{ - return(rhs * lhs); -} +const Vector3D operator*(const Field3D& lhs, const Vector3D& rhs) { return (rhs * lhs); } /*************************************************************** * NON-MEMBER FUNCTIONS ***************************************************************/ // Return the magnitude of a vector -const Field3D abs(const Vector3D &v, const std::string& region) { - return sqrt(v*v, region); +const Field3D abs(const Vector3D& v, const std::string& region) { + return sqrt(v * v, region); } Vector3D toFieldAligned(const Vector3D& v, const std::string& region) { diff --git a/src/field/where.cxx b/src/field/where.cxx index 30763cb1a4..9360b63d80 100644 --- a/src/field/where.cxx +++ b/src/field/where.cxx @@ -24,4 +24,4 @@ **************************************************************************/ #include -#include +#include diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx index 044379188b..f158fa3d7a 100644 --- a/src/invert/fft_fftw.cxx +++ b/src/invert/fft_fftw.cxx @@ -27,23 +27,23 @@ #include "bout/build_config.hxx" -#include -#include -#include -#include +#include +#include +#include +#include #if BOUT_HAS_FFTW #include #include -#include #include +#include #if BOUT_USE_OPENMP #include #endif // _OPENMP #else -#include +#include #endif // BOUT_HAS_FFTW namespace bout { @@ -62,8 +62,9 @@ void fft_init(Options* options) { options = Options::getRoot()->getSection("fft"); } fft_measurement_flag = (*options)["fft_measurement_flag"] - .doc("Level speed measurements to optimise FFT settings: [estimate], measure, exhaustive") - .withDefault(FFT_MEASUREMENT_FLAG::estimate); + .doc("Level speed measurements to optimise FFT settings: " + "[estimate], measure, exhaustive") + .withDefault(FFT_MEASUREMENT_FLAG::estimate); fft_init(fft_measurement_flag); } @@ -105,20 +106,21 @@ void fft_init(bool fft_measure) { #if !BOUT_USE_OPENMP // Serial code -void rfft(MAYBE_UNUSED(const BoutReal *in), MAYBE_UNUSED(int length), MAYBE_UNUSED(dcomplex *out)) { +void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), + MAYBE_UNUSED(dcomplex* out)) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else // static variables initialized once - static double *fin; - static fftw_complex *fout; + static double* fin; + static fftw_complex* fout; static fftw_plan p; static int n = 0; // If the current length mismatches n - if(length != n) { + if (length != n) { // If n has been used before - if(n > 0) { + if (n > 0) { // Free the previously initialized data fftw_destroy_plan(p); fftw_free(fin); @@ -134,7 +136,8 @@ void rfft(MAYBE_UNUSED(const BoutReal *in), MAYBE_UNUSED(int length), MAYBE_UNUS * I.e the offset and the positive frequencies (so no mirroring * around the Nyquist frequency) */ - fout = static_cast(fftw_malloc(sizeof(fftw_complex) * (length/2 + 1))); + fout = + static_cast(fftw_malloc(sizeof(fftw_complex) * (length / 2 + 1))); auto flags = get_measurement_flag(fft_measurement_flag); @@ -149,36 +152,39 @@ void rfft(MAYBE_UNUSED(const BoutReal *in), MAYBE_UNUSED(int length), MAYBE_UNUS } // Put the input to fin - for(int i=0;i 0) { + if (n > 0) { // Free the previously initialized data fftw_destroy_plan(p); fftw_free(fin); @@ -192,7 +198,8 @@ void irfft(MAYBE_UNUSED(const dcomplex *in), MAYBE_UNUSED(int length), MAYBE_UNU * I.e the offset and the positive frequencies (so no mirroring * around the Nyquist frequency) */ - fin = static_cast(fftw_malloc(sizeof(fftw_complex) * (length/2 + 1))); + fin = + static_cast(fftw_malloc(sizeof(fftw_complex) * (length / 2 + 1))); // Initialize the output of the fourier transformation fout = static_cast(fftw_malloc(sizeof(double) * length)); @@ -209,8 +216,8 @@ void irfft(MAYBE_UNUSED(const dcomplex *in), MAYBE_UNUSED(int length), MAYBE_UNU } // Store the real and imaginary parts in the proper way - const int nmodes = (n/2) + 1; - for(int i=0;i 0) { + if (size > 0) { // Free all memory - for(int i=0;i(fftw_malloc(sizeof(double) * length * n_th)); - foutall = static_cast( + finall = static_cast(fftw_malloc(sizeof(double) * length * n_th)); + foutall = static_cast( fftw_malloc(sizeof(fftw_complex) * (length / 2 + 1) * n_th)); p = new fftw_plan[n_th]; //Never freed auto flags = get_measurement_flag(fft_measurement_flag); - for(int i=0;i(size); const int nmodes = (size / 2) + 1; - for(int i=0;i 0) { // Free all memory - for (int i = 0; i < nthreads; i++) + for (int i = 0; i < nthreads; i++) { fftw_destroy_plan(p[i]); + } delete[] p; fftw_free(finall); fftw_free(foutall); @@ -334,29 +349,30 @@ void irfft(MAYBE_UNUSED(const dcomplex *in), MAYBE_UNUSED(int length), MAYBE_UNU fft_init(); - finall = static_cast( + finall = static_cast( fftw_malloc(sizeof(fftw_complex) * (length / 2 + 1) * n_th)); - foutall = static_cast(fftw_malloc(sizeof(double) * length * n_th)); + foutall = static_cast(fftw_malloc(sizeof(double) * length * n_th)); p = new fftw_plan[n_th]; // Never freed auto flags = get_measurement_flag(fft_measurement_flag); - for (int i = 0; i < n_th; i++) + for (int i = 0; i < n_th; i++) { p[i] = fftw_plan_dft_c2r_1d(length, finall + i * (length / 2 + 1), foutall + i * length, flags); + } size = length; nthreads = n_th; } } // Get working arrays for this thread - fftw_complex *fin = finall + th_id * (size / 2 + 1); - double *fout = foutall + th_id * size; + fftw_complex* fin = finall + th_id * (size / 2 + 1); + double* fout = foutall + th_id * size; const int nmodes = (size / 2) + 1; - for(int i=0;i 0); - if(length != n) { - if(n > 0) { + if (length != n) { + if (n > 0) { fftw_destroy_plan(p); fftw_free(fin); fftw_free(fout); - } + } // fft_init(); // Could be optimized better - fin = static_cast(fftw_malloc(sizeof(double) * 2 * length)); - fout = static_cast(fftw_malloc(sizeof(fftw_complex) * 2 * length)); + fin = static_cast(fftw_malloc(sizeof(double) * 2 * length)); + fout = static_cast(fftw_malloc(sizeof(fftw_complex) * 2 * length)); auto flags = get_measurement_flag(fft_measurement_flag); // fftw call // Plan a real-input/complex-output discrete Fourier transform (DFT) // in 1 dimensions. Returns a fftw_plan (containing pointers etc.) - p = fftw_plan_dft_r2c_1d(2*(length-1), fin, fout, flags); + p = fftw_plan_dft_r2c_1d(2 * (length - 1), fin, fout, flags); n = length; } - for(int i=0;i(length) - 1); // Normalise + } #endif } -void DST_rev(MAYBE_UNUSED(dcomplex *in), MAYBE_UNUSED(int length), MAYBE_UNUSED(BoutReal *out)) { +void DST_rev(MAYBE_UNUSED(dcomplex* in), MAYBE_UNUSED(int length), + MAYBE_UNUSED(BoutReal* out)) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else - static fftw_complex *fin; - static double *fout; + static fftw_complex* fin; + static double* fout; static fftw_plan p; static int n = 0; ASSERT1(length > 0); - if(length != n) { - if(n > 0) { + if (length != n) { + if (n > 0) { fftw_destroy_plan(p); fftw_free(fin); fftw_free(fout); @@ -448,36 +469,41 @@ void DST_rev(MAYBE_UNUSED(dcomplex *in), MAYBE_UNUSED(int length), MAYBE_UNUSED( // Could be optimized better fin = - static_cast(fftw_malloc(sizeof(fftw_complex) * 2 * (length - 1))); - fout = static_cast(fftw_malloc(sizeof(double) * 2 * (length - 1))); + static_cast(fftw_malloc(sizeof(fftw_complex) * 2 * (length - 1))); + fout = static_cast(fftw_malloc(sizeof(double) * 2 * (length - 1))); auto flags = get_measurement_flag(fft_measurement_flag); - p = fftw_plan_dft_c2r_1d(2*(length-1), fin, fout, flags); + p = fftw_plan_dft_c2r_1d(2 * (length - 1), fin, fout, flags); n = length; } - for(int i=0;i irfft(const Array& in, int length) { } // namespace fft } // namespace bout - diff --git a/src/invert/lapack_routines.cxx b/src/invert/lapack_routines.cxx index 05d722e897..144a478b65 100644 --- a/src/invert/lapack_routines.cxx +++ b/src/invert/lapack_routines.cxx @@ -36,26 +36,30 @@ #include "bout/build_config.hxx" -#include -#include -#include -#include +#include +#include +#include +#include #if BOUT_HAS_LAPACK // LAPACK prototypes extern "C" { - /// Complex tridiagonal inversion - void zgtsv_(int *n, int *nrhs, fcmplx *dl, fcmplx *d, fcmplx *du, fcmplx * b, int *ldb, int *info); - /// BoutReal (double) tridiagonal inversion - void dgtsv_(int *n, int *nrhs, BoutReal *dl, BoutReal *d, BoutReal *du, BoutReal *b, int *ldb, int *info); - /// Complex band solver - void zgbsv_(int *n, int *kl, int *ku, int *nrhs, fcmplx *ab, int *ldab, int *ipiv, fcmplx *b, int *ldb, int *info); +/// Complex tridiagonal inversion +void zgtsv_(int* n, int* nrhs, fcmplx* dl, fcmplx* d, fcmplx* du, fcmplx* b, int* ldb, + int* info); +/// BoutReal (double) tridiagonal inversion +void dgtsv_(int* n, int* nrhs, BoutReal* dl, BoutReal* d, BoutReal* du, BoutReal* b, + int* ldb, int* info); +/// Complex band solver +void zgbsv_(int* n, int* kl, int* ku, int* nrhs, fcmplx* ab, int* ldab, int* ipiv, + fcmplx* b, int* ldb, int* info); } /// Use LAPACK routine ZGTSV -int tridag(const dcomplex *a, const dcomplex *b, const dcomplex *c, const dcomplex *r, dcomplex *u, int n) { - +int tridag(const dcomplex* a, const dcomplex* b, const dcomplex* c, const dcomplex* r, + dcomplex* u, int n) { + // Lapack routines overwrite their inputs, so need to copy // allocate memory @@ -70,7 +74,7 @@ int tridag(const dcomplex *a, const dcomplex *b, const dcomplex *c, const dcompl if (i != (n - 1)) { dl[i].r = a[i + 1].real(); dl[i].i = a[i + 1].imag(); - + du[i].r = c[i].real(); du[i].i = c[i].imag(); } @@ -92,7 +96,7 @@ int tridag(const dcomplex *a, const dcomplex *b, const dcomplex *c, const dcompl int nrhs = 1; int info; zgtsv_(&n, &nrhs, dl.begin(), d.begin(), du.begin(), x.begin(), &n, &info); - + if (info != 0) { // Some sort of problem throw BoutException("Problem in LAPACK ZGTSV routine\n"); @@ -110,7 +114,8 @@ int tridag(const dcomplex *a, const dcomplex *b, const dcomplex *c, const dcompl * * Returns true on success */ -bool tridag(const BoutReal *a, const BoutReal *b, const BoutReal *c, const BoutReal *r, BoutReal *u, int n) { +bool tridag(const BoutReal* a, const BoutReal* b, const BoutReal* c, const BoutReal* r, + BoutReal* u, int n) { // Lapack routines overwrite their inputs, so need to copy Array dl(n), d(n), du(n), x(n); @@ -142,7 +147,7 @@ bool tridag(const BoutReal *a, const BoutReal *b, const BoutReal *c, const BoutR int nrhs = 1; int info; dgtsv_(&n, &nrhs, dl.begin(), d.begin(), du.begin(), x.begin(), &n, &info); - + if (info != 0) { // Some sort of problem throw BoutException("Problem in LAPACK DGTSV routine\n"); @@ -160,7 +165,8 @@ bool tridag(const BoutReal *a, const BoutReal *b, const BoutReal *c, const BoutR * * Uses Sherman-Morrison formula */ -void cyclic_tridag(BoutReal *a, BoutReal *b, BoutReal *c, BoutReal *r, BoutReal *x, int n) { +void cyclic_tridag(BoutReal* a, BoutReal* b, BoutReal* c, BoutReal* r, BoutReal* x, + int n) { if (n <= 2) { throw BoutException("n too small in cyclic_tridag"); } @@ -178,8 +184,9 @@ void cyclic_tridag(BoutReal *a, BoutReal *b, BoutReal *c, BoutReal *r, BoutReal b[n - 1] = b[n - 1] - c[n - 1] * a[0] / gamma; // Solve tridiagonal system Ax=r - if (!tridag(a, b, c, r, x, n)) + if (!tridag(a, b, c, r, x, n)) { throw BoutException("ERROR: first tridag call failed in cyclic_tridag\n"); + } u[0] = gamma; u[n - 1] = c[n - 1]; @@ -191,7 +198,7 @@ void cyclic_tridag(BoutReal *a, BoutReal *b, BoutReal *c, BoutReal *r, BoutReal if (!tridag(a, b, c, u.begin(), z.begin(), n)) { throw BoutException("ERROR: second tridag call failed in cyclic_tridag\n"); } - + BoutReal fact = (x[0] + a[0] * x[n - 1] / gamma) / (1.0 + z[0] + a[0] * z[n - 1] / gamma); @@ -218,13 +225,13 @@ void cyclic_tridag(BoutReal *a, BoutReal *b, BoutReal *c, BoutReal *r, BoutReal * info output status * */ -void cband_solve(Matrix &a, int n, int m1, int m2, Array &b) { +void cband_solve(Matrix& a, int n, int m1, int m2, Array& b) { int nrhs = 1; int kl = m1; int ku = m2; int ldab = 2 * kl + ku + 1; int ldb = n; - + Array AB(ldab * n); Array ipiv(n); Array x(n); @@ -234,7 +241,7 @@ void cband_solve(Matrix &a, int n, int m1, int m2, Array &b) x[i].r = b[i].real(); x[i].i = b[i].imag(); } - + // Put matrix elements into AB(ldab, N) (FORTRAN -> loops over ldab fastest) // A is organised into rows, but AB is in columns. First kl not set for (int j = 0; j < n; j++) { @@ -261,22 +268,28 @@ void cband_solve(Matrix &a, int n, int m1, int m2, Array &b) // No LAPACK available. Routines throw exceptions /// Tri-diagonal complex matrix inversion -int tridag(const dcomplex*, const dcomplex*, const dcomplex*, const dcomplex*, dcomplex*, int) { - throw BoutException("complex tridag function not available. Compile BOUT++ with Lapack support."); +int tridag(const dcomplex*, const dcomplex*, const dcomplex*, const dcomplex*, dcomplex*, + int) { + throw BoutException( + "complex tridag function not available. Compile BOUT++ with Lapack support."); } /// Tri-diagonal matrix inversion (BoutReal) -bool tridag(const BoutReal*, const BoutReal*, const BoutReal*, const BoutReal*, BoutReal*, int) { - throw BoutException("tridag function not available. Compile BOUT++ with Lapack support."); +bool tridag(const BoutReal*, const BoutReal*, const BoutReal*, const BoutReal*, BoutReal*, + int) { + throw BoutException( + "tridag function not available. Compile BOUT++ with Lapack support."); } /// Solve a cyclic tridiagonal matrix void cyclic_tridag(BoutReal*, BoutReal*, BoutReal*, BoutReal*, BoutReal*, int) { - throw BoutException("cyclic_tridag function not available. Compile BOUT++ with Lapack support."); + throw BoutException( + "cyclic_tridag function not available. Compile BOUT++ with Lapack support."); } void cband_solve(Matrix&, int, int, int, Array&) { - throw BoutException("cband_solve function not available. Compile BOUT++ with Lapack support."); + throw BoutException( + "cband_solve function not available. Compile BOUT++ with Lapack support."); } #endif // BOUT_HAS_LAPACK @@ -284,42 +297,48 @@ void cband_solve(Matrix&, int, int, int, Array&) { // Common functions /// Solve a cyclic tridiagonal matrix -void cyclic_tridag(dcomplex *a, dcomplex *b, dcomplex *c, dcomplex *r, dcomplex *x, int n) { - if (n <= 2) +void cyclic_tridag(dcomplex* a, dcomplex* b, dcomplex* c, dcomplex* r, dcomplex* x, + int n) { + if (n <= 2) { throw BoutException("n too small in cyclic_tridag(dcomplex)"); - + } + Array u(n), z(n); - + dcomplex gamma = -b[0]; - + // Save original values of b (restore after) dcomplex b0 = b[0]; - dcomplex bn = b[n-1]; - + dcomplex bn = b[n - 1]; + // Modify b b[0] = b[0] - gamma; - b[n-1] = b[n-1] - c[n-1]*a[0]/gamma; - + b[n - 1] = b[n - 1] - c[n - 1] * a[0] / gamma; + // Solve tridiagonal system Ax=r - if(tridag(a, b, c, r, x, n)) + if (tridag(a, b, c, r, x, n)) { throw BoutException("First tridag call failed in cyclic_tridag(dcomplex)"); - + } + u[0] = gamma; - u[n-1] = c[n-1]; - for(int i=1;i<(n-1);i++) + u[n - 1] = c[n - 1]; + for (int i = 1; i < (n - 1); i++) { u[i] = 0.; - + } + // Solve Az = u - if(tridag(a, b, c, u.begin(), z.begin(), n)) + if (tridag(a, b, c, u.begin(), z.begin(), n)) { throw BoutException("Second tridag call failed in cyclic_tridag(dcomplex)\n"); - - dcomplex fact = (x[0] + a[0]*x[n-1]/gamma) / // v.x / (1 + v.z) - (1.0 + z[0] + a[0]*z[n-1]/gamma); - - for(int i=0;i #include #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "cyclic_laplace.hxx" @@ -152,8 +152,9 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } // Copy into array, transposing so kz is first index - for (int kz = 0; kz < nmode; kz++) + for (int kz = 0; kz < nmode; kz++) { bcmplx(kz, ix - xs) = k1d[kz]; + } } // Get elements of the tridiagonal matrix diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx index 3d8db8601d..314f9942ed 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx @@ -31,7 +31,7 @@ class LaplaceCyclic; #ifndef __LAP_CYCLIC_H__ #define __LAP_CYCLIC_H__ -#include "invert_laplace.hxx" +#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" #if BOUT_USE_METRIC_3D @@ -43,11 +43,11 @@ RegisterUnavailableLaplace registerlaplacecycle(LAPLACE_CYCLIC, #else -#include -#include -#include +#include +#include +#include -#include "utils.hxx" +#include "bout/utils.hxx" namespace { RegisterLaplace registerlaplacecycle(LAPLACE_CYCLIC); @@ -63,65 +63,65 @@ public: Mesh* mesh_in = nullptr, Solver* solver = nullptr, Datafile* dump = nullptr); ~LaplaceCyclic(); - + using Laplacian::setCoefA; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Acoef = val; } using Laplacian::setCoefC; - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { setCoefC1(val); setCoefC2(val); } using Laplacian::setCoefC1; - void setCoefC1(const Field2D &val) override { + void setCoefC1(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1coef = val; } using Laplacian::setCoefC2; - void setCoefC2(const Field2D &val) override { + void setCoefC2(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2coef = val; } using Laplacian::setCoefD; - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Dcoef = val; } using Laplacian::setCoefEx; - void setCoefEx(const Field2D &UNUSED(val)) override { + void setCoefEx(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceCyclic does not have Ex coefficient"); } using Laplacian::setCoefEz; - void setCoefEz(const Field2D &UNUSED(val)) override { + void setCoefEz(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceCyclic does not have Ez coefficient"); } using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override {return solve(b,b);} - FieldPerp solve(const FieldPerp &b, const FieldPerp &x0) override; + FieldPerp solve(const FieldPerp& b) override { return solve(b, b); } + FieldPerp solve(const FieldPerp& b, const FieldPerp& x0) override; - Field3D solve(const Field3D &b) override {return solve(b,b);} - Field3D solve(const Field3D &b, const Field3D &x0) override; + Field3D solve(const Field3D& b) override { return solve(b, b); } + Field3D solve(const Field3D& b, const Field3D& x0) override; void verify_solution(const Matrix& a_ver, const Matrix& b_ver, const Matrix& c_ver, const Matrix& r_ver, const Matrix& x_sol, int nsys); private: Field2D Acoef, C1coef, C2coef, Dcoef; - + int nmode; // Number of modes being solved int xs, xe; // Start and end X indices Matrix a, b, c, bcmplx, xcmplx; - + bool dst; - - CyclicReduce *cr; ///< Tridiagonal solver + + CyclicReduce* cr; ///< Tridiagonal solver }; #endif // BOUT_USE_METRIC_3D diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx index 7a6402c807..99946a64dd 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx @@ -36,10 +36,10 @@ #include #include #include -#include +#include #include -#include -#include +#include +#include LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* solver, Datafile* dump) @@ -249,16 +249,28 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) { Field3D result = solution.toField(); localmesh->communicate(result); if (result.hasParallelSlices()) { - BOUT_FOR(i, indexer->getRegionLowerY()) { result.ydown()[i] = result[i]; } - BOUT_FOR(i, indexer->getRegionUpperY()) { result.yup()[i] = result[i]; } + BOUT_FOR (i, indexer->getRegionLowerY()) { + result.ydown()[i] = result[i]; + } + BOUT_FOR (i, indexer->getRegionUpperY()) { + result.yup()[i] = result[i]; + } for (int b = 1; b < localmesh->ystart; b++) { - BOUT_FOR(i, indexer->getRegionLowerY()) { result.ydown(b)[i.ym(b)] = result[i]; } - BOUT_FOR(i, indexer->getRegionUpperY()) { result.yup(b)[i.yp(b)] = result[i]; } + BOUT_FOR (i, indexer->getRegionLowerY()) { + result.ydown(b)[i.ym(b)] = result[i]; + } + BOUT_FOR (i, indexer->getRegionUpperY()) { + result.yup(b)[i.yp(b)] = result[i]; + } } } for (int b = 1; b < localmesh->xstart; b++) { - BOUT_FOR(i, indexer->getRegionInnerX()) { result[i.xm(b)] = result[i]; } - BOUT_FOR(i, indexer->getRegionOuterX()) { result[i.xp(b)] = result[i]; } + BOUT_FOR (i, indexer->getRegionInnerX()) { + result[i.xm(b)] = result[i]; + } + BOUT_FOR (i, indexer->getRegionOuterX()) { + result[i.xp(b)] = result[i]; + } } CALI_MARK_END("LaplaceHypre3d_solve:createField"); diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx index 11656c3269..9fc2864f84 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx @@ -38,11 +38,11 @@ class LaplaceHypre3d; #include #include #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include class LaplaceHypre3d; diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx index e55438dd82..261ea2089a 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx @@ -29,21 +29,21 @@ #if not BOUT_USE_METRIC_3D -#include "globals.hxx" +#include "bout/globals.hxx" #include #include #include #include #include -#include +#include #include -#include -#include -#include +#include +#include +#include -#include "boutcomm.hxx" -#include +#include "bout/boutcomm.hxx" +#include #include @@ -84,7 +84,8 @@ LaplaceIPT::LaplaceIPT(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED } // Cannot use multigrid on 1 core if (n == 1 and max_level != 0) { - throw BoutException("LaplaceIPT error: must have max_level=0 if using one processor. "); + throw BoutException( + "LaplaceIPT error: must have max_level=0 if using one processor. "); } static int ipt_solver_count = 1; @@ -492,10 +493,8 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { cycle_eta = 0; for (int kz = 0; kz < nmode; kz++) { const BoutReal ratio = errornorm[kz] / errornorm_old[kz]; - const int eta = - std::ceil(std::log(1.0 / errornorm[kz]) / std::log(ratio)); + const int eta = std::ceil(std::log(1.0 / errornorm[kz]) / std::log(ratio)); cycle_eta = (cycle_eta > eta) ? cycle_eta : eta; - } } } @@ -581,8 +580,9 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { for (int ix = 0; ix < 4; ix++) { for (int kz = 0; kz < nmode; kz++) { if (!finite(levels[0].xloc(ix, kz).real()) - or !finite(levels[0].xloc(ix, kz).imag())) + or !finite(levels[0].xloc(ix, kz).imag())) { throw BoutException("Non-finite xloc at {:d}, {:d}, {:d}", ix, jy, kz); + } } } #endif @@ -599,8 +599,9 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { #if CHECK > 2 for (int ix = 0; ix < ncx; ix++) { for (int kz = 0; kz < nmode; kz++) { - if (!finite(xk1d(kz, ix).real()) or !finite(xk1d(kz, ix).imag())) + if (!finite(xk1d(kz, ix).real()) or !finite(xk1d(kz, ix).imag())) { throw BoutException("Non-finite xloc at {:d}, {:d}, {:d}", ix, jy, kz); + } } } #endif @@ -638,9 +639,11 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { irfft(&xk(ix, 0), ncz, x[ix]); #if CHECK > 2 - for (int kz = 0; kz < ncz; kz++) - if (!finite(x(ix, kz))) + for (int kz = 0; kz < ncz; kz++) { + if (!finite(x(ix, kz))) { throw BoutException("Non-finite at {:d}, {:d}, {:d}", ix, jy, kz); + } + } #endif } @@ -1225,12 +1228,17 @@ void LaplaceIPT::Level::calculate_total_residual(const LaplaceIPT& l, if (!converged[kz]) { errornorm[kz] = 0.0; - BoutReal w = pow( l.rtol*sqrt(pow(xloc(1, kz).real(), 2) + pow(xloc(1, kz).imag(), 2)) + l.atol , 2); - subtotal[kz] = ( pow(residual(1, kz).real(), 2) + pow(residual(1, kz).imag(), 2) ) / w; + BoutReal w = pow( + l.rtol * sqrt(pow(xloc(1, kz).real(), 2) + pow(xloc(1, kz).imag(), 2)) + l.atol, + 2); + subtotal[kz] = + (pow(residual(1, kz).real(), 2) + pow(residual(1, kz).imag(), 2)) / w; if (l.localmesh->lastX()) { - w = pow( l.rtol*sqrt(pow(xloc(2, kz).real(), 2) + pow(xloc(2, kz).imag(), 2)) + l.atol , 2); + w = pow(l.rtol * sqrt(pow(xloc(2, kz).real(), 2) + pow(xloc(2, kz).imag(), 2)) + + l.atol, + 2); subtotal[kz] += - ( pow(residual(2, kz).real(), 2) + pow(residual(2, kz).imag(), 2) ) / w; + (pow(residual(2, kz).real(), 2) + pow(residual(2, kz).imag(), 2)) / w; } } } @@ -1241,7 +1249,7 @@ void LaplaceIPT::Level::calculate_total_residual(const LaplaceIPT& l, for (int kz = 0; kz < l.nmode; kz++) { if (!converged[kz]) { - errornorm[kz] = sqrt(errornorm[kz]/BoutReal(l.ncx)); + errornorm[kz] = sqrt(errornorm[kz] / BoutReal(l.ncx)); if (errornorm[kz] < 1.0) { converged[kz] = true; } diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx index 6b57e00abf..5f78ac89d1 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx @@ -29,7 +29,7 @@ class LaplaceIPT; #ifndef __IPT_H__ #define __IPT_H__ -#include "invert_laplace.hxx" +#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" #if BOUT_USE_METRIC_3D @@ -41,9 +41,9 @@ RegisterUnavailableLaplace registerlaplaceipt(LAPLACE_IPT, #else -#include -#include -#include +#include +#include +#include namespace { RegisterLaplace registerlaplaceipt(LAPLACE_IPT); diff --git a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx index 10ac88ad2c..3670b314c7 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx @@ -33,7 +33,7 @@ #include "multigrid_laplace.hxx" #include -#include "unused.hxx" +#include "bout/unused.hxx" // Define basic multigrid algorithm diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx index e136613d26..953c52bcbe 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx @@ -33,21 +33,21 @@ #if not BOUT_USE_METRIC_3D #include -#include #include +#include #if BOUT_USE_OPENMP #include #endif -BoutReal soltime=0.0,settime=0.0; +BoutReal soltime = 0.0, settime = 0.0; LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED(solver), Datafile* UNUSED(dump)) : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0) { TRACE("LaplaceMultigrid::LaplaceMultigrid(Options *opt)"); - + // periodic x-direction not handled: see MultigridAlg::communications ASSERT1(!localmesh->periodicX); @@ -57,83 +57,97 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ D.setLocation(location); // Get Options in Laplace Section - if (!opt) opts = Options::getRoot()->getSection("laplace"); - else opts=opt; - opts->get("multigridlevel",mglevel,100,true); - opts->get("rtol",rtol,pow(10.0,-8),true); - opts->get("atol",atol,pow(10.0,-20),true); - opts->get("dtol",dtol,pow(10.0,5),true); - opts->get("smtype",mgsm,1,true); + if (!opt) { + opts = Options::getRoot()->getSection("laplace"); + } else { + opts = opt; + } + opts->get("multigridlevel", mglevel, 100, true); + opts->get("rtol", rtol, pow(10.0, -8), true); + opts->get("atol", atol, pow(10.0, -20), true); + opts->get("dtol", dtol, pow(10.0, 5), true); + opts->get("smtype", mgsm, 1, true); #if BOUT_USE_OPENMP - if (mgsm != 0 && omp_get_max_threads()>1) { - output_warn << "WARNING: in multigrid Laplace solver, for smtype!=0 the smoothing cannot be parallelised with OpenMP threads."< 1) { + output_warn << "WARNING: in multigrid Laplace solver, for smtype!=0 the smoothing " + "cannot be parallelised with OpenMP threads." + << endl + << " Consider using smtype=0 instead when using OpenMP threads." + << endl; } #endif - opts->get("jacomega",omega,0.8,true); - opts->get("solvertype",mgplag,1,true); - opts->get("cftype",cftype,0,true); - opts->get("mergempi",mgmpi,63,true); - opts->get("checking",pcheck,0,true); + opts->get("jacomega", omega, 0.8, true); + opts->get("solvertype", mgplag, 1, true); + opts->get("cftype", cftype, 0, true); + opts->get("mergempi", mgmpi, 63, true); + opts->get("checking", pcheck, 0, true); mgcount = 0; // Initialize, allocate memory, etc. comms_tagbase = 385; // Some random number - + int implemented_global_flags = INVERT_START_NEW; - if ( global_flags & ~implemented_global_flags ) { - throw BoutException("Attempted to set Laplacian inversion flag that is not implemented in LaplaceMultigrid."); + if (global_flags & ~implemented_global_flags) { + throw BoutException("Attempted to set Laplacian inversion flag that is not " + "implemented in LaplaceMultigrid."); } - int implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_DC_GRAD; // INVERT_DC_GRAD does not actually do anything, but harmless to set while comparing to Fourier solver with Neumann boundary conditions - if ( inner_boundary_flags & ~implemented_boundary_flags ) { - throw BoutException("Attempted to set Laplacian inner boundary inversion flag that is not implemented in LaplaceMultigrid."); + int implemented_boundary_flags = + INVERT_AC_GRAD + INVERT_SET + + INVERT_DC_GRAD; // INVERT_DC_GRAD does not actually do anything, but harmless to set while comparing to Fourier solver with Neumann boundary conditions + if (inner_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set Laplacian inner boundary inversion flag that " + "is not implemented in LaplaceMultigrid."); } - if ( outer_boundary_flags & ~implemented_boundary_flags ) { - throw BoutException("Attempted to set Laplacian outer boundary inversion flag that is not implemented in LaplaceMultigrid."); + if (outer_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set Laplacian outer boundary inversion flag that " + "is not implemented in LaplaceMultigrid."); } - + commX = localmesh->getXcomm(); - - Nx_local = localmesh->xend - localmesh->xstart + 1; // excluding guard cells - Nx_global = localmesh->GlobalNx - 2*localmesh->xstart; // excluding guard cells - + + Nx_local = localmesh->xend - localmesh->xstart + 1; // excluding guard cells + Nx_global = localmesh->GlobalNx - 2 * localmesh->xstart; // excluding guard cells + if (mgcount == 0) { - output <<"Nx="<GlobalNz; Nz_local = Nz_global; // No parallelization in z-direction (for now) - // + // //else { // Nz_local = localmesh->zend - localmesh->zstart + 1; // excluding guard cells // Nz_global = localmesh->GlobalNz - 2*localmesh->zstart; // excluding guard cells // } - if (mgcount==0) { - output <<"Nz="<1) { + if (mglevel > 1) { int nn = Nx_global; - for (int n = mglevel;n > 1; n--) { - if ( nn%2 != 0 ) { - output<<"Size of global x-domain is not a multiple of 2^"< 1; n--) { + if (nn % 2 != 0) { + output << "Size of global x-domain is not a multiple of 2^" << mglevel - 1 + << " mglevel is changed to " << mglevel - n + 1 << endl; mglevel = mglevel - n + 1; break; } - nn = nn/2; + nn = nn / 2; } // ... and check the same for z-direction nn = Nz_global; - for (int n = mglevel;n > 1; n--) { - if ( nn%2 != 0 ) { - output<<"Size of global z-domain is not a multiple of 2^ "< 1; n--) { + if (nn % 2 != 0) { + output << "Size of global z-domain is not a multiple of 2^ " << mglevel - 1 + << " mglevel is changed to " << mglevel - n + 1 << endl; mglevel = mglevel - n + 1; break; } - nn = nn/2; + nn = nn / 2; } + } else { + mglevel = 1; } - else mglevel = 1; // Compute available levels on each processor along x-direction // aclevel is the number of levels that can be used in parallel, i.e. set by @@ -141,36 +155,39 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ // If the number of levels is higher than aclevel, then the grid is collected // to a single processor, and a new multigrid solver (called sMG) is created // to run in serial to compute the coarsest (mglevel-aclevel) levels - int aclevel,adlevel; - if (mglevel >1) { + int aclevel, adlevel; + if (mglevel > 1) { int nn = Nx_local; aclevel = mglevel; - for (int n = aclevel;n > 1; n--) { - if ( nn%2 != 0 ) { - output<<"Size of local x-domain is not a multiple of 2^"< 1; n--) { + if (nn % 2 != 0) { + output << "Size of local x-domain is not a multiple of 2^" << aclevel + << " aclevel is changed to " << aclevel - n + 1 << endl; aclevel = aclevel - n + 1; break; } - nn = nn/2; + nn = nn / 2; } // ... and check the same for z-direction nn = Nz_local; - for (int n = aclevel;n > 1; n--) { - if ( nn%2 != 0 ) { - output<<"Size of local z-domain is not a multiple of 2^ "< 1; n--) { + if (nn % 2 != 0) { + output << "Size of local z-domain is not a multiple of 2^ " << aclevel + << " aclevel is changed to " << aclevel - n << endl; aclevel = aclevel - n + 1; break; } - nn = nn/2; + nn = nn / 2; } + } else { + aclevel = 1; } - else aclevel = 1; adlevel = mglevel - aclevel; kMG = bout::utils::make_unique(aclevel, Nx_local, Nz_local, Nx_global, adlevel, mgmpi, commX, pcheck); kMG->mgplag = mgplag; - kMG->mgsm = mgsm; + kMG->mgsm = mgsm; kMG->cftype = cftype; kMG->rtol = rtol; kMG->atol = atol; @@ -183,18 +200,24 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ x.reallocate((Nx_local + 2) * (Nz_local + 2)); b.reallocate((Nx_local + 2) * (Nz_local + 2)); - if (mgcount == 0) { - output<<" Smoothing type is "; + if (mgcount == 0) { + output << " Smoothing type is "; if (mgsm == 0) { - output<<"Jacobi smoother"; - output<<"with omega = "<rProcI); - output<<"Out file= "<matmg[level][i*9+j]); - fprintf(outf,"\n"); - } - fclose(outf); +if (kMG->xNP > 1) { +bout::globals::mpi->MPI_Barrier(commX); +} + +if ((pcheck == 3) && (mgcount == 0)) { +FILE* outf; +char outfile[256]; +sprintf(outfile, "test_matF_%d.mat", kMG->rProcI); +output << "Out file= " << outfile << endl; +outf = fopen(outfile, "w"); +int dim = (lxx + 2) * (lzz + 2); +fprintf(outf, "dim = %d (%d, %d)\n", dim, lxx, lzz); + +for (int i = 0; i < dim; i++) { + fprintf(outf, "%d ==", i); + for (int j = 0; j < 9; j++) { +fprintf(outf, "%12.6f,", kMG->matmg[level][i * 9 + j]); } + fprintf(outf, "\n"); +} +fclose(outf); +} - if (level > 0) kMG->setMultigridC(0); - - if((pcheck == 3) && (mgcount == 0)) { - for(int i = level; i> 0;i--) { - output<lnx[i-1]<<"("<gnx[i-1]<<"),"<lnz[i-1]<rProcI); - output<<"Out file= "<lnx[i-1]+2)*(kMG->lnz[i-1]+2); - fprintf(outf,"dim = %d (%d,%d)\n",dim,kMG->lnx[i-1],kMG->lnz[i-1]); - - for(int ii = 0;iimatmg[i-1][ii*9+j]); - fprintf(outf,"\n"); - } - fclose(outf); - } +if (level > 0) { +kMG->setMultigridC(0); +} + +if ((pcheck == 3) && (mgcount == 0)) { +for (int i = level; i > 0; i--) { + output << i << "dimension= " << kMG->lnx[i - 1] << "(" << kMG->gnx[i - 1] << ")," + << kMG->lnz[i - 1] << endl; + + FILE* outf; + char outfile[256]; + sprintf(outfile, "test_matC%1d_%d.mat", i, kMG->rProcI); + output << "Out file= " << outfile << endl; + outf = fopen(outfile, "w"); + int dim = (kMG->lnx[i - 1] + 2) * (kMG->lnz[i - 1] + 2); + fprintf(outf, "dim = %d (%d,%d)\n", dim, kMG->lnx[i - 1], kMG->lnz[i - 1]); + + for (int ii = 0; ii < dim; ii++) { +fprintf(outf, "%d ==", ii); +for (int j = 0; j < 9; j++) { + fprintf(outf, "%12.6f,", kMG->matmg[i - 1][ii * 9 + j]); +} +fprintf(outf, "\n"); } + fclose(outf); +} +} - t1 = bout::globals::mpi->MPI_Wtime(); - settime += t1-t0; +t1 = bout::globals::mpi->MPI_Wtime(); +settime += t1 - t0; - // Compute solution. +// Compute solution. - mgcount++; - if (pcheck > 0) - t0 = bout::globals::mpi->MPI_Wtime(); +mgcount++; +if (pcheck > 0) { +t0 = bout::globals::mpi->MPI_Wtime(); +} - kMG->getSolution(std::begin(x), std::begin(b), 0); +kMG->getSolution(std::begin(x), std::begin(b), 0); - if (pcheck > 0) { - t1 = bout::globals::mpi->MPI_Wtime(); - soltime += t1-t0; - if(mgcount%300 == 0) { - output<<"Accumulated execution time at "< 0) { +t1 = bout::globals::mpi->MPI_Wtime(); +soltime += t1 - t0; +if (mgcount % 300 == 0) { + output << "Accumulated execution time at " << mgcount << " Sol " << soltime << " ( " + << settime << " )" << endl; + settime = 0.; + soltime = 0.; +} +} - FieldPerp result{emptyFrom(b_in)}; +FieldPerp result{emptyFrom(b_in)}; #if CHECK > 2 - // Make any unused elements NaN so that user does not try to do calculations with them - BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = BoutNaN; } +// Make any unused elements NaN so that user does not try to do calculations with them +BOUT_FOR (i, result.getRegion("RGN_ALL")) { +result[i] = BoutNaN; +} #endif - // Copy solution into a FieldPerp to return -BOUT_OMP(parallel default(shared) ) +// Copy solution into a FieldPerp to return +BOUT_OMP(parallel default(shared)) BOUT_OMP(for collapse(2)) - for (int i=1; ixstart; - int k2 = k-1; - result(i2, k2) = x[i*lz2+k]; - } - } - if (localmesh->firstX()) { - if ( inner_boundary_flags & INVERT_AC_GRAD ) { - // Neumann boundary condition - if ( inner_boundary_flags & INVERT_SET ) { - // guard cells of x0 specify gradient to set at inner boundary - int i2 = -1+localmesh->xstart; -BOUT_OMP(parallel default(shared) ) +for (int i = 1; i < lxx + 1; i++) { +for (int k = 1; k < lzz + 1; k++) { + int i2 = i - 1 + localmesh->xstart; + int k2 = k - 1; + result(i2, k2) = x[i * lz2 + k]; +} +} +if (localmesh->firstX()) { +if (inner_boundary_flags & INVERT_AC_GRAD) { + // Neumann boundary condition + if (inner_boundary_flags & INVERT_SET) { +// guard cells of x0 specify gradient to set at inner boundary +int i2 = -1 + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kxstart-1, k2)*sqrt(coords->g_11(localmesh->xstart, yindex))*coords->dx(localmesh->xstart, yindex); - } - } - else { - // zero gradient inner boundary condition - int i2 = -1+localmesh->xstart; -BOUT_OMP(parallel default(shared) ) +for (int k = 1; k < lzz + 1; k++) { + int k2 = k - 1; + result(i2, k2) = x[lz2 + k] + - x0(localmesh->xstart - 1, k2) + * sqrt(coords->g_11(localmesh->xstart, yindex)) + * coords->dx(localmesh->xstart, yindex); +} + } else { +// zero gradient inner boundary condition +int i2 = -1 + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kxstart; -BOUT_OMP(parallel default(shared) ) +for (int k = 1; k < lzz + 1; k++) { + int k2 = k - 1; + result(i2, k2) = x[lz2 + k]; +} + } +} else { + // Dirichlet boundary condition + if (inner_boundary_flags & INVERT_SET) { +// guard cells of x0 specify value to set at inner boundary +int i2 = -1 + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kxstart-1,k2) - x[lz2+k]; - } - } - else { - // zero value inner boundary condition - int i2 = -1+localmesh->xstart; -BOUT_OMP(parallel default(shared) ) +for (int k = 1; k < lzz + 1; k++) { + int k2 = k - 1; + result(i2, k2) = 2. * x0(localmesh->xstart - 1, k2) - x[lz2 + k]; +} + } else { +// zero value inner boundary condition +int i2 = -1 + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; klastX()) { - if ( outer_boundary_flags & INVERT_AC_GRAD ) { - // Neumann boundary condition - if ( inner_boundary_flags & INVERT_SET ) { - // guard cells of x0 specify gradient to set at outer boundary - int i2 = lxx+localmesh->xstart; -BOUT_OMP(parallel default(shared) ) +} +} +if (localmesh->lastX()) { +if (outer_boundary_flags & INVERT_AC_GRAD) { + // Neumann boundary condition + if (inner_boundary_flags & INVERT_SET) { +// guard cells of x0 specify gradient to set at outer boundary +int i2 = lxx + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kxend+1, k2)*sqrt(coords->g_11(localmesh->xend, yindex))*coords->dx(localmesh->xend, yindex); - } - } - else { - // zero gradient outer boundary condition - int i2 = lxx+localmesh->xstart; -BOUT_OMP(parallel default(shared) ) +for (int k = 1; k < lzz + 1; k++) { + int k2 = k - 1; + result(i2, k2) = x[lxx * lz2 + k] + + x0(localmesh->xend + 1, k2) + * sqrt(coords->g_11(localmesh->xend, yindex)) + * coords->dx(localmesh->xend, yindex); +} + } else { +// zero gradient outer boundary condition +int i2 = lxx + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kxstart; -BOUT_OMP(parallel default(shared) ) +for (int k = 1; k < lzz + 1; k++) { + int k2 = k - 1; + result(i2, k2) = x[lxx * lz2 + k]; +} + } +} else { + // Dirichlet boundary condition + if (outer_boundary_flags & INVERT_SET) { +// guard cells of x0 specify value to set at outer boundary +int i2 = lxx + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kxend+1,k2) - x[lxx*lz2+k]; - } - } - else { - // zero value inner boundary condition - int i2 = lxx+localmesh->xstart; -BOUT_OMP(parallel default(shared) ) +for (int k = 1; k < lzz + 1; k++) { + int k2 = k - 1; + result(i2, k2) = 2. * x0(localmesh->xend + 1, k2) - x[lxx * lz2 + k]; +} + } else { +// zero value inner boundary condition +int i2 = lxx + localmesh->xstart; +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for (int k=1; kmatmg[level]; - int llx = kMG->lnx[level]; - int llz = kMG->lnz[level]; +BoutReal* mat; +mat = kMG->matmg[level]; +int llx = kMG->lnx[level]; +int llz = kMG->lnz[level]; BOUT_OMP(parallel default(shared)) BOUT_OMP(for collapse(2)) - for (int i=1; ixstart; - int k2 = k-1; - int k2p = (k2+1)%Nz_global; - int k2m = (k2+Nz_global-1)%Nz_global; - - BoutReal dz = coords->dz(i2, yindex); - BoutReal ddx_C = (C2(i2+1, yindex, k2) - C2(i2-1, yindex, k2))/2./coords->dx(i2, yindex)/C1(i2, yindex, k2); - BoutReal ddz_C = - (C2(i2, yindex, k2p) - C2(i2, yindex, k2m)) / 2. / dz / C1(i2, yindex, k2); - - BoutReal ddx = D(i2, yindex, k2)*coords->g11(i2, yindex)/coords->dx(i2, yindex)/coords->dx(i2, yindex); - // coefficient of 2nd derivative stencil (x-direction) - - BoutReal ddz = D(i2, yindex, k2) * coords->g33(i2, yindex) / SQ(dz); - // coefficient of 2nd derivative stencil (z-direction) - - BoutReal dxdz = - D(i2, yindex, k2) * 2. * coords->g13(i2, yindex) / coords->dx(i2, yindex) / dz; - // coefficient of mixed derivative stencil (could assume zero, at least initially, - // if easier; then check this is true in constructor) - - BoutReal dxd = (D(i2, yindex, k2)*coords->G1(i2, yindex) - + coords->g11(i2, yindex)*ddx_C - + coords->g13(i2, yindex)*ddz_C // (could assume zero, at least initially, if easier; then check this is true in constructor) - )/coords->dx(i2, yindex); // coefficient of 1st derivative stencil (x-direction) - if (nonuniform) { - // add correction for non-uniform dx - dxd += D(i2, yindex, k2)*coords->d1_dx(i2, yindex); - } - - BoutReal dzd = - (D(i2, yindex, k2) * coords->G3(i2, yindex) + coords->g33(i2, yindex) * ddz_C - + coords->g13(i2, yindex) - * ddx_C // (could assume zero, at least initially, if easier; then check - // this is true in constructor) - ) - / dz; // coefficient of 1st derivative stencil (z-direction) - - int ic = i*(llz+2)+k; - mat[ic*9] = dxdz/4.; - mat[ic*9+1] = ddx - dxd/2.; - mat[ic*9+2] = -dxdz/4.; - mat[ic*9+3] = ddz - dzd/2.; - mat[ic*9+4] = A(i2, yindex, k2) - 2.*(ddx+ddz); // coefficient of no-derivative component - mat[ic*9+5] = ddz + dzd/2.; - mat[ic*9+6] = -dxdz/4.; - mat[ic*9+7] = ddx+dxd/2.; - mat[ic*9+8] = dxdz/4.; - } +for (int i = 1; i < llx + 1; i++) { +for (int k = 1; k < llz + 1; k++) { + int i2 = i - 1 + localmesh->xstart; + int k2 = k - 1; + int k2p = (k2 + 1) % Nz_global; + int k2m = (k2 + Nz_global - 1) % Nz_global; + + BoutReal dz = coords->dz(i2, yindex); + BoutReal ddx_C = (C2(i2 + 1, yindex, k2) - C2(i2 - 1, yindex, k2)) / 2. + / coords->dx(i2, yindex) / C1(i2, yindex, k2); + BoutReal ddz_C = + (C2(i2, yindex, k2p) - C2(i2, yindex, k2m)) / 2. / dz / C1(i2, yindex, k2); + + BoutReal ddx = D(i2, yindex, k2) * coords->g11(i2, yindex) / coords->dx(i2, yindex) + / coords->dx(i2, yindex); + // coefficient of 2nd derivative stencil (x-direction) + + BoutReal ddz = D(i2, yindex, k2) * coords->g33(i2, yindex) / SQ(dz); + // coefficient of 2nd derivative stencil (z-direction) + + BoutReal dxdz = + D(i2, yindex, k2) * 2. * coords->g13(i2, yindex) / coords->dx(i2, yindex) / dz; + // coefficient of mixed derivative stencil (could assume zero, at least initially, + // if easier; then check this is true in constructor) + + BoutReal dxd = + (D(i2, yindex, k2) * coords->G1(i2, yindex) + coords->g11(i2, yindex) * ddx_C + + coords->g13(i2, yindex) + * ddz_C // (could assume zero, at least initially, if easier; then check this is true in constructor) + ) + / coords->dx(i2, yindex); // coefficient of 1st derivative stencil (x-direction) + if (nonuniform) { +// add correction for non-uniform dx +dxd += D(i2, yindex, k2) * coords->d1_dx(i2, yindex); } - // Here put boundary conditions + BoutReal dzd = + (D(i2, yindex, k2) * coords->G3(i2, yindex) + coords->g33(i2, yindex) * ddz_C + + coords->g13(i2, yindex) + * ddx_C // (could assume zero, at least initially, if easier; then check + // this is true in constructor) + ) + / dz; // coefficient of 1st derivative stencil (z-direction) + + int ic = i * (llz + 2) + k; + mat[ic * 9] = dxdz / 4.; + mat[ic * 9 + 1] = ddx - dxd / 2.; + mat[ic * 9 + 2] = -dxdz / 4.; + mat[ic * 9 + 3] = ddz - dzd / 2.; + mat[ic * 9 + 4] = + A(i2, yindex, k2) - 2. * (ddx + ddz); // coefficient of no-derivative component + mat[ic * 9 + 5] = ddz + dzd / 2.; + mat[ic * 9 + 6] = -dxdz / 4.; + mat[ic * 9 + 7] = ddx + dxd / 2.; + mat[ic * 9 + 8] = dxdz / 4.; +} +} + +// Here put boundary conditions - if (kMG->rProcI == 0) { - if ( inner_boundary_flags & INVERT_AC_GRAD ) { - // Neumann boundary condition -BOUT_OMP(parallel default(shared)) +if (kMG->rProcI == 0) { +if (inner_boundary_flags & INVERT_AC_GRAD) { + // Neumann boundary condition + BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int k = 1;krProcI == kMG->xNP-1) { - if ( outer_boundary_flags & INVERT_AC_GRAD ) { - // Neumann boundary condition +for (int k = 1; k < llz + 1; k++) { +int ic = llz + 2 + k; +mat[ic * 9 + 3] -= mat[ic * 9]; +mat[ic * 9 + 4] -= mat[ic * 9 + 1]; +mat[ic * 9 + 5] -= mat[ic * 9 + 2]; +b[ic] -= mat[ic * 9] * x[k - 1]; +b[ic] -= mat[ic * 9 + 1] * x[k]; +b[ic] -= mat[ic * 9 + 2] * x[k + 1]; +mat[ic * 9] = 0.; +mat[ic * 9 + 1] = 0.; +mat[ic * 9 + 2] = 0.; +} +} +} +if (kMG->rProcI == kMG->xNP - 1) { +if (outer_boundary_flags & INVERT_AC_GRAD) { +// Neumann boundary condition BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int k = 1;k -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #define MAXGM 15 // In multigrid_alg.cxx -class MultigridAlg{ +class MultigridAlg { public: - MultigridAlg(int ,int ,int ,int ,int ,MPI_Comm ,int); + MultigridAlg(int, int, int, int, int, MPI_Comm, int); virtual ~MultigridAlg(); - void setMultigridC(int ); - void getSolution(BoutReal *,BoutReal *,int ); + void setMultigridC(int); + void getSolution(BoutReal*, BoutReal*, int); - int mglevel,mgplag,cftype,mgsm,pcheck,xNP,zNP,rProcI; - BoutReal rtol,atol,dtol,omega; + int mglevel, mgplag, cftype, mgsm, pcheck, xNP, zNP, rProcI; + BoutReal rtol, atol, dtol, omega; Array gnx, gnz, lnx, lnz; - BoutReal **matmg; + BoutReal** matmg; protected: /******* Start implementation ********/ - int numP,xProcI,zProcI,xProcP,xProcM,zProcP,zProcM; + int numP, xProcI, zProcI, xProcP, xProcM, zProcP, zProcM; MPI_Comm commMG; - void communications(BoutReal *, int ); - void setMatrixC(int ); - - void cycleMG(int ,BoutReal *, BoutReal *); - void smoothings(int , BoutReal *, BoutReal *); - void projection(int , BoutReal *, BoutReal *); - void prolongation(int ,BoutReal *, BoutReal *); - void pGMRES(BoutReal *, BoutReal *, int , int); - void solveMG(BoutReal *, BoutReal *, int ); - void multiAVec(int , BoutReal *, BoutReal *); - void residualVec(int , BoutReal *, BoutReal *, BoutReal *); - BoutReal vectorProd(int , BoutReal *, BoutReal *); - - virtual void lowestSolver(BoutReal *, BoutReal *, int ); - -}; + void communications(BoutReal*, int); + void setMatrixC(int); + + void cycleMG(int, BoutReal*, BoutReal*); + void smoothings(int, BoutReal*, BoutReal*); + void projection(int, BoutReal*, BoutReal*); + void prolongation(int, BoutReal*, BoutReal*); + void pGMRES(BoutReal*, BoutReal*, int, int); + void solveMG(BoutReal*, BoutReal*, int); + void multiAVec(int, BoutReal*, BoutReal*); + void residualVec(int, BoutReal*, BoutReal*, BoutReal*); + BoutReal vectorProd(int, BoutReal*, BoutReal*); + virtual void lowestSolver(BoutReal*, BoutReal*, int); +}; // Define three different type of multigrid solver // in multigrid_solver.cxx -class MultigridSerial: public MultigridAlg{ +class MultigridSerial : public MultigridAlg { public: MultigridSerial(int level, int gx, int gz, MPI_Comm comm, int check); - ~MultigridSerial() {}; + ~MultigridSerial(){}; - void convertMatrixF(BoutReal *); + void convertMatrixF(BoutReal*); }; -class Multigrid2DPf1D: public MultigridAlg{ +class Multigrid2DPf1D : public MultigridAlg { public: - Multigrid2DPf1D(int ,int ,int ,int ,int ,int ,int ,int ,MPI_Comm ,int ); - ~Multigrid2DPf1D() {}; + Multigrid2DPf1D(int, int, int, int, int, int, int, int, MPI_Comm, int); + ~Multigrid2DPf1D(){}; - void setMultigridC(int ); - void setPcheck(int ); + void setMultigridC(int); + void setPcheck(int); void setValueS(); int kflag; private: std::unique_ptr sMG; - void convertMatrixFS(int ); - void lowestSolver(BoutReal *, BoutReal *, int ); - + void convertMatrixFS(int); + void lowestSolver(BoutReal*, BoutReal*, int); }; -class Multigrid1DP: public MultigridAlg{ +class Multigrid1DP : public MultigridAlg { public: - Multigrid1DP(int ,int ,int ,int ,int ,int, MPI_Comm ,int ); - ~Multigrid1DP() {}; - void setMultigridC(int ); - void setPcheck(int ); + Multigrid1DP(int, int, int, int, int, int, MPI_Comm, int); + ~Multigrid1DP(){}; + void setMultigridC(int); + void setPcheck(int); void setValueS(); int kflag; @@ -133,21 +130,18 @@ private: MPI_Comm comm2D; std::unique_ptr sMG; std::unique_ptr rMG; - void convertMatrixF2D(int ); - void convertMatrixFS(int ); - void lowestSolver(BoutReal *, BoutReal *, int ); - + void convertMatrixF2D(int); + void convertMatrixFS(int); + void lowestSolver(BoutReal*, BoutReal*, int); }; - - class LaplaceMultigrid : public Laplacian { public: LaplaceMultigrid(Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE, Mesh* mesh_in = nullptr, Solver* solver = nullptr, Datafile* dump = nullptr); - ~LaplaceMultigrid() {}; - + ~LaplaceMultigrid(){}; + using Laplacian::setCoefA; using Laplacian::setCoefC; using Laplacian::setCoefC1; @@ -156,28 +150,28 @@ public: using Laplacian::setCoefEx; using Laplacian::setCoefEz; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; } - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; C2 = val; } - void setCoefC1(const Field2D &val) override { + void setCoefC1(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; } - void setCoefC2(const Field2D &val) override { + void setCoefC2(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2 = val; } - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; @@ -189,28 +183,28 @@ public: throw BoutException("setCoefEz is not implemented in LaplaceMultigrid"); } - void setCoefA(const Field3D &val) override { + void setCoefA(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; } - void setCoefC(const Field3D &val) override { + void setCoefC(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; C2 = val; } - void setCoefC1(const Field3D &val) override { + void setCoefC1(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; } - void setCoefC2(const Field3D &val) override { + void setCoefC2(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2 = val; } - void setCoefD(const Field3D &val) override { + void setCoefD(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; @@ -219,27 +213,27 @@ public: bool uses3DCoefs() const override { return true; } using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override { + FieldPerp solve(const FieldPerp& b) override { ASSERT1(localmesh == b.getMesh()); return solve(b, zeroFrom(b)); } - FieldPerp solve(const FieldPerp &b_in, const FieldPerp &x0) override; + FieldPerp solve(const FieldPerp& b_in, const FieldPerp& x0) override; private: - Field3D A,C1,C2,D; // ODE Coefficients + Field3D A, C1, C2, D; // ODE Coefficients int Nx_local, Nx_global, Nz_local, Nz_global; // Local and global grid sizes - int yindex; // y-position of the current solution phase + int yindex; // y-position of the current solution phase Array x; // solution vector Array b; // RHS vector std::unique_ptr kMG; /******* Start implementation ********/ - int mglevel,mgplag,cftype,mgsm,pcheck; - int mgcount,mgmpi; + int mglevel, mgplag, cftype, mgsm, pcheck; + int mgcount, mgmpi; - Options *opts; - BoutReal rtol,atol,dtol,omega; + Options* opts; + BoutReal rtol, atol, dtol, omega; MPI_Comm commX; int comms_tagbase; diff --git a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx index a1892f09cd..eb7e2bdb6c 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx @@ -32,27 +32,34 @@ #if not BOUT_USE_METRIC_3D #include "multigrid_laplace.hxx" -#include "unused.hxx" +#include "bout/unused.hxx" #include -Multigrid1DP::Multigrid1DP(int level,int lx, int lz, int gx, int dl, int merge, - MPI_Comm comm,int check) : - MultigridAlg(level,lx,lz,gx,lz,comm,check) { +Multigrid1DP::Multigrid1DP(int level, int lx, int lz, int gx, int dl, int merge, + MPI_Comm comm, int check) + : MultigridAlg(level, lx, lz, gx, lz, comm, check) { mglevel = level; - if(pcheck > 0) output<<"Construct MG1DP "< 0) { + output << "Construct MG1DP " << endl; + } commMG = comm; - MPI_Comm_size(commMG,&xNP); - MPI_Comm_rank(commMG,&rProcI); + MPI_Comm_size(commMG, &xNP); + MPI_Comm_rank(commMG, &rProcI); xProcI = rProcI; - if(xNP > 1) { - if(xProcI == 0) xProcM = xNP-1; - else xProcM = xProcI-1; - if(xProcI == xNP-1) xProcP = 0; - else xProcP = xProcI+1; - } - else { + if (xNP > 1) { + if (xProcI == 0) { + xProcM = xNP - 1; + } else { + xProcM = xProcI - 1; + } + if (xProcI == xNP - 1) { + xProcP = 0; + } else { + xProcP = xProcI + 1; + } + } else { xProcI = 0; xProcM = 0; xProcP = 0; @@ -61,155 +68,175 @@ Multigrid1DP::Multigrid1DP(int level,int lx, int lz, int gx, int dl, int merge, numP = xNP; zProcI = xProcI; zProcP = xProcI; - zProcM = xProcI; + zProcM = xProcI; - if(pcheck == 1) { - output <<"In MG1DP level "< 0) { + int nz, kk, nx; + if (dl > 0) { // Find levels for more coarser spaces - if(numP > merge) { + if (numP > merge) { int nn = numP; int mm = static_cast(sqrt(numP)); - kk = 1; - for(int n = nn; n>1;n--) { - if(nn%2 != 0) n = 1; - else { + kk = 1; + for (int n = nn; n > 1; n--) { + if (nn % 2 != 0) { + n = 1; + } else { kk += 1; - nn = nn/2; - } + nn = nn / 2; + } } nn = lnz[0]; int kz = 1; - for(int n = nn; n>1;n--) { - if(nn%2 != 0) n =1; - else { + for (int n = nn; n > 1; n--) { + if (nn % 2 != 0) { + n = 1; + } else { kz += 1; - nn = nn/2; - } + nn = nn / 2; + } + } + + if (kz < kk) { + kk = kz; } - - if(kz < kk) kk = kz; nz = 1; nx = xNP; - for(int n = 0;n0;n--) { - if((llx%2 == 0) && (llz%2 == 0)) { + for (int n = dl; n > 0; n--) { + if ((llx % 2 == 0) && (llz % 2 == 0)) { kk += 1; - llx = llx/2; - llz = llz/2; + llx = llx / 2; + llz = llz / 2; + } else { + n = 1; } - else n = 1; } - if(kk > 0) kflag = 1; - else kflag = 2; + if (kk > 0) { + kflag = 1; + } else { + kflag = 2; + } + } else { + kflag = 2; } - else kflag = 2; - if(kflag == 1) { - if(pcheck == 1) { - output <<"To MG2DP "<( kk, lx, lz, gnx[0], lnz[0], dl - kk + 1, nx, nz, commMG, pcheck); } else { int nn = gnx[0]; int mm = gnz[0]; - int kk = 1; - for(int n = dl; n>0;n--) { - if((nn%2 == 0) && (mm%2 == 0)) { + int kk = 1; + for (int n = dl; n > 0; n--) { + if ((nn % 2 == 0) && (mm % 2 == 0)) { kk += 1; - nn = nn/2; - mm = mm/2; + nn = nn / 2; + mm = mm / 2; + } else { + n = 1; } - else n = 1; - } - if(pcheck == 1) { - output <<"To Ser "<(kk, gnx[0], lnz[0], commMG, pcheck); - } + } + } else { + kflag = 0; } - else kflag = 0; } void Multigrid1DP::setMultigridC(int UNUSED(plag)) { int level = mglevel - 1; - for(int n = level;n>0;n--) { - if(pcheck == 2) { - output< 0; n--) { + if (pcheck == 2) { + output << n << "matrix in 1DP = " << lnx[n - 1] << "," << lnz[n - 1] << endl; + output << gnx[n - 1] << "," << gnz[n - 1] << endl; } setMatrixC(n); } - if(kflag == 1) { - level = rMG->mglevel-1; + if (kflag == 1) { + level = rMG->mglevel - 1; convertMatrixF2D(level); - if(level > 0) rMG->setMultigridC(0); + if (level > 0) { + rMG->setMultigridC(0); + } - if(pcheck == 2) { - for(int i = level; i >= 0;i--) { - FILE *outf; + if (pcheck == 2) { + for (int i = level; i >= 0; i--) { + FILE* outf; char outfile[256]; - sprintf(outfile,"2DP_matC%1d_%d.mat",i,rMG->rProcI); - output<<"Out file= "<lnx[i]+2)*(rMG->lnz[i]+2); - fprintf(outf,"dim = %d (%d, %d)\n",dim,rMG->lnx[i],rMG->lnz[i]); - - for(int ii = 0;iimatmg[i][ii*9+j]); - fprintf(outf,"\n"); - } + sprintf(outfile, "2DP_matC%1d_%d.mat", i, rMG->rProcI); + output << "Out file= " << outfile << endl; + outf = fopen(outfile, "w"); + int dim = (rMG->lnx[i] + 2) * (rMG->lnz[i] + 2); + fprintf(outf, "dim = %d (%d, %d)\n", dim, rMG->lnx[i], rMG->lnz[i]); + + for (int ii = 0; ii < dim; ii++) { + fprintf(outf, "%d ==", ii); + for (int j = 0; j < 9; j++) { + fprintf(outf, "%12.6f,", rMG->matmg[i][ii * 9 + j]); + } + fprintf(outf, "\n"); + } fclose(outf); } } - } - else if(kflag == 2) { - level = sMG->mglevel-1; + } else if (kflag == 2) { + level = sMG->mglevel - 1; convertMatrixFS(level); - if(level > 0) sMG->setMultigridC(0); - if(pcheck == 3) { - for(int i = level; i >= 0;i--) { - FILE *outf; + if (level > 0) { + sMG->setMultigridC(0); + } + if (pcheck == 3) { + for (int i = level; i >= 0; i--) { + FILE* outf; char outfile[256]; - sprintf(outfile,"S1D_matC%1d_%d.mat",i,sMG->rProcI); - output<<"Out file= "<lnx[i]+2)*(sMG->lnz[i]+2); - fprintf(outf,"dim = %d\n",dim); - - for(int ii = 0;iimatmg[i][ii*9+j]); - fprintf(outf,"\n"); - } + sprintf(outfile, "S1D_matC%1d_%d.mat", i, sMG->rProcI); + output << "Out file= " << outfile << endl; + outf = fopen(outfile, "w"); + int dim = (sMG->lnx[i] + 2) * (sMG->lnz[i] + 2); + fprintf(outf, "dim = %d\n", dim); + + for (int ii = 0; ii < dim; ii++) { + fprintf(outf, "%d ==", ii); + for (int j = 0; j < 9; j++) { + fprintf(outf, "%12.6f,", sMG->matmg[i][ii * 9 + j]); + } + fprintf(outf, "\n"); + } fclose(outf); } } @@ -218,7 +245,7 @@ void Multigrid1DP::setMultigridC(int UNUSED(plag)) { void Multigrid1DP::setValueS() { - if(kflag == 1) { + if (kflag == 1) { rMG->mgplag = mgplag; rMG->mgsm = mgsm; rMG->cftype = cftype; @@ -227,8 +254,7 @@ void Multigrid1DP::setValueS() { rMG->dtol = dtol; rMG->omega = omega; rMG->setValueS(); - } - else if(kflag == 2) { + } else if (kflag == 2) { sMG->mgplag = mgplag; sMG->mgsm = mgsm; sMG->cftype = cftype; @@ -242,465 +268,473 @@ void Multigrid1DP::setValueS() { void Multigrid1DP::setPcheck(int check) { pcheck = check; - if(kflag == 1) { + if (kflag == 1) { rMG->setPcheck(check); - } - else if(kflag == 2) { + } else if (kflag == 2) { sMG->pcheck = check; } } -void Multigrid1DP::lowestSolver(BoutReal *x, BoutReal *b, int UNUSED(plag)) { +void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { - if(kflag == 1) { - int level = rMG->mglevel-1; - int dim = (rMG->lnx[level]+2)*(rMG->lnz[level]+2); + if (kflag == 1) { + int level = rMG->mglevel - 1; + int dim = (rMG->lnx[level] + 2) * (rMG->lnz[level] + 2); Array y(dim); Array r(dim); int ggx = rMG->lnx[level]; - int dimg = (ggx+2)*(gnz[0]+2); + int dimg = (ggx + 2) * (gnz[0] + 2); Array yl(dimg); Array yg(dimg); - int nx = (xProcI%rMG->zNP)*lnx[0]; + int nx = (xProcI % rMG->zNP) * lnx[0]; -BOUT_OMP(parallel default(shared)) - { + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;iMPI_Allreduce(std::begin(yl), std::begin(yg), dimg, MPI_DOUBLE, MPI_SUM, comm2D); - int nz = (xProcI%rMG->zNP)*(rMG->lnz[level]); -BOUT_OMP(parallel default(shared)) - { - int xend = rMG->lnx[level]+1; - int zend = rMG->lnz[level]+1; + int nz = (xProcI % rMG->zNP) * (rMG->lnz[level]); + BOUT_OMP(parallel default(shared)) { +int xend = rMG->lnx[level] + 1; +int zend = rMG->lnz[level] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = ix*(lnz[0]+2)+nz+iz; - int mm = ix*(rMG->lnz[level]+2)+iz; - r[mm] = yg[nn]; - } - } +for (int ix = 1; ix < xend; ix++) { + for (int iz = 1; iz < zend; iz++) { + int nn = ix * (lnz[0] + 2) + nz + iz; + int mm = ix * (rMG->lnz[level] + 2) + iz; + r[mm] = yg[nn]; + } +} } rMG->getSolution(std::begin(y), std::begin(r), 1); BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;ilnx[level]+1; - int zend = rMG->lnz[level]+1; +for (int i = 0; i < dimg; i++) { + yl[i] = 0.0; + yg[i] = 0.0; +} + +int xend = rMG->lnx[level] + 1; +int zend = rMG->lnz[level] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = ix*(lnz[0]+2)+nz+iz; - int mm = ix*(rMG->lnz[level]+2)+iz; - yl[nn] = y[mm]; - } - } +for (int ix = 1; ix < xend; ix++) { + for (int iz = 1; iz < zend; iz++) { + int nn = ix * (lnz[0] + 2) + nz + iz; + int mm = ix * (rMG->lnz[level] + 2) + iz; + yl[nn] = y[mm]; + } +} } bout::globals::mpi->MPI_Allreduce(std::begin(yl), std::begin(yg), dimg, MPI_DOUBLE, MPI_SUM, comm2D); - BOUT_OMP(parallel default(shared)) - { - int xend = lnx[0]+1; - int zend = lnz[0]+1; + BOUT_OMP(parallel default(shared)) { +int xend = lnx[0] + 1; +int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = (nx+ix)*(lnz[0]+2)+iz; - int mm = ix*(lnz[0]+2)+iz; - x[mm] = yg[nn]; - } - } - } - communications(x,0); +for (int ix = 1; ix < xend; ix++) { + for (int iz = 1; iz < zend; iz++) { + int nn = (nx + ix) * (lnz[0] + 2) + iz; + int mm = ix * (lnz[0] + 2) + iz; + x[mm] = yg[nn]; } - else if(kflag == 2) { - int level = sMG->mglevel-1; - int dim = (sMG->lnx[level]+2)*(sMG->lnz[level]+2); +} + } + communications(x, 0); + } else if (kflag == 2) { + int level = sMG->mglevel - 1; + int dim = (sMG->lnx[level] + 2) * (sMG->lnz[level] + 2); Array y(dim); Array r(dim); - int nx = xProcI*lnx[0]; -BOUT_OMP(parallel default(shared)) - { + int nx = xProcI * lnx[0]; + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;iMPI_Allreduce(std::begin(y), std::begin(r), dim, MPI_DOUBLE, MPI_SUM, commMG); BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i = 0;igetSolution(std::begin(y), std::begin(r), 1); +for (int i = 0; i < dim; i++) { +y[i] = 0.0; +} +sMG->getSolution(std::begin(y), std::begin(r), 1); - BOUT_OMP(parallel default(shared)) - { - int xend = lnx[0]+1; - int zend = lnz[0]+1; +BOUT_OMP(parallel default(shared)) { +int xend = lnx[0] + 1; +int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = (nx+ix)*(lnz[0]+2)+iz; - int mm = ix*(lnz[0]+2)+iz; - x[mm] = y[nn]; - } - } - } - communications(x,0); +for (int ix = 1; ix < xend; ix++) { + for (int iz = 1; iz < zend; iz++) { + int nn = (nx + ix) * (lnz[0] + 2) + iz; + int mm = ix * (lnz[0] + 2) + iz; + x[mm] = y[nn]; } - else { - pGMRES(x,b,0,0); +} +} +communications(x, 0); + } else { +pGMRES(x, b, 0, 0); } - } - void Multigrid1DP::convertMatrixF2D(int level) { int ggx = rMG->lnx[level]; - int dim = (ggx+2)*(gnz[0]+2); + int dim = (ggx + 2) * (gnz[0] + 2); Array yl(dim * 9); Array yg(dim * 9); - int nx = (xProcI%rMG->zNP)*lnx[0]; -BOUT_OMP(parallel default(shared)) - { + int nx = (xProcI % rMG->zNP) * lnx[0]; + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;ilnx[level]+2)*(rMG->lnz[level]+2)*9;i++) { - rMG->matmg[level][i] = 0.0; - } - - int xend = lnx[0]+1; - int zend = lnz[0]+1; +for (int i = 0; i < (rMG->lnx[level] + 2) * (rMG->lnz[level] + 2) * 9; i++) { +rMG->matmg[level][i] = 0.0; +} + +int xend = lnx[0] + 1; +int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = (nx+ix)*(lnz[0]+2)+iz; - int mm = ix*(lnz[0]+2)+iz; - for(int k = 0;k<9;k++) { - yl[nn*9+k] = matmg[0][mm*9+k]; - } - } - } +for (int ix = 1; ix < xend; ix++) { +for (int iz = 1; iz < zend; iz++) { + int nn = (nx + ix) * (lnz[0] + 2) + iz; + int mm = ix * (lnz[0] + 2) + iz; + for (int k = 0; k < 9; k++) { + yl[nn * 9 + k] = matmg[0][mm * 9 + k]; + } +} +} } - if(pcheck == 3) { - FILE *outf; - char outfile[256]; - sprintf(outfile,"2DP_CP_%d.mat",rProcI); - output<<"Out file= "<MPI_Allreduce(std::begin(yl), std::begin(yg), dim * 9, MPI_DOUBLE, MPI_SUM, comm2D); - if(pcheck == 3) { - FILE *outf; - char outfile[256]; - sprintf(outfile,"2DP_Conv_%d.mat",rProcI); - output<<"Out file= "<zNP)*(rMG->lnz[level]); + if (pcheck == 3) { +FILE* outf; +char outfile[256]; +sprintf(outfile, "2DP_Conv_%d.mat", rProcI); +output << "Out file= " << outfile << endl; +outf = fopen(outfile, "w"); +fprintf(outf, "dim = (%d, %d)\n", ggx, gnz[0]); + +for (int ii = 0; ii < dim; ii++) { +fprintf(outf, "%d ==", ii); +for (int j = 0; j < 9; j++) { + fprintf(outf, "%12.6f,", yg[ii * 9 + j]); +} +fprintf(outf, "\n"); +} +fclose(outf); + } + int nz = (xProcI % rMG->zNP) * (rMG->lnz[level]); -BOUT_OMP(parallel default(shared)) - { - int xend = rMG->lnx[level]+1; - int zend = rMG->lnz[level]+1; + BOUT_OMP(parallel default(shared)) { +int xend = rMG->lnx[level] + 1; +int zend = rMG->lnz[level] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = ix*(lnz[0]+2)+nz+iz; - int mm = ix*(rMG->lnz[level]+2)+iz; - for(int k = 0;k<9;k++) { - rMG->matmg[level][mm*9+k] = yg[nn*9+k]; - } - } - } +for (int ix = 1; ix < xend; ix++) { +for (int iz = 1; iz < zend; iz++) { + int nn = ix * (lnz[0] + 2) + nz + iz; + int mm = ix * (rMG->lnz[level] + 2) + iz; + for (int k = 0; k < 9; k++) { + rMG->matmg[level][mm * 9 + k] = yg[nn * 9 + k]; + } +} +} } } void Multigrid1DP::convertMatrixFS(int level) { - int dim = (gnx[0]+2)*(gnz[0]+2); + int dim = (gnx[0] + 2) * (gnz[0] + 2); Array yl(dim * 9); - BoutReal *yg = sMG->matmg[level]; - int nx = xProcI*lnx[0]; -BOUT_OMP(parallel default(shared)) - { + BoutReal* yg = sMG->matmg[level]; + int nx = xProcI * lnx[0]; + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;iMPI_Allreduce(std::begin(yl), yg, dim * 9, MPI_DOUBLE, MPI_SUM, commMG); } -Multigrid2DPf1D::Multigrid2DPf1D(int level,int lx,int lz, int gx, int gz, - int dl,int px,int pz, MPI_Comm comm,int check) : - MultigridAlg(level,lx,lz,gx,gz,comm,check) { +Multigrid2DPf1D::Multigrid2DPf1D(int level, int lx, int lz, int gx, int gz, int dl, + int px, int pz, MPI_Comm comm, int check) + : MultigridAlg(level, lx, lz, gx, gz, comm, check) { mglevel = level; /* Momory allocate for Multigrid */ xNP = px; zNP = pz; - numP = px*pz; + numP = px * pz; commMG = comm; - MPI_Comm_rank(comm,&rProcI); - xProcI = rProcI/zNP; - zProcI = rProcI%zNP; - if(xProcI == 0) xProcM = numP-zNP+zProcI; - else xProcM = rProcI-zNP; - if(xProcI == xNP-1) xProcP = zProcI; - else xProcP = rProcI + zNP; - if(zProcI == 0) zProcM = rProcI+zNP-1; - else zProcM = rProcI-1; - if(zProcI ==zNP-1) zProcP = xProcI*zNP; - else zProcP = rProcI + 1; - if(pcheck == 2) { - output<<"In 2DP "<=0;i--) { - output< 0) { - int nn = gnx[0]; - int mm = gnz[0]; - int kk = 1; - for(int n = dl; n>0;n--) { - if((nn%2 == 0) && (mm%2 == 0)) { - kk += 1; - nn = nn/2; - mm = mm/2; - } - else n = 0; - } - if(pcheck == 2) { - output <<"In 2DP To Ser"<(kk, gnx[0], gnz[0], commMG, pcheck); + MPI_Comm_rank(comm, &rProcI); + xProcI = rProcI / zNP; + zProcI = rProcI % zNP; + if (xProcI == 0) { +xProcM = numP - zNP + zProcI; + } else { +xProcM = rProcI - zNP; + } + if (xProcI == xNP - 1) { +xProcP = zProcI; + } else { +xProcP = rProcI + zNP; + } + if (zProcI == 0) { +zProcM = rProcI + zNP - 1; + } else { +zProcM = rProcI - 1; + } + if (zProcI == zNP - 1) { +zProcP = xProcI * zNP; + } else { +zProcP = rProcI + 1; + } + if (pcheck == 2) { +output << "In 2DP " << mglevel << "xNP=" << xNP << "(" << zNP << ")" << dl << endl; +for (int i = mglevel - 1; i >= 0; i--) { +output << i << " loc dim " << lnx[i] << "," << lnz[i] << endl; +output << i << " glo dim " << gnx[i] << "," << gnz[i] << endl; +} + } + + if (dl > 0) { +int nn = gnx[0]; +int mm = gnz[0]; +int kk = 1; +for (int n = dl; n > 0; n--) { +if ((nn % 2 == 0) && (mm % 2 == 0)) { + kk += 1; + nn = nn / 2; + mm = mm / 2; +} else { + n = 0; +} +} +if (pcheck == 2) { +output << "In 2DP To Ser" << kk << "xNP=" << xNP << "(" << zNP << ")" << endl; +output << "total dim" << gnx[0] << "(" << gnz[0] << ")" << endl; +} +kflag = 2; +sMG = bout::utils::make_unique(kk, gnx[0], gnz[0], commMG, pcheck); + } else { +kflag = 0; } - else kflag = 0; } void Multigrid2DPf1D::setMultigridC(int UNUSED(plag)) { int level = mglevel - 1; - for(int n = level;n>0;n--) { - setMatrixC(n); - if(pcheck == 2) { - output< 0; n--) { +setMatrixC(n); +if (pcheck == 2) { +output << n << "Cmatrix in 2DP = " << lnx[n - 1] << "," << lnz[n - 1] << endl; +output << gnx[n - 1] << "," << gnz[n - 1] << endl; +} } - if(kflag == 2) { - level = sMG->mglevel-1; - convertMatrixFS(level); - if(level > 0) sMG->setMultigridC(0); - if(pcheck == 2) { - for(int i = level; i >= 0;i--) { - FILE *outf; - char outfile[256]; - sprintf(outfile,"S2D_matC%1d_%d.mat",i,sMG->rProcI); - outf = fopen(outfile,"w"); - output<<"Out file= "<lnx[i]+2)*(sMG->lnz[i]+2); - fprintf(outf,"dim = %d\n",dim); - - for(int ii = 0;iimatmg[i][ii*9+j]); - fprintf(outf,"\n"); - } - fclose(outf); - } + if (kflag == 2) { +level = sMG->mglevel - 1; +convertMatrixFS(level); +if (level > 0) { +sMG->setMultigridC(0); +} +if (pcheck == 2) { +for (int i = level; i >= 0; i--) { + FILE* outf; + char outfile[256]; + sprintf(outfile, "S2D_matC%1d_%d.mat", i, sMG->rProcI); + outf = fopen(outfile, "w"); + output << "Out file= " << outfile << endl; + int dim = (sMG->lnx[i] + 2) * (sMG->lnz[i] + 2); + fprintf(outf, "dim = %d\n", dim); + + for (int ii = 0; ii < dim; ii++) { + fprintf(outf, "%d ==", ii); + for (int j = 0; j < 9; j++) { + fprintf(outf, "%12.6f,", sMG->matmg[i][ii * 9 + j]); } + fprintf(outf, "\n"); + } + fclose(outf); +} +} } } void Multigrid2DPf1D::setValueS() { - if(kflag == 2) { - sMG->mgplag = mgplag; - sMG->mgsm = mgsm; - sMG->cftype = cftype; - sMG->rtol = rtol; - sMG->atol = atol; - sMG->dtol = dtol; - sMG->omega = omega; + if (kflag == 2) { +sMG->mgplag = mgplag; +sMG->mgsm = mgsm; +sMG->cftype = cftype; +sMG->rtol = rtol; +sMG->atol = atol; +sMG->dtol = dtol; +sMG->omega = omega; } } void Multigrid2DPf1D::setPcheck(int check) { pcheck = check; - if(kflag == 2) { - sMG->pcheck = check; + if (kflag == 2) { +sMG->pcheck = check; } } -void Multigrid2DPf1D::lowestSolver(BoutReal *x, BoutReal *b, int UNUSED(plag)) { +void Multigrid2DPf1D::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { - if(kflag == 2) { - int level = sMG->mglevel-1; - int dim = (sMG->lnx[level]+2)*(sMG->lnz[level]+2); - Array y(dim); - Array r(dim); - int nx = xProcI*lnx[0]; - int nz = zProcI*lnz[0]; -BOUT_OMP(parallel default(shared) ) - { + if (kflag == 2) { +int level = sMG->mglevel - 1; +int dim = (sMG->lnx[level] + 2) * (sMG->lnz[level] + 2); +Array y(dim); +Array r(dim); +int nx = xProcI * lnx[0]; +int nz = zProcI * lnz[0]; +BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;iMPI_Allreduce(std::begin(y), std::begin(r), dim, MPI_DOUBLE, - MPI_SUM, commMG); - BOUT_OMP(parallel default(shared)) +for (int ix = 1; ix < xend; ix++) { + for (int iz = 1; iz < zend; iz++) { + int nn = (nx + ix) * (gnz[0] + 2) + nz + iz; + int mm = ix * (lnz[0] + 2) + iz; + y[nn] = b[mm]; + } +} +} +bout::globals::mpi->MPI_Allreduce(std::begin(y), std::begin(r), dim, MPI_DOUBLE, MPI_SUM, + commMG); +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i = 0;igetSolution(std::begin(y), std::begin(r), 1); - BOUT_OMP(parallel default(shared)) - { - int xend = lnx[0]+1; - int zend = lnz[0]+1; +for (int i = 0; i < dim; i++) { +y[i] = 0.0; +} +sMG->getSolution(std::begin(y), std::begin(r), 1); +BOUT_OMP(parallel default(shared)) { +int xend = lnx[0] + 1; +int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) - for(int ix = 1;ix < xend ;ix++) { - for(int iz = 1;iz < zend;iz++) { - int nn = (nx+ix)*(gnz[0]+2)+nz+iz; - int mm = ix*(lnz[0]+2)+iz; - x[mm] = y[nn]; - } - } - } - communications(x,0); +for (int ix = 1; ix < xend; ix++) { + for (int iz = 1; iz < zend; iz++) { + int nn = (nx + ix) * (gnz[0] + 2) + nz + iz; + int mm = ix * (lnz[0] + 2) + iz; + x[mm] = y[nn]; } - else { - pGMRES(x,b,0,0); +} +} +communications(x, 0); + } else { +pGMRES(x, b, 0, 0); } - } void Multigrid2DPf1D::convertMatrixFS(int level) { - int dim = (gnx[0]+2)*(gnz[0]+2); + int dim = (gnx[0] + 2) * (gnz[0] + 2); Array yl(dim * 9); - BoutReal *yg = sMG->matmg[level]; - int nx = xProcI*lnx[0]; - int nz = zProcI*lnz[0]; -BOUT_OMP(parallel default(shared) ) - { + BoutReal* yg = sMG->matmg[level]; + int nx = xProcI * lnx[0]; + int nz = zProcI * lnz[0]; + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i = 0;iMPI_Allreduce(std::begin(yl), yg, dim * 9, MPI_DOUBLE, MPI_SUM, commMG); @@ -719,12 +753,12 @@ MultigridSerial::MultigridSerial(int level, int gx, int gz, MPI_Comm comm, int c xProcP = rProcI; zProcM = rProcI; zProcP = rProcI; - if(pcheck == 2) { - output<<"In SerMG "<=0;i--) { - output<= 0; i--) { +output << i << " Ser loc dim " << lnx[i] << "," << lnz[i] << endl; +output << i << " Ser glo dim " << gnx[i] << "," << gnz[i] << endl; +} } } diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx index c4c05e7db2..0811e6a6f6 100644 --- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx +++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx @@ -136,13 +136,13 @@ * * Stop: Function returns phiNext */ -#include -#include #include +#include #include -#include -#include -#include +#include +#include +#include +#include #include "naulin_laplace.hxx" @@ -151,7 +151,8 @@ LaplaceNaulin::LaplaceNaulin(Options* opt, const CELL_LOC loc, Mesh* mesh_in, : Laplacian(opt, loc, mesh_in), Acoef(0.0), C1coef(1.0), C2coef(0.0), Dcoef(1.0), delp2solver(nullptr), naulinsolver_mean_its(0.), ncalls(0) { - ASSERT1(opt != nullptr); // An Options pointer should always be passed in by LaplaceFactory + ASSERT1(opt + != nullptr); // An Options pointer should always be passed in by LaplaceFactory Acoef.setLocation(location); C1coef.setLocation(location); @@ -169,7 +170,7 @@ LaplaceNaulin::LaplaceNaulin(Options* opt, const CELL_LOC loc, Mesh* mesh_in, opt->getSection("delp2solver")->get("type", delp2type, "cyclic"); // Check delp2solver is using an FFT scheme, otherwise it will not exactly // invert Delp2 and we will not converge - ASSERT0( delp2type=="cyclic" || delp2type=="spt" || delp2type=="tri" ); + ASSERT0(delp2type == "cyclic" || delp2type == "spt" || delp2type == "tri"); // Use same flags for FFT solver as for NaulinSolver delp2solver->setGlobalFlags(global_flags); delp2solver->setInnerBoundaryFlags(inner_boundary_flags); @@ -194,21 +195,20 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) { ASSERT1(Acoef.getLocation() == location); ASSERT1(localmesh == rhs.getMesh() && localmesh == x0.getMesh()); - Field3D rhsOverD = rhs/Dcoef; + Field3D rhsOverD = rhs / Dcoef; - Field3D C1TimesD = C1coef*Dcoef; // This is needed several times + Field3D C1TimesD = C1coef * Dcoef; // This is needed several times // x-component of 1./(C1*D) * Grad_perp(C2) - Field3D coef_x = DDX(C2coef, location, "C2")/C1TimesD; + Field3D coef_x = DDX(C2coef, location, "C2") / C1TimesD; // y-component of 1./(C1*D) * Grad_perp(C2) - Field3D coef_y = DDY(C2coef, location, "C2")/C1TimesD; + Field3D coef_y = DDY(C2coef, location, "C2") / C1TimesD; // z-component of 1./(C1*D) * Grad_perp(C2) - Field3D coef_z = DDZ(C2coef, location, "FFT")/C1TimesD; - - Field3D AOverD = Acoef/Dcoef; + Field3D coef_z = DDZ(C2coef, location, "FFT") / C1TimesD; + Field3D AOverD = Acoef / Dcoef; // Split coefficients into DC and AC parts so that delp2solver can use DC part. // This allows all-Neumann boundary conditions as long as AOverD_DC is non-zero @@ -221,39 +221,42 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) { // necessarily in phase. // This is the piece that cannot be passed to an FFT-based Laplacian solver // (through our current interface). - Field3D coef_x_AC = coef_x - DDX(C2coef_DC, location, "C2")/C1coefTimesD_DC; + Field3D coef_x_AC = coef_x - DDX(C2coef_DC, location, "C2") / C1coefTimesD_DC; // coef_z is a z-derivative so must already have zero DC component Field2D AOverD_DC = DC(AOverD); Field3D AOverD_AC = AOverD - AOverD_DC; - delp2solver->setCoefA(AOverD_DC); delp2solver->setCoefC1(C1coefTimesD_DC); delp2solver->setCoefC2(C2coef_DC); // Use this below to normalize error for relative error estimate - BoutReal RMS_rhsOverD = sqrt(mean(SQ(rhsOverD), true, "RGN_NOBNDRY")); // use sqrt(mean(SQ)) to make sure we do not divide by zero at a point + BoutReal RMS_rhsOverD = sqrt(mean( + SQ(rhsOverD), true, + "RGN_NOBNDRY")); // use sqrt(mean(SQ)) to make sure we do not divide by zero at a point - BoutReal error_rel = 1e20, error_abs=1e20, last_error=error_abs; + BoutReal error_rel = 1e20, error_abs = 1e20, last_error = error_abs; int count = 0; int underrelax_count = 0; BoutReal underrelax_factor = initial_underrelax_factor; - auto calc_b_guess = [&] (const Field3D& x_in) { + auto calc_b_guess = [&](const Field3D& x_in) { // Derivatives of x Field3D ddx_x = DDX(x_in, location, "C2"); Field3D ddz_x = DDZ(x_in, location, "FFT"); - return rhsOverD - (coords->g11*coef_x_AC*ddx_x + coords->g33*coef_z*ddz_x - + coords->g13*(coef_x_AC*ddz_x + coef_z*ddx_x)) - AOverD_AC*x_in; + return rhsOverD + - (coords->g11 * coef_x_AC * ddx_x + coords->g33 * coef_z * ddz_x + + coords->g13 * (coef_x_AC * ddz_x + coef_z * ddx_x)) + - AOverD_AC * x_in; }; - auto calc_b_x_pair = [&, this] (Field3D b, Field3D x_guess) { + auto calc_b_x_pair = [&, this](Field3D b, Field3D x_guess) { // Note take a copy of the 'b' argument, because we want to return a copy of it in the // result - if ( (inner_boundary_flags & INVERT_SET) || (outer_boundary_flags & INVERT_SET) ) { + if ((inner_boundary_flags & INVERT_SET) || (outer_boundary_flags & INVERT_SET)) { // This passes in the boundary conditions from x0's guard cells copy_x_boundaries(x_guess, x0, localmesh); } @@ -278,10 +281,12 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) { error_abs = max(abs(error3D, "RGN_NOBNDRY"), true, "RGN_NOBNDRY"); error_rel = error_abs / RMS_rhsOverD; - if (error_relmaxits) { + if (count > maxits) { throw BoutException( "LaplaceNaulin error: Not converged within maxits={:d} iterations.", maxits); } @@ -293,7 +298,9 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) { // Restart from b_x_pair_old - that was our best guess bnew = calc_b_guess(b_x_pair_old.second); - b_x_pair = calc_b_x_pair(underrelax_factor*bnew + (1. - underrelax_factor)*b_x_pair_old.first, b_x_pair_old.second); + b_x_pair = calc_b_x_pair(underrelax_factor * bnew + + (1. - underrelax_factor) * b_x_pair_old.first, + b_x_pair_old.second); bnew = calc_b_guess(b_x_pair.second); @@ -303,44 +310,55 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) { // effectively another iteration, so increment the counter ++count; - if (count>maxits) { + if (count > maxits) { throw BoutException( "LaplaceNaulin error: Not converged within maxits={:d} iterations.", maxits); } } // Might have met convergence criterion while in underrelaxation loop - if (error_relfirstX()) { - for (int i=localmesh->xstart-1; i>=0; --i) - for (int j=localmesh->ystart; j<=localmesh->yend; ++j) - for (int k=0; kLocalNz; ++k) + for (int i = localmesh->xstart - 1; i >= 0; --i) { + for (int j = localmesh->ystart; j <= localmesh->yend; ++j) { + for (int k = 0; k < localmesh->LocalNz; ++k) { x(i, j, k) = x0(i, j, k); + } + } + } } if (localmesh->lastX()) { - for (int i=localmesh->xend+1; iLocalNx; ++i) - for (int j=localmesh->ystart; j<=localmesh->yend; ++j) - for (int k=0; kLocalNz; ++k) + for (int i = localmesh->xend + 1; i < localmesh->LocalNx; ++i) { + for (int j = localmesh->ystart; j <= localmesh->yend; ++j) { + for (int k = 0; k < localmesh->LocalNz; ++k) { x(i, j, k) = x0(i, j, k); + } + } + } } } diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx index d2948346a5..99f433e30c 100644 --- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx +++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx @@ -28,8 +28,8 @@ class LaplaceNaulin; #ifndef __LAP_NAULIN_H__ #define __LAP_NAULIN_H__ -#include -#include +#include +#include namespace { RegisterLaplace registerlaplacenaulin(LAPLACE_NAULIN); @@ -45,7 +45,7 @@ public: Mesh* mesh_in = nullptr, Solver* solver = nullptr, Datafile* dump = nullptr); ~LaplaceNaulin() = default; - + using Laplacian::setCoefA; using Laplacian::setCoefC; using Laplacian::setCoefC1; @@ -57,62 +57,62 @@ public: // ACoef is not implemented because the delp2solver that we use can probably // only handle a Field2D for Acoef, but we would have to pass Acoef/Dcoef, // where we allow Dcoef to be a Field3D - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Acoef = val; } - void setCoefA(const Field3D &val) override { + void setCoefA(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Acoef = val; } - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); setCoefC1(val); setCoefC2(val); } - void setCoefC(const Field3D &val) override { + void setCoefC(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); setCoefC1(val); setCoefC2(val); } - void setCoefC1(const Field3D &val) override { + void setCoefC1(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1coef = val; } - void setCoefC1(const Field2D &val) override { + void setCoefC1(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1coef = val; } - void setCoefC2(const Field3D &val) override { + void setCoefC2(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2coef = val; } - void setCoefC2(const Field2D &val) override { + void setCoefC2(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2coef = val; } - void setCoefD(const Field3D &val) override { + void setCoefD(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Dcoef = val; } - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Dcoef = val; } - void setCoefEx(const Field2D &UNUSED(val)) override { + void setCoefEx(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceNaulin does not have Ex coefficient"); } - void setCoefEz(const Field2D &UNUSED(val)) override { + void setCoefEz(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceNaulin does not have Ez coefficient"); } @@ -120,21 +120,27 @@ public: using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override {return solve(b,b);} - FieldPerp solve(const FieldPerp &UNUSED(b), - const FieldPerp &UNUSED(x0)) override { + FieldPerp solve(const FieldPerp& b) override { return solve(b, b); } + FieldPerp solve(const FieldPerp& UNUSED(b), const FieldPerp& UNUSED(x0)) override { throw BoutException( "LaplaceNaulin has no solve(FieldPerp), must call solve(Field3D)"); } - Field3D solve(const Field3D &b, const Field3D &x0) override; - Field3D solve(const Field3D &b) override { - return solve(b, zeroFrom(b)); - } + Field3D solve(const Field3D& b, const Field3D& x0) override; + Field3D solve(const Field3D& b) override { return solve(b, zeroFrom(b)); } // Override flag-setting methods to set delp2solver's flags as well - void setGlobalFlags(int f) override { Laplacian::setGlobalFlags(f); delp2solver->setGlobalFlags(f); } - void setInnerBoundaryFlags(int f) override { Laplacian::setInnerBoundaryFlags(f); delp2solver->setInnerBoundaryFlags(f); } - void setOuterBoundaryFlags(int f) override { Laplacian::setOuterBoundaryFlags(f); delp2solver->setOuterBoundaryFlags(f); } + void setGlobalFlags(int f) override { + Laplacian::setGlobalFlags(f); + delp2solver->setGlobalFlags(f); + } + void setInnerBoundaryFlags(int f) override { + Laplacian::setInnerBoundaryFlags(f); + delp2solver->setInnerBoundaryFlags(f); + } + void setOuterBoundaryFlags(int f) override { + Laplacian::setOuterBoundaryFlags(f); + delp2solver->setOuterBoundaryFlags(f); + } BoutReal getMeanIterations() const { return naulinsolver_mean_its; } void resetMeanIterations() { naulinsolver_mean_its = 0; } @@ -171,7 +177,7 @@ private: /// Copy the boundary guard cells from the input 'initial guess' x0 into x. /// These may be used to set non-zero-value boundary conditions - void copy_x_boundaries(Field3D &x, const Field3D &x0, Mesh *mesh); + void copy_x_boundaries(Field3D& x, const Field3D& x0, Mesh* mesh); }; #endif // __LAP_NAULIN_H__ diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx index d80cafde17..5d141cc1a4 100644 --- a/src/invert/laplace/impls/pcr/pcr.cxx +++ b/src/invert/laplace/impls/pcr/pcr.cxx @@ -37,20 +37,20 @@ **************************************************************************/ #include "pcr.hxx" -#include "globals.hxx" +#include "bout/globals.hxx" #include #include #include #include -#include +#include #include -#include -#include -#include +#include +#include +#include -#include "boutcomm.hxx" -#include +#include "bout/boutcomm.hxx" +#include #include @@ -620,8 +620,7 @@ void LaplacePCR ::cr_pcr_solver(Matrix& a_mpi, Matrix& b_mpi * to ensure we pass a square system of interior rows to the PCR library. */ void LaplacePCR ::eliminate_boundary_rows(Matrix& a, Matrix& b, - Matrix& c, - Matrix& r) { + Matrix& c, Matrix& r) { if (localmesh->firstX()) { for (int kz = 0; kz < nsys; kz++) { @@ -629,10 +628,8 @@ void LaplacePCR ::eliminate_boundary_rows(Matrix& a, Matrix& // This fixes the case where INVERT_BNDRY_ONE is true, but there are more // than 1 guard cells. for (int ix = 1; ix < localmesh->xstart + 1; ix++) { - b(kz, ix) = - b(kz, ix) - c(kz, ix - 1) * a(kz, ix) / b(kz, ix - 1); - r(kz, ix) = - r(kz, ix) - r(kz, ix - 1) * a(kz, ix) / b(kz, ix - 1); + b(kz, ix) = b(kz, ix) - c(kz, ix - 1) * a(kz, ix) / b(kz, ix - 1); + r(kz, ix) = r(kz, ix) - r(kz, ix - 1) * a(kz, ix) / b(kz, ix - 1); a(kz, ix) = 0.0; } } @@ -1086,23 +1083,25 @@ void LaplacePCR ::verify_solution(const Matrix& a_ver, y_ver(kz, i) = a_ver(kz, i) * x_ver(kz, i) + b_ver(kz, i) * x_ver(kz, i + 1) + c_ver(kz, i) * x_ver(kz, i + 2); error(kz, i) = y_ver(kz, i) - r_ver(kz, i); - if(std::abs(error(kz, i)) > max_error){ + if (std::abs(error(kz, i)) > max_error) { max_loc_x = i; max_loc_z = kz; } max_error = std::max(max_error, std::abs(error(kz, i))); - if( error(kz, i).real() > 0.01 || error(kz, i).imag() > 0.01 ){ - output.write("abs error {}, r={}, y={}, kz {}, i {}, a={}, b={}, c={}, x-= {}, " - "x={}, x+ = {}\n", - error(kz, i).real(), r_ver(kz, i).real(), y_ver(kz, i).real(), kz, i, - a_ver(kz, i).real(), b_ver(kz, i).real(), c_ver(kz, i).real(), - x_ver(kz, i).real(), x_ver(kz, i + 1).real(), x_ver(kz, i + 2).real()); - output.write("abs error imag {}, r={}, y={}, kz {}, i {}, a={}, b={}, c={}, x-= {}, " - "x={}, x+ = {}\n", - error(kz, i).imag(), r_ver(kz, i).imag(), y_ver(kz, i).imag(), kz, i, - a_ver(kz, i).imag(), b_ver(kz, i).imag(), c_ver(kz, i).imag(), - x_ver(kz, i).imag(), x_ver(kz, i + 1).imag(), x_ver(kz, i + 2).imag()); + if (error(kz, i).real() > 0.01 || error(kz, i).imag() > 0.01) { + output.write("abs error {}, r={}, y={}, kz {}, i {}, a={}, b={}, c={}, x-= {}, " + "x={}, x+ = {}\n", + error(kz, i).real(), r_ver(kz, i).real(), y_ver(kz, i).real(), kz, i, + a_ver(kz, i).real(), b_ver(kz, i).real(), c_ver(kz, i).real(), + x_ver(kz, i).real(), x_ver(kz, i + 1).real(), + x_ver(kz, i + 2).real()); + output.write( + "abs error imag {}, r={}, y={}, kz {}, i {}, a={}, b={}, c={}, x-= {}, " + "x={}, x+ = {}\n", + error(kz, i).imag(), r_ver(kz, i).imag(), y_ver(kz, i).imag(), kz, i, + a_ver(kz, i).imag(), b_ver(kz, i).imag(), c_ver(kz, i).imag(), + x_ver(kz, i).imag(), x_ver(kz, i + 1).imag(), x_ver(kz, i + 2).imag()); } } } diff --git a/src/invert/laplace/impls/pcr/pcr.hxx b/src/invert/laplace/impls/pcr/pcr.hxx index aeb969d093..4a98bd0024 100644 --- a/src/invert/laplace/impls/pcr/pcr.hxx +++ b/src/invert/laplace/impls/pcr/pcr.hxx @@ -29,10 +29,10 @@ class LaplacePCR; #ifndef BOUT_PCR_H #define BOUT_PCR_H -#include -#include -#include -#include +#include +#include +#include +#include namespace { RegisterLaplace registerlaplacepcr(LAPLACE_PCR); diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx index 86a8b94f8e..21df752f3a 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx @@ -37,19 +37,19 @@ **************************************************************************/ #include "pcr_thomas.hxx" -#include "globals.hxx" +#include "bout/globals.hxx" -#include "boutcomm.hxx" +#include "bout/boutcomm.hxx" #include #include #include #include #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include #include diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx index e4d4833473..eba3cfeec1 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx @@ -29,10 +29,10 @@ class LaplacePCR_THOMAS; #ifndef BOUT_PCR_THOMAS_H #define BOUT_PCR_THOMAS_H -#include -#include -#include -#include +#include +#include +#include +#include namespace { RegisterLaplace registerlaplacepcrthomas(LAPLACE_PCR_THOMAS); diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx index fc2210df61..b027664be1 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx @@ -29,32 +29,32 @@ #include "petsc_laplace.hxx" +#include #include #include -#include -#include -#include +#include +#include #define KSP_RICHARDSON "richardson" -#define KSP_CHEBYSHEV "chebyshev" -#define KSP_CG "cg" -#define KSP_GMRES "gmres" -#define KSP_TCQMR "tcqmr" -#define KSP_BCGS "bcgs" -#define KSP_CGS "cgs" -#define KSP_TFQMR "tfqmr" -#define KSP_CR "cr" -#define KSP_LSQR "lsqr" -#define KSP_BICG "bicg" -#define KSP_PREONLY "preonly" - - -static PetscErrorCode laplacePCapply(PC pc,Vec x,Vec y) { +#define KSP_CHEBYSHEV "chebyshev" +#define KSP_CG "cg" +#define KSP_GMRES "gmres" +#define KSP_TCQMR "tcqmr" +#define KSP_BCGS "bcgs" +#define KSP_CGS "cgs" +#define KSP_TFQMR "tfqmr" +#define KSP_CR "cr" +#define KSP_LSQR "lsqr" +#define KSP_BICG "bicg" +#define KSP_PREONLY "preonly" + +static PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) { int ierr; // Get the context - LaplacePetsc *s; - ierr = PCShellGetContext(pc, reinterpret_cast(&s)); CHKERRQ(ierr); + LaplacePetsc* s; + ierr = PCShellGetContext(pc, reinterpret_cast(&s)); + CHKERRQ(ierr); PetscFunctionReturn(s->precon(x, y)); } @@ -72,32 +72,41 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Ez.setLocation(location); // Get Options in Laplace Section - if (!opt) opts = Options::getRoot()->getSection("laplace"); - else opts=opt; - - #if CHECK > 0 - // These are the implemented flags - implemented_flags = INVERT_START_NEW; - implemented_boundary_flags = INVERT_AC_GRAD - + INVERT_SET - + INVERT_RHS - ; - // Checking flags are set to something which is not implemented - // This is done binary (which is possible as each flag is a power of 2) - if ( global_flags & ~implemented_flags ) { - if (global_flags&INVERT_4TH_ORDER) output<<"For PETSc based Laplacian inverter, use 'fourth_order=true' instead of setting INVERT_4TH_ORDER flag"<getSection("laplace"); + } else { + opts = opt; + } + +#if CHECK > 0 + // These are the implemented flags + implemented_flags = INVERT_START_NEW; + implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_RHS; + // Checking flags are set to something which is not implemented + // This is done binary (which is possible as each flag is a power of 2) + if (global_flags & ~implemented_flags) { + if (global_flags & INVERT_4TH_ORDER) { + output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " + "setting INVERT_4TH_ORDER flag" + << endl; } - if(localmesh->periodicX) { - throw BoutException("LaplacePetsc does not work with periodicity in the x direction (localmesh->PeriodicX == true). Change boundary conditions or use serial-tri or cyclic solver instead"); - } - #endif + throw BoutException("Attempted to set Laplacian inversion flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (inner_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (outer_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (localmesh->periodicX) { + throw BoutException("LaplacePetsc does not work with periodicity in the x direction " + "(localmesh->PeriodicX == true). Change boundary conditions or " + "use serial-tri or cyclic solver instead"); + } +#endif // Get communicator for group of processors in X - all points in z-x plane for fixed y. comm = localmesh->getXcomm(); @@ -105,35 +114,42 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, // Need to determine local size to use based on prior parallelisation // Coefficient values are stored only on local processors. localN = (localmesh->xend - localmesh->xstart + 1) * (localmesh->LocalNz); - if(localmesh->firstX()) - localN += localmesh->xstart * (localmesh->LocalNz); // If on first processor add on width of boundary region - if(localmesh->lastX()) - localN += localmesh->xstart * (localmesh->LocalNz); // If on last processor add on width of boundary region + if (localmesh->firstX()) { + localN += + localmesh->xstart + * (localmesh->LocalNz); // If on first processor add on width of boundary region + } + if (localmesh->lastX()) { + localN += + localmesh->xstart + * (localmesh->LocalNz); // If on last processor add on width of boundary region + } // Calculate 'size' (the total number of points in physical grid) if (bout::globals::mpi->MPI_Allreduce(&localN, &size, 1, MPI_INT, MPI_SUM, comm) - != MPI_SUCCESS) + != MPI_SUCCESS) { throw BoutException("Error in MPI_Allreduce during LaplacePetsc initialisation"); + } // Calculate total (physical) grid dimensions meshz = localmesh->LocalNz; meshx = size / meshz; // Create PETSc type of vectors for the solution and the RHS vector - VecCreate( comm, &xs ); - VecSetSizes( xs, localN, size ); - VecSetFromOptions( xs ); - VecDuplicate( xs , &bs ); + VecCreate(comm, &xs); + VecSetSizes(xs, localN, size); + VecSetFromOptions(xs); + VecDuplicate(xs, &bs); // Get 4th order solver switch opts->get("fourth_order", fourth_order, false); // Set size of (the PETSc) Matrix on each processor to localN x localN - MatCreate( comm, &MatA ); - MatSetSizes( MatA, localN, localN, size, size ); + MatCreate(comm, &MatA); + MatSetSizes(MatA, localN, localN, size, size); MatSetFromOptions(MatA); // if (fourth_order) MatMPIAIJSetPreallocation( MatA, 25, PETSC_NULL, 10, PETSC_NULL ); -// else MatMPIAIJSetPreallocation( MatA, 9, PETSC_NULL, 3, PETSC_NULL ); + // else MatMPIAIJSetPreallocation( MatA, 9, PETSC_NULL, 3, PETSC_NULL ); /* Pre allocate memory * nnz denotes an array containing the number of non-zeros in the various rows @@ -143,134 +159,127 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, * parallel) */ PetscInt *d_nnz, *o_nnz; - PetscMalloc( (localN)*sizeof(PetscInt), &d_nnz ); - PetscMalloc( (localN)*sizeof(PetscInt), &o_nnz ); + PetscMalloc((localN) * sizeof(PetscInt), &d_nnz); + PetscMalloc((localN) * sizeof(PetscInt), &o_nnz); if (fourth_order) { // first and last 2*localmesh-LocalNz entries are the edge x-values that (may) have 'off-diagonal' components (i.e. on another processor) - if ( localmesh->firstX() && localmesh->lastX() ) { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=15; - d_nnz[localN-1-i]=15; - o_nnz[i]=0; - o_nnz[localN-1-i]=0; + if (localmesh->firstX() && localmesh->lastX()) { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 15; + d_nnz[localN - 1 - i] = 15; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 0; } - for (int i=(localmesh->LocalNz); i<2*(localmesh->LocalNz); i++) { - d_nnz[i]=20; - d_nnz[localN-1-i]=20; - o_nnz[i]=0; - o_nnz[localN-1-i]=0; + for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) { + d_nnz[i] = 20; + d_nnz[localN - 1 - i] = 20; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 0; } - } - else if ( localmesh->firstX() ) { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=15; - d_nnz[localN-1-i]=15; - o_nnz[i]=0; - o_nnz[localN-1-i]=10; + } else if (localmesh->firstX()) { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 15; + d_nnz[localN - 1 - i] = 15; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 10; } - for (int i=(localmesh->LocalNz); i<2*(localmesh->LocalNz); i++) { - d_nnz[i]=20; - d_nnz[localN-1-i]=20; - o_nnz[i]=0; - o_nnz[localN-1-i]=5; + for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) { + d_nnz[i] = 20; + d_nnz[localN - 1 - i] = 20; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 5; } - } - else if ( localmesh->lastX() ) { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=15; - d_nnz[localN-1-i]=15; - o_nnz[i]=10; - o_nnz[localN-1-i]=0; + } else if (localmesh->lastX()) { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 15; + d_nnz[localN - 1 - i] = 15; + o_nnz[i] = 10; + o_nnz[localN - 1 - i] = 0; } - for (int i=(localmesh->LocalNz); i<2*(localmesh->LocalNz); i++) { - d_nnz[i]=20; - d_nnz[localN-1-i]=20; - o_nnz[i]=5; - o_nnz[localN-1-i]=0; + for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) { + d_nnz[i] = 20; + d_nnz[localN - 1 - i] = 20; + o_nnz[i] = 5; + o_nnz[localN - 1 - i] = 0; } - } - else { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=15; - d_nnz[localN-1-i]=15; - o_nnz[i]=10; - o_nnz[localN-1-i]=10; + } else { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 15; + d_nnz[localN - 1 - i] = 15; + o_nnz[i] = 10; + o_nnz[localN - 1 - i] = 10; } - for (int i=(localmesh->LocalNz); i<2*(localmesh->LocalNz); i++) { - d_nnz[i]=20; - d_nnz[localN-1-i]=20; - o_nnz[i]=5; - o_nnz[localN-1-i]=5; + for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) { + d_nnz[i] = 20; + d_nnz[localN - 1 - i] = 20; + o_nnz[i] = 5; + o_nnz[localN - 1 - i] = 5; } } - for (int i=2*(localmesh->LocalNz); iLocalNz));i++) { - d_nnz[i]=25; - d_nnz[localN-1-i]=25; - o_nnz[i]=0; - o_nnz[localN-1-i]=0; + for (int i = 2 * (localmesh->LocalNz); i < localN - 2 * ((localmesh->LocalNz)); i++) { + d_nnz[i] = 25; + d_nnz[localN - 1 - i] = 25; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 0; } // Use d_nnz and o_nnz for preallocating the matrix if (localmesh->firstX() && localmesh->lastX()) { // Only one processor in X - MatSeqAIJSetPreallocation( MatA, 0, d_nnz ); - }else { - MatMPIAIJSetPreallocation( MatA, 0, d_nnz, 0, o_nnz ); + MatSeqAIJSetPreallocation(MatA, 0, d_nnz); + } else { + MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz); } - } - else { + } else { // first and last localmesh->LocalNz entries are the edge x-values that (may) have 'off-diagonal' components (i.e. on another processor) - if ( localmesh->firstX() && localmesh->lastX() ) { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=6; - d_nnz[localN-1-i]=6; - o_nnz[i]=0; - o_nnz[localN-1-i]=0; + if (localmesh->firstX() && localmesh->lastX()) { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 6; + d_nnz[localN - 1 - i] = 6; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 0; } - } - else if ( localmesh->firstX() ) { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=6; - d_nnz[localN-1-i]=6; - o_nnz[i]=0; - o_nnz[localN-1-i]=3; + } else if (localmesh->firstX()) { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 6; + d_nnz[localN - 1 - i] = 6; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 3; } - } - else if ( localmesh->lastX() ) { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=6; - d_nnz[localN-1-i]=6; - o_nnz[i]=3; - o_nnz[localN-1-i]=0; + } else if (localmesh->lastX()) { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 6; + d_nnz[localN - 1 - i] = 6; + o_nnz[i] = 3; + o_nnz[localN - 1 - i] = 0; } - } - else { - for (int i=0; iLocalNz; i++) { - d_nnz[i]=6; - d_nnz[localN-1-i]=6; - o_nnz[i]=3; - o_nnz[localN-1-i]=3; + } else { + for (int i = 0; i < localmesh->LocalNz; i++) { + d_nnz[i] = 6; + d_nnz[localN - 1 - i] = 6; + o_nnz[i] = 3; + o_nnz[localN - 1 - i] = 3; } } - for (int i=localmesh->LocalNz; iLocalNz);i++) { - d_nnz[i]=9; - d_nnz[localN-1-i]=9; - o_nnz[i]=0; - o_nnz[localN-1-i]=0; + for (int i = localmesh->LocalNz; i < localN - (localmesh->LocalNz); i++) { + d_nnz[i] = 9; + d_nnz[localN - 1 - i] = 9; + o_nnz[i] = 0; + o_nnz[localN - 1 - i] = 0; } // Use d_nnz and o_nnz for preallocating the matrix if (localmesh->firstX() && localmesh->lastX()) { - MatSeqAIJSetPreallocation( MatA, 0, d_nnz ); + MatSeqAIJSetPreallocation(MatA, 0, d_nnz); } else { - MatMPIAIJSetPreallocation( MatA, 0, d_nnz, 0, o_nnz ); + MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz); } } // Free the d_nnz and o_nnz arrays, as these are will not be used anymore - PetscFree( d_nnz ); - PetscFree( o_nnz ); + PetscFree(d_nnz); + PetscFree(o_nnz); // Sets up the internal matrix data structures for the later use. MatSetUp(MatA); @@ -292,12 +301,12 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, if (pctype == "user") { pctype = PCSHELL; } - + // Get Options specific to particular solver types - opts->get("richardson_damping_factor",richardson_damping_factor,1.0,true); - opts->get("chebyshev_max",chebyshev_max,100,true); - opts->get("chebyshev_min",chebyshev_min,0.01,true); - opts->get("gmres_max_steps",gmres_max_steps,30,true); + opts->get("richardson_damping_factor", richardson_damping_factor, 1.0, true); + opts->get("chebyshev_max", chebyshev_max, 100, true); + opts->get("chebyshev_min", chebyshev_min, 0.01, true); + opts->get("gmres_max_steps", gmres_max_steps, 30, true); // Get Tolerances for KSP solver rtol = (*opts)["rtol"].doc("Relative tolerance for KSP solver").withDefault(1e-5); @@ -308,7 +317,9 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, // Get direct solver switch direct = (*opts)["direct"].doc("Use direct (LU) solver?").withDefault(false); if (direct) { - output << endl << "Using LU decompostion for direct solution of system" << endl << endl; + output << endl + << "Using LU decompostion for direct solution of system" << endl + << endl; } if (pctype == PCSHELL) { @@ -349,35 +360,43 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { ASSERT1(localmesh == b.getMesh() && localmesh == x0.getMesh()); ASSERT1(b.getLocation() == location); ASSERT1(x0.getLocation() == location); - - #if CHECK > 0 - // Checking flags are set to something which is not implemented (see - // constructor for details) - if ( global_flags & !implemented_flags) { - if (global_flags&INVERT_4TH_ORDER) output<<"For PETSc based Laplacian inverter, use 'fourth_order=true' instead of setting INVERT_4TH_ORDER flag"< 0 + // Checking flags are set to something which is not implemented (see + // constructor for details) + if (global_flags & !implemented_flags) { + if (global_flags & INVERT_4TH_ORDER) { + output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " + "setting INVERT_4TH_ORDER flag" + << endl; } - #endif + throw BoutException("Attempted to set Laplacian inversion flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (inner_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (outer_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } +#endif int y = b.getIndex(); // Get the Y index sol.setIndex(y); // Initialize the solution field. sol = 0.; // Determine which row/columns of the matrix are locally owned - MatGetOwnershipRange( MatA, &Istart, &Iend ); + MatGetOwnershipRange(MatA, &Istart, &Iend); - int i = Istart; // The row in the PETSc matrix - { Timer timer("petscsetup"); + int i = Istart; // The row in the PETSc matrix + { + Timer timer("petscsetup"); // if ((fourth_order) && !(lastflag&INVERT_4TH_ORDER)) throw BoutException("Should not change INVERT_4TH_ORDER flag in LaplacePetsc: 2nd order and 4th order require different pre-allocation to optimize PETSc solver"); - /* Set Matrix Elements + /* Set Matrix Elements * * Loop over locally owned rows of matrix A * i labels NODE POINT from @@ -391,107 +410,103 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { * In other word the indexing is done in a row-major order, but starting at * bottom left rather than top left */ - // X=0 to localmesh->xstart-1 defines the boundary region of the domain. - // Set the values for the inner boundary region - if( localmesh->firstX() ) { - for(int x=0; xxstart; x++) { - for(int z=0; zLocalNz; z++) { - PetscScalar val; // Value of element to be set in the matrix - // If Neumann Boundary Conditions are set. - if(inner_boundary_flags & INVERT_AC_GRAD) { - // Set values corresponding to nodes adjacent in x - if( fourth_order ) { - // Fourth Order Accuracy on Boundary - Element(i, x, z, 0, 0, - -25.0 / (12.0 * coords->dx(x, y, z)) - / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, 1, 0, - 4.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, 2, 0, - -3.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, 3, 0, - 4.0 / (3.0 * coords->dx(x, y, z)) - / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, 4, 0, - -1.0 / (4.0 * coords->dx(x, y, z)) - / sqrt(coords->g_11(x, y, z)), - MatA); - } else { - // Second Order Accuracy on Boundary - // Element(i,x,z, 0, 0, -3.0 / (2.0*coords->dx(x,y)), MatA ); - // Element(i,x,z, 1, 0, 2.0 / coords->dx(x,y), MatA ); - // Element(i,x,z, 2, 0, -1.0 / (2.0*coords->dx(x,y)), MatA ); - // Element(i,x,z, 3, 0, 0.0, MatA ); // Reset these elements to 0 - // in case 4th order flag was used previously: not allowed now - // Element(i,x,z, 4, 0, 0.0, MatA ); - // Second Order Accuracy on Boundary, set half-way between grid points - Element(i, x, z, 0, 0, - -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, 1, 0, - 1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, 2, 0, 0.0, MatA); - // Element(i,x,z, 3, 0, 0.0, MatA ); // Reset - // these elements to 0 in case 4th order flag was - // used previously: not allowed now - // Element(i,x,z, 4, 0, 0.0, MatA ); - } - } else { - if (fourth_order) { - // Set Diagonal Values to 1 - Element(i,x,z, 0, 0, 1., MatA ); - - // Set off diagonal elements to zero - Element(i,x,z, 1, 0, 0.0, MatA ); - Element(i,x,z, 2, 0, 0.0, MatA ); - Element(i,x,z, 3, 0, 0.0, MatA ); - Element(i,x,z, 4, 0, 0.0, MatA ); - } else { - Element(i,x,z, 0, 0, 0.5, MatA ); - Element(i,x,z, 1, 0, 0.5, MatA ); - Element(i,x,z, 2, 0, 0., MatA ); - } - } - - val=0; // Initialize val - - // Set Components of RHS - // If the inner boundary value should be set by b or x0 - if( inner_boundary_flags & INVERT_RHS ) val = b[x][z]; - else if( inner_boundary_flags & INVERT_SET ) val = x0[x][z]; - - // Set components of the RHS (the PETSc vector bs) - // 1 element is being set in row i to val - // INSERT_VALUES replaces existing entries with new values - VecSetValues( bs, 1, &i, &val, INSERT_VALUES ); - - // Set components of the and trial solution (the PETSc vector xs) - // 1 element is being set in row i to val - // INSERT_VALUES replaces existing entries with new values - val = x0[x][z]; - VecSetValues( xs, 1, &i, &val, INSERT_VALUES ); - - i++; // Increment row in Petsc matrix + // X=0 to localmesh->xstart-1 defines the boundary region of the domain. + // Set the values for the inner boundary region + if (localmesh->firstX()) { + for (int x = 0; x < localmesh->xstart; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val; // Value of element to be set in the matrix + // If Neumann Boundary Conditions are set. + if (inner_boundary_flags & INVERT_AC_GRAD) { + // Set values corresponding to nodes adjacent in x + if (fourth_order) { + // Fourth Order Accuracy on Boundary + Element(i, x, z, 0, 0, + -25.0 / (12.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)), + MatA); + Element(i, x, z, 1, 0, + 4.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, 2, 0, + -3.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, 3, 0, + 4.0 / (3.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)), + MatA); + Element(i, x, z, 4, 0, + -1.0 / (4.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)), + MatA); + } else { + // Second Order Accuracy on Boundary + // Element(i,x,z, 0, 0, -3.0 / (2.0*coords->dx(x,y)), MatA ); + // Element(i,x,z, 1, 0, 2.0 / coords->dx(x,y), MatA ); + // Element(i,x,z, 2, 0, -1.0 / (2.0*coords->dx(x,y)), MatA ); + // Element(i,x,z, 3, 0, 0.0, MatA ); // Reset these elements to 0 + // in case 4th order flag was used previously: not allowed now + // Element(i,x,z, 4, 0, 0.0, MatA ); + // Second Order Accuracy on Boundary, set half-way between grid points + Element(i, x, z, 0, 0, + -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, 1, 0, + 1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, 2, 0, 0.0, MatA); + // Element(i,x,z, 3, 0, 0.0, MatA ); // Reset + // these elements to 0 in case 4th order flag was + // used previously: not allowed now + // Element(i,x,z, 4, 0, 0.0, MatA ); } + } else { + if (fourth_order) { + // Set Diagonal Values to 1 + Element(i, x, z, 0, 0, 1., MatA); + + // Set off diagonal elements to zero + Element(i, x, z, 1, 0, 0.0, MatA); + Element(i, x, z, 2, 0, 0.0, MatA); + Element(i, x, z, 3, 0, 0.0, MatA); + Element(i, x, z, 4, 0, 0.0, MatA); + } else { + Element(i, x, z, 0, 0, 0.5, MatA); + Element(i, x, z, 1, 0, 0.5, MatA); + Element(i, x, z, 2, 0, 0., MatA); + } + } + + val = 0; // Initialize val + + // Set Components of RHS + // If the inner boundary value should be set by b or x0 + if (inner_boundary_flags & INVERT_RHS) { + val = b[x][z]; + } else if (inner_boundary_flags & INVERT_SET) { + val = x0[x][z]; + } + + // Set components of the RHS (the PETSc vector bs) + // 1 element is being set in row i to val + // INSERT_VALUES replaces existing entries with new values + VecSetValues(bs, 1, &i, &val, INSERT_VALUES); + + // Set components of the and trial solution (the PETSc vector xs) + // 1 element is being set in row i to val + // INSERT_VALUES replaces existing entries with new values + val = x0[x][z]; + VecSetValues(xs, 1, &i, &val, INSERT_VALUES); + + i++; // Increment row in Petsc matrix } + } } - // Set the values for the main domain - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { - for(int z=0; zLocalNz; z++) { + // Set the values for the main domain + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // NOTE: Only A0 is the A from setCoefA () BoutReal A0, A1, A2, A3, A4, A5; - A0 = A(x,y,z); + A0 = A(x, y, z); ASSERT3(finite(A0)); - + // Set the matrix coefficients - Coeffs( x, y, z, A1, A2, A3, A4, A5 ); + Coeffs(x, y, z, A1, A2, A3, A4, A5); BoutReal dx = coords->dx(x, y, z); BoutReal dx2 = SQ(dx); @@ -504,383 +519,383 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { ASSERT3(finite(A3)); ASSERT3(finite(A4)); ASSERT3(finite(A5)); - - // Set Matrix Elements - PetscScalar val=0.; - if (fourth_order) { - // f(i,j) = f(x,z) - val = A0 - (5.0/2.0)*( (A1 / dx2) + (A2 / dz2) ); - Element(i,x,z, 0, 0, val, MatA ); - - // f(i-2,j-2) - val = A3 / ( 144.0 * dxdz ); - Element(i,x,z, -2, -2, val, MatA ); - - // f(i-2,j-1) - val = -1.0 * A3 / ( 18.0 * dxdz ); - Element(i,x,z, -2, -1, val, MatA ); - - // f(i-2,j) - val = (1.0/12.0) * ( (-1.0 * A1 / dx2 ) + (A4 / dx) ); - Element(i,x,z, -2, 0, val, MatA ); - - // f(i-2,j+1) - val = A3 / ( 18.0 * dxdz ); - Element(i,x,z, -2, 1, val, MatA ); - - // f(i-2,j+2) - val = -1.0 * A3 / ( 144.0 * dxdz ); - Element(i,x,z, -2, 2, val, MatA ); - - // f(i-1,j-2) - val = -1.0 * A3 / ( 18.0 * dxdz ); - Element(i,x,z, -1, -2, val, MatA ); - - // f(i-1,j-1) - val = 4.0 * A3 / ( 9.0 * dxdz ); - Element(i,x,z, -1, -1, val, MatA ); - - // f(i-1,j) - val = ( 4.0 * A1 / ( 3.0 * dx2 ) ) - ( 2.0 * A4 / ( 3.0 * dx ) ); - Element(i,x,z, -1, 0, val, MatA ); - - // f(i-1,j+1) - val = -4.0 * A3 / ( 9.0 * dxdz ); - Element(i,x,z, -1, 1, val, MatA ); - - // f(i-1,j+2) - val = A3 / ( 18.0 * dxdz ); - Element(i,x,z, -1, 2, val, MatA ); - - // f(i,j-2) - val = (1.0/12.0) * ( ( -1.0 * A2 / dz2 ) + ( A5 / dz ) ); - Element(i,x,z, 0, -2, val, MatA ); - - // f(i,j-1) - val = ( 4.0 * A2 / ( 3.0 * dz2 ) ) - ( 2.0 * A5 / ( 3.0 * dz ) ); - Element(i,x,z, 0, -1, val, MatA ); - - // f(i,j+1) - val = ( 4.0 * A2 / ( 3.0 * dz2 ) ) + ( 2.0 * A5 / ( 3.0 * dz ) ); - Element(i,x,z, 0, 1, val, MatA ); - - // f(i,j+2) - val = (-1.0/12.0) * ( ( A2 / dz2 ) + ( A5 / dz ) ); - Element(i,x,z, 0, 2, val, MatA ); - - // f(i+1,j-2) - val = A3 / ( 18.0 * dxdz ); - Element(i,x,z, 1, -2, val, MatA ); - - // f(i+1,j-1) - val = -4.0 * A3 / ( 9.0 * dxdz ); - Element(i,x,z, 1, -1, val, MatA ); - - // f(i+1,j) - val = ( 4.0 * A1 / ( 3.0*dx2 ) ) + ( 2.0 * A4 / ( 3.0 * dx ) ); - Element(i,x,z, 1, 0, val, MatA ); - - // f(i+1,j+1) - val = 4.0 * A3 / ( 9.0 * dxdz ); - Element(i,x,z, 1, 1, val, MatA ); - - // f(i+1,j+2) - val = -1.0 * A3 / ( 18.0 * dxdz ); - Element(i,x,z, 1, 2, val, MatA ); - - // f(i+2,j-2) - val = -1.0 * A3 / ( 144.0 * dxdz ); - Element(i,x,z, 2, -2, val, MatA ); - - // f(i+2,j-1) - val = A3 / ( 18.0 * dxdz ); - Element(i,x,z, 2, -1, val, MatA ); - - // f(i+2,j) - val = (-1.0/12.0) * ( (A1 / dx2) + (A4 / dx) ); - Element(i,x,z, 2, 0, val, MatA ); - - // f(i+2,j+1) - val = -1.0 * A3 / ( 18.0 * dxdz ); - Element(i,x,z, 2, 1, val, MatA ); - - // f(i+2,j+2) - val = A3 / ( 144.0 * dxdz ); - Element(i,x,z, 2, 2, val, MatA ); - } else { - // Second order - - // f(i,j) = f(x,z) - val = A0 - 2.0*( (A1 / dx2) + (A2 / dz2) ); - Element(i,x,z, 0, 0, val, MatA ); - - // f(i-1,j-1) - val = A3 / (4.0 * dxdz); - Element(i,x,z, -1, -1, val, MatA ); - - // f(i-1,j) - val = ( A1 / dx2 ) - A4 / ( 2.0 * dx ); - Element(i,x,z, -1, 0, val, MatA ); - - // f(i-1,j+1) - val = -1.0 * A3 / ( 4.0 * dxdz ); - Element(i,x,z, -1, 1, val, MatA ); - - // f(i,j-1) - val = ( A2 / dz2 ) - ( A5 / ( 2.0 * dz ) ); - Element(i,x,z, 0, -1, val, MatA ); - - // f(i,j+1) - val = ( A2 / dz2 ) + ( A5 / ( 2.0 * dz ) ); - Element(i,x,z, 0, 1, val, MatA ); - - // f(i+1,j-1) - val = -1.0 * A3 / ( 4.0 * dxdz ); - Element(i,x,z, 1, -1, val, MatA ); - - // f(i+1,j) - val = ( A1 / dx2 ) + ( A4 / ( 2.0 * dx ) ); - Element(i,x,z, 1, 0, val, MatA ); - - // f(i+1,j+1) - val = A3 / ( 4.0 * dxdz ); - Element(i,x,z, 1, 1, val, MatA ); - } - // Set Components of RHS Vector - val = b[x][z]; - VecSetValues( bs, 1, &i, &val, INSERT_VALUES ); - // Set Components of Trial Solution Vector - val = x0[x][z]; - VecSetValues( xs, 1, &i, &val, INSERT_VALUES ); - i++; + // Set Matrix Elements + PetscScalar val = 0.; + if (fourth_order) { + // f(i,j) = f(x,z) + val = A0 - (5.0 / 2.0) * ((A1 / dx2) + (A2 / dz2)); + Element(i, x, z, 0, 0, val, MatA); + + // f(i-2,j-2) + val = A3 / (144.0 * dxdz); + Element(i, x, z, -2, -2, val, MatA); + + // f(i-2,j-1) + val = -1.0 * A3 / (18.0 * dxdz); + Element(i, x, z, -2, -1, val, MatA); + + // f(i-2,j) + val = (1.0 / 12.0) * ((-1.0 * A1 / dx2) + (A4 / dx)); + Element(i, x, z, -2, 0, val, MatA); + + // f(i-2,j+1) + val = A3 / (18.0 * dxdz); + Element(i, x, z, -2, 1, val, MatA); + + // f(i-2,j+2) + val = -1.0 * A3 / (144.0 * dxdz); + Element(i, x, z, -2, 2, val, MatA); + + // f(i-1,j-2) + val = -1.0 * A3 / (18.0 * dxdz); + Element(i, x, z, -1, -2, val, MatA); + + // f(i-1,j-1) + val = 4.0 * A3 / (9.0 * dxdz); + Element(i, x, z, -1, -1, val, MatA); + + // f(i-1,j) + val = (4.0 * A1 / (3.0 * dx2)) - (2.0 * A4 / (3.0 * dx)); + Element(i, x, z, -1, 0, val, MatA); + + // f(i-1,j+1) + val = -4.0 * A3 / (9.0 * dxdz); + Element(i, x, z, -1, 1, val, MatA); + + // f(i-1,j+2) + val = A3 / (18.0 * dxdz); + Element(i, x, z, -1, 2, val, MatA); + + // f(i,j-2) + val = (1.0 / 12.0) * ((-1.0 * A2 / dz2) + (A5 / dz)); + Element(i, x, z, 0, -2, val, MatA); + + // f(i,j-1) + val = (4.0 * A2 / (3.0 * dz2)) - (2.0 * A5 / (3.0 * dz)); + Element(i, x, z, 0, -1, val, MatA); + + // f(i,j+1) + val = (4.0 * A2 / (3.0 * dz2)) + (2.0 * A5 / (3.0 * dz)); + Element(i, x, z, 0, 1, val, MatA); + + // f(i,j+2) + val = (-1.0 / 12.0) * ((A2 / dz2) + (A5 / dz)); + Element(i, x, z, 0, 2, val, MatA); + + // f(i+1,j-2) + val = A3 / (18.0 * dxdz); + Element(i, x, z, 1, -2, val, MatA); + + // f(i+1,j-1) + val = -4.0 * A3 / (9.0 * dxdz); + Element(i, x, z, 1, -1, val, MatA); + + // f(i+1,j) + val = (4.0 * A1 / (3.0 * dx2)) + (2.0 * A4 / (3.0 * dx)); + Element(i, x, z, 1, 0, val, MatA); + + // f(i+1,j+1) + val = 4.0 * A3 / (9.0 * dxdz); + Element(i, x, z, 1, 1, val, MatA); + + // f(i+1,j+2) + val = -1.0 * A3 / (18.0 * dxdz); + Element(i, x, z, 1, 2, val, MatA); + + // f(i+2,j-2) + val = -1.0 * A3 / (144.0 * dxdz); + Element(i, x, z, 2, -2, val, MatA); + + // f(i+2,j-1) + val = A3 / (18.0 * dxdz); + Element(i, x, z, 2, -1, val, MatA); + + // f(i+2,j) + val = (-1.0 / 12.0) * ((A1 / dx2) + (A4 / dx)); + Element(i, x, z, 2, 0, val, MatA); + + // f(i+2,j+1) + val = -1.0 * A3 / (18.0 * dxdz); + Element(i, x, z, 2, 1, val, MatA); + + // f(i+2,j+2) + val = A3 / (144.0 * dxdz); + Element(i, x, z, 2, 2, val, MatA); + } else { + // Second order + + // f(i,j) = f(x,z) + val = A0 - 2.0 * ((A1 / dx2) + (A2 / dz2)); + Element(i, x, z, 0, 0, val, MatA); + + // f(i-1,j-1) + val = A3 / (4.0 * dxdz); + Element(i, x, z, -1, -1, val, MatA); + + // f(i-1,j) + val = (A1 / dx2) - A4 / (2.0 * dx); + Element(i, x, z, -1, 0, val, MatA); + + // f(i-1,j+1) + val = -1.0 * A3 / (4.0 * dxdz); + Element(i, x, z, -1, 1, val, MatA); + + // f(i,j-1) + val = (A2 / dz2) - (A5 / (2.0 * dz)); + Element(i, x, z, 0, -1, val, MatA); + + // f(i,j+1) + val = (A2 / dz2) + (A5 / (2.0 * dz)); + Element(i, x, z, 0, 1, val, MatA); + + // f(i+1,j-1) + val = -1.0 * A3 / (4.0 * dxdz); + Element(i, x, z, 1, -1, val, MatA); + + // f(i+1,j) + val = (A1 / dx2) + (A4 / (2.0 * dx)); + Element(i, x, z, 1, 0, val, MatA); + + // f(i+1,j+1) + val = A3 / (4.0 * dxdz); + Element(i, x, z, 1, 1, val, MatA); } + // Set Components of RHS Vector + val = b[x][z]; + VecSetValues(bs, 1, &i, &val, INSERT_VALUES); + + // Set Components of Trial Solution Vector + val = x0[x][z]; + VecSetValues(xs, 1, &i, &val, INSERT_VALUES); + i++; + } } - // X=localmesh->xend+1 to localmesh->LocalNx-1 defines the upper boundary region of the domain. - // Set the values for the outer boundary region - if( localmesh->lastX() ) { - for(int x=localmesh->xend+1; xLocalNx; x++) { - for(int z=0; zLocalNz; z++) { - // Set Diagonal Values to 1 - PetscScalar val = 1; - Element(i,x,z, 0, 0, val, MatA ); - - // If Neumann Boundary Conditions are set. - if(outer_boundary_flags & INVERT_AC_GRAD) { - // Set values corresponding to nodes adjacent in x - if( fourth_order ) { - // Fourth Order Accuracy on Boundary - Element(i, x, z, 0, 0, - 25.0 / (12.0 * coords->dx(x, y, z)) - / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, -1, 0, - -4.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, -2, 0, - 3.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, -3, 0, - -4.0 / (3.0 * coords->dx(x, y, z)) - / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, -4, 0, - 1.0 / (4.0 * coords->dx(x, y, z)) - / sqrt(coords->g_11(x, y, z)), - MatA); - } - else { - // // Second Order Accuracy on Boundary - // Element(i,x,z, 0, 0, 3.0 / (2.0*coords->dx(x,y)), MatA ); - // Element(i,x,z, -1, 0, -2.0 / coords->dx(x,y), MatA ); - // Element(i,x,z, -2, 0, 1.0 / (2.0*coords->dx(x,y)), MatA ); - // Element(i,x,z, -3, 0, 0.0, MatA ); // Reset these elements to 0 - // in case 4th order flag was used previously: not allowed now - // Element(i,x,z, -4, 0, 0.0, MatA ); - // Second Order Accuracy on Boundary, set half-way between grid - // points - Element(i, x, z, 0, 0, - 1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, -1, 0, - -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), - MatA); - Element(i, x, z, -2, 0, 0.0, MatA); - // Element(i,x,z, -3, 0, 0.0, MatA ); // Reset these elements to 0 - // in case 4th order flag was used previously: not allowed now - // Element(i,x,z, -4, 0, 0.0, MatA ); - } - } - else { - if (fourth_order) { - // Set off diagonal elements to zero - Element(i,x,z, -1, 0, 0.0, MatA ); - Element(i,x,z, -2, 0, 0.0, MatA ); - Element(i,x,z, -3, 0, 0.0, MatA ); - Element(i,x,z, -4, 0, 0.0, MatA ); - } - else { - Element(i,x,z, 0, 0, 0.5 , MatA ); - Element(i,x,z, -1, 0, 0.5 , MatA ); - Element(i,x,z, -2, 0, 0., MatA ); - } - } - - // Set Components of RHS - // If the inner boundary value should be set by b or x0 - val=0; - if( outer_boundary_flags & INVERT_RHS ) val = b[x][z]; - else if( outer_boundary_flags & INVERT_SET ) val = x0[x][z]; - - // Set components of the RHS (the PETSc vector bs) - // 1 element is being set in row i to val - // INSERT_VALUES replaces existing entries with new values - VecSetValues( bs, 1, &i, &val, INSERT_VALUES ); - - // Set components of the and trial solution (the PETSc vector xs) - // 1 element is being set in row i to val - // INSERT_VALUES replaces existing entries with new values - val = x0[x][z]; - VecSetValues( xs, 1, &i, &val, INSERT_VALUES ); - - i++; // Increment row in Petsc matrix + // X=localmesh->xend+1 to localmesh->LocalNx-1 defines the upper boundary region of the domain. + // Set the values for the outer boundary region + if (localmesh->lastX()) { + for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + // Set Diagonal Values to 1 + PetscScalar val = 1; + Element(i, x, z, 0, 0, val, MatA); + + // If Neumann Boundary Conditions are set. + if (outer_boundary_flags & INVERT_AC_GRAD) { + // Set values corresponding to nodes adjacent in x + if (fourth_order) { + // Fourth Order Accuracy on Boundary + Element(i, x, z, 0, 0, + 25.0 / (12.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)), + MatA); + Element(i, x, z, -1, 0, + -4.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, -2, 0, + 3.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, -3, 0, + -4.0 / (3.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)), + MatA); + Element(i, x, z, -4, 0, + 1.0 / (4.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)), + MatA); + } else { + // // Second Order Accuracy on Boundary + // Element(i,x,z, 0, 0, 3.0 / (2.0*coords->dx(x,y)), MatA ); + // Element(i,x,z, -1, 0, -2.0 / coords->dx(x,y), MatA ); + // Element(i,x,z, -2, 0, 1.0 / (2.0*coords->dx(x,y)), MatA ); + // Element(i,x,z, -3, 0, 0.0, MatA ); // Reset these elements to 0 + // in case 4th order flag was used previously: not allowed now + // Element(i,x,z, -4, 0, 0.0, MatA ); + // Second Order Accuracy on Boundary, set half-way between grid + // points + Element(i, x, z, 0, 0, + 1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, -1, 0, + -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA); + Element(i, x, z, -2, 0, 0.0, MatA); + // Element(i,x,z, -3, 0, 0.0, MatA ); // Reset these elements to 0 + // in case 4th order flag was used previously: not allowed now + // Element(i,x,z, -4, 0, 0.0, MatA ); } + } else { + if (fourth_order) { + // Set off diagonal elements to zero + Element(i, x, z, -1, 0, 0.0, MatA); + Element(i, x, z, -2, 0, 0.0, MatA); + Element(i, x, z, -3, 0, 0.0, MatA); + Element(i, x, z, -4, 0, 0.0, MatA); + } else { + Element(i, x, z, 0, 0, 0.5, MatA); + Element(i, x, z, -1, 0, 0.5, MatA); + Element(i, x, z, -2, 0, 0., MatA); + } + } + + // Set Components of RHS + // If the inner boundary value should be set by b or x0 + val = 0; + if (outer_boundary_flags & INVERT_RHS) { + val = b[x][z]; + } else if (outer_boundary_flags & INVERT_SET) { + val = x0[x][z]; + } + + // Set components of the RHS (the PETSc vector bs) + // 1 element is being set in row i to val + // INSERT_VALUES replaces existing entries with new values + VecSetValues(bs, 1, &i, &val, INSERT_VALUES); + + // Set components of the and trial solution (the PETSc vector xs) + // 1 element is being set in row i to val + // INSERT_VALUES replaces existing entries with new values + val = x0[x][z]; + VecSetValues(xs, 1, &i, &val, INSERT_VALUES); + + i++; // Increment row in Petsc matrix } + } } - if(i != Iend) { - throw BoutException("Petsc index sanity check failed"); - } + if (i != Iend) { + throw BoutException("Petsc index sanity check failed"); + } - // Assemble Matrix - MatAssemblyBegin( MatA, MAT_FINAL_ASSEMBLY ); - MatAssemblyEnd( MatA, MAT_FINAL_ASSEMBLY ); + // Assemble Matrix + MatAssemblyBegin(MatA, MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(MatA, MAT_FINAL_ASSEMBLY); -// // Record which flags were used for this matrix -// lastflag = flags; + // // Record which flags were used for this matrix + // lastflag = flags; - // Assemble RHS Vector - VecAssemblyBegin(bs); - VecAssemblyEnd(bs); + // Assemble RHS Vector + VecAssemblyBegin(bs); + VecAssemblyEnd(bs); - // Assemble Trial Solution Vector - VecAssemblyBegin(xs); - VecAssemblyEnd(xs); + // Assemble Trial Solution Vector + VecAssemblyBegin(xs); + VecAssemblyEnd(xs); - // Configure Linear Solver -#if PETSC_VERSION_GE(3,5,0) - KSPSetOperators( ksp,MatA,MatA); + // Configure Linear Solver +#if PETSC_VERSION_GE(3, 5, 0) + KSPSetOperators(ksp, MatA, MatA); #else - KSPSetOperators( ksp,MatA,MatA,DIFFERENT_NONZERO_PATTERN ); + KSPSetOperators(ksp, MatA, MatA, DIFFERENT_NONZERO_PATTERN); #endif - PC pc; // The preconditioner option - - if(direct) { // If a direct solver has been chosen - // Get the preconditioner - KSPGetPC(ksp,&pc); - // Set the preconditioner - PCSetType(pc,PCLU); - // Set the solver type -#if PETSC_VERSION_GE(3,9,0) - PCFactorSetMatSolverType(pc,"mumps"); + PC pc; // The preconditioner option + + if (direct) { // If a direct solver has been chosen + // Get the preconditioner + KSPGetPC(ksp, &pc); + // Set the preconditioner + PCSetType(pc, PCLU); + // Set the solver type +#if PETSC_VERSION_GE(3, 9, 0) + PCFactorSetMatSolverType(pc, "mumps"); #else - PCFactorSetMatSolverPackage(pc,"mumps"); + PCFactorSetMatSolverPackage(pc, "mumps"); #endif - }else { // If a iterative solver has been chosen - KSPSetType( ksp, ksptype.c_str() ); // Set the type of the solver + } else { // If a iterative solver has been chosen + KSPSetType(ksp, ksptype.c_str()); // Set the type of the solver - if( ksptype == KSPRICHARDSON ) KSPRichardsonSetScale( ksp, richardson_damping_factor ); + if (ksptype == KSPRICHARDSON) { + KSPRichardsonSetScale(ksp, richardson_damping_factor); + } #ifdef KSPCHEBYSHEV - else if( ksptype == KSPCHEBYSHEV ) KSPChebyshevSetEigenvalues( ksp, chebyshev_max, chebyshev_min ); + else if (ksptype == KSPCHEBYSHEV) { + KSPChebyshevSetEigenvalues(ksp, chebyshev_max, chebyshev_min); + } #endif - else if( ksptype == KSPGMRES ) KSPGMRESSetRestart( ksp, gmres_max_steps ); + else if (ksptype == KSPGMRES) { + KSPGMRESSetRestart(ksp, gmres_max_steps); + } - // Set the relative and absolute tolerances - KSPSetTolerances( ksp, rtol, atol, dtol, maxits ); + // Set the relative and absolute tolerances + KSPSetTolerances(ksp, rtol, atol, dtol, maxits); - // If the initial guess is not set to zero - if (!(global_flags & INVERT_START_NEW)) { - KSPSetInitialGuessNonzero(ksp, static_cast(true)); - } + // If the initial guess is not set to zero + if (!(global_flags & INVERT_START_NEW)) { + KSPSetInitialGuessNonzero(ksp, static_cast(true)); + } - // Get the preconditioner - KSPGetPC(ksp,&pc); - - // Set the type of the preconditioner - PCSetType(pc, pctype.c_str()); - - // If pctype = user in BOUT.inp, it will be translated to PCSHELL upon - // construction of the object - if (pctype == PCSHELL) { - // User-supplied preconditioner function - PCShellSetApply(pc,laplacePCapply); - PCShellSetContext(pc,this); - if(rightprec) { - KSPSetPCSide(ksp, PC_RIGHT); // Right preconditioning - }else - KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning - //ierr = PCShellSetApply(pc,laplacePCapply);CHKERRQ(ierr); - //ierr = PCShellSetContext(pc,this);CHKERRQ(ierr); - //ierr = KSPSetPCSide(ksp, PC_RIGHT);CHKERRQ(ierr); - } + // Get the preconditioner + KSPGetPC(ksp, &pc); + + // Set the type of the preconditioner + PCSetType(pc, pctype.c_str()); + + // If pctype = user in BOUT.inp, it will be translated to PCSHELL upon + // construction of the object + if (pctype == PCSHELL) { + // User-supplied preconditioner function + PCShellSetApply(pc, laplacePCapply); + PCShellSetContext(pc, this); + if (rightprec) { + KSPSetPCSide(ksp, PC_RIGHT); // Right preconditioning + } else { + KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning + } + //ierr = PCShellSetApply(pc,laplacePCapply);CHKERRQ(ierr); + //ierr = PCShellSetContext(pc,this);CHKERRQ(ierr); + //ierr = KSPSetPCSide(ksp, PC_RIGHT);CHKERRQ(ierr); + } - lib.setOptionsFromInputFile(ksp); - } + lib.setOptionsFromInputFile(ksp); + } } // Call the actual solver - { Timer timer("petscsolve"); - KSPSolve( ksp, bs, xs ); // Call the solver to solve the system + { + Timer timer("petscsolve"); + KSPSolve(ksp, bs, xs); // Call the solver to solve the system } KSPConvergedReason reason; - KSPGetConvergedReason( ksp, &reason ); - if (reason==-3) { // Too many iterations, might be fixed by taking smaller timestep + KSPGetConvergedReason(ksp, &reason); + if (reason == -3) { // Too many iterations, might be fixed by taking smaller timestep throw BoutIterationFail("petsc_laplace: too many iterations"); - } - else if (reason<=0) { - output<<"KSPConvergedReason is "<firstX()) { - for(int x=0; xxstart; x++) { - for(int z=0; zLocalNz; z++) { - PetscScalar val = 0; - VecGetValues(xs, 1, &i, &val ); - sol[x][z] = val; - i++; // Increment row in Petsc matrix - } - } + if (localmesh->firstX()) { + for (int x = 0; x < localmesh->xstart; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val = 0; + VecGetValues(xs, 1, &i, &val); + sol[x][z] = val; + i++; // Increment row in Petsc matrix + } } + } // Set the main domain values - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { - for(int z=0; zLocalNz; z++) { - PetscScalar val = 0; - VecGetValues(xs, 1, &i, &val ); - sol[x][z] = val; - i++; // Increment row in Petsc matrix - } + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val = 0; + VecGetValues(xs, 1, &i, &val); + sol[x][z] = val; + i++; // Increment row in Petsc matrix } + } // Set the outer boundary values - if(localmesh->lastX()) { - for(int x=localmesh->xend+1; xLocalNx; x++) { - for(int z=0;z < localmesh->LocalNz; z++) { - PetscScalar val = 0; - VecGetValues(xs, 1, &i, &val ); - sol[x][z] = val; - i++; // Increment row in Petsc matrix - } - } + if (localmesh->lastX()) { + for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val = 0; + VecGetValues(xs, 1, &i, &val); + sol[x][z] = val; + i++; // Increment row in Petsc matrix + } } + } - if(i != Iend) { + if (i != Iend) { throw BoutException("Petsc index sanity check 2 failed"); } @@ -905,24 +920,29 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { * * \param[out] MatA The matrix A used in the inversion */ -void LaplacePetsc::Element(int i, int x, int z, - int xshift, int zshift, - PetscScalar ele, Mat &MatA ) { +void LaplacePetsc::Element(int i, int x, int z, int xshift, int zshift, PetscScalar ele, + Mat& MatA) { // Need to convert LOCAL x to GLOBAL x in order to correctly calculate // PETSC Matrix Index. int xoffset = Istart / meshz; - if( Istart % meshz != 0 ) - throw BoutException("Petsc index sanity check 3 failed"); + if (Istart % meshz != 0) { + throw BoutException("Petsc index sanity check 3 failed"); + } // Calculate the row to be set int row_new = x + xshift; // should never be out of range. - if( !localmesh->firstX() ) row_new += (xoffset - localmesh->xstart); + if (!localmesh->firstX()) { + row_new += (xoffset - localmesh->xstart); + } // Calculate the column to be set int col_new = z + zshift; - if( col_new < 0 ) col_new += meshz; - else if( col_new > meshz-1 ) col_new -= meshz; + if (col_new < 0) { + col_new += meshz; + } else if (col_new > meshz - 1) { + col_new -= meshz; + } // Convert to global indices int index = (row_new * meshz) + col_new; @@ -933,7 +953,7 @@ void LaplacePetsc::Element(int i, int x, int z, z, i, index); } #endif - + /* Inserts or adds a block of values into a matrix * Input: * MatA - The matrix to set the values in @@ -944,7 +964,7 @@ void LaplacePetsc::Element(int i, int x, int z, * &ele - The vlaue to be set * INSERT_VALUES replaces existing entries with new values */ - MatSetValues(MatA,1,&i,1,&index,&ele,INSERT_VALUES); + MatSetValues(MatA, 1, &i, 1, &index, &ele, INSERT_VALUES); } /*! @@ -979,7 +999,8 @@ void LaplacePetsc::Element(int i, int x, int z, * \param[out] coef5 Convenient variable used to set matrix * (see manual for details) */ -void LaplacePetsc::Coeffs( int x, int y, int z, BoutReal &coef1, BoutReal &coef2, BoutReal &coef3, BoutReal &coef4, BoutReal &coef5 ) { +void LaplacePetsc::Coeffs(int x, int y, int z, BoutReal& coef1, BoutReal& coef2, + BoutReal& coef3, BoutReal& coef4, BoutReal& coef5) { coef1 = coords->g11(x, y, z); // X 2nd derivative coefficient coef2 = coords->g33(x, y, z); // Z 2nd derivative coefficient @@ -996,9 +1017,9 @@ void LaplacePetsc::Coeffs( int x, int y, int z, BoutReal &coef1, BoutReal &coef2 ASSERT3(finite(coef5)); } - if(nonuniform) { + if (nonuniform) { // non-uniform mesh correction - if((x != 0) && (x != (localmesh->LocalNx-1))) { + if ((x != 0) && (x != (localmesh->LocalNx - 1))) { coef4 -= 0.5 * ((coords->dx(x + 1, y, z) - coords->dx(x - 1, y, z)) / SQ(coords->dx(x, y, z))) @@ -1006,7 +1027,7 @@ void LaplacePetsc::Coeffs( int x, int y, int z, BoutReal &coef1, BoutReal &coef2 } } - if(localmesh->IncIntShear) { + if (localmesh->IncIntShear) { // d2dz2 term coef2 += coords->g11(x, y, z) * coords->IntShiftTorsion(x, y, z) * coords->IntShiftTorsion(x, y, z); @@ -1015,51 +1036,57 @@ void LaplacePetsc::Coeffs( int x, int y, int z, BoutReal &coef1, BoutReal &coef2 } if (issetD) { - coef1 *= D(x,y,z); - coef2 *= D(x,y,z); - coef3 *= D(x,y,z); - coef4 *= D(x,y,z); - coef5 *= D(x,y,z); + coef1 *= D(x, y, z); + coef2 *= D(x, y, z); + coef3 *= D(x, y, z); + coef4 *= D(x, y, z); + coef5 *= D(x, y, z); } // A second/fourth order derivative term if (issetC) { -// if( (x > 0) && (x < (localmesh->LocalNx-1)) ) //Valid if doing second order derivative, not if fourth: should only be called for xstart<=x<=xend anyway - if( (x > 1) && (x < (localmesh->LocalNx-2)) ) { - int zp = z+1; // z plus 1 - if (zp > meshz-1) zp -= meshz; - int zm = z-1; // z minus 1 - if (zm<0) zm += meshz; - BoutReal ddx_C; - BoutReal ddz_C; - - if (fourth_order) { - int zpp = z+2; // z plus 1 plus 1 - if (zpp > meshz-1) zpp -= meshz; - int zmm = z-2; // z minus 1 minus 1 - if (zmm<0) zmm += meshz; - // Fourth order discretization of C in x - ddx_C = (-C2(x + 2, y, z) + 8. * C2(x + 1, y, z) - 8. * C2(x - 1, y, z) - + C2(x - 2, y, z)) - / (12. * coords->dx(x, y, z) * (C1(x, y, z))); - // Fourth order discretization of C in z - ddz_C = - (-C2(x, y, zpp) + 8. * C2(x, y, zp) - 8. * C2(x, y, zm) + C2(x, y, zmm)) - / (12. * coords->dz(x, y, z) * (C1(x, y, z))); - } - else { - // Second order discretization of C in x - ddx_C = (C2(x + 1, y, z) - C2(x - 1, y, z)) - / (2. * coords->dx(x, y, z) * (C1(x, y, z))); - // Second order discretization of C in z - ddz_C = (C2(x, y, zp) - C2(x, y, zm)) - / (2. * coords->dz(x, y, z) * (C1(x, y, z))); - } + // if( (x > 0) && (x < (localmesh->LocalNx-1)) ) //Valid if doing second order derivative, not if fourth: should only be called for xstart<=x<=xend anyway + if ((x > 1) && (x < (localmesh->LocalNx - 2))) { + int zp = z + 1; // z plus 1 + if (zp > meshz - 1) { + zp -= meshz; + } + int zm = z - 1; // z minus 1 + if (zm < 0) { + zm += meshz; + } + BoutReal ddx_C; + BoutReal ddz_C; - coef4 += coords->g11(x, y, z) * ddx_C + coords->g13(x, y, z) * ddz_C; - coef5 += coords->g13(x, y, z) * ddx_C + coords->g33(x, y, z) * ddz_C; + if (fourth_order) { + int zpp = z + 2; // z plus 1 plus 1 + if (zpp > meshz - 1) { + zpp -= meshz; } + int zmm = z - 2; // z minus 1 minus 1 + if (zmm < 0) { + zmm += meshz; + } + // Fourth order discretization of C in x + ddx_C = (-C2(x + 2, y, z) + 8. * C2(x + 1, y, z) - 8. * C2(x - 1, y, z) + + C2(x - 2, y, z)) + / (12. * coords->dx(x, y, z) * (C1(x, y, z))); + // Fourth order discretization of C in z + ddz_C = (-C2(x, y, zpp) + 8. * C2(x, y, zp) - 8. * C2(x, y, zm) + C2(x, y, zmm)) + / (12. * coords->dz(x, y, z) * (C1(x, y, z))); + } else { + // Second order discretization of C in x + ddx_C = (C2(x + 1, y, z) - C2(x - 1, y, z)) + / (2. * coords->dx(x, y, z) * (C1(x, y, z))); + // Second order discretization of C in z + ddz_C = + (C2(x, y, zp) - C2(x, y, zm)) / (2. * coords->dz(x, y, z) * (C1(x, y, z))); + } + + coef4 += coords->g11(x, y, z) * ddx_C + coords->g13(x, y, z) * ddz_C; + coef5 += coords->g13(x, y, z) * ddx_C + coords->g33(x, y, z) * ddz_C; } + } /* Ex and Ez * Additional 1st derivative terms to allow for solution field to be @@ -1071,86 +1098,77 @@ void LaplacePetsc::Coeffs( int x, int y, int z, BoutReal &coef1, BoutReal &coef2 */ if (issetE) { // These coefficients are 0 by default - coef4 += Ex(x,y,z); - coef5 += Ez(x,y,z); + coef4 += Ex(x, y, z); + coef5 += Ez(x, y, z); } } - -void LaplacePetsc::vecToField(Vec xs, FieldPerp &f) { +void LaplacePetsc::vecToField(Vec xs, FieldPerp& f) { ASSERT1(localmesh == f.getMesh()); f.allocate(); int i = Istart; - if(localmesh->firstX()) - { - for(int x=0; xxstart; x++) - { - for(int z=0; zLocalNz; z++) - { - PetscScalar val; - VecGetValues(xs, 1, &i, &val ); - f[x][z] = val; - i++; // Increment row in Petsc matrix - } - } + if (localmesh->firstX()) { + for (int x = 0; x < localmesh->xstart; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val; + VecGetValues(xs, 1, &i, &val); + f[x][z] = val; + i++; // Increment row in Petsc matrix + } } + } - for(int x=localmesh->xstart; x <= localmesh->xend; x++) - { - for(int z=0; zLocalNz; z++) - { - PetscScalar val; - VecGetValues(xs, 1, &i, &val ); - f[x][z] = val; - i++; // Increment row in Petsc matrix - } + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val; + VecGetValues(xs, 1, &i, &val); + f[x][z] = val; + i++; // Increment row in Petsc matrix } + } - if(localmesh->lastX()) - { - for(int x=localmesh->xend+1; xLocalNx; x++) - { - for(int z=0;z < localmesh->LocalNz; z++) - { - PetscScalar val; - VecGetValues(xs, 1, &i, &val ); - f[x][z] = val; - i++; // Increment row in Petsc matrix - } - } + if (localmesh->lastX()) { + for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val; + VecGetValues(xs, 1, &i, &val); + f[x][z] = val; + i++; // Increment row in Petsc matrix + } } + } ASSERT1(i == Iend); } -void LaplacePetsc::fieldToVec(const FieldPerp &f, Vec bs) { +void LaplacePetsc::fieldToVec(const FieldPerp& f, Vec bs) { ASSERT1(localmesh == f.getMesh()); int i = Istart; - if(localmesh->firstX()) { - for(int x=0; xxstart; x++) { - for(int z=0; zLocalNz; z++) { + if (localmesh->firstX()) { + for (int x = 0; x < localmesh->xstart; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = f[x][z]; - VecSetValues( bs, 1, &i, &val, INSERT_VALUES ); + VecSetValues(bs, 1, &i, &val, INSERT_VALUES); i++; // Increment row in Petsc matrix } } } - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { - for(int z=0; zLocalNz; z++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = f[x][z]; - VecSetValues( bs, 1, &i, &val, INSERT_VALUES ); + VecSetValues(bs, 1, &i, &val, INSERT_VALUES); i++; // Increment row in Petsc matrix } } - if(localmesh->lastX()) { - for(int x=localmesh->xend+1; xLocalNx; x++) { - for(int z=0;z < localmesh->LocalNz; z++) { + if (localmesh->lastX()) { + for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = f[x][z]; - VecSetValues( bs, 1, &i, &val, INSERT_VALUES ); + VecSetValues(bs, 1, &i, &val, INSERT_VALUES); i++; // Increment row in Petsc matrix } } diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx index 92a1ddb33b..416db62c92 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx @@ -29,8 +29,8 @@ #ifndef __PETSC_LAPLACE_H__ #define __PETSC_LAPLACE_H__ +#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" -#include "invert_laplace.hxx" #if not BOUT_HAS_PETSC @@ -41,12 +41,12 @@ RegisterUnavailableLaplace registerlaplacepetsc(LAPLACE_PETSC, #else -#include -#include -#include -#include #include -#include +#include +#include +#include +#include +#include // PETSc creates macros for MPI calls, which interfere with the MpiWrapper class #undef MPI_Allreduce @@ -72,10 +72,10 @@ public: Mesh* mesh_in = nullptr, Solver* solver = nullptr, Datafile* dump = nullptr); ~LaplacePetsc() { - KSPDestroy( &ksp ); - VecDestroy( &xs ); - VecDestroy( &bs ); - MatDestroy( &MatA ); + KSPDestroy(&ksp); + VecDestroy(&xs); + VecDestroy(&bs); + MatDestroy(&MatA); } using Laplacian::setCoefA; @@ -86,113 +86,134 @@ public: using Laplacian::setCoefEx; using Laplacian::setCoefEz; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; /*Acoefchanged = true;*/ - if(pcsolve) pcsolve->setCoefA(val); + if (pcsolve) { + pcsolve->setCoefA(val); + } } - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; C2 = val; issetC = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefC(val); + if (pcsolve) { + pcsolve->setCoefC(val); + } } - void setCoefC1(const Field2D &val) override { + void setCoefC1(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; issetC = true; } - void setCoefC2(const Field2D &val) override { + void setCoefC2(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2 = val; issetC = true; } - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; issetD = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefD(val); + if (pcsolve) { + pcsolve->setCoefD(val); + } } - void setCoefEx(const Field2D &val) override { + void setCoefEx(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ex = val; issetE = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefEx(val); + if (pcsolve) { + pcsolve->setCoefEx(val); + } } - void setCoefEz(const Field2D &val) override { + void setCoefEz(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ez = val; issetE = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefEz(val); + if (pcsolve) { + pcsolve->setCoefEz(val); + } } - void setCoefA(const Field3D &val) override { + void setCoefA(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; /*Acoefchanged = true;*/ - if(pcsolve) pcsolve->setCoefA(val); + if (pcsolve) { + pcsolve->setCoefA(val); + } } - void setCoefC(const Field3D &val) override { + void setCoefC(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; C2 = val; issetC = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefC(val); + if (pcsolve) { + pcsolve->setCoefC(val); + } } - void setCoefC1(const Field3D &val) override { + void setCoefC1(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; issetC = true; } - void setCoefC2(const Field3D &val) override { + void setCoefC2(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2 = val; issetC = true; } - void setCoefD(const Field3D &val) override { + void setCoefD(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; issetD = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefD(val); + if (pcsolve) { + pcsolve->setCoefD(val); + } } - void setCoefEx(const Field3D &val) override { + void setCoefEx(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ex = val; issetE = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefEx(val); + if (pcsolve) { + pcsolve->setCoefEx(val); + } } - void setCoefEz(const Field3D &val) override { + void setCoefEz(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ez = val; issetE = true; /*coefchanged = true;*/ - if(pcsolve) pcsolve->setCoefEz(val); + if (pcsolve) { + pcsolve->setCoefEz(val); + } } using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override; - FieldPerp solve(const FieldPerp &b, const FieldPerp &x0) override; + FieldPerp solve(const FieldPerp& b) override; + FieldPerp solve(const FieldPerp& b, const FieldPerp& x0) override; int precon(Vec x, Vec y); ///< Preconditioner function private: - void Element(int i, int x, int z, int xshift, int zshift, PetscScalar ele, Mat &MatA ); - void Coeffs( int x, int y, int z, BoutReal &A1, BoutReal &A2, BoutReal &A3, BoutReal &A4, BoutReal &A5 ); + void Element(int i, int x, int z, int xshift, int zshift, PetscScalar ele, Mat& MatA); + void Coeffs(int x, int y, int z, BoutReal& A1, BoutReal& A2, BoutReal& A3, BoutReal& A4, + BoutReal& A5); /* Ex and Ez * Additional 1st derivative terms to allow for solution field to be @@ -201,26 +222,27 @@ private: * See LaplacePetsc::Coeffs for details an potential pit falls */ Field3D A, C1, C2, D, Ex, Ez; -// Metrics are not constant in y-direction, so matrix always changes as you loop over the grid -// Hence using coefchanged switch to avoid recomputing the mmatrix is not a useful thing to do (unless maybe in a cylindrical machine, but not worth implementing just for that) -// bool coefchanged; // Set to true when C, D, Ex or Ez coefficients are changed -// bool Acoefchanged; // Set to true when A coefficient is changed + // Metrics are not constant in y-direction, so matrix always changes as you loop over the grid + // Hence using coefchanged switch to avoid recomputing the mmatrix is not a useful thing to do (unless maybe in a cylindrical machine, but not worth implementing just for that) + // bool coefchanged; // Set to true when C, D, Ex or Ez coefficients are changed + // bool Acoefchanged; // Set to true when A coefficient is changed bool issetD; bool issetC; bool issetE; - FieldPerp sol; // solution Field + FieldPerp sol; // solution Field // Istart is the first row of MatA owned by the process, Iend is 1 greater than the last row. int Istart, Iend; - int meshx, meshz, size, localN; // Mesh sizes, total size, no of points on this processor + int meshx, meshz, size, + localN; // Mesh sizes, total size, no of points on this processor MPI_Comm comm; Mat MatA; - Vec xs, bs; // Solution and RHS vectors + Vec xs, bs; // Solution and RHS vectors KSP ksp; - Options *opts; // Laplace Section Options Object + Options* opts; // Laplace Section Options Object std::string ksptype; ///< KSP solver type std::string pctype; ///< Preconditioner type @@ -232,22 +254,22 @@ private: // Convergence Parameters. Solution is considered converged if |r_k| < max( rtol * |b| , atol ) // where r_k = b - Ax_k. The solution is considered diverged if |r_k| > dtol * |b|. BoutReal rtol, atol, dtol; - int maxits; // Maximum number of iterations in solver. + int maxits; // Maximum number of iterations in solver. bool direct; //Use direct LU solver if true. bool fourth_order; PetscLib lib; - bool rightprec; // Right preconditioning + bool rightprec; // Right preconditioning std::unique_ptr pcsolve; // Laplacian solver for preconditioning - void vecToField(Vec x, FieldPerp &f); // Copy a vector into a fieldperp - void fieldToVec(const FieldPerp &f, Vec x); // Copy a fieldperp into a vector + void vecToField(Vec x, FieldPerp& f); // Copy a vector into a fieldperp + void fieldToVec(const FieldPerp& f, Vec x); // Copy a fieldperp into a vector - #if CHECK > 0 - int implemented_flags; - int implemented_boundary_flags; - #endif +#if CHECK > 0 + int implemented_flags; + int implemented_boundary_flags; +#endif }; #endif //BOUT_HAS_PETSC diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 210e41cbb3..646703e9a9 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -35,9 +35,9 @@ #include #include #include -#include -#include -#include +#include +#include +#include LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED(solver), Datafile* UNUSED(dump)) @@ -273,13 +273,19 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { Field3D solution = guess.toField(); localmesh->communicate(solution); if (solution.hasParallelSlices()) { - BOUT_FOR(i, indexer->getRegionLowerY()) { solution.ydown()[i] = solution[i]; } - BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup()[i] = solution[i]; } + BOUT_FOR (i, indexer->getRegionLowerY()) { + solution.ydown()[i] = solution[i]; + } + BOUT_FOR (i, indexer->getRegionUpperY()) { + solution.yup()[i] = solution[i]; + } for (int b = 1; b < localmesh->ystart; b++) { - BOUT_FOR(i, indexer->getRegionLowerY()) { + BOUT_FOR (i, indexer->getRegionLowerY()) { solution.ydown(b)[i.ym(b)] = solution[i]; } - BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup(b)[i.yp(b)] = solution[i]; } + BOUT_FOR (i, indexer->getRegionUpperY()) { + solution.yup(b)[i.yp(b)] = solution[i]; + } } } @@ -287,18 +293,20 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // from single boundary cell which is set by the solver // Note: RegionInnerX is the set of points just outside the domain // (in the first boundary cell) so one boundary cell is already set - BOUT_FOR(i, indexer->getRegionInnerX()) { + BOUT_FOR (i, indexer->getRegionInnerX()) { for (int b = 1; b < localmesh->xstart; b++) { - solution[i.xm(b)] = 3.*solution[i.xm(b-1)] - 3.*solution[i.xm(b-2)] + solution[i.xm(b-3)]; + solution[i.xm(b)] = + 3. * solution[i.xm(b - 1)] - 3. * solution[i.xm(b - 2)] + solution[i.xm(b - 3)]; } } // Set outer boundary cells by extrapolating // Note: RegionOuterX is the set of points just outside the domain // (in the first boundary cell) so one boundary cell is already set - BOUT_FOR(i, indexer->getRegionOuterX()) { + BOUT_FOR (i, indexer->getRegionOuterX()) { for (int b = 1; b < localmesh->xstart; b++) { - solution[i.xp(b)] = 3.*solution[i.xp(b-1)] - 3.*solution[i.xp(b-2)] + solution[i.xp(b-3)]; + solution[i.xp(b)] = + 3. * solution[i.xp(b - 1)] - 3. * solution[i.xp(b - 2)] + solution[i.xp(b - 3)]; } } @@ -432,9 +440,10 @@ void LaplacePetsc3dAmg::updateMatrix3D() { } C_df_dy /= 2 * coords->dy[l]; C_d2f_dy2 /= SQ(coords->dy[l]); - C_d2f_dxdy /= 4*coords->dx[l]; // NOTE: This value is not completed here. It needs to - // be divide by dx(i +/- 1, j, k) when using to set a - // matrix element + C_d2f_dxdy /= + 4 * coords->dx[l]; // NOTE: This value is not completed here. It needs to + // be divide by dx(i +/- 1, j, k) when using to set a + // matrix element C_d2f_dydz /= 4 * coords->dy[l] * coords->dz[l]; // The values stored in the y-boundary are already interpolated diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx index 0744013b9f..81c5893e20 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx @@ -30,25 +30,25 @@ class LaplacePetsc3dAmg; #ifndef __PETSC_LAPLACE_3DAMG_H__ #define __PETSC_LAPLACE_3DAMG_H__ +#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" -#include "invert_laplace.hxx" #if not BOUT_HAS_PETSC namespace { -RegisterUnavailableLaplace registerlaplacepetsc3damg(LAPLACE_PETSC3DAMG, - "BOUT++ was not configured with PETSc"); +RegisterUnavailableLaplace + registerlaplacepetsc3damg(LAPLACE_PETSC3DAMG, "BOUT++ was not configured with PETSc"); } #else -#include -#include -#include -#include #include -#include #include +#include +#include +#include +#include +#include #include class LaplacePetsc3dAmg; @@ -64,115 +64,112 @@ public: Datafile* dump = nullptr); ~LaplacePetsc3dAmg() override; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; updateRequired = true; } - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; C2 = val; updateRequired = issetC = true; } - void setCoefC1(const Field2D &val) override { + void setCoefC1(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; issetC = true; } - void setCoefC2(const Field2D &val) override { + void setCoefC2(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2 = val; updateRequired = issetC = true; } - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; updateRequired = issetD = true; } - void setCoefEx(const Field2D &val) override { + void setCoefEx(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ex = val; updateRequired = issetE = true; } - void setCoefEz(const Field2D &val) override { + void setCoefEz(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ez = val; updateRequired = issetE = true; } - void setCoefA(const Field3D &val) override { + void setCoefA(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; updateRequired = true; } - void setCoefC(const Field3D &val) override { + void setCoefC(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; C2 = val; updateRequired = issetC = true; } - void setCoefC1(const Field3D &val) override { + void setCoefC1(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C1 = val; updateRequired = issetC = true; } - void setCoefC2(const Field3D &val) override { + void setCoefC2(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C2 = val; updateRequired = issetC = true; } - void setCoefD(const Field3D &val) override { + void setCoefD(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; updateRequired = issetD = true; } - void setCoefEx(const Field3D &val) override { + void setCoefEx(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ex = val; updateRequired = issetE = true; } - void setCoefEz(const Field3D &val) override { + void setCoefEz(const Field3D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ez = val; updateRequired = issetE = true; } - // Return a reference to the matrix objects representing the Laplace // operator. These will be (re)construct if necessary. PetscMatrix& getMatrix3D(); IndexerPtr getIndexer() { return indexer; } - virtual Field2D solve(const Field2D &b) override; + virtual Field2D solve(const Field2D& b) override; - virtual Field3D solve(const Field3D &b) override { + virtual Field3D solve(const Field3D& b) override { Field3D zero = zeroFrom(b); return solve(b, zero); } - virtual Field3D solve(const Field3D &b_in, const Field3D &x0) override; - + virtual Field3D solve(const Field3D& b_in, const Field3D& x0) override; virtual FieldPerp solve(const FieldPerp& UNUSED(b)) override { throw BoutException("LaplacePetsc3DAmg cannot solve for FieldPerp"); } private: - // (Re)compute the values of the matrix representing the Laplacian operator void updateMatrix3D(); @@ -201,7 +198,7 @@ private: int lower_boundary_flags; int upper_boundary_flags; - Options *opts; // Laplace Section Options Object + Options* opts; // Laplace Section Options Object std::string ksptype; ///< KSP solver type std::string pctype; ///< Preconditioner type @@ -213,7 +210,7 @@ private: // Convergence Parameters. Solution is considered converged if |r_k| < max( rtol * |b| , atol ) // where r_k = b - Ax_k. The solution is considered diverged if |r_k| > dtol * |b|. BoutReal rtol, atol, dtol; - int maxits; // Maximum number of iterations in solver. + int maxits; // Maximum number of iterations in solver. bool direct; //Use direct LU solver if true. RangeIterator lowerY, upperY; @@ -226,7 +223,8 @@ private: // These are the implemented flags static constexpr int implemented_flags = INVERT_START_NEW, - implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_RHS; + implemented_boundary_flags = + INVERT_AC_GRAD + INVERT_SET + INVERT_RHS; }; #endif //BOUT_HAS_PETSC diff --git a/src/invert/laplace/impls/serial_band/serial_band.cxx b/src/invert/laplace/impls/serial_band/serial_band.cxx index f6639af013..1eaad7359f 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.cxx +++ b/src/invert/laplace/impls/serial_band/serial_band.cxx @@ -32,13 +32,13 @@ #include #include #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include -#include +#include //#define SECONDORDER // Define to use 2nd order differencing @@ -49,11 +49,14 @@ LaplaceSerialBand::LaplaceSerialBand(Options* opt, const CELL_LOC loc, Mesh* mes Ccoef.setLocation(location); Dcoef.setLocation(location); - if(!localmesh->firstX() || !localmesh->lastX()) + if (!localmesh->firstX() || !localmesh->lastX()) { throw BoutException("LaplaceSerialBand only works for localmesh->NXPE = 1"); - if(localmesh->periodicX) { - throw BoutException("LaplaceSerialBand does not work with periodicity in the x direction (localmesh->PeriodicX == true). Change boundary conditions or use serial-tri or cyclic solver instead"); - } + } + if (localmesh->periodicX) { + throw BoutException("LaplaceSerialBand does not work with periodicity in the x " + "direction (localmesh->PeriodicX == true). Change boundary " + "conditions or use serial-tri or cyclic solver instead"); + } // Allocate memory int ncz = localmesh->LocalNz; @@ -61,8 +64,8 @@ LaplaceSerialBand::LaplaceSerialBand(Options* opt, const CELL_LOC loc, Mesh* mes bk1d.reallocate(localmesh->LocalNx); //Initialise bk to 0 as we only visit 0<= kz <= maxmode in solve - for(int kz=maxmode+1; kz < ncz/2 + 1; kz++){ - for (int ix=0; ixLocalNx; ix++){ + for (int kz = maxmode + 1; kz < ncz / 2 + 1; kz++) { + for (int ix = 0; ix < localmesh->LocalNx; ix++) { bk(ix, kz) = 0.0; } } @@ -92,57 +95,60 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { int jy = b.getIndex(); int ncz = localmesh->LocalNz; - int ncx = localmesh->LocalNx-1; + int ncx = localmesh->LocalNx - 1; int xbndry = localmesh->xstart; // Width of the x boundary // If the flags to assign that only one guard cell should be used is set - if((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) + if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; + } BOUT_OMP(parallel for) - for(int ix=0;ixLocalNx;ix++) { + for (int ix = 0; ix < localmesh->LocalNx; ix++) { // for fixed ix,jy set a complex vector rho(z) - - if(((ix < xbndry) && (inner_boundary_flags & INVERT_SET)) || - ((ncx-ix < xbndry) && (outer_boundary_flags & INVERT_SET))) { + + if (((ix < xbndry) && (inner_boundary_flags & INVERT_SET)) + || ((ncx - ix < xbndry) && (outer_boundary_flags & INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0[ix], ncz, &bk(ix, 0)); - }else + } else { rfft(b[ix], ncz, &bk(ix, 0)); + } } - + int xstart, xend; // Get range for 4th order: Need at least 2 each side - if(xbndry > 1) { + if (xbndry > 1) { xstart = xbndry; - xend = ncx-xbndry; - }else { + xend = ncx - xbndry; + } else { xstart = 2; - xend = localmesh->LocalNx-2; + xend = localmesh->LocalNx - 2; } const auto kwave_fac = TWOPI / coords->zlength(); // wave number is 1/[rad] - for(int iz=0;iz<=maxmode;iz++) { + for (int iz = 0; iz <= maxmode; iz++) { // solve differential equation in x BoutReal coef1 = 0.0, coef2 = 0.0, coef3 = 0.0, coef4 = 0.0, coef5 = 0.0, coef6 = 0.0; ///////// PERFORM INVERSION ///////// - + // shift freqs according to FFT convention const Field2D kwave_ = iz * kwave_fac; // set bk1d - for(int ix=0;ixLocalNx;ix++) + for (int ix = 0; ix < localmesh->LocalNx; ix++) { bk1d[ix] = bk(ix, iz); + } // Fill in interior points - for(int ix=xstart;ix<=xend;ix++) { + for (int ix = xstart; ix <= xend; ix++) { BoutReal kwave = kwave_(ix, jy); -#ifdef SECONDORDER +#ifdef SECONDORDER // Use second-order differencing. Useful for testing the tridiagonal solver // with different boundary conditions - dcomplex a,b,c; + dcomplex a, b, c; tridagCoefs(ix, jy, iz, a, b, c, &Ccoef, &Dcoef); A(ix, 0) = 0.; @@ -152,39 +158,46 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ix, 4) = 0.; #else // Set coefficients - coef1 = coords->g11(ix,jy); // X 2nd derivative - coef2 = coords->g33(ix,jy); // Z 2nd derivative - coef3 = coords->g13(ix,jy); // X-Z mixed derivatives - coef4 = 0.0; // X 1st derivative - coef5 = 0.0; // Z 1st derivative - coef6 = Acoef(ix,jy); // Constant + coef1 = coords->g11(ix, jy); // X 2nd derivative + coef2 = coords->g33(ix, jy); // Z 2nd derivative + coef3 = coords->g13(ix, jy); // X-Z mixed derivatives + coef4 = 0.0; // X 1st derivative + coef5 = 0.0; // Z 1st derivative + coef6 = Acoef(ix, jy); // Constant // Multiply Delp2 component by a factor - coef1 *= Dcoef(ix,jy); - coef2 *= Dcoef(ix,jy); - coef3 *= Dcoef(ix,jy); + coef1 *= Dcoef(ix, jy); + coef2 *= Dcoef(ix, jy); + coef3 *= Dcoef(ix, jy); - if(all_terms) { - coef4 = coords->G1(ix,jy); - coef5 = coords->G3(ix,jy); + if (all_terms) { + coef4 = coords->G1(ix, jy); + coef5 = coords->G3(ix, jy); } - if(nonuniform) { + if (nonuniform) { // non-uniform localmesh correction - if((ix != 0) && (ix != ncx)) - coef4 += coords->g11(ix,jy)*( (1.0/coords->dx(ix+1,jy)) - (1.0/coords->dx(ix-1,jy)) )/(2.0*coords->dx(ix,jy)); + if ((ix != 0) && (ix != ncx)) { + coef4 += coords->g11(ix, jy) + * ((1.0 / coords->dx(ix + 1, jy)) - (1.0 / coords->dx(ix - 1, jy))) + / (2.0 * coords->dx(ix, jy)); + } } // A first order derivative term (1/c)\nabla_perp c\cdot\nabla_\perp x - - if((ix > 1) && (ix < (localmesh->LocalNx-2))) - coef4 += coords->g11(ix,jy) * (Ccoef(ix-2,jy) - 8.*Ccoef(ix-1,jy) + 8.*Ccoef(ix+1,jy) - Ccoef(ix+2,jy)) / (12.*coords->dx(ix,jy)*(Ccoef(ix,jy))); + + if ((ix > 1) && (ix < (localmesh->LocalNx - 2))) { + coef4 += coords->g11(ix, jy) + * (Ccoef(ix - 2, jy) - 8. * Ccoef(ix - 1, jy) + 8. * Ccoef(ix + 1, jy) + - Ccoef(ix + 2, jy)) + / (12. * coords->dx(ix, jy) * (Ccoef(ix, jy))); + } // Put into matrix - coef1 /= 12.* SQ(coords->dx(ix,jy)); + coef1 /= 12. * SQ(coords->dx(ix, jy)); coef2 *= SQ(kwave); - coef3 *= kwave / (12. * coords->dx(ix,jy)); - coef4 /= 12. * coords->dx(ix,jy); + coef3 *= kwave / (12. * coords->dx(ix, jy)); + coef4 /= 12. * coords->dx(ix, jy); coef5 *= kwave; A(ix, 0) = dcomplex(-coef1 + coef4, coef3); @@ -195,20 +208,20 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { #endif } - if(xbndry < 2) { + if (xbndry < 2) { // Use 2nd order near edges int ix = 1; auto kwave = kwave_(ix, jy); - coef1=coords->g11(ix,jy)/(SQ(coords->dx(ix,jy))); - coef2=coords->g33(ix,jy); - coef3= kwave * coords->g13(ix,jy)/(2. * coords->dx(ix,jy)); - + coef1 = coords->g11(ix, jy) / (SQ(coords->dx(ix, jy))); + coef2 = coords->g33(ix, jy); + coef3 = kwave * coords->g13(ix, jy) / (2. * coords->dx(ix, jy)); + // Multiply Delp2 component by a factor - coef1 *= Dcoef(ix,jy); - coef2 *= Dcoef(ix,jy); - coef3 *= Dcoef(ix,jy); + coef1 *= Dcoef(ix, jy); + coef2 *= Dcoef(ix, jy); + coef3 *= Dcoef(ix, jy); A(ix, 0) = 0.0; // Should never be used A(ix, 1) = dcomplex(coef1, -coef3); @@ -216,11 +229,11 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ix, 3) = dcomplex(coef1, coef3); A(ix, 4) = 0.0; - ix = ncx-1; + ix = ncx - 1; - coef1=coords->g11(ix,jy)/(SQ(coords->dx(ix,jy))); - coef2=coords->g33(ix,jy); - coef3= kwave * coords->g13(ix,jy)/(2. * coords->dx(ix,jy)); + coef1 = coords->g11(ix, jy) / (SQ(coords->dx(ix, jy))); + coef2 = coords->g33(ix, jy); + coef3 = kwave * coords->g13(ix, jy) / (2. * coords->dx(ix, jy)); A(ix, 0) = 0.0; A(ix, 1) = dcomplex(coef1, -coef3); @@ -231,13 +244,15 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { // Boundary conditions - for(int ix=0;ixg_11(ix, jy)) / coords->dx(ix, jy); A(ix, 3) = .5 / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); A(ix, 4) = 0.; } - - } - else if(inner_boundary_flags & INVERT_DC_GRAD) { + + } else if (inner_boundary_flags & INVERT_DC_GRAD) { // Zero gradient at inner boundary. 2nd-order accurate // Boundary at midpoint - for (int ix=0;ixg_22(ix, jy)); A(ix, 3) = 4. / sqrt(coords->g_22(ix + 1, jy)); A(ix, 4) = -1. / sqrt(coords->g_22(ix + 2, jy)); } - } - else if(inner_boundary_flags & INVERT_DC_GRADPARINV) { - for (int ix=0;ixg_22(ix, jy)); A(ix, 3) = 4. * sqrt(coords->g_22(ix + 1, jy)); A(ix, 4) = -sqrt(coords->g_22(ix + 2, jy)); } - } - else if (inner_boundary_flags & INVERT_DC_LAP) { - for (int ix=0;ixg11(ix,jy)/(12.* SQ(coords->dx(ix,jy))); - - coef2=coords->g33(ix,jy); - - coef3= kwave * coords->g13(ix,jy)/(2. * coords->dx(ix,jy)); - - coef4 = Acoef(ix,jy); - + coef1 = coords->g11(ix, jy) / (12. * SQ(coords->dx(ix, jy))); + + coef2 = coords->g33(ix, jy); + + coef3 = kwave * coords->g13(ix, jy) / (2. * coords->dx(ix, jy)); + + coef4 = Acoef(ix, jy); + // Combine 4th order at 1 with 2nd order at 0 A(1, 0) = 0.0; // Not used A(1, 1) = dcomplex( - (14. - SQ(coords->dx(0, jy) * kwave) * coords->g33(0, jy) / coords->g11(0, jy)) * - coef1, + (14. + - SQ(coords->dx(0, jy) * kwave) * coords->g33(0, jy) / coords->g11(0, jy)) + * coef1, -coef3); A(1, 2) = dcomplex(-29. * coef1 - SQ(kwave) * coef2 + coef4, 0.0); A(1, 3) = dcomplex(16. * coef1, coef3); A(1, 4) = dcomplex(-coef1, 0.0); - coef1=coords->g11(ix,jy)/(SQ(coords->dx(ix,jy))); - coef2=coords->g33(ix,jy); - coef3= kwave * coords->g13(ix,jy)/(2. * coords->dx(ix,jy)); + coef1 = coords->g11(ix, jy) / (SQ(coords->dx(ix, jy))); + coef2 = coords->g33(ix, jy); + coef3 = kwave * coords->g13(ix, jy) / (2. * coords->dx(ix, jy)); // Use 2nd order at 1 A(0, 0) = 0.0; // Should never be used @@ -352,42 +367,43 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(0, 3) = dcomplex(-2.0 * coef1 - SQ(kwave) * coef2 + coef4, 0.0); A(0, 4) = dcomplex(coef1, coef3); } - + // Outer boundary - if(outer_boundary_flags & INVERT_AC_GRAD) { + if (outer_boundary_flags & INVERT_AC_GRAD) { // Zero gradient at outer boundary - for (int ix=0;ixg11(ix,jy)/(12.* SQ(coords->dx(ix,jy))); - - coef2=coords->g33(ix,jy); + int ix = ncx - 1; + + coef1 = coords->g11(ix, jy) / (12. * SQ(coords->dx(ix, jy))); + + coef2 = coords->g33(ix, jy); auto kwave = kwave_(ix, jy); - coef3= kwave * coords->g13(ix,jy)/(2. * coords->dx(ix,jy)); - - coef4 = Acoef(ix,jy); - + coef3 = kwave * coords->g13(ix, jy) / (2. * coords->dx(ix, jy)); + + coef4 = Acoef(ix, jy); + // Combine 4th order at ncx-1 with 2nd order at ncx A(ix, 0) = dcomplex(-coef1, 0.0); A(ix, 1) = dcomplex(16. * coef1, -coef3); A(ix, 2) = dcomplex(-29. * coef1 - SQ(kwave) * coef2 + coef4, 0.0); - A(ix, 3) = dcomplex( - (14. - - SQ(coords->dx(ncx, jy) * kwave) * coords->g33(ncx, jy) / coords->g11(ncx, jy)) * - coef1, - coef3); + A(ix, 3) = dcomplex((14. + - SQ(coords->dx(ncx, jy) * kwave) * coords->g33(ncx, jy) + / coords->g11(ncx, jy)) + * coef1, + coef3); A(ix, 4) = 0.0; // Not used - coef1=coords->g11(ix,jy)/(SQ(coords->dx(ix,jy))); - coef2=coords->g33(ix,jy); - coef3= kwave * coords->g13(ix,jy)/(2. * coords->dx(ix,jy)); + coef1 = coords->g11(ix, jy) / (SQ(coords->dx(ix, jy))); + coef2 = coords->g33(ix, jy); + coef3 = kwave * coords->g13(ix, jy) / (2. * coords->dx(ix, jy)); // Use 2nd order at ncx - 1 A(ncx, 0) = dcomplex(coef1, -coef3); @@ -397,32 +413,36 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ncx, 4) = 0.0; } } - + // Perform inversion cband_solve(A, localmesh->LocalNx, 2, 2, bk1d); - if((global_flags & INVERT_KX_ZERO) && (iz == 0)) { + if ((global_flags & INVERT_KX_ZERO) && (iz == 0)) { // Set the Kx = 0, n = 0 component to zero. For now just subtract // Should do in the inversion e.g. Sherman-Morrison formula - + dcomplex offset(0.0); - for(int ix=0;ix<=ncx;ix++) + for (int ix = 0; ix <= ncx; ix++) { offset += bk1d[ix]; + } offset /= static_cast(ncx + 1); - for(int ix=0;ix<=ncx;ix++) + for (int ix = 0; ix <= ncx; ix++) { bk1d[ix] -= offset; + } } - + // Fill xk - for (int ix=0; ix<=ncx; ix++) + for (int ix = 0; ix <= ncx; ix++) { xk(ix, iz) = bk1d[ix]; + } } - + // Done inversion, transform back - for(int ix=0; ix<=ncx; ix++){ - if(global_flags & INVERT_ZERO_DC) + for (int ix = 0; ix <= ncx; ix++) { + if (global_flags & INVERT_ZERO_DC) { xk(ix, 0) = 0.0; + } irfft(&xk(ix, 0), ncz, x[ix]); } diff --git a/src/invert/laplace/impls/serial_band/serial_band.hxx b/src/invert/laplace/impls/serial_band/serial_band.hxx index a5298d7b5e..1eb35322ce 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.hxx +++ b/src/invert/laplace/impls/serial_band/serial_band.hxx @@ -29,7 +29,7 @@ class LaplaceSerialBand; #ifndef __SERIAL_BAND_H__ #define __SERIAL_BAND_H__ -#include "invert_laplace.hxx" +#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" #if BOUT_USE_METRIC_3D @@ -41,9 +41,9 @@ RegisterUnavailableLaplace #else -#include -#include -#include +#include +#include +#include namespace { RegisterLaplace registerlaplaceserialband(LAPLACE_BAND); @@ -55,40 +55,41 @@ public: Mesh* mesh_in = nullptr, Solver* solver = nullptr, Datafile* dump = nullptr); ~LaplaceSerialBand(){}; - + using Laplacian::setCoefA; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Acoef = val; } using Laplacian::setCoefC; - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ccoef = val; } using Laplacian::setCoefD; - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Dcoef = val; } using Laplacian::setCoefEx; - void setCoefEx(const Field2D &UNUSED(val)) override { + void setCoefEx(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceSerialBand does not have Ex coefficient"); } using Laplacian::setCoefEz; - void setCoefEz(const Field2D &UNUSED(val)) override { + void setCoefEz(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceSerialBand does not have Ez coefficient"); } using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override; - FieldPerp solve(const FieldPerp &b, const FieldPerp &x0) override; + FieldPerp solve(const FieldPerp& b) override; + FieldPerp solve(const FieldPerp& b, const FieldPerp& x0) override; + private: Field2D Acoef, Ccoef, Dcoef; - + Matrix bk, xk, A; Array bk1d, xk1d; }; diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx index 7b852f1243..f61223bb50 100644 --- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx +++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx @@ -24,19 +24,19 @@ * **************************************************************************/ -#include "globals.hxx" #include "serial_tri.hxx" +#include "bout/globals.hxx" -#include -#include -#include -#include -#include #include +#include #include +#include #include +#include +#include +#include -#include +#include LaplaceSerialTri::LaplaceSerialTri(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED(solver), Datafile* UNUSED(dump)) @@ -45,7 +45,7 @@ LaplaceSerialTri::LaplaceSerialTri(Options* opt, CELL_LOC loc, Mesh* mesh_in, C.setLocation(location); D.setLocation(location); - if(!localmesh->firstX() || !localmesh->lastX()) { + if (!localmesh->firstX() || !localmesh->lastX()) { throw BoutException("LaplaceSerialTri only works for localmesh->NXPE = 1"); } } @@ -88,16 +88,18 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { // Setting the width of the boundary. // NOTE: The default is a width of 2 guard cells - int inbndry = localmesh->xstart, outbndry=localmesh->xstart; + int inbndry = localmesh->xstart, outbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if (inner_boundary_flags & INVERT_BNDRY_ONE) + if (inner_boundary_flags & INVERT_BNDRY_ONE) { inbndry = 1; - if (outer_boundary_flags & INVERT_BNDRY_ONE) + } + if (outer_boundary_flags & INVERT_BNDRY_ONE) { outbndry = 1; + } /* Allocation fo * bk = The fourier transformed of b, where b is one of the inputs in @@ -138,8 +140,8 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { * If the INVERT_SET flag is set (meaning that x0 will be used to set the * bounadry values), */ - if (((ix < inbndry) && (inner_boundary_flags & INVERT_SET)) || - ((ncx - 1 - ix < outbndry) && (outer_boundary_flags & INVERT_SET))) { + if (((ix < inbndry) && (inner_boundary_flags & INVERT_SET)) + || ((ncx - 1 - ix < outbndry) && (outer_boundary_flags & INVERT_SET))) { // Use the values in x0 in the boundary // x0 is the input @@ -226,15 +228,18 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { // Done inversion, transform back for (int ix = 0; ix < ncx; ix++) { - if(global_flags & INVERT_ZERO_DC) + if (global_flags & INVERT_ZERO_DC) { xk(ix, 0) = 0.0; + } irfft(&xk(ix, 0), ncz, x[ix]); #if CHECK > 2 - for(int kz=0;kz -#include -#include +#include +#include +#include namespace { RegisterLaplace registerlaplaceserialtri(LAPLACE_TRI); @@ -45,35 +45,36 @@ public: ~LaplaceSerialTri(){}; using Laplacian::setCoefA; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); A = val; } using Laplacian::setCoefC; - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); C = val; } using Laplacian::setCoefD; - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); D = val; } using Laplacian::setCoefEx; - void setCoefEx(const Field2D &UNUSED(val)) override { + void setCoefEx(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceSerialTri does not have Ex coefficient"); } using Laplacian::setCoefEz; - void setCoefEz(const Field2D &UNUSED(val)) override { + void setCoefEz(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceSerialTri does not have Ez coefficient"); } using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override; - FieldPerp solve(const FieldPerp &b, const FieldPerp &x0) override; + FieldPerp solve(const FieldPerp& b) override; + FieldPerp solve(const FieldPerp& b, const FieldPerp& x0) override; + private: // The coefficents in // D*grad_perp^2(x) + (1/C)*(grad_perp(C))*grad_perp(x) + A*x = b diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index d3bfbba39a..975655ca81 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -35,10 +35,10 @@ #include #include #include -#include -#include -#include -#include +#include +#include +#include +#include #include "spt.hxx" @@ -49,21 +49,25 @@ LaplaceSPT::LaplaceSPT(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Ccoef.setLocation(location); Dcoef.setLocation(location); - if(localmesh->periodicX) { - throw BoutException("LaplaceSPT does not work with periodicity in the x direction (localmesh->PeriodicX == true). Change boundary conditions or use serial-tri or cyclic solver instead"); - } - + if (localmesh->periodicX) { + throw BoutException("LaplaceSPT does not work with periodicity in the x direction " + "(localmesh->PeriodicX == true). Change boundary conditions or " + "use serial-tri or cyclic solver instead"); + } + // Get start and end indices ys = localmesh->ystart; ye = localmesh->yend; - if(localmesh->hasBndryLowerY() && include_yguards) + if (localmesh->hasBndryLowerY() && include_yguards) { ys = 0; // Mesh contains a lower boundary - if(localmesh->hasBndryUpperY() && include_yguards) - ye = localmesh->LocalNy-1; // Contains upper boundary - + } + if (localmesh->hasBndryUpperY() && include_yguards) { + ye = localmesh->LocalNy - 1; // Contains upper boundary + } + alldata = new SPT_data[ye - ys + 1]; alldata -= ys; // Re-number indices to start at ys - for(int jy=ys;jy<=ye;jy++) { + for (int jy = ys; jy <= ye; jy++) { alldata[jy].comm_tag = SPT_DATA + jy; // Give each one a different tag } @@ -85,33 +89,39 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) { ASSERT1(x0.getLocation() == location); FieldPerp x{emptyFrom(b)}; - - if( (inner_boundary_flags & INVERT_SET) || (outer_boundary_flags & INVERT_SET) ) { + + if ((inner_boundary_flags & INVERT_SET) || (outer_boundary_flags & INVERT_SET)) { FieldPerp bs = copy(b); - + int xbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) + if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; - if((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) { + } + if ((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) { // Copy x0 inner boundary into bs - for(int ix=0;ixLocalNz;iz++) + for (int ix = 0; ix < xbndry; ix++) { + for (int iz = 0; iz < localmesh->LocalNz; iz++) { bs[ix][iz] = x0[ix][iz]; + } + } } - if((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) { + if ((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) { // Copy x0 outer boundary into bs - for(int ix=localmesh->LocalNx-1;ix>=localmesh->LocalNx-xbndry;ix--) - for(int iz=0;izLocalNz;iz++) + for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) { + for (int iz = 0; iz < localmesh->LocalNz; iz++) { bs[ix][iz] = x0[ix][iz]; + } + } } start(bs, slicedata); - }else + } else { start(b, slicedata); + } finish(slicedata, x); checkData(x); - + return x; } @@ -128,65 +138,74 @@ Field3D LaplaceSPT::solve(const Field3D& b) { Timer timer("invert"); Field3D x{emptyFrom(b)}; - - for(int jy=ys; jy <= ye; jy++) { + + for (int jy = ys; jy <= ye; jy++) { // And start another one going start(sliceXZ(b, jy), alldata[jy]); - + // Move each calculation along one processor - for(int jy2=ys; jy2 < jy; jy2++) + for (int jy2 = ys; jy2 < jy; jy2++) { next(alldata[jy2]); + } } - + bool running = true; do { // Move each calculation along until the last one is finished - for(int jy=ys; jy <= ye; jy++) + for (int jy = ys; jy <= ye; jy++) { running = next(alldata[jy]) == 0; - }while(running); + } + } while (running); FieldPerp xperp(localmesh); xperp.setLocation(location); xperp.allocate(); - + // All calculations finished. Get result - for(int jy=ys; jy <= ye; jy++) { + for (int jy = ys; jy <= ye; jy++) { finish(alldata[jy], xperp); x = xperp; } - + return x; } Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { ASSERT1(localmesh == b.getMesh() && localmesh == x0.getMesh()); - if( ((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) || - ((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) ) { + if (((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) + || ((outer_boundary_flags & INVERT_SET) && localmesh->lastX())) { Field3D bs = copy(b); - + int xbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) + if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; - - if((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) { + } + + if ((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) { // Copy x0 inner boundary into bs - for(int ix=0;ixLocalNy;iy++) - for(int iz=0;izLocalNz;iz++) - bs(ix,iy,iz) = x0(ix,iy,iz); + for (int ix = 0; ix < xbndry; ix++) { + for (int iy = 0; iy < localmesh->LocalNy; iy++) { + for (int iz = 0; iz < localmesh->LocalNz; iz++) { + bs(ix, iy, iz) = x0(ix, iy, iz); + } + } + } } - if((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) { + if ((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) { // Copy x0 outer boundary into bs - for(int ix=localmesh->LocalNx-1;ix>=localmesh->LocalNx-xbndry;ix--) - for(int iy=0;iyLocalNy;iy++) - for(int iz=0;izLocalNz;iz++) - bs(ix,iy,iz) = x0(ix,iy,iz); + for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) { + for (int iy = 0; iy < localmesh->LocalNy; iy++) { + for (int iz = 0; iz < localmesh->LocalNz; iz++) { + bs(ix, iy, iz) = x0(ix, iy, iz); + } + } + } } return solve(bs); } - + return solve(b); } @@ -207,31 +226,31 @@ Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { * @param[inout] um * @param[in] start */ -void LaplaceSPT::tridagForward(dcomplex *a, dcomplex *b, dcomplex *c, - dcomplex *r, dcomplex *u, int n, - dcomplex *gam, - dcomplex &bet, dcomplex &um, bool start) { +void LaplaceSPT::tridagForward(dcomplex* a, dcomplex* b, dcomplex* c, dcomplex* r, + dcomplex* u, int n, dcomplex* gam, dcomplex& bet, + dcomplex& um, bool start) { int j; - - if(start) { + + if (start) { bet = b[0]; u[0] = r[0] / bet; - }else { + } else { gam[0] = c[-1] / bet; // NOTE: ASSUMES C NOT CHANGING - bet = b[0] - a[0]*gam[0]; - u[0] = (r[0]-a[0]*um)/bet; + bet = b[0] - a[0] * gam[0]; + u[0] = (r[0] - a[0] * um) / bet; } - - for(j=1;jPE_XIND + 1, and returned to localmesh->PE_XIND - 1 * @param[inout] up u from processor localmesh->PE_XIND + 1, and returned to localmesh->PE_XIND - 1 */ -void LaplaceSPT::tridagBack(dcomplex *u, int n, - dcomplex *gam, dcomplex &gp, dcomplex &up) { +void LaplaceSPT::tridagBack(dcomplex* u, int n, dcomplex* gam, dcomplex& gp, + dcomplex& up) { int j; - u[n-1] = u[n-1] - gp*up; + u[n - 1] = u[n - 1] - gp * up; - for(j=n-2;j>=0;j--) { - u[j] = u[j]-gam[j+1]*u[j+1]; + for (j = n - 2; j >= 0; j--) { + u[j] = u[j] - gam[j + 1] * u[j + 1]; } gp = gam[0]; up = u[0]; @@ -273,25 +292,30 @@ void LaplaceSPT::tridagBack(dcomplex *u, int n, /// /// @param[in] b RHS values (Ax = b) /// @param[out] data Structure containing data needed for second half of inversion -int LaplaceSPT::start(const FieldPerp &b, SPT_data &data) { - if(localmesh->firstX() && localmesh->lastX()) +int LaplaceSPT::start(const FieldPerp& b, SPT_data& data) { + if (localmesh->firstX() && localmesh->lastX()) { throw BoutException("Error: SPT method only works for localmesh->NXPE > 1\n"); + } ASSERT1(b.getLocation() == location); data.jy = b.getIndex(); - int mm = localmesh->LocalNz/2 + 1; - data.allocate(mm, localmesh->LocalNx); // Make sure data is allocated. Already allocated -> does nothing - + int mm = localmesh->LocalNz / 2 + 1; + data.allocate( + mm, + localmesh + ->LocalNx); // Make sure data is allocated. Already allocated -> does nothing + /// Take FFTs of data int ncz = localmesh->LocalNz; - - for(int ix=0; ix < localmesh->LocalNx; ix++) { + + for (int ix = 0; ix < localmesh->LocalNx; ix++) { rfft(b[ix], ncz, std::begin(dc1d)); - for(int kz = 0; kz <= maxmode; kz++) + for (int kz = 0; kz <= maxmode; kz++) { data.bk(kz, ix) = dc1d[kz]; + } } BoutReal kwaveFactor = 2.0 * PI / getUniform(coords->zlength()); @@ -305,35 +329,36 @@ int LaplaceSPT::start(const FieldPerp &b, SPT_data &data) { data.proc = 0; //< Starts at processor 0 data.dir = 1; - - if(localmesh->firstX()) { + + if (localmesh->firstX()) { BOUT_OMP(parallel for) - for(int kz = 0; kz <= maxmode; kz++) { + for (int kz = 0; kz <= maxmode; kz++) { dcomplex bet, u0; // Start tridiagonal solve tridagForward(&data.avec(kz, 0), &data.bvec(kz, 0), &data.cvec(kz, 0), - &data.bk(kz, 0), &data.xk(kz, 0), localmesh->xend + 1, &data.gam(kz, 0), - bet, u0, true); + &data.bk(kz, 0), &data.xk(kz, 0), localmesh->xend + 1, + &data.gam(kz, 0), bet, u0, true); // Load intermediate values into buffers - data.buffer[4*kz] = bet.real(); - data.buffer[4*kz + 1] = bet.imag(); - data.buffer[4*kz + 2] = u0.real(); - data.buffer[4*kz + 3] = u0.imag(); + data.buffer[4 * kz] = bet.real(); + data.buffer[4 * kz + 1] = bet.imag(); + data.buffer[4 * kz + 2] = u0.real(); + data.buffer[4 * kz + 3] = u0.imag(); } - + // Send data localmesh->sendXOut(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag); - }else if(localmesh->PE_XIND == 1) { + } else if (localmesh->PE_XIND == 1) { // Post a receive data.recv_handle = localmesh->irecvXIn(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag); } - + data.proc++; // Now moved onto the next processor - if(localmesh->NXPE == 2) + if (localmesh->NXPE == 2) { data.dir = -1; // Special case. Otherwise reversal handled in spt_continue - + } + return 0; } @@ -343,114 +368,122 @@ int LaplaceSPT::start(const FieldPerp &b, SPT_data &data) { @param[inout] data Structure which keeps track of the calculation */ -int LaplaceSPT::next(SPT_data &data) { - if(data.proc < 0) // Already finished +int LaplaceSPT::next(SPT_data& data) { + if (data.proc < 0) { // Already finished return 1; - - if(localmesh->PE_XIND == data.proc) { + } + + if (localmesh->PE_XIND == data.proc) { /// This processor's turn to do inversion // Wait for data to arrive localmesh->wait(data.recv_handle); - if(localmesh->lastX()) { + if (localmesh->lastX()) { // Last processor, turn-around - + BOUT_OMP(parallel for) - for(int kz = 0; kz <= maxmode; kz++) { + for (int kz = 0; kz <= maxmode; kz++) { dcomplex bet, u0; dcomplex gp, up; - bet = dcomplex(data.buffer[4*kz], data.buffer[4*kz + 1]); - u0 = dcomplex(data.buffer[4*kz + 2], data.buffer[4*kz + 3]); - tridagForward(&data.avec(kz, localmesh->xstart), &data.bvec(kz, localmesh->xstart), + bet = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); + u0 = dcomplex(data.buffer[4 * kz + 2], data.buffer[4 * kz + 3]); + tridagForward(&data.avec(kz, localmesh->xstart), + &data.bvec(kz, localmesh->xstart), &data.cvec(kz, localmesh->xstart), &data.bk(kz, localmesh->xstart), &data.xk(kz, localmesh->xstart), localmesh->xend + 1, &data.gam(kz, localmesh->xstart), bet, u0); // Back-substitute - gp = 0.0; - up = 0.0; - tridagBack(&data.xk(kz, localmesh->xstart), localmesh->LocalNx - localmesh->xstart, + gp = 0.0; + up = 0.0; + tridagBack(&data.xk(kz, localmesh->xstart), + localmesh->LocalNx - localmesh->xstart, &data.gam(kz, localmesh->xstart), gp, up); - data.buffer[4*kz] = gp.real(); - data.buffer[4*kz + 1] = gp.imag(); - data.buffer[4*kz + 2] = up.real(); - data.buffer[4*kz + 3] = up.imag(); + data.buffer[4 * kz] = gp.real(); + data.buffer[4 * kz + 1] = gp.imag(); + data.buffer[4 * kz + 2] = up.real(); + data.buffer[4 * kz + 3] = up.imag(); } - }else if(data.dir > 0) { + } else if (data.dir > 0) { // In the middle of X, forward direction BOUT_OMP(parallel for) - for(int kz = 0; kz <= maxmode; kz++) { - dcomplex bet, u0; - bet = dcomplex(data.buffer[4*kz], data.buffer[4*kz + 1]); - u0 = dcomplex(data.buffer[4*kz + 2], data.buffer[4*kz + 3]); - tridagForward(&data.avec(kz, localmesh->xstart), &data.bvec(kz, localmesh->xstart), - &data.cvec(kz, localmesh->xstart), &data.bk(kz, localmesh->xstart), - &data.xk(kz, localmesh->xstart), localmesh->xend - localmesh->xstart + 1, - &data.gam(kz, localmesh->xstart), bet, u0); + for (int kz = 0; kz <= maxmode; kz++) { + dcomplex bet, u0; + bet = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); + u0 = dcomplex(data.buffer[4 * kz + 2], data.buffer[4 * kz + 3]); + tridagForward( + &data.avec(kz, localmesh->xstart), &data.bvec(kz, localmesh->xstart), + &data.cvec(kz, localmesh->xstart), &data.bk(kz, localmesh->xstart), + &data.xk(kz, localmesh->xstart), localmesh->xend - localmesh->xstart + 1, + &data.gam(kz, localmesh->xstart), bet, u0); // Load intermediate values into buffers - data.buffer[4*kz] = bet.real(); - data.buffer[4*kz + 1] = bet.imag(); - data.buffer[4*kz + 2] = u0.real(); - data.buffer[4*kz + 3] = u0.imag(); + data.buffer[4 * kz] = bet.real(); + data.buffer[4 * kz + 1] = bet.imag(); + data.buffer[4 * kz + 2] = u0.real(); + data.buffer[4 * kz + 3] = u0.imag(); } - - }else if(localmesh->firstX()) { + + } else if (localmesh->firstX()) { // Back to the start BOUT_OMP(parallel for) - for(int kz = 0; kz <= maxmode; kz++) { - dcomplex gp, up; - gp = dcomplex(data.buffer[4*kz], data.buffer[4*kz + 1]); - up = dcomplex(data.buffer[4*kz + 2], data.buffer[4*kz + 3]); +for (int kz = 0; kz <= maxmode; kz++) { + dcomplex gp, up; + gp = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); + up = dcomplex(data.buffer[4 * kz + 2], data.buffer[4 * kz + 3]); - tridagBack(&data.xk(kz, 0), localmesh->xend + 1, &data.gam(kz, 0), gp, up); - } + tridagBack(&data.xk(kz, 0), localmesh->xend + 1, &data.gam(kz, 0), gp, up); +} - }else { - // Middle of X, back-substitution stage + } else { +// Middle of X, back-substitution stage BOUT_OMP(parallel for) - for(int kz = 0; kz <= maxmode; kz++) { - dcomplex gp = dcomplex(data.buffer[4*kz], data.buffer[4*kz + 1]); - dcomplex up = dcomplex(data.buffer[4*kz + 2], data.buffer[4*kz + 3]); + for (int kz = 0; kz <= maxmode; kz++) { + dcomplex gp = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); + dcomplex up = dcomplex(data.buffer[4 * kz + 2], data.buffer[4 * kz + 3]); - tridagBack(&data.xk(kz, localmesh->xstart), localmesh->xend - localmesh->xstart + 1, + tridagBack(&data.xk(kz, localmesh->xstart), + localmesh->xend - localmesh->xstart + 1, &data.gam(kz, localmesh->xstart), gp, up); - data.buffer[4*kz] = gp.real(); - data.buffer[4*kz + 1] = gp.imag(); - data.buffer[4*kz + 2] = up.real(); - data.buffer[4*kz + 3] = up.imag(); + data.buffer[4 * kz] = gp.real(); + data.buffer[4 * kz + 1] = gp.imag(); + data.buffer[4 * kz + 2] = up.real(); + data.buffer[4 * kz + 3] = up.imag(); } } - if(localmesh->PE_XIND != 0) { // If not finished yet + if (localmesh->PE_XIND != 0) { // If not finished yet /// Send data - - if(data.dir > 0) { + + if (data.dir > 0) { localmesh->sendXOut(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag); - }else + } else { localmesh->sendXIn(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag); + } } - }else if(localmesh->PE_XIND == data.proc + data.dir) { + } else if (localmesh->PE_XIND == data.proc + data.dir) { // This processor is next, post receive - - if(data.dir > 0) { + + if (data.dir > 0) { data.recv_handle = localmesh->irecvXIn(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag); - }else + } else { data.recv_handle = localmesh->irecvXOut(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag); + } } - + data.proc += data.dir; - - if(data.proc == localmesh->NXPE-1) + + if (data.proc == localmesh->NXPE - 1) { data.dir = -1; // Reverses direction at the end + } return 0; } @@ -459,8 +492,8 @@ BOUT_OMP(parallel for) /// /// @param[inout] data Structure keeping track of calculation /// @param[out] x The result -void LaplaceSPT::finish(SPT_data &data, FieldPerp &x) { - int ncx = localmesh->LocalNx-1; +void LaplaceSPT::finish(SPT_data& data, FieldPerp& x) { + int ncx = localmesh->LocalNx - 1; int ncz = localmesh->LocalNz; ASSERT1(x.getLocation() == location); @@ -469,36 +502,41 @@ void LaplaceSPT::finish(SPT_data &data, FieldPerp &x) { x.setIndex(data.jy); // Make sure calculation has finished - while(next(data) == 0) {} + while (next(data) == 0) { + } // Have result in Fourier space. Convert back to real space - - for(int ix=0; ix<=ncx; ix++){ - - for(int kz = 0; kz<= maxmode; kz++) { + + for (int ix = 0; ix <= ncx; ix++) { + + for (int kz = 0; kz <= maxmode; kz++) { dc1d[kz] = data.xk(kz, ix); } - for(int kz = maxmode + 1; kz <= ncz/2; kz++) + for (int kz = maxmode + 1; kz <= ncz / 2; kz++) { dc1d[kz] = 0.0; + } - if(global_flags & INVERT_ZERO_DC) + if (global_flags & INVERT_ZERO_DC) { dc1d[0] = 0.0; + } irfft(std::begin(dc1d), ncz, x[ix]); } - if(!localmesh->firstX()) { + if (!localmesh->firstX()) { // Set left boundary to zero (Prevent unassigned values in corners) - for(int ix=0; ixxstart; ix++){ - for(int kz=0;kzLocalNz;kz++) - x(ix,kz) = 0.0; + for (int ix = 0; ix < localmesh->xstart; ix++) { + for (int kz = 0; kz < localmesh->LocalNz; kz++) { + x(ix, kz) = 0.0; + } } } - if(!localmesh->lastX()) { + if (!localmesh->lastX()) { // Same for right boundary - for(int ix=localmesh->xend+1; ixLocalNx; ix++){ - for(int kz=0;kzLocalNz;kz++) - x(ix,kz) = 0.0; + for (int ix = localmesh->xend + 1; ix < localmesh->LocalNx; ix++) { + for (int kz = 0; kz < localmesh->LocalNz; kz++) { + x(ix, kz) = 0.0; + } } } } @@ -519,4 +557,3 @@ void LaplaceSPT::SPT_data::allocate(int mm, int nx) { buffer.reallocate(4 * mm); } - diff --git a/src/invert/laplace/impls/spt/spt.hxx b/src/invert/laplace/impls/spt/spt.hxx index 2ddc28633d..c000e1991b 100644 --- a/src/invert/laplace/impls/spt/spt.hxx +++ b/src/invert/laplace/impls/spt/spt.hxx @@ -42,10 +42,10 @@ class LaplaceSPT; #define __SPT_H__ #include -#include -#include -#include -#include +#include +#include +#include +#include /// Simple parallelisation of the Thomas tridiagonal solver algorithm (serial code) /*! @@ -70,43 +70,44 @@ public: LaplaceSPT(Options* opt = nullptr, const CELL_LOC = CELL_CENTRE, Mesh* mesh_in = nullptr, Solver* solver = nullptr, Datafile* dump = nullptr); ~LaplaceSPT(); - + using Laplacian::setCoefA; - void setCoefA(const Field2D &val) override { + void setCoefA(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Acoef = val; } using Laplacian::setCoefC; - void setCoefC(const Field2D &val) override { + void setCoefC(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Ccoef = val; } using Laplacian::setCoefD; - void setCoefD(const Field2D &val) override { + void setCoefD(const Field2D& val) override { ASSERT1(val.getLocation() == location); ASSERT1(localmesh == val.getMesh()); Dcoef = val; } using Laplacian::setCoefEx; - void setCoefEx(const Field2D &UNUSED(val)) override { + void setCoefEx(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceSPT does not have Ex coefficient"); } using Laplacian::setCoefEz; - void setCoefEz(const Field2D &UNUSED(val)) override { + void setCoefEz(const Field2D& UNUSED(val)) override { throw BoutException("LaplaceSPT does not have Ez coefficient"); } using Laplacian::solve; - FieldPerp solve(const FieldPerp &b) override; - FieldPerp solve(const FieldPerp &b, const FieldPerp &x0) override; - - Field3D solve(const Field3D &b) override; - Field3D solve(const Field3D &b, const Field3D &x0) override; + FieldPerp solve(const FieldPerp& b) override; + FieldPerp solve(const FieldPerp& b, const FieldPerp& x0) override; + + Field3D solve(const Field3D& b) override; + Field3D solve(const Field3D& b, const Field3D& x0) override; + private: enum { SPT_DATA = 1123 }; ///< 'magic' number for SPT MPI messages - + Field2D Acoef, Ccoef, Dcoef; /// Data structure for SPT algorithm @@ -140,19 +141,16 @@ private: Array dc1d; ///< 1D in Z for taking FFTs - void tridagForward(dcomplex *a, dcomplex *b, dcomplex *c, - dcomplex *r, dcomplex *u, int n, - dcomplex *gam, - dcomplex &bet, dcomplex &um, bool start=false); - void tridagBack(dcomplex *u, int n, - dcomplex *gam, dcomplex &gp, dcomplex &up); - - int start(const FieldPerp &b, SPT_data &data); - - int next(SPT_data &data); - - void finish(SPT_data &data, FieldPerp &x); + void tridagForward(dcomplex* a, dcomplex* b, dcomplex* c, dcomplex* r, dcomplex* u, + int n, dcomplex* gam, dcomplex& bet, dcomplex& um, + bool start = false); + void tridagBack(dcomplex* u, int n, dcomplex* gam, dcomplex& gp, dcomplex& up); + + int start(const FieldPerp& b, SPT_data& data); + + int next(SPT_data& data); + void finish(SPT_data& data, FieldPerp& x); }; namespace { diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index cadacb37a0..43d540a261 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -36,15 +36,15 @@ #include #include #include -#include -#include +#include +#include #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include // Implementations: #include "impls/cyclic/cyclic_laplace.hxx" @@ -142,14 +142,13 @@ Laplacian::Laplacian(Options* options, const CELL_LOC loc, Mesh* mesh_in, std::unique_ptr Laplacian::instance = nullptr; Laplacian* Laplacian::defaultInstance() { - if (instance == nullptr) + if (instance == nullptr) { instance = create(); + } return instance.get(); } -void Laplacian::cleanup() { - instance.reset(); -} +void Laplacian::cleanup() { instance.reset(); } /********************************************************************************** * Solve routines @@ -164,15 +163,18 @@ Field3D Laplacian::solve(const Field3D& b) { Timer timer("invert"); int ys = localmesh->ystart, ye = localmesh->yend; - if(localmesh->hasBndryLowerY()) { - if (include_yguards) + if (localmesh->hasBndryLowerY()) { + if (include_yguards) { ys = 0; // Mesh contains a lower boundary and we are solving in the guard cells + } ys += extra_yguards_lower; } - if(localmesh->hasBndryUpperY()) { - if (include_yguards) - ye = localmesh->LocalNy-1; // Contains upper boundary and we are solving in the guard cells + if (localmesh->hasBndryUpperY()) { + if (include_yguards) { + ye = localmesh->LocalNy + - 1; // Contains upper boundary and we are solving in the guard cells + } ye -= extra_yguards_upper; } @@ -181,10 +183,10 @@ Field3D Laplacian::solve(const Field3D& b) { int status = 0; try { - for(int jy=ys; jy <= ye; jy++) { + for (int jy = ys; jy <= ye; jy++) { // 1. Slice b (i.e. take a X-Z plane out of the field) // 2. Send it to the solver of the implementation (determined during creation) - x = solve(sliceXZ(b,jy)); + x = solve(sliceXZ(b, jy)); } } catch (const BoutIterationFail&) { status = 1; @@ -224,19 +226,21 @@ Field3D Laplacian::solve(const Field3D& b, const Field3D& x0) { // Setting the start and end range of the y-slices int ys = localmesh->ystart, ye = localmesh->yend; - if(localmesh->hasBndryLowerY() && include_yguards) + if (localmesh->hasBndryLowerY() && include_yguards) { ys = 0; // Mesh contains a lower boundary - if(localmesh->hasBndryUpperY() && include_yguards) - ye = localmesh->LocalNy-1; // Contains upper boundary + } + if (localmesh->hasBndryUpperY() && include_yguards) { + ye = localmesh->LocalNy - 1; // Contains upper boundary + } Field3D x{emptyFrom(b)}; int status = 0; try { - for(int jy=ys; jy <= ye; jy++) { + for (int jy = ys; jy <= ye; jy++) { // 1. Slice b and x (i.e. take a X-Z plane out of the field) // 2. Send them to the solver of the implementation (determined during creation) - x = solve(sliceXZ(b,jy), sliceXZ(x0,jy)); + x = solve(sliceXZ(b, jy), sliceXZ(x0, jy)); } } catch (const BoutIterationFail&) { status = 1; @@ -256,20 +260,18 @@ Field2D Laplacian::solve(const Field2D& b, const Field2D& x0) { * MATRIX ELEMENTS **********************************************************************************/ -void Laplacian::tridagCoefs(int jx, int jy, int jz, - dcomplex &a, dcomplex &b, dcomplex &c, - const Field2D *ccoef, const Field2D *d, - CELL_LOC loc) { +void Laplacian::tridagCoefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcomplex& c, + const Field2D* ccoef, const Field2D* d, CELL_LOC loc) { - if (loc == CELL_DEFAULT) loc = location; + if (loc == CELL_DEFAULT) { + loc = location; + } ASSERT1(ccoef == nullptr || ccoef->getLocation() == loc); ASSERT1(d == nullptr || d->getLocation() == loc); BoutReal kwave = jz * 2.0 * PI / coords->zlength()(jx, jy); // wave number is 1/[rad] - tridagCoefs(jx, jy, kwave, - a, b, c, - ccoef, d, loc); + tridagCoefs(jx, jy, kwave, a, b, c, ccoef, d, loc); } #if BOUT_USE_METRIC_3D @@ -280,10 +282,9 @@ void Laplacian::tridagCoefs(int /* jx */, int /* jy */, BoutReal /* kwave */, throw BoutException("Laplacian::tridagCoefs() does not support 3d metrics."); } #else -void Laplacian::tridagCoefs(int jx, int jy, BoutReal kwave, - dcomplex &a, dcomplex &b, dcomplex &c, - const Field2D *c1coef, const Field2D *c2coef, - const Field2D *d, CELL_LOC loc) { +void Laplacian::tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, + dcomplex& c, const Field2D* c1coef, const Field2D* c2coef, + const Field2D* d, CELL_LOC loc) { /* Function: Laplacian::tridagCoef * Purpose: - Set the matrix components of A in Ax=b, solving * @@ -323,57 +324,62 @@ void Laplacian::tridagCoefs(int jx, int jy, BoutReal kwave, BoutReal coef1, coef2, coef3, coef4, coef5; - coef1=localcoords->g11(jx,jy); ///< X 2nd derivative coefficient - coef2=localcoords->g33(jx,jy); ///< Z 2nd derivative coefficient - coef3=2.*localcoords->g13(jx,jy); ///< X-Z mixed derivative coefficient + coef1 = localcoords->g11(jx, jy); ///< X 2nd derivative coefficient + coef2 = localcoords->g33(jx, jy); ///< Z 2nd derivative coefficient + coef3 = 2. * localcoords->g13(jx, jy); ///< X-Z mixed derivative coefficient coef4 = 0.0; coef5 = 0.0; // If global flag all_terms are set (true by default) - if(all_terms) { - coef4 = localcoords->G1(jx,jy); // X 1st derivative - coef5 = localcoords->G3(jx,jy); // Z 1st derivative + if (all_terms) { + coef4 = localcoords->G1(jx, jy); // X 1st derivative + coef5 = localcoords->G3(jx, jy); // Z 1st derivative } if (d != nullptr) { // Multiply Delp2 component by a factor - coef1 *= (*d)(jx,jy); - coef2 *= (*d)(jx,jy); - coef3 *= (*d)(jx,jy); - coef4 *= (*d)(jx,jy); - coef5 *= (*d)(jx,jy); + coef1 *= (*d)(jx, jy); + coef2 *= (*d)(jx, jy); + coef3 *= (*d)(jx, jy); + coef4 *= (*d)(jx, jy); + coef5 *= (*d)(jx, jy); } - if(nonuniform) { + if (nonuniform) { // non-uniform mesh correction - if((jx != 0) && (jx != (localmesh->LocalNx-1))) { - coef4 -= 0.5*((localcoords->dx(jx+1,jy) - localcoords->dx(jx-1,jy))/SQ(localcoords->dx(jx,jy)))*coef1; + if ((jx != 0) && (jx != (localmesh->LocalNx - 1))) { + coef4 -= 0.5 + * ((localcoords->dx(jx + 1, jy) - localcoords->dx(jx - 1, jy)) + / SQ(localcoords->dx(jx, jy))) + * coef1; } } if (c1coef != nullptr) { // First derivative terms - if((jx > 0) && (jx < (localmesh->LocalNx-1))) { - BoutReal dc2dx_over_c1 = ((*c2coef)(jx+1,jy) - (*c2coef)(jx-1,jy)) / (2.*localcoords->dx(jx,jy)*((*c1coef)(jx,jy))); - coef4 += localcoords->g11(jx,jy) * dc2dx_over_c1; - coef5 += localcoords->g13(jx,jy) * dc2dx_over_c1; + if ((jx > 0) && (jx < (localmesh->LocalNx - 1))) { + BoutReal dc2dx_over_c1 = ((*c2coef)(jx + 1, jy) - (*c2coef)(jx - 1, jy)) + / (2. * localcoords->dx(jx, jy) * ((*c1coef)(jx, jy))); + coef4 += localcoords->g11(jx, jy) * dc2dx_over_c1; + coef5 += localcoords->g13(jx, jy) * dc2dx_over_c1; } } - if(localmesh->IncIntShear) { + if (localmesh->IncIntShear) { // d2dz2 term - coef2 += localcoords->g11(jx,jy) * localcoords->IntShiftTorsion(jx,jy) * localcoords->IntShiftTorsion(jx,jy); + coef2 += localcoords->g11(jx, jy) * localcoords->IntShiftTorsion(jx, jy) + * localcoords->IntShiftTorsion(jx, jy); // Mixed derivative coef3 = 0.0; // This cancels out } - coef1 /= SQ(localcoords->dx(jx,jy)); - coef3 /= 2.*localcoords->dx(jx,jy); - coef4 /= 2.*localcoords->dx(jx,jy); + coef1 /= SQ(localcoords->dx(jx, jy)); + coef3 /= 2. * localcoords->dx(jx, jy); + coef4 /= 2. * localcoords->dx(jx, jy); - a = dcomplex(coef1 - coef4,-kwave*coef3); - b = dcomplex(-2.0*coef1 - SQ(kwave)*coef2,kwave*coef5); - c = dcomplex(coef1 + coef4,kwave*coef3); + a = dcomplex(coef1 - coef4, -kwave * coef3); + b = dcomplex(-2.0 * coef1 - SQ(kwave) * coef2, kwave * coef5); + c = dcomplex(coef1 + coef4, kwave * coef3); } #endif @@ -441,104 +447,108 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco ASSERT3((c1coef == nullptr and c2coef == nullptr) or (c1coef != nullptr and c2coef != nullptr)) - int xs = 0; // xstart set to the start of x on this processor (including ghost points) - int xe = localmesh->LocalNx-1; // xend set to the end of x on this processor (including ghost points) + int xs = 0; // xstart set to the start of x on this processor (including ghost points) + int xe = localmesh->LocalNx + - 1; // xend set to the end of x on this processor (including ghost points) // Do not want boundary cells if x is periodic for cyclic solver. Only other solver which // works with periodicX is serial_tri, which uses includeguards==true, so the below isn't called. - if(!includeguards) { - if(!localmesh->firstX() || localmesh->periodicX) + if (!includeguards) { + if (!localmesh->firstX() || localmesh->periodicX) { xs = localmesh->xstart; // Inner edge is a guard cell - if(!localmesh->lastX() || localmesh->periodicX) + } + if (!localmesh->lastX() || localmesh->periodicX) { xe = localmesh->xend; // Outer edge is a guard cell + } } int ncx = xe - xs; // Total number of points in x to be used // Setting the width of the boundary. // NOTE: The default is a width of (localmesh->xstart) guard cells - int inbndry = localmesh->xstart, outbndry=localmesh->xstart; + int inbndry = localmesh->xstart, outbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if(inner_boundary_flags & INVERT_BNDRY_ONE) + if (inner_boundary_flags & INVERT_BNDRY_ONE) { inbndry = 1; - if(outer_boundary_flags & INVERT_BNDRY_ONE) + } + if (outer_boundary_flags & INVERT_BNDRY_ONE) { outbndry = 1; + } // Loop through our specified x-domain. // The boundaries will be set according to the if-statements below. - for(int ix=0;ix<=ncx;ix++) { + for (int ix = 0; ix <= ncx; ix++) { // Actually set the metric coefficients - tridagCoefs(xs+ix, jy, kwave, avec[ix], bvec[ix], cvec[ix], c1coef, c2coef, d); - if (a != nullptr) + tridagCoefs(xs + ix, jy, kwave, avec[ix], bvec[ix], cvec[ix], c1coef, c2coef, d); + if (a != nullptr) { // Add A to bvec (the main diagonal in the matrix) - bvec[ix] += (*a)(xs+ix,jy); + bvec[ix] += (*a)(xs + ix, jy); + } } // Set the boundary conditions if x is not periodic - if(!localmesh->periodicX) { - if(localmesh->firstX()) { + if (!localmesh->periodicX) { + if (localmesh->firstX()) { // INNER BOUNDARY ON THIS PROCESSOR // If no user specified value is set on inner boundary, set the first // element in b (in the equation AX=b) to 0 - if(!(inner_boundary_flags & (INVERT_RHS | INVERT_SET))) { - for(int ix=0;ixg_11(ix,jy))/coords->dx(ix,jy); - cvec[ix] = 1./sqrt(coords->g_11(ix,jy))/coords->dx(ix,jy); + for (int ix = 0; ix < inbndry; ix++) { + avec[ix] = 0.; + bvec[ix] = -1. / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); + cvec[ix] = 1. / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); } - } - else if(inner_boundary_flags & INVERT_DC_GRAD) { + } else if (inner_boundary_flags & INVERT_DC_GRAD) { // Zero gradient at inner boundary - for (int ix=0;ixg_22(ix,jy)); - cvec[ix] = -1.0/sqrt(coords->g_22(ix+1,jy)); + } else if (inner_boundary_flags & INVERT_DC_GRADPAR) { + for (int ix = 0; ix < inbndry; ix++) { + avec[ix] = 0.0; + bvec[ix] = 1.0 / sqrt(coords->g_22(ix, jy)); + cvec[ix] = -1.0 / sqrt(coords->g_22(ix + 1, jy)); } - } - else if(inner_boundary_flags & INVERT_DC_GRADPARINV) { - for (int ix=0;ixg_22(ix,jy)); - cvec[ix] = -sqrt(coords->g_22(ix+1,jy)); + } else if (inner_boundary_flags & INVERT_DC_GRADPARINV) { + for (int ix = 0; ix < inbndry; ix++) { + avec[ix] = 0.0; + bvec[ix] = sqrt(coords->g_22(ix, jy)); + cvec[ix] = -sqrt(coords->g_22(ix + 1, jy)); } - } - else if (inner_boundary_flags & INVERT_DC_LAP) { + } else if (inner_boundary_flags & INVERT_DC_LAP) { // Decaying boundary conditions BoutReal k = 0.0; if (a != nullptr) { BoutReal ksq = -((*a)(inbndry, jy)); - if(ksq < 0.0) + if (ksq < 0.0) { throw BoutException("ksq must be positive"); + } k = sqrt(ksq); } - for (int ix=0;ixdx(ix,jy)/sqrt(coords->g11(ix,jy))); + for (int ix = 0; ix < inbndry; ix++) { + avec[ix] = 0.; + bvec[ix] = 1.; + cvec[ix] = -exp(-k * coords->dx(ix, jy) / sqrt(coords->g11(ix, jy))); } - } - else if (inner_boundary_flags & INVERT_IN_CYLINDER){ + } else if (inner_boundary_flags & INVERT_IN_CYLINDER) { // Condition for inner radial boundary for cylindrical coordinates /* Explanation: * The discrete fourier transform is defined as @@ -574,16 +584,15 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco * = F(x,y)_k if k is even * = - F(x,y)_k if k is odd */ - for (int ix=0;ixg_11(ix,jy))/coords->dx(ix,jy); - cvec[ix] = dcomplex(1.,0.)/sqrt(coords->g_11(ix,jy))/coords->dx(ix,jy); + for (int ix = 0; ix < inbndry; ix++) { + avec[ix] = dcomplex(0., 0.); + bvec[ix] = + dcomplex(-1., 0.) / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); + cvec[ix] = dcomplex(1., 0.) / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); } - } - else if(inner_boundary_flags & INVERT_AC_GRAD) { + } else if (inner_boundary_flags & INVERT_AC_GRAD) { // Zero gradient at inner boundary - for (int ix=0;ixg33(ix,jy)/coords->g11(ix,jy))*kwave*coords->dx(ix,jy)); + cvec[ix] = -exp(-1.0 * sqrt(coords->g33(ix, jy) / coords->g11(ix, jy)) * kwave + * coords->dx(ix, jy)); } - } - else if (inner_boundary_flags & INVERT_IN_CYLINDER) { + } else if (inner_boundary_flags & INVERT_IN_CYLINDER) { // Condition for inner radial boundary for cylindrical coordinates // Explanation under "if (inner_boundary_flags & INVERT_IN_CYLINDER)" - for (int ix=0;ixlastX()) { + if (localmesh->lastX()) { // OUTER BOUNDARY ON THIS PROCESSOR // If no user specified value is set on outer boundary, set the last // element in b (in the equation AX=b) to 0 - if(!(outer_boundary_flags & (INVERT_RHS | INVERT_SET))) { - for (int ix=0;ixg_11(ncx-ix,jy))/coords->dx(ncx-ix,jy); - bvec[ncx-ix]=dcomplex(1.,0.)/sqrt(coords->g_11(ncx-ix,jy))/coords->dx(ncx-ix,jy); - cvec[ncx-ix]=dcomplex(0.,0.); + for (int ix = 0; ix < outbndry; ix++) { + avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) + / coords->dx(ncx - ix, jy); + bvec[ncx - ix] = dcomplex(1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) + / coords->dx(ncx - ix, jy); + cvec[ncx - ix] = dcomplex(0., 0.); } - } - else if(outer_boundary_flags & INVERT_DC_GRAD) { + } else if (outer_boundary_flags & INVERT_DC_GRAD) { // Zero gradient at outer boundary - for (int ix=0;ixg_22(ncx-ix+1,jy)); - bvec[ncx-ix] = -1.0/sqrt(coords->g_22(ncx-ix,jy)); - cvec[ncx-ix] = 0.0; + } else if (inner_boundary_flags & INVERT_DC_GRADPAR) { + for (int ix = 0; ix < inbndry; ix++) { + avec[ncx - ix] = 1.0 / sqrt(coords->g_22(ncx - ix + 1, jy)); + bvec[ncx - ix] = -1.0 / sqrt(coords->g_22(ncx - ix, jy)); + cvec[ncx - ix] = 0.0; } - } - else if(inner_boundary_flags & INVERT_DC_GRADPARINV) { - for (int ix=0;ixg_22(ncx-ix-1,jy)); - bvec[ncx-ix] = -sqrt(coords->g_22(ncx-ix,jy)); - cvec[ncx-ix] = 0.0; + } else if (inner_boundary_flags & INVERT_DC_GRADPARINV) { + for (int ix = 0; ix < inbndry; ix++) { + avec[ncx - ix] = sqrt(coords->g_22(ncx - ix - 1, jy)); + bvec[ncx - ix] = -sqrt(coords->g_22(ncx - ix, jy)); + cvec[ncx - ix] = 0.0; } - } - else if (inner_boundary_flags & INVERT_DC_LAP) { + } else if (inner_boundary_flags & INVERT_DC_LAP) { // Decaying boundary conditions BoutReal k = 0.0; if (a != nullptr) { BoutReal ksq = -((*a)(inbndry, jy)); - if(ksq < 0.0) + if (ksq < 0.0) { throw BoutException("ksq must be positive"); + } k = sqrt(ksq); } - for (int ix=0;ixdx(ncx-ix,jy)/sqrt(coords->g11(ncx-ix,jy))); + for (int ix = 0; ix < inbndry; ix++) { + cvec[ncx - ix] = 0.; + bvec[ncx - ix] = 1.; + avec[ncx - ix] = + -exp(-k * coords->dx(ncx - ix, jy) / sqrt(coords->g11(ncx - ix, jy))); } - } - else { + } else { // Order 2 dirichlet BC (boundary half between points) // Zero value at outer boundary - for (int ix=0;ixg_11(ncx-ix,jy))/coords->dx(ncx-ix,jy); - bvec[ncx-ix]=dcomplex(1.,0.)/sqrt(coords->g_11(ncx-ix,jy))/coords->dx(ncx-ix,jy); - cvec[ncx-ix]=dcomplex(0.,0.); + for (int ix = 0; ix < outbndry; ix++) { + avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) + / coords->dx(ncx - ix, jy); + bvec[ncx - ix] = dcomplex(1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) + / coords->dx(ncx - ix, jy); + cvec[ncx - ix] = dcomplex(0., 0.); } - } - else if(outer_boundary_flags & INVERT_AC_GRAD) { + } else if (outer_boundary_flags & INVERT_AC_GRAD) { // Zero gradient at outer boundary - for (int ix=0;ixg33(xe-ix,jy)/coords->g11(xe-ix,jy))*kwave*coords->dx(xe-ix,jy)); - bvec[ncx-ix] = 1.0; - cvec[ncx-ix] = 0.0; + for (int ix = 0; ix < outbndry; ix++) { + avec[ncx - ix] = + -exp(-1.0 * sqrt(coords->g33(xe - ix, jy) / coords->g11(xe - ix, jy)) + * kwave * coords->dx(xe - ix, jy)); + bvec[ncx - ix] = 1.0; + cvec[ncx - ix] = 0.0; } - } - else { + } else { // Order 2 dirichlet BC (boundary half between points) // Zero value at outer boundary - for (int ix=0;ixtridagCoefs(jx,jy, jz, a, b, c, ccoef, d, loc); +void laplace_tridag_coefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcomplex& c, + const Field2D* ccoef, const Field2D* d, CELL_LOC loc) { + Laplacian::defaultInstance()->tridagCoefs(jx, jy, jz, a, b, c, ccoef, d, loc); } constexpr decltype(LaplaceFactory::type_name) LaplaceFactory::type_name; constexpr decltype(LaplaceFactory::section_name) LaplaceFactory::section_name; diff --git a/src/invert/laplacexy/laplacexy.cxx b/src/invert/laplacexy/laplacexy.cxx index 5e407164f7..3714d1b1df 100644 --- a/src/invert/laplacexy/laplacexy.cxx +++ b/src/invert/laplacexy/laplacexy.cxx @@ -8,40 +8,41 @@ #include -#include -#include -#include -#include #include +#include +#include +#include +#include -#include +#include #include - -static PetscErrorCode laplacePCapply(PC pc,Vec x,Vec y) { +static PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) { int ierr; - + // Get the context - LaplaceXY *s; - ierr = PCShellGetContext(pc, reinterpret_cast(&s)); CHKERRQ(ierr); - + LaplaceXY* s; + ierr = PCShellGetContext(pc, reinterpret_cast(&s)); + CHKERRQ(ierr); + PetscFunctionReturn(s->precon(x, y)); } -LaplaceXY::LaplaceXY(Mesh *m, Options *opt, const CELL_LOC loc) - : lib(opt==nullptr ? &(Options::root()["laplacexy"]) : opt), - localmesh(m==nullptr ? bout::globals::mesh : m), location(loc), monitor(*this) { +LaplaceXY::LaplaceXY(Mesh* m, Options* opt, const CELL_LOC loc) + : lib(opt == nullptr ? &(Options::root()["laplacexy"]) : opt), + localmesh(m == nullptr ? bout::globals::mesh : m), location(loc), monitor(*this) { Timer timer("invert"); if (opt == nullptr) { // If no options supplied, use default opt = &(Options::root()["laplacexy"]); } - - finite_volume = (*opt)["finite_volume"].doc( - "Use finite volume rather than finite difference discretisation." - ).withDefault(true); + + finite_volume = + (*opt)["finite_volume"] + .doc("Use finite volume rather than finite difference discretisation.") + .withDefault(true); /////////////////////////////////////////////////// // Boundary condititions options @@ -60,10 +61,7 @@ LaplaceXY::LaplaceXY(Mesh *m, Options *opt, const CELL_LOC loc) } // Check value of y_bndry is a supported option - if (not( - y_bndry == "dirichlet" - or y_bndry == "neumann" - or y_bndry == "free_o3")) { + if (not(y_bndry == "dirichlet" or y_bndry == "neumann" or y_bndry == "free_o3")) { throw BoutException("Unrecognized option '{}' for laplacexy:ybndry", y_bndry); } @@ -82,74 +80,77 @@ LaplaceXY::LaplaceXY(Mesh *m, Options *opt, const CELL_LOC loc) // Get MPI communicator auto comm = BoutComm::get(); - + // Local size const int localN = localSize(); - // Create Vectors - VecCreate( comm, &xs ); - VecSetSizes( xs, localN, PETSC_DETERMINE ); - VecSetFromOptions( xs ); - VecDuplicate( xs , &bs ); + // Create Vectors + VecCreate(comm, &xs); + VecSetSizes(xs, localN, PETSC_DETERMINE); + VecSetFromOptions(xs); + VecDuplicate(xs, &bs); // Set size of Matrix on each processor to localN x localN - MatCreate( comm, &MatA ); - MatSetSizes( MatA, localN, localN, PETSC_DETERMINE, PETSC_DETERMINE ); + MatCreate(comm, &MatA); + MatSetSizes(MatA, localN, localN, PETSC_DETERMINE, PETSC_DETERMINE); MatSetFromOptions(MatA); - + ////////////////////////////////////////////////// // Specify local indices. This creates a mapping // from local indices to index, using a Field2D object - indexXY = -1; // Set all points to -1, indicating out of domain + indexXY = -1; // Set all points to -1, indicating out of domain int ind = 0; - + // Y boundaries - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - indexXY(it.ind, localmesh->ystart-1) = ind++; + indexXY(it.ind, localmesh->ystart - 1) = ind++; } if ((not finite_volume) and localmesh->hasBndryLowerY()) { // Corner boundary cells if (localmesh->firstX()) { - indexXY(localmesh->xstart-1, localmesh->ystart-1) = ind++; + indexXY(localmesh->xstart - 1, localmesh->ystart - 1) = ind++; } if (localmesh->lastX()) { - indexXY(localmesh->xend+1, localmesh->ystart-1) = ind++; + indexXY(localmesh->xend + 1, localmesh->ystart - 1) = ind++; } } - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - indexXY(it.ind, localmesh->yend+1) = ind++; + indexXY(it.ind, localmesh->yend + 1) = ind++; } if ((not finite_volume) and localmesh->hasBndryUpperY()) { // Corner boundary cells if (localmesh->firstX()) { - indexXY(localmesh->xstart-1, localmesh->yend+1) = ind++; + indexXY(localmesh->xstart - 1, localmesh->yend + 1) = ind++; } if (localmesh->lastX()) { - indexXY(localmesh->xend+1, localmesh->yend+1) = ind++; + indexXY(localmesh->xend + 1, localmesh->yend + 1) = ind++; } } - + xstart = localmesh->xstart; - if(localmesh->firstX()) + if (localmesh->firstX()) { xstart -= 1; // Include X guard cells + } xend = localmesh->xend; - if(localmesh->lastX()) + if (localmesh->lastX()) { xend += 1; - for(int x=xstart;x<=xend;x++) - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { - indexXY(x,y) = ind++; + } + for (int x = xstart; x <= xend; x++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { + indexXY(x, y) = ind++; } - + } + ASSERT1(ind == localN); // Reached end of range ////////////////////////////////////////////////// @@ -169,95 +170,100 @@ LaplaceXY::LaplaceXY(Mesh *m, Options *opt, const CELL_LOC loc) ////////////////////////////////////////////////// // Pre-allocate PETSc storage - + PetscInt *d_nnz, *o_nnz; - PetscMalloc( (localN)*sizeof(PetscInt), &d_nnz ); - PetscMalloc( (localN)*sizeof(PetscInt), &o_nnz ); - + PetscMalloc((localN) * sizeof(PetscInt), &d_nnz); + PetscMalloc((localN) * sizeof(PetscInt), &o_nnz); + if (finite_volume) { setPreallocationFiniteVolume(d_nnz, o_nnz); } else { setPreallocationFiniteDifference(d_nnz, o_nnz); } // Pre-allocate - MatMPIAIJSetPreallocation( MatA, 0, d_nnz, 0, o_nnz ); - MatSetUp(MatA); - - PetscFree( d_nnz ); - PetscFree( o_nnz ); - + MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz); + MatSetUp(MatA); + + PetscFree(d_nnz); + PetscFree(o_nnz); + // Determine which row/columns of the matrix are locally owned int Istart, Iend; - MatGetOwnershipRange( MatA, &Istart, &Iend ); - + MatGetOwnershipRange(MatA, &Istart, &Iend); + // Convert indexXY from local index to global index indexXY += Istart; - + // Now communicate to fill guard cells // Note, this includes corner cells if necessary localmesh->communicate(indexXY); ////////////////////////////////////////////////// // Set up KSP - - // Declare KSP Context - KSPCreate( comm, &ksp ); - + + // Declare KSP Context + KSPCreate(comm, &ksp); + // Configure Linear Solver - + const bool direct = (*opt)["direct"].doc("Use a direct LU solver").withDefault(false); - - if(direct) { - KSPGetPC(ksp,&pc); - PCSetType(pc,PCLU); -#if PETSC_VERSION_GE(3,9,0) - PCFactorSetMatSolverType(pc,"mumps"); + + if (direct) { + KSPGetPC(ksp, &pc); + PCSetType(pc, PCLU); +#if PETSC_VERSION_GE(3, 9, 0) + PCFactorSetMatSolverType(pc, "mumps"); #else - PCFactorSetMatSolverPackage(pc,"mumps"); + PCFactorSetMatSolverPackage(pc, "mumps"); #endif - }else { - + } else { + // Convergence Parameters. Solution is considered converged if |r_k| < max( rtol * |b| , atol ) // where r_k = b - Ax_k. The solution is considered diverged if |r_k| > dtol * |b|. const BoutReal rtol = (*opt)["rtol"].doc("Relative tolerance").withDefault(1e-5); - const BoutReal atol = (*opt)["atol"] + const BoutReal atol = + (*opt)["atol"] .doc("Absolute tolerance. The solution is considered converged if |Ax-b| " "< max( rtol * |b| , atol )") .withDefault(1e-10); - const BoutReal dtol = (*opt)["dtol"] - .doc("The solution is considered diverged if |Ax-b| > dtol * |b|") - .withDefault(1e3); + const BoutReal dtol = + (*opt)["dtol"] + .doc("The solution is considered diverged if |Ax-b| > dtol * |b|") + .withDefault(1e3); const int maxits = (*opt)["maxits"].doc("Maximum iterations").withDefault(100000); // Get KSP Solver Type - const std::string ksptype = (*opt)["ksptype"].doc("KSP solver type").withDefault("gmres"); - + const std::string ksptype = + (*opt)["ksptype"].doc("KSP solver type").withDefault("gmres"); + // Get PC type - const std::string pctype = (*opt)["pctype"].doc("Preconditioner type").withDefault("none"); + const std::string pctype = + (*opt)["pctype"].doc("Preconditioner type").withDefault("none"); - KSPSetType( ksp, ksptype.c_str() ); - KSPSetTolerances( ksp, rtol, atol, dtol, maxits ); + KSPSetType(ksp, ksptype.c_str()); + KSPSetTolerances(ksp, rtol, atol, dtol, maxits); KSPSetInitialGuessNonzero(ksp, static_cast(true)); - KSPGetPC(ksp,&pc); + KSPGetPC(ksp, &pc); PCSetType(pc, pctype.c_str()); if (pctype == "shell") { // Using tridiagonal solver as preconditioner - PCShellSetApply(pc,laplacePCapply); - PCShellSetContext(pc,this); - - const bool rightprec = (*opt)["rightprec"].doc("Use right preconditioning?").withDefault(true); + PCShellSetApply(pc, laplacePCapply); + PCShellSetContext(pc, this); + + const bool rightprec = + (*opt)["rightprec"].doc("Use right preconditioning?").withDefault(true); if (rightprec) { KSPSetPCSide(ksp, PC_RIGHT); // Right preconditioning } else { - KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning + KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning } } } - + lib.setOptionsFromInputFile(ksp); /////////////////////////////////////////////////// @@ -280,7 +286,7 @@ void LaplaceXY::setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz) { const int localN = localSize(); // This discretisation uses a 5-point stencil - for(int i=0;ifirstX()) { + if (localmesh->firstX()) { // Lower X boundary - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xstart - 1, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 2; // Diagonal sub-matrix o_nnz[localIndex] = 0; // Off-diagonal sub-matrix } - }else { + } else { // On another processor - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xstart, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] -= 1; o_nnz[localIndex] += 1; } } - if(localmesh->lastX()) { + if (localmesh->lastX()) { // Upper X boundary - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xend + 1, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 2; // Diagonal sub-matrix o_nnz[localIndex] = 0; // Off-diagonal sub-matrix } - }else { + } else { // On another processor - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xend, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] -= 1; o_nnz[localIndex] += 1; } } // Y boundaries - for(int x=localmesh->xstart; x <=localmesh->xend; x++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { // Default to no boundary // NOTE: This assumes that communications in Y are to other // processors. If Y is communicated with this processor (e.g. NYPE=1) @@ -344,7 +350,7 @@ void LaplaceXY::setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz) { } } - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; @@ -362,7 +368,7 @@ void LaplaceXY::setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz) { o_nnz[localIndex] -= 1; } } - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; @@ -386,7 +392,7 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn const int localN = localSize(); // This discretisation uses a 9-point stencil - for(int i=0;ifirstX()) { + if (localmesh->firstX()) { // Lower X boundary - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xstart - 1, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 2; // Diagonal sub-matrix o_nnz[localIndex] = 0; // Off-diagonal sub-matrix } - }else { + } else { // On another processor - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xstart, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] -= 3; o_nnz[localIndex] += 3; } } - if(localmesh->lastX()) { + if (localmesh->lastX()) { // Upper X boundary - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xend + 1, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 2; // Diagonal sub-matrix o_nnz[localIndex] = 0; // Off-diagonal sub-matrix } - }else { + } else { // On another processor - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int localIndex = globalIndex(localmesh->xend, y); - ASSERT1( (localIndex >= 0) && (localIndex < localN) ); + ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] -= 3; o_nnz[localIndex] += 3; } @@ -432,7 +438,7 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn // Y boundaries const int y_bndry_stencil_size = (y_bndry == "free_o3") ? 4 : 2; - for(int x=localmesh->xstart; x <=localmesh->xend; x++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { // Default to no boundary // NOTE: This assumes that communications in Y are to other // processors. If Y is communicated with this processor (e.g. NYPE=1) @@ -451,7 +457,7 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn } } - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, they are handled specially below if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; @@ -460,7 +466,7 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn const int localIndex = globalIndex(it.ind, localmesh->ystart - 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = y_bndry_stencil_size; // Diagonal sub-matrix - o_nnz[localIndex] = 0; // Off-diagonal sub-matrix + o_nnz[localIndex] = 0; // Off-diagonal sub-matrix } { const int localIndex = globalIndex(it.ind, localmesh->ystart); @@ -474,29 +480,29 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn // special handling for the corners, since we use a free_o3 y-boundary // condition just in the corners when y_bndry=="dirichlet" if (localmesh->firstX()) { - const int localIndex = globalIndex(localmesh->xstart-1, localmesh->ystart-1); + const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 4; } if (localmesh->lastX()) { - const int localIndex = globalIndex(localmesh->xend+1, localmesh->ystart-1); + const int localIndex = globalIndex(localmesh->xend + 1, localmesh->ystart - 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 4; } } else { if (localmesh->firstX()) { - const int localIndex = globalIndex(localmesh->xstart-1, localmesh->ystart-1); + const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = y_bndry_stencil_size; } if (localmesh->lastX()) { - const int localIndex = globalIndex(localmesh->xend+1, localmesh->ystart-1); + const int localIndex = globalIndex(localmesh->xend + 1, localmesh->ystart - 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = y_bndry_stencil_size; } } } - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, they are handled specially below if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; @@ -505,7 +511,7 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn const int localIndex = globalIndex(it.ind, localmesh->yend + 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = y_bndry_stencil_size; // Diagonal sub-matrix - o_nnz[localIndex] = 0; // Off-diagonal sub-matrix + o_nnz[localIndex] = 0; // Off-diagonal sub-matrix } { const int localIndex = globalIndex(it.ind, localmesh->yend); @@ -519,23 +525,23 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn // special handling for the corners, since we use a free_o3 y-boundary // condition just in the corners when y_bndry=="dirichlet" if (localmesh->firstX()) { - const int localIndex = globalIndex(localmesh->xstart-1, localmesh->yend+1); + const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->yend + 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 4; } if (localmesh->lastX()) { - const int localIndex = globalIndex(localmesh->xend+1, localmesh->yend+1); + const int localIndex = globalIndex(localmesh->xend + 1, localmesh->yend + 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = 4; } } else { if (localmesh->firstX()) { - const int localIndex = globalIndex(localmesh->xstart-1, localmesh->yend+1); + const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->yend + 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = y_bndry_stencil_size; } if (localmesh->lastX()) { - const int localIndex = globalIndex(localmesh->xend+1, localmesh->yend+1); + const int localIndex = globalIndex(localmesh->xend + 1, localmesh->yend + 1); ASSERT1((localIndex >= 0) && (localIndex < localN)); d_nnz[localIndex] = y_bndry_stencil_size; } @@ -543,7 +549,7 @@ void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nn } } -void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { +void LaplaceXY::setCoefs(const Field2D& A, const Field2D& B) { Timer timer("invert"); ASSERT1(A.getMesh() == localmesh); @@ -556,54 +562,54 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { } else { setMatrixElementsFiniteDifference(A, B); } - + // X boundaries - if(localmesh->firstX()) { - if(x_inner_dirichlet) { + if (localmesh->firstX()) { + if (x_inner_dirichlet) { // Dirichlet on inner X boundary - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { - int row = globalIndex(localmesh->xstart-1,y); + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { + int row = globalIndex(localmesh->xstart - 1, y); PetscScalar val = 0.5; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); - - int col = globalIndex(localmesh->xstart,y); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); - + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); + + int col = globalIndex(localmesh->xstart, y); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); + // Preconditioner bcoef(y - localmesh->ystart, 0) = 0.5; ccoef(y - localmesh->ystart, 0) = 0.5; } - - }else { - + + } else { + // Neumann on inner X boundary - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { - int row = globalIndex(localmesh->xstart-1,y); + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { + int row = globalIndex(localmesh->xstart - 1, y); PetscScalar val = 1.0; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); - - int col = globalIndex(localmesh->xstart,y); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); + + int col = globalIndex(localmesh->xstart, y); val = -1.0; - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); - + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); + // Preconditioner bcoef(y - localmesh->ystart, 0) = 1.0; ccoef(y - localmesh->ystart, 0) = -1.0; } } } - if(localmesh->lastX()) { + if (localmesh->lastX()) { // Dirichlet on outer X boundary - - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { - int row = globalIndex(localmesh->xend+1,y); + + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { + int row = globalIndex(localmesh->xend + 1, y); PetscScalar val = 0.5; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); - - int col = globalIndex(localmesh->xend,y); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); - + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); + + int col = globalIndex(localmesh->xend, y); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); + // Preconditioner acoef(y - localmesh->ystart, localmesh->xend + 1 - xstart) = 0.5; bcoef(y - localmesh->ystart, localmesh->xend + 1 - xstart) = 0.5; @@ -612,105 +618,105 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { if (y_bndry == "dirichlet") { // Dirichlet on Y boundaries - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - int row = globalIndex(it.ind, localmesh->ystart-1); + int row = globalIndex(it.ind, localmesh->ystart - 1); PetscScalar val = 0.5; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); - + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); + int col = globalIndex(it.ind, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } - - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - int row = globalIndex(it.ind, localmesh->yend+1); + int row = globalIndex(it.ind, localmesh->yend + 1); PetscScalar val = 0.5; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); - + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); + int col = globalIndex(it.ind, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } } else if (y_bndry == "neumann") { // Neumann on Y boundaries - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - int row = globalIndex(it.ind, localmesh->ystart-1); + int row = globalIndex(it.ind, localmesh->ystart - 1); PetscScalar val = 1.0; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -1.0; int col = globalIndex(it.ind, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } - - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - int row = globalIndex(it.ind, localmesh->yend+1); + int row = globalIndex(it.ind, localmesh->yend + 1); PetscScalar val = 1.0; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -1.0; int col = globalIndex(it.ind, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } } else if (y_bndry == "free_o3") { // 'free_o3' extrapolating boundary condition on Y boundaries - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - int row = globalIndex(it.ind, localmesh->ystart-1); + int row = globalIndex(it.ind, localmesh->ystart - 1); PetscScalar val = 1.0; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -3.0; int col = globalIndex(it.ind, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = 3.0; - col = globalIndex(it.ind, localmesh->ystart+1); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(it.ind, localmesh->ystart + 1); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = -1.0; - col = globalIndex(it.ind, localmesh->ystart+2); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(it.ind, localmesh->ystart + 2); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; } - int row = globalIndex(it.ind, localmesh->yend+1); + int row = globalIndex(it.ind, localmesh->yend + 1); PetscScalar val = 1.0; - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -3.0; int col = globalIndex(it.ind, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = 3.0; - col = globalIndex(it.ind, localmesh->yend-1); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(it.ind, localmesh->yend - 1); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = -1.0; - col = globalIndex(it.ind, localmesh->yend-2); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(it.ind, localmesh->yend - 2); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } } else { throw BoutException("Unsupported option for y_bndry"); @@ -727,12 +733,12 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Neumann y-bc // f(xs-1,ys-1) = f(xs-1,ys) PetscScalar val = 1.0; - int row = globalIndex(localmesh->xstart-1, localmesh->ystart-1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -1.0; - int col = globalIndex(localmesh->xstart-1, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xstart - 1, localmesh->ystart); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") { // 'free_o3' extrapolating boundary condition on Y boundaries // f(xs-1,ys-1) = 3*f(xs-1,ys) - 3*f(xs-1,ys+1) + f(xs-1,ys+2) @@ -740,20 +746,20 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know // what value to pass for the corner PetscScalar val = 1.0; - int row = globalIndex(localmesh->xstart-1, localmesh->ystart-1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -3.0; - int col = globalIndex(localmesh->xstart-1, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xstart - 1, localmesh->ystart); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = 3.0; - col = globalIndex(localmesh->xstart-1, localmesh->ystart+1); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xstart - 1, localmesh->ystart + 1); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = -1.0; - col = globalIndex(localmesh->xstart-1, localmesh->ystart+2); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xstart - 1, localmesh->ystart + 2); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else { throw BoutException("Unsupported option for y_bndry"); } @@ -763,12 +769,12 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Neumann y-bc // f(xe+1,ys-1) = f(xe+1,ys) PetscScalar val = 1.0; - int row = globalIndex(localmesh->xend+1, localmesh->ystart-1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xend + 1, localmesh->ystart - 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -1.0; - int col = globalIndex(localmesh->xend+1, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xend + 1, localmesh->ystart); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") { // 'free_o3' extrapolating boundary condition on Y boundaries // f(xe+1,ys-1) = 3*f(xe+1,ys) - 3*f(xe+1,ys+1) + f(xe+1,ys+2) @@ -776,24 +782,23 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know // what value to pass for the corner PetscScalar val = 1.0; - int row = globalIndex(localmesh->xend+1, localmesh->ystart-1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xend + 1, localmesh->ystart - 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -3.0; - int col = globalIndex(localmesh->xend+1, localmesh->ystart); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xend + 1, localmesh->ystart); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = 3.0; - col = globalIndex(localmesh->xend+1, localmesh->ystart+1); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xend + 1, localmesh->ystart + 1); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = -1.0; - col = globalIndex(localmesh->xend+1, localmesh->ystart+2); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xend + 1, localmesh->ystart + 2); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else { throw BoutException("Unsupported option for y_bndry"); } - } } if (localmesh->hasBndryUpperY()) { @@ -802,12 +807,12 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Neumann y-bc // f(xs-1,ys-1) = f(xs-1,ys) PetscScalar val = 1.0; - int row = globalIndex(localmesh->xstart-1, localmesh->yend+1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xstart - 1, localmesh->yend + 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -1.0; - int col = globalIndex(localmesh->xstart-1, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xstart - 1, localmesh->yend); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") { // 'free_o3' extrapolating boundary condition on Y boundaries // f(xs-1,ys-1) = 3*f(xs-1,ys) - 3*f(xs-1,ys+1) + f(xs-1,ys+2) @@ -815,20 +820,20 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know // what value to pass for the corner PetscScalar val = 1.0; - int row = globalIndex(localmesh->xstart-1, localmesh->yend+1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xstart - 1, localmesh->yend + 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -3.0; - int col = globalIndex(localmesh->xstart-1, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xstart - 1, localmesh->yend); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = 3.0; - col = globalIndex(localmesh->xstart-1, localmesh->yend-1); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xstart - 1, localmesh->yend - 1); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = -1.0; - col = globalIndex(localmesh->xstart-1, localmesh->yend-2); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xstart - 1, localmesh->yend - 2); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else { throw BoutException("Unsupported option for y_bndry"); } @@ -838,12 +843,12 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Neumann y-bc // f(xe+1,ys-1) = f(xe+1,ys) PetscScalar val = 1.0; - int row = globalIndex(localmesh->xend+1, localmesh->yend+1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xend + 1, localmesh->yend + 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -1.0; - int col = globalIndex(localmesh->xend+1, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xend + 1, localmesh->yend); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") { // 'free_o3' extrapolating boundary condition on Y boundaries // f(xe+1,ys-1) = 3*f(xe+1,ys) - 3*f(xe+1,ys+1) + f(xe+1,ys+2) @@ -851,44 +856,43 @@ void LaplaceXY::setCoefs(const Field2D &A, const Field2D &B) { // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know // what value to pass for the corner PetscScalar val = 1.0; - int row = globalIndex(localmesh->xend+1, localmesh->yend+1); - MatSetValues(MatA,1,&row,1,&row,&val,INSERT_VALUES); + int row = globalIndex(localmesh->xend + 1, localmesh->yend + 1); + MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES); val = -3.0; - int col = globalIndex(localmesh->xend+1, localmesh->yend); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + int col = globalIndex(localmesh->xend + 1, localmesh->yend); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = 3.0; - col = globalIndex(localmesh->xend+1, localmesh->yend-1); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xend + 1, localmesh->yend - 1); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); val = -1.0; - col = globalIndex(localmesh->xend+1, localmesh->yend-2); - MatSetValues(MatA,1,&row,1,&col,&val,INSERT_VALUES); + col = globalIndex(localmesh->xend + 1, localmesh->yend - 2); + MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES); } else { throw BoutException("Unsupported option for y_bndry"); } - } } } - + // Assemble Matrix - MatAssemblyBegin( MatA, MAT_FINAL_ASSEMBLY ); - MatAssemblyEnd( MatA, MAT_FINAL_ASSEMBLY ); + MatAssemblyBegin(MatA, MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(MatA, MAT_FINAL_ASSEMBLY); // Set the operator -#if PETSC_VERSION_GE(3,5,0) - KSPSetOperators( ksp,MatA,MatA ); +#if PETSC_VERSION_GE(3, 5, 0) + KSPSetOperators(ksp, MatA, MatA); #else - KSPSetOperators( ksp,MatA,MatA,DIFFERENT_NONZERO_PATTERN ); + KSPSetOperators(ksp, MatA, MatA, DIFFERENT_NONZERO_PATTERN); #endif - + // Set coefficients for preconditioner cr->setCoefs(acoef, bcoef, ccoef); } -void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B) { +void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D& A, const Field2D& B) { ////////////////////////////////////////////////// // Set Matrix elements // @@ -903,8 +907,8 @@ void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B const Field2D g_23_DC = DC(coords->g_23); const Field2D g23_DC = DC(coords->g23); - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { - for(int y=localmesh->ystart;y<=localmesh->yend;y++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { // stencil entries PetscScalar c, xm, xp, ym, yp; @@ -914,30 +918,30 @@ void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B BoutReal J = 0.5 * (J_DC(x, y) + J_DC(x + 1, y)); BoutReal g11 = 0.5 * (g11_DC(x, y) + g11_DC(x + 1, y)); BoutReal dx = 0.5 * (dx_DC(x, y) + dx_DC(x + 1, y)); - BoutReal Acoef = 0.5*(A(x,y) + A(x+1,y)); + BoutReal Acoef = 0.5 * (A(x, y) + A(x + 1, y)); BoutReal val = Acoef * J * g11 / (J_DC(x, y) * dx * dx_DC(x, y)); xp = val; - c = -val; + c = -val; // Metrics on x-1/2 boundary J = 0.5 * (J_DC(x, y) + J_DC(x - 1, y)); g11 = 0.5 * (g11_DC(x, y) + g11_DC(x - 1, y)); dx = 0.5 * (dx_DC(x, y) + dx_DC(x - 1, y)); - Acoef = 0.5*(A(x,y) + A(x-1,y)); + Acoef = 0.5 * (A(x, y) + A(x - 1, y)); val = Acoef * J * g11 / (J_DC(x, y) * dx * dx_DC(x, y)); xm = val; - c -= val; + c -= val; - c += B(x,y); + c += B(x, y); // Put values into the preconditioner, X derivatives only acoef(y - localmesh->ystart, x - xstart) = xm; bcoef(y - localmesh->ystart, x - xstart) = c; ccoef(y - localmesh->ystart, x - xstart) = xp; - if( include_y_derivs ) { + if (include_y_derivs) { // YY component // Metrics at y+1/2 J = 0.5 * (J_DC(x, y) + J_DC(x, y + 1)); @@ -945,7 +949,7 @@ void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B BoutReal g23 = 0.5 * (g23_DC(x, y) + g23_DC(x, y + 1)); BoutReal g_23 = 0.5 * (g_23_DC(x, y) + g_23_DC(x, y + 1)); BoutReal dy = 0.5 * (dy_DC(x, y) + dy_DC(x, y + 1)); - Acoef = 0.5*(A(x,y+1) + A(x,y)); + Acoef = 0.5 * (A(x, y + 1) + A(x, y)); val = -Acoef * J * g23 * g_23 / (g_22 * J_DC(x, y) * dy * dy_DC(x, y)); yp = val; @@ -957,7 +961,7 @@ void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B g23 = 0.5 * (g23_DC(x, y) + g23_DC(x, y - 1)); g_23 = 0.5 * (g_23_DC(x, y) + g_23_DC(x, y - 1)); dy = 0.5 * (dy_DC(x, y) + dy_DC(x, y - 1)); - Acoef = 0.5*(A(x,y-1) + A(x,y)); + Acoef = 0.5 * (A(x, y - 1) + A(x, y)); val = -Acoef * J * g23 * g_23 / (g_22 * J_DC(x, y) * dy * dy_DC(x, y)); ym = val; @@ -967,33 +971,33 @@ void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D &A, const Field2D &B ///////////////////////////////////////////////// // Now have a 5-point stencil for the Laplacian - int row = globalIndex(x,y); + int row = globalIndex(x, y); // Set the centre (diagonal) - MatSetValues(MatA,1,&row,1,&row,&c,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &row, &c, INSERT_VALUES); // X + 1 - int col = globalIndex(x+1, y); - MatSetValues(MatA,1,&row,1,&col,&xp,INSERT_VALUES); + int col = globalIndex(x + 1, y); + MatSetValues(MatA, 1, &row, 1, &col, &xp, INSERT_VALUES); // X - 1 - col = globalIndex(x-1, y); - MatSetValues(MatA,1,&row,1,&col,&xm,INSERT_VALUES); + col = globalIndex(x - 1, y); + MatSetValues(MatA, 1, &row, 1, &col, &xm, INSERT_VALUES); - if( include_y_derivs ) { + if (include_y_derivs) { // Y + 1 - col = globalIndex(x, y+1); - MatSetValues(MatA,1,&row,1,&col,&yp,INSERT_VALUES); + col = globalIndex(x, y + 1); + MatSetValues(MatA, 1, &row, 1, &col, &yp, INSERT_VALUES); // Y - 1 - col = globalIndex(x, y-1); - MatSetValues(MatA,1,&row,1,&col,&ym,INSERT_VALUES); + col = globalIndex(x, y - 1); + MatSetValues(MatA, 1, &row, 1, &col, &ym, INSERT_VALUES); } } } } -void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D &A, const Field2D &B) { +void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D& A, const Field2D& B) { ////////////////////////////////////////////////// // Set Matrix elements // @@ -1019,8 +1023,8 @@ void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D &A, const Field2 const Field2D coef_dfdy = G2_2D - DC(DDY(J_2D / g_22_2D) / J_2D); - for(int x = localmesh->xstart; x <= localmesh->xend; x++) { - for(int y = localmesh->ystart; y <= localmesh->yend; y++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { // stencil entries PetscScalar c, xm, xp, ym, yp, xpyp, xpym, xmyp, xmym; @@ -1034,7 +1038,7 @@ void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D &A, const Field2 // A*g11*d2fdx2 val = A(x, y) * g11_2D(x, y) / SQ(dx); xp += val; - c = -2.*val; + c = -2. * val; xm += val; // Non-uniform grid correction val = A(x, y) * g11_2D(x, y) * d1_dx_2D(x, y) / (2. * dx); @@ -1047,27 +1051,27 @@ void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D &A, const Field2 xm -= val; // B*f - c += B(x,y); + c += B(x, y); // Put values into the preconditioner, X derivatives only acoef(y - localmesh->ystart, x - xstart) = xm; bcoef(y - localmesh->ystart, x - xstart) = c; ccoef(y - localmesh->ystart, x - xstart) = xp; - if(include_y_derivs) { + if (include_y_derivs) { BoutReal dy = dy_2D(x, y); - BoutReal dAdx = (A(x+1, y) - A(x-1, y))/(2.*dx); - BoutReal dAdy = (A(x, y+1) - A(x, y-1))/(2.*dy); + BoutReal dAdx = (A(x + 1, y) - A(x - 1, y)) / (2. * dx); + BoutReal dAdy = (A(x, y + 1) - A(x, y - 1)) / (2. * dy); // A*(G2-1/J*d/dy(J/g_22))*dfdy - val = A(x, y)*coef_dfdy(x, y)/(2.*dy); + val = A(x, y) * coef_dfdy(x, y) / (2. * dy); yp = val; ym = -val; // A*(g22-1/g_22)*d2fdy2 val = A(x, y) * (g22_2D(x, y) - 1. / g_22_2D(x, y)) / SQ(dy); yp += val; - c -= 2.*val; + c -= 2. * val; ym += val; // Non-uniform mesh correction val = A(x, y) * (g22_2D(x, y) - 1. / g_22_2D(x, y)) * d1_dy_2D(x, y) / (2. * dy); @@ -1098,43 +1102,43 @@ void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D &A, const Field2 ///////////////////////////////////////////////// // Now have a 9-point stencil for the Laplacian - int row = globalIndex(x,y); + int row = globalIndex(x, y); // Set the centre (diagonal) - MatSetValues(MatA,1,&row,1,&row,&c,INSERT_VALUES); + MatSetValues(MatA, 1, &row, 1, &row, &c, INSERT_VALUES); // X + 1 - int col = globalIndex(x+1, y); - MatSetValues(MatA,1,&row,1,&col,&xp,INSERT_VALUES); + int col = globalIndex(x + 1, y); + MatSetValues(MatA, 1, &row, 1, &col, &xp, INSERT_VALUES); // X - 1 - col = globalIndex(x-1, y); - MatSetValues(MatA,1,&row,1,&col,&xm,INSERT_VALUES); + col = globalIndex(x - 1, y); + MatSetValues(MatA, 1, &row, 1, &col, &xm, INSERT_VALUES); - if( include_y_derivs ) { + if (include_y_derivs) { // Y + 1 - col = globalIndex(x, y+1); - MatSetValues(MatA,1,&row,1,&col,&yp,INSERT_VALUES); + col = globalIndex(x, y + 1); + MatSetValues(MatA, 1, &row, 1, &col, &yp, INSERT_VALUES); // Y - 1 - col = globalIndex(x, y-1); - MatSetValues(MatA,1,&row,1,&col,&ym,INSERT_VALUES); + col = globalIndex(x, y - 1); + MatSetValues(MatA, 1, &row, 1, &col, &ym, INSERT_VALUES); // X + 1, Y + 1 - col = globalIndex(x+1, y+1); - MatSetValues(MatA,1,&row,1,&col,&xpyp,INSERT_VALUES); + col = globalIndex(x + 1, y + 1); + MatSetValues(MatA, 1, &row, 1, &col, &xpyp, INSERT_VALUES); // X + 1, Y - 1 - col = globalIndex(x+1, y-1); - MatSetValues(MatA,1,&row,1,&col,&xpym,INSERT_VALUES); + col = globalIndex(x + 1, y - 1); + MatSetValues(MatA, 1, &row, 1, &col, &xpym, INSERT_VALUES); // X - 1, Y + 1 - col = globalIndex(x-1, y+1); - MatSetValues(MatA,1,&row,1,&col,&xmyp,INSERT_VALUES); + col = globalIndex(x - 1, y + 1); + MatSetValues(MatA, 1, &row, 1, &col, &xmyp, INSERT_VALUES); // X - 1, Y - 1 - col = globalIndex(x-1, y-1); - MatSetValues(MatA,1,&row,1,&col,&xmym,INSERT_VALUES); + col = globalIndex(x - 1, y - 1); + MatSetValues(MatA, 1, &row, 1, &col, &xmym, INSERT_VALUES); } } } @@ -1234,8 +1238,9 @@ const Field2D LaplaceXY::solve(const Field2D& rhs, const Field2D& x0) { int ind = globalIndex(localmesh->xstart - 1, y); PetscScalar val; VecGetValues(xs, 1, &ind, &val); - for (int x = localmesh->xstart - 1; x >= 0; x--) + for (int x = localmesh->xstart - 1; x >= 0; x--) { result(x, y) = val; + } } } @@ -1245,47 +1250,48 @@ const Field2D LaplaceXY::solve(const Field2D& rhs, const Field2D& x0) { int ind = globalIndex(localmesh->xend + 1, y); PetscScalar val; VecGetValues(xs, 1, &ind, &val); - for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) + for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) { result(x, y) = val; + } } } // Lower Y boundary for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { if ( - // Should not go into corner cells, finite-volume LaplaceXY stencil does not include - // them - (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend)) + // Should not go into corner cells, finite-volume LaplaceXY stencil does not include + // them + (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend)) - // Only go into first corner cell for finite-difference - or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1) - ) { + // Only go into first corner cell for finite-difference + or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1)) { continue; } int ind = globalIndex(it.ind, localmesh->ystart - 1); PetscScalar val; VecGetValues(xs, 1, &ind, &val); - for (int y = localmesh->ystart - 1; y >= 0; y--) + for (int y = localmesh->ystart - 1; y >= 0; y--) { result(it.ind, y) = val; + } } // Upper Y boundary for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { if ( - // Should not go into corner cells, finite-volume LaplaceXY stencil does not include - // them - (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend)) + // Should not go into corner cells, finite-volume LaplaceXY stencil does not include + // them + (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend)) - // Only go into first corner cell for finite-difference - or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1) - ) { + // Only go into first corner cell for finite-difference + or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1)) { continue; } int ind = globalIndex(it.ind, localmesh->yend + 1); PetscScalar val; VecGetValues(xs, 1, &ind, &val); - for (int y = localmesh->yend + 1; y < localmesh->LocalNy; y++) + for (int y = localmesh->yend + 1; y < localmesh->LocalNy; y++) { result(it.ind, y) = val; + } } return result; @@ -1741,47 +1747,47 @@ void LaplaceXY::solveFiniteDifference(const Field2D& x0) { * indexing patterns, so incrementing an integer would be tricky. */ int LaplaceXY::precon(Vec input, Vec result) { - - for(auto itdwn=localmesh->iterateBndryLowerY(); !itdwn.isDone(); itdwn++) { + + for (auto itdwn = localmesh->iterateBndryLowerY(); !itdwn.isDone(); itdwn++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (itdwn.ind < localmesh->xstart or itdwn.ind > localmesh->xend) { continue; } - const int ind = globalIndex(itdwn.ind, localmesh->ystart-1); + const int ind = globalIndex(itdwn.ind, localmesh->ystart - 1); PetscScalar val; - VecGetValues(input, 1, &ind, &val ); - VecSetValues(result, 1, &ind, &val, INSERT_VALUES ); + VecGetValues(input, 1, &ind, &val); + VecSetValues(result, 1, &ind, &val, INSERT_VALUES); } - for(auto itup=localmesh->iterateBndryUpperY(); !itup.isDone(); itup++) { + for (auto itup = localmesh->iterateBndryUpperY(); !itup.isDone(); itup++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (itup.ind < localmesh->xstart or itup.ind > localmesh->xend) { continue; } - const int ind = globalIndex(itup.ind, localmesh->yend+1); + const int ind = globalIndex(itup.ind, localmesh->yend + 1); PetscScalar val; - VecGetValues(input, 1, &ind, &val ); - VecSetValues(result, 1, &ind, &val, INSERT_VALUES ); + VecGetValues(input, 1, &ind, &val); + VecSetValues(result, 1, &ind, &val, INSERT_VALUES); } - + // Load vector x into bvals array - for(int x=xstart; x<=xend; x++) { - for(int y=localmesh->ystart; y<=localmesh->yend; y++) { + for (int x = xstart; x <= xend; x++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int ind = globalIndex(x, y); PetscScalar val; - VecGetValues(input, 1, &ind, &val ); + VecGetValues(input, 1, &ind, &val); bvals(y - localmesh->ystart, x - xstart) = val; } } - + // Solve tridiagonal systems using CR solver cr->solve(bvals, xvals); // Save result xvals into y array - for(int x=xstart; x<=xend; x++) { - for(int y=localmesh->ystart; y<=localmesh->yend; y++) { + for (int x = xstart; x <= xend; x++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { const int ind = globalIndex(x, y); PetscScalar val = xvals(y - localmesh->ystart, x - xstart); - VecSetValues(result, 1, &ind, &val, INSERT_VALUES ); + VecSetValues(result, 1, &ind, &val, INSERT_VALUES); } } VecAssemblyBegin(result); @@ -1792,21 +1798,23 @@ int LaplaceXY::precon(Vec input, Vec result) { /////////////////////////////////////////////////////////////// int LaplaceXY::localSize() { - + // Bulk of points const int nx = localmesh->xend - localmesh->xstart + 1; const int ny = localmesh->yend - localmesh->ystart + 1; - - int n = nx * ny; - + + int n = nx * ny; + // X boundaries - if(localmesh->firstX()) + if (localmesh->firstX()) { n += ny; - if(localmesh->lastX()) + } + if (localmesh->lastX()) { n += ny; - + } + // Y boundaries - for(RangeIterator it=localmesh->iterateBndryLowerY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; @@ -1821,7 +1829,7 @@ int LaplaceXY::localSize() { n++; } } - for(RangeIterator it=localmesh->iterateBndryUpperY(); !it.isDone(); it++) { + for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { // Should not go into corner cells, LaplaceXY stencil does not include them if (it.ind < localmesh->xstart or it.ind > localmesh->xend) { continue; @@ -1836,15 +1844,15 @@ int LaplaceXY::localSize() { n++; } } - + return n; } int LaplaceXY::globalIndex(int x, int y) { - if( (x < 0) || (x >= localmesh->LocalNx) || - (y < 0) || (y >= localmesh->LocalNy) ) + if ((x < 0) || (x >= localmesh->LocalNx) || (y < 0) || (y >= localmesh->LocalNy)) { return -1; // Out of range - + } + // Get the index from a Field2D, round to integer return static_cast(std::round(indexXY(x, y))); } diff --git a/src/invert/laplacexy2/laplacexy2.cxx b/src/invert/laplacexy2/laplacexy2.cxx index 23969dab20..88334982a2 100644 --- a/src/invert/laplacexy2/laplacexy2.cxx +++ b/src/invert/laplacexy2/laplacexy2.cxx @@ -9,11 +9,11 @@ #include #include -#include -#include -#include +#include +#include +#include -#include +#include #include diff --git a/src/invert/laplacexy2/laplacexy2_hypre.cxx b/src/invert/laplacexy2/laplacexy2_hypre.cxx index 5179bac2c3..fc36b77aaa 100644 --- a/src/invert/laplacexy2/laplacexy2_hypre.cxx +++ b/src/invert/laplacexy2/laplacexy2_hypre.cxx @@ -2,10 +2,10 @@ #if BOUT_HAS_HYPRE -#include "boutcomm.hxx" -#include "globals.hxx" -#include "output.hxx" -#include "utils.hxx" +#include "bout/boutcomm.hxx" +#include "bout/globals.hxx" +#include "bout/output.hxx" +#include "bout/utils.hxx" #include "bout/assert.hxx" #include "bout/mesh.hxx" #include "bout/sys/timer.hxx" @@ -18,8 +18,9 @@ inline void gpuAssert(cudaError_t code, const char* file, int line, bool abort = true) { if (code != cudaSuccess) { fprintf(stderr, "GPUassert: %s %s %d\n", cudaGetErrorString(code), file, line); - if (abort) + if (abort) { exit(code); + } } } #endif @@ -312,29 +313,33 @@ Field2D LaplaceXY2Hypre::solve(Field2D& rhs, Field2D& x0) { // Inner X boundary if (localmesh->firstX()) { for (int y = localmesh->ystart; y <= localmesh->yend; y++) { - for (int x = localmesh->xstart - 2; x >= 0; x--) + for (int x = localmesh->xstart - 2; x >= 0; x--) { sol(x, y) = sol(localmesh->xstart - 1, y); + } } } // Outer X boundary if (localmesh->lastX()) { for (int y = localmesh->ystart; y <= localmesh->yend; y++) { - for (int x = localmesh->xend + 2; x < localmesh->LocalNx; x++) + for (int x = localmesh->xend + 2; x < localmesh->LocalNx; x++) { sol(x, y) = sol(localmesh->xend + 1, y); + } } } // Lower Y boundary for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) { - for (int y = localmesh->ystart - 2; y >= 0; y--) + for (int y = localmesh->ystart - 2; y >= 0; y--) { sol(it.ind, y) = sol(it.ind, localmesh->ystart - 1); + } } // Upper Y boundary for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) { - for (int y = localmesh->yend + 2; y < localmesh->LocalNy; y++) + for (int y = localmesh->yend + 2; y < localmesh->LocalNy; y++) { sol(it.ind, y) = sol(it.ind, localmesh->yend + 1); + } } return sol; } diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx index f168b9c34c..9c32f4743e 100644 --- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx +++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx @@ -3,15 +3,16 @@ #if not BOUT_USE_METRIC_3D -#include -#include #include #include -#include +#include +#include +#include -#include +#include -LaplaceXZcyclic::LaplaceXZcyclic(Mesh *m, Options *options, const CELL_LOC loc) : LaplaceXZ(m, options, loc) { +LaplaceXZcyclic::LaplaceXZcyclic(Mesh* m, Options* options, const CELL_LOC loc) + : LaplaceXZ(m, options, loc) { // Note: `m` may be nullptr, but localmesh is set in LaplaceXZ base constructor // Number of Z Fourier modes, including DC @@ -59,7 +60,7 @@ LaplaceXZcyclic::LaplaceXZcyclic(Mesh *m, Options *options, const CELL_LOC loc) LaplaceXZcyclic::setCoefs(one, zero); } -void LaplaceXZcyclic::setCoefs(const Field2D &A2D, const Field2D &B2D) { +void LaplaceXZcyclic::setCoefs(const Field2D& A2D, const Field2D& B2D) { TRACE("LaplaceXZcyclic::setCoefs"); Timer timer("invert"); @@ -67,30 +68,30 @@ void LaplaceXZcyclic::setCoefs(const Field2D &A2D, const Field2D &B2D) { ASSERT1(B2D.getMesh() == localmesh); ASSERT1(A2D.getLocation() == location); ASSERT1(B2D.getLocation() == location); - + // Set coefficients - Coordinates *coord = localmesh->getCoordinates(location); + Coordinates* coord = localmesh->getCoordinates(location); // NOTE: For now the X-Z terms are omitted, so check that they are small ASSERT2(max(abs(coord->g13)) < 1e-5); - + int ind = 0; const BoutReal zlength = getUniform(coord->zlength()); - for(int y=localmesh->ystart; y <= localmesh->yend; y++) { - for(int kz = 0; kz < nmode; kz++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { + for (int kz = 0; kz < nmode; kz++) { BoutReal kwave = kz * 2.0 * PI / zlength; - if(localmesh->firstX()) { + if (localmesh->firstX()) { // Inner X boundary - - if( ((kz == 0) && (inner_boundary_flags & INVERT_DC_GRAD)) || - ((kz != 0) && (inner_boundary_flags & INVERT_AC_GRAD)) ) { + + if (((kz == 0) && (inner_boundary_flags & INVERT_DC_GRAD)) + || ((kz != 0) && (inner_boundary_flags & INVERT_AC_GRAD))) { // Neumann acoef(ind, 0) = 0.0; bcoef(ind, 0) = 1.0; ccoef(ind, 0) = -1.0; - }else { + } else { // Dirichlet // This includes cases where the boundary is set to a value acoef(ind, 0) = 0.0; @@ -100,7 +101,7 @@ void LaplaceXZcyclic::setCoefs(const Field2D &A2D, const Field2D &B2D) { } // Bulk of the domain - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { acoef(ind, x - xstart) = 0.0; // X-1 bcoef(ind, x - xstart) = 0.0; // Diagonal ccoef(ind, x - xstart) = 0.0; // X+1 @@ -115,23 +116,23 @@ void LaplaceXZcyclic::setCoefs(const Field2D &A2D, const Field2D &B2D) { // XX component // Metrics on x+1/2 boundary - BoutReal J = 0.5*(coord->J(x,y) + coord->J(x+1,y)); - BoutReal g11 = 0.5*(coord->g11(x,y) + coord->g11(x+1,y)); - BoutReal dx = 0.5*(coord->dx(x,y) + coord->dx(x+1,y)); - BoutReal A = 0.5*(A2D(x,y) + A2D(x+1,y)); + BoutReal J = 0.5 * (coord->J(x, y) + coord->J(x + 1, y)); + BoutReal g11 = 0.5 * (coord->g11(x, y) + coord->g11(x + 1, y)); + BoutReal dx = 0.5 * (coord->dx(x, y) + coord->dx(x + 1, y)); + BoutReal A = 0.5 * (A2D(x, y) + A2D(x + 1, y)); - BoutReal val = A * J * g11 / (coord->J(x,y) * dx * coord->dx(x,y)); + BoutReal val = A * J * g11 / (coord->J(x, y) * dx * coord->dx(x, y)); ccoef(ind, x - xstart) += val; bcoef(ind, x - xstart) -= val; // Metrics on x-1/2 boundary - J = 0.5*(coord->J(x,y) + coord->J(x-1,y)); - g11 = 0.5*(coord->g11(x,y) + coord->g11(x-1,y)); - dx = 0.5*(coord->dx(x,y) + coord->dx(x-1,y)); - A = 0.5*(A2D(x,y) + A2D(x-1,y)); + J = 0.5 * (coord->J(x, y) + coord->J(x - 1, y)); + g11 = 0.5 * (coord->g11(x, y) + coord->g11(x - 1, y)); + dx = 0.5 * (coord->dx(x, y) + coord->dx(x - 1, y)); + A = 0.5 * (A2D(x, y) + A2D(x - 1, y)); - val = A * J * g11 / (coord->J(x,y) * dx * coord->dx(x,y)); + val = A * J * g11 / (coord->J(x, y) * dx * coord->dx(x, y)); acoef(ind, x - xstart) += val; bcoef(ind, x - xstart) -= val; @@ -140,22 +141,22 @@ void LaplaceXZcyclic::setCoefs(const Field2D &A2D, const Field2D &B2D) { } // Outer X boundary - if(localmesh->lastX()) { + if (localmesh->lastX()) { // Outer X boundary - if( ((kz == 0) && (outer_boundary_flags & INVERT_DC_GRAD)) || - ((kz != 0) && (outer_boundary_flags & INVERT_AC_GRAD)) ) { + if (((kz == 0) && (outer_boundary_flags & INVERT_DC_GRAD)) + || ((kz != 0) && (outer_boundary_flags & INVERT_AC_GRAD))) { // Neumann acoef(ind, nloc - 1) = -1.0; bcoef(ind, nloc - 1) = 1.0; ccoef(ind, nloc - 1) = 0.0; - }else { + } else { // Dirichlet acoef(ind, nloc - 1) = 0.5; bcoef(ind, nloc - 1) = 0.5; ccoef(ind, nloc - 1) = 0.0; } } - + ind++; } } @@ -163,7 +164,7 @@ void LaplaceXZcyclic::setCoefs(const Field2D &A2D, const Field2D &B2D) { cr->setCoefs(acoef, bcoef, ccoef); } -Field3D LaplaceXZcyclic::solve(const Field3D &rhs, const Field3D &x0) { +Field3D LaplaceXZcyclic::solve(const Field3D& rhs, const Field3D& x0) { Timer timer("invert"); ASSERT1(rhs.getMesh() == localmesh); @@ -173,77 +174,77 @@ Field3D LaplaceXZcyclic::solve(const Field3D &rhs, const Field3D &x0) { // Create the rhs array int ind = 0; - for(int y=localmesh->ystart; y <= localmesh->yend; y++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { - if(localmesh->firstX()) { + if (localmesh->firstX()) { // Inner X boundary - - if(inner_boundary_flags & INVERT_SET) { + + if (inner_boundary_flags & INVERT_SET) { // Fourier transform x0 in Z at xstart-1 and xstart rfft(&x0(localmesh->xstart - 1, y, 0), localmesh->LocalNz, std::begin(k1d)); rfft(&x0(localmesh->xstart, y, 0), localmesh->LocalNz, std::begin(k1d_2)); - for(int kz = 0; kz < nmode; kz++) { + for (int kz = 0; kz < nmode; kz++) { // Use the same coefficients as applied to the solution // so can either set gradient or value rhscmplx(ind + kz, 0) = bcoef(ind + kz, 0) * k1d[kz] + ccoef(ind + kz, 0) * k1d_2[kz]; } - }else if(inner_boundary_flags & INVERT_RHS) { + } else if (inner_boundary_flags & INVERT_RHS) { // Fourier transform rhs in Z at xstart-1 and xstart rfft(&rhs(localmesh->xstart - 1, y, 0), localmesh->LocalNz, std::begin(k1d)); rfft(&rhs(localmesh->xstart, y, 0), localmesh->LocalNz, std::begin(k1d_2)); - for(int kz = 0; kz < nmode; kz++) { + for (int kz = 0; kz < nmode; kz++) { // Use the same coefficients as applied to the solution // so can either set gradient or value rhscmplx(ind + kz, 0) = bcoef(ind + kz, 0) * k1d[kz] + ccoef(ind + kz, 0) * k1d_2[kz]; } - }else { - for(int kz = 0; kz < nmode; kz++) { + } else { + for (int kz = 0; kz < nmode; kz++) { rhscmplx(ind + kz, 0) = 0.0; } } } // Bulk of the domain - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { // Fourier transform RHS rfft(&rhs(x, y, 0), localmesh->LocalNz, std::begin(k1d)); - for(int kz = 0; kz < nmode; kz++) { + for (int kz = 0; kz < nmode; kz++) { rhscmplx(ind + kz, x - xstart) = k1d[kz]; } } // Outer X boundary - if(localmesh->lastX()) { + if (localmesh->lastX()) { // Outer X boundary - if(outer_boundary_flags & INVERT_SET) { + if (outer_boundary_flags & INVERT_SET) { // Fourier transform x0 in Z at xend and xend+1 rfft(&x0(localmesh->xend, y, 0), localmesh->LocalNz, std::begin(k1d)); rfft(&x0(localmesh->xend + 1, y, 0), localmesh->LocalNz, std::begin(k1d_2)); - for(int kz = 0; kz < nmode; kz++) { + for (int kz = 0; kz < nmode; kz++) { // Use the same coefficients as applied to the solution // so can either set gradient or value rhscmplx(ind + kz, nloc - 1) = acoef(ind + kz, nloc - 1) * k1d[kz] + bcoef(ind + kz, nloc - 1) * k1d_2[kz]; } - }else if(outer_boundary_flags & INVERT_RHS) { + } else if (outer_boundary_flags & INVERT_RHS) { // Fourier transform rhs in Z at xstart-1 and xstart rfft(&rhs(localmesh->xend, y, 0), localmesh->LocalNz, std::begin(k1d)); rfft(&rhs(localmesh->xend + 1, y, 0), localmesh->LocalNz, std::begin(k1d_2)); - for(int kz = 0; kz < nmode; kz++) { + for (int kz = 0; kz < nmode; kz++) { // Use the same coefficients as applied to the solution // so can either set gradient or value rhscmplx(ind + kz, nloc - 1) = acoef(ind + kz, nloc - 1) * k1d[kz] + bcoef(ind + kz, nloc - 1) * k1d_2[kz]; } - }else { - for(int kz = 0; kz < nmode; kz++) { + } else { + for (int kz = 0; kz < nmode; kz++) { rhscmplx(ind + kz, nloc - 1) = 0.0; } } - - for(int kz = 0; kz < nmode; kz++) { + + for (int kz = 0; kz < nmode; kz++) { rhscmplx(ind + kz, nloc - 1) = 0.0; } } @@ -258,9 +259,9 @@ Field3D LaplaceXZcyclic::solve(const Field3D &rhs, const Field3D &x0) { Field3D result{emptyFrom(rhs)}; ind = 0; - for(int y=localmesh->ystart; y <= localmesh->yend; y++) { - for(int x=xstart;x<=xend;x++) { - for(int kz = 0; kz < nmode; kz++) { + for (int y = localmesh->ystart; y <= localmesh->yend; y++) { + for (int x = xstart; x <= xend; x++) { + for (int kz = 0; kz < nmode; kz++) { k1d[kz] = xcmplx(ind + kz, x - xstart); } @@ -269,7 +270,7 @@ Field3D LaplaceXZcyclic::solve(const Field3D &rhs, const Field3D &x0) { } ind += nmode; } - + return result; } diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx index 0b6a24156b..af7760f9c1 100644 --- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx +++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx @@ -13,22 +13,23 @@ RegisterUnavailableLaplaceXZ registerlaplacexzcylic{ #else -#include -#include -#include -#include "utils.hxx" +#include "bout/utils.hxx" +#include +#include +#include class LaplaceXZcyclic : public LaplaceXZ { public: - LaplaceXZcyclic(Mesh *m = nullptr, Options *options = nullptr, - const CELL_LOC loc = CELL_CENTRE); + LaplaceXZcyclic(Mesh* m = nullptr, Options* options = nullptr, + const CELL_LOC loc = CELL_CENTRE); ~LaplaceXZcyclic() {} - + using LaplaceXZ::setCoefs; - void setCoefs(const Field2D &A, const Field2D &B) override; - + void setCoefs(const Field2D& A, const Field2D& B) override; + using LaplaceXZ::solve; - Field3D solve(const Field3D &b, const Field3D &x0) override; + Field3D solve(const Field3D& b, const Field3D& x0) override; + private: int xstart, xend; int nmode, nloc, nsys; diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx index f59500ba6c..ff28f6d51a 100644 --- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx +++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx @@ -17,13 +17,12 @@ #include #include -#include -#include +#include +#include -LaplaceXZpetsc::LaplaceXZpetsc(Mesh *m, Options *opt, const CELL_LOC loc) - : LaplaceXZ(m, opt, loc), - lib(opt==nullptr ? &(Options::root()["laplacexz"]) : opt), - coefs_set(false) { +LaplaceXZpetsc::LaplaceXZpetsc(Mesh* m, Options* opt, const CELL_LOC loc) + : LaplaceXZ(m, opt, loc), lib(opt == nullptr ? &(Options::root()["laplacexz"]) : opt), + coefs_set(false) { /* Constructor: LaplaceXZpetsc * Purpose: - Setting inversion solver options @@ -135,22 +134,27 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh *m, Options *opt, const CELL_LOC loc) // where r_k = b - Ax_k. The solution is considered diverged if |r_k| > dtol * |b|. const BoutReal rtol = (*opt)["rtol"].doc("Relative tolerance").withDefault(1e-5); - const BoutReal atol = (*opt)["atol"] + const BoutReal atol = + (*opt)["atol"] .doc("Absolute tolerance. The solution is considered converged if |Ax-b| " "< max( rtol * |b| , atol )") .withDefault(1e-10); - const BoutReal dtol = (*opt)["dtol"] - .doc("The solution is considered diverged if |Ax-b| > dtol * |b|") - .withDefault(1e3); + const BoutReal dtol = + (*opt)["dtol"] + .doc("The solution is considered diverged if |Ax-b| > dtol * |b|") + .withDefault(1e3); const int maxits = (*opt)["maxits"].doc("Maximum iterations").withDefault(100000); // Get KSP Solver Type - const std::string ksptype = (*opt)["ksptype"].doc("KSP solver type").withDefault("gmres"); + const std::string ksptype = + (*opt)["ksptype"].doc("KSP solver type").withDefault("gmres"); // Get PC type - const std::string pctype = (*opt)["pctype"].doc("Preconditioner type").withDefault("none"); + const std::string pctype = + (*opt)["pctype"].doc("Preconditioner type").withDefault("none"); - const std::string factor_package = (*opt)["factor_package"] + const std::string factor_package = + (*opt)["factor_package"] .doc("Package to use in preconditioner. Passed to PCFactorSetMatSolver") .withDefault("petsc"); @@ -167,10 +171,10 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh *m, Options *opt, const CELL_LOC loc) } // Create Vectors - VecCreate( comm, &xs ); - VecSetSizes( xs, localN, PETSC_DETERMINE ); - VecSetFromOptions( xs ); - VecDuplicate( xs , &bs ); + VecCreate(comm, &xs); + VecSetSizes(xs, localN, PETSC_DETERMINE); + VecSetFromOptions(xs); + VecDuplicate(xs, &bs); for (int y = localmesh->ystart; y <= localmesh->yend; y++) { YSlice data; @@ -178,18 +182,18 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh *m, Options *opt, const CELL_LOC loc) data.yindex = y; // Set size of Matrix on each processor to localN x localN - MatCreate( comm, &data.MatA ); - MatSetSizes( data.MatA, localN, localN, PETSC_DETERMINE, PETSC_DETERMINE ); + MatCreate(comm, &data.MatA); + MatSetSizes(data.MatA, localN, localN, PETSC_DETERMINE, PETSC_DETERMINE); MatSetFromOptions(data.MatA); ////////////////////////////////////////////////// // Pre-allocate space for matrix elements PetscInt *d_nnz, *o_nnz; - PetscMalloc( (localN)*sizeof(PetscInt), &d_nnz ); - PetscMalloc( (localN)*sizeof(PetscInt), &o_nnz ); + PetscMalloc((localN) * sizeof(PetscInt), &d_nnz); + PetscMalloc((localN) * sizeof(PetscInt), &o_nnz); - for (int i=0;i 0 - // Checking flags are set to something which is not implemented - // This is done binary (which is possible as each flag is a power of 2) - if ( inner_boundary_flags & ~implemented_boundary_flags ) { - throw BoutException("Attempted to set LaplaceXZ inversion boundary flag that is not implemented in petsc_laplace.cxx"); - } - if ( outer_boundary_flags & ~implemented_boundary_flags ) { - throw BoutException("Attempted to set LaplaceXZ inversion boundary flag that is not implemented in petsc_laplace.cxx"); - } - #endif +#if CHECK > 0 + // Checking flags are set to something which is not implemented + // This is done binary (which is possible as each flag is a power of 2) + if (inner_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set LaplaceXZ inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (outer_boundary_flags & ~implemented_boundary_flags) { + throw BoutException("Attempted to set LaplaceXZ inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } +#endif Timer timer("invert"); // Set coefficients @@ -314,7 +319,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { Field3D B = Bin; // Each Y slice is handled as a separate set of matrices and KSP context - for (auto &it : slice) { + for (auto& it : slice) { // Get Y index int y = it.yindex; @@ -324,13 +329,13 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { //////////////////////////////////////////////// // Inner X boundary (see note about BC in LaplaceXZ constructor) int row = Istart; - if(localmesh->firstX()) { - if (inner_boundary_flags & INVERT_AC_GRAD){ + if (localmesh->firstX()) { + if (inner_boundary_flags & INVERT_AC_GRAD) { // Neumann 0 /* NOTE: Sign of the elements are opposite of what one might expect, * see note about BC in LaplaceXZ constructor for more details */ - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 1.0; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -340,10 +345,9 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { row++; } - } - else if(inner_boundary_flags & INVERT_SET){ + } else if (inner_boundary_flags & INVERT_SET) { // Setting BC from x0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 1.0; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -353,10 +357,9 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { row++; } - } - else if(inner_boundary_flags & INVERT_RHS){ + } else if (inner_boundary_flags & INVERT_RHS) { // Setting BC from b - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 1.0; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -366,13 +369,12 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { row++; } - } - else{ + } else { // Default: Dirichlet on inner x boundary /* NOTE: Sign of the elements are opposite of what one might expect, * see note about BC in LaplaceXZ constructor for more details */ - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 0.5; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -388,10 +390,10 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { // Set matrix elements // // (1/J) d/dx ( A * J * g11 d/dx ) + (1/J) d/dz ( A * J * g33 d/dz ) + B - Coordinates *coords = localmesh->getCoordinates(location); + Coordinates* coords = localmesh->getCoordinates(location); - for(int x=localmesh->xstart; x <= localmesh->xend; x++) { - for(int z=0; z < localmesh->LocalNz; z++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // stencil entries PetscScalar c, xm, xp, zm, zp; // Diagonal entries @@ -588,7 +590,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { } // B term - c += B(x,y,z); + c += B(x, y, z); ///////////////////////////////////////////////// // Now have a 9-point stencil for the Laplacian @@ -615,8 +617,8 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { // Z + 1 col = row + 1; - if(z == localmesh->LocalNz-1) { - col -= localmesh->LocalNz; // Wrap around + if (z == localmesh->LocalNz - 1) { + col -= localmesh->LocalNz; // Wrap around } MatSetValues(it.MatA, 1, &row, 1, &col, &zp, INSERT_VALUES); @@ -631,8 +633,8 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { // Z - 1 col = row - 1; - if(z == 0) { - col += localmesh->LocalNz; // Wrap around + if (z == 0) { + col += localmesh->LocalNz; // Wrap around } MatSetValues(it.MatA, 1, &row, 1, &col, &zm, INSERT_VALUES); @@ -650,10 +652,10 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { //////////////////////////////////////////////// // Outer X boundary (see note about BC in LaplaceXZ constructor) - if(localmesh->lastX()) { - if (outer_boundary_flags & INVERT_AC_GRAD){ + if (localmesh->lastX()) { + if (outer_boundary_flags & INVERT_AC_GRAD) { // Neumann 0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 1.0; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -663,10 +665,9 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { row++; } - } - else if (outer_boundary_flags & INVERT_SET){ + } else if (outer_boundary_flags & INVERT_SET) { // Setting BC from x0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 1.0; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -676,10 +677,9 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { row++; } - } - else if (outer_boundary_flags & INVERT_RHS){ + } else if (outer_boundary_flags & INVERT_RHS) { // Setting BC from b - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val = 1.0; MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); @@ -689,12 +689,11 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { row++; } - } - else{ + } else { //Default: Dirichlet on outer X boundary PetscScalar val = 0.5; - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES); int col = row - (localmesh->LocalNz); // -1 in X @@ -714,14 +713,14 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { // Increase reuse count reuse_count++; - if(reuse_count > reuse_limit) { + if (reuse_count > reuse_limit) { // Reuse limit exceeded. Reset count reuse_count = 0; // Modifying preconditioner matrix - for (auto &it : slice) { + for (auto& it : slice) { // Copy matrix into preconditioner - if(coefs_set) { + if (coefs_set) { // Preconditioner already set MatDestroy(&it.MatP); } @@ -729,20 +728,20 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { } // Set operators - for (auto &it : slice) { + for (auto& it : slice) { // Note: This is a hack to force update of the preconditioner matrix -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) KSPSetOperators(it.ksp, it.MatA, it.MatP); #else KSPSetOperators(it.ksp, it.MatA, it.MatP, SAME_NONZERO_PATTERN); #endif } - }else { - for (auto &it : slice) { + } else { + for (auto& it : slice) { /// Reuse the preconditioner, even if the operator changes -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) KSPSetReusePreconditioner(it.ksp, PETSC_TRUE); #else KSPSetOperators(it.ksp, it.MatA, it.MatP, SAME_PRECONDITIONER); @@ -753,7 +752,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D &Ain, const Field3D &Bin) { coefs_set = true; } -Field3D LaplaceXZpetsc::solve(const Field3D &bin, const Field3D &x0in) { +Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) { /* Function: LaplaceXZpetsc::solve * Purpose: - Set the values of b in Ax=b * - Set the initial guess x0, and use this for x in Ax=b @@ -775,7 +774,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D &bin, const Field3D &x0in) { ASSERT1(bin.getLocation() == location); ASSERT1(x0in.getLocation() == location); - if(!coefs_set) { + if (!coefs_set) { throw BoutException("LaplaceXZpetsc: solve called before setCoefs"); } @@ -786,7 +785,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D &bin, const Field3D &x0in) { Field3D result{emptyFrom(bin)}; - for (auto &it : slice) { + for (auto& it : slice) { /// Get y index int y = it.yindex; @@ -802,127 +801,121 @@ Field3D LaplaceXZpetsc::solve(const Field3D &bin, const Field3D &x0in) { int ind = Istart; // Inner X boundary (see note about BC in LaplaceXZ constructor) - if(localmesh->firstX()) { - if (inner_boundary_flags & INVERT_AC_GRAD){ + if (localmesh->firstX()) { + if (inner_boundary_flags & INVERT_AC_GRAD) { // Neumann 0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xstart-1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xstart - 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b val = 0.0; - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } - } - else if (inner_boundary_flags & INVERT_SET){ + } else if (inner_boundary_flags & INVERT_SET) { // Setting BC from x0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xstart-1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xstart - 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b - val = x0(localmesh->xstart,y,z); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = x0(localmesh->xstart, y, z); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } - } - else if (inner_boundary_flags & INVERT_RHS){ + } else if (inner_boundary_flags & INVERT_RHS) { // Setting BC from b - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xstart-1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xstart - 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b - val = b(localmesh->xstart,y,z); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = b(localmesh->xstart, y, z); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } - } - else{ + } else { // Default: Neumann on inner x boundary - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xstart-1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xstart - 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b - val = x0(localmesh->xstart-1,y,z) - x0(localmesh->xstart,y,z); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = x0(localmesh->xstart - 1, y, z) - x0(localmesh->xstart, y, z); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } } } // Set the inner points - for(int x=localmesh->xstart;x<= localmesh->xend;x++) { - for(int z=0; z < localmesh->LocalNz; z++) { - PetscScalar val = x0(x,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { + PetscScalar val = x0(x, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); - val = b(x,y,z); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = b(x, y, z); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } } // Outer X boundary (see note about BC in LaplaceXZ constructor) - if(localmesh->lastX()) { - if (outer_boundary_flags & INVERT_AC_GRAD){ + if (localmesh->lastX()) { + if (outer_boundary_flags & INVERT_AC_GRAD) { // Neumann 0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xend+1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xend + 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b val = 0.0; - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } - } - else if (outer_boundary_flags & INVERT_SET){ + } else if (outer_boundary_flags & INVERT_SET) { // Setting BC from x0 - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xend+1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xend + 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b - val = x0(localmesh->xend+1,y,z); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = x0(localmesh->xend + 1, y, z); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } - } - else if (outer_boundary_flags & INVERT_RHS){ + } else if (outer_boundary_flags & INVERT_RHS) { // Setting BC from b - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xend+1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xend + 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b - val = b(localmesh->xend+1,y,z); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = b(localmesh->xend + 1, y, z); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } - } - else{ + } else { //Default: Dirichlet on outer X boundary - for(int z=0; z < localmesh->LocalNz; z++) { + for (int z = 0; z < localmesh->LocalNz; z++) { // Setting the initial guess x0 - PetscScalar val = x0(localmesh->xend+1,y,z); - VecSetValues( xs, 1, &ind, &val, INSERT_VALUES ); + PetscScalar val = x0(localmesh->xend + 1, y, z); + VecSetValues(xs, 1, &ind, &val, INSERT_VALUES); // Setting the solution b - val = 0.5*(x0(localmesh->xend,y,z) + x0(localmesh->xend+1,y,z)); - VecSetValues( bs, 1, &ind, &val, INSERT_VALUES ); + val = 0.5 * (x0(localmesh->xend, y, z) + x0(localmesh->xend + 1, y, z)); + VecSetValues(bs, 1, &ind, &val, INSERT_VALUES); ind++; } @@ -948,7 +941,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D &bin, const Field3D &x0in) { KSPConvergedReason reason; KSPGetConvergedReason(it.ksp, &reason); - if(reason <= 0) { + if (reason <= 0) { throw BoutException("LaplaceXZ failed to converge. Reason {:d}", reason); } @@ -957,34 +950,34 @@ Field3D LaplaceXZpetsc::solve(const Field3D &bin, const Field3D &x0in) { ind = Istart; // Inner X boundary - if(localmesh->firstX()) { - for(int z=0; z < localmesh->LocalNz; z++) { + if (localmesh->firstX()) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val; - VecGetValues(xs, 1, &ind, &val ); - for (int x = localmesh->xstart - 1; x >= 0; --x){ - result(x,y,z) = val; - } + VecGetValues(xs, 1, &ind, &val); + for (int x = localmesh->xstart - 1; x >= 0; --x) { + result(x, y, z) = val; + } ind++; } } - for(int x=localmesh->xstart;x<= localmesh->xend;x++) { - for(int z=0; z < localmesh->LocalNz; z++) { + for (int x = localmesh->xstart; x <= localmesh->xend; x++) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val; - VecGetValues(xs, 1, &ind, &val ); - result(x,y,z) = val; + VecGetValues(xs, 1, &ind, &val); + result(x, y, z) = val; ind++; } } // Outer X boundary - if(localmesh->lastX()) { - for(int z=0; z < localmesh->LocalNz; z++) { + if (localmesh->lastX()) { + for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val; - VecGetValues(xs, 1, &ind, &val ); - for(int x=localmesh->xend+1; xLocalNx; ++x){ - result(x,y,z) = val; - } + VecGetValues(xs, 1, &ind, &val); + for (int x = localmesh->xend + 1; x < localmesh->LocalNx; ++x) { + result(x, y, z) = val; + } ind++; } } diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx index 40c35e5f73..47967390f9 100644 --- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx +++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx @@ -29,53 +29,48 @@ RegisterLaplaceXZ registerlaplacexzpetsc{"petsc"}; class LaplaceXZpetsc : public LaplaceXZ { public: - LaplaceXZpetsc(Mesh *m = nullptr, Options *options = nullptr, const CELL_LOC loc = CELL_CENTRE); + LaplaceXZpetsc(Mesh* m = nullptr, Options* options = nullptr, + const CELL_LOC loc = CELL_CENTRE); ~LaplaceXZpetsc(); - void setCoefs(const Field3D &A, const Field3D &B); + void setCoefs(const Field3D& A, const Field3D& B); - void setCoefs(const Field2D &A, const Field2D &B) { - setCoefs(Field3D(A), Field3D(B)); - } + void setCoefs(const Field2D& A, const Field2D& B) { setCoefs(Field3D(A), Field3D(B)); } /*! * Solve Laplacian in X-Z */ - Field3D solve(const Field3D &b, const Field3D &x0); + Field3D solve(const Field3D& b, const Field3D& x0); private: - PetscLib lib; ///< Requires PETSc library + PetscLib lib; ///< Requires PETSc library /*! * Data for a single Y slice */ struct YSlice { int yindex; /// Y index - Mat MatA; ///< Matrix to be inverted - Mat MatP; ///< Matrix for preconditioner - KSP ksp; ///< Krylov Subspace solver context + Mat MatA; ///< Matrix to be inverted + Mat MatP; ///< Matrix for preconditioner + KSP ksp; ///< Krylov Subspace solver context }; std::vector slice; - Vec xs, bs; ///< Solution and RHS vectors + Vec xs, bs; ///< Solution and RHS vectors int reuse_limit; ///< How many times can the preconditioner be reused? int reuse_count; ///< How many times has it been reused? bool coefs_set; ///< Have coefficients been set? - - #if CHECK > 0 - // Currently implemented flags - static const int implemented_boundary_flags = INVERT_AC_GRAD - + INVERT_SET - + INVERT_RHS - ; - #endif + +#if CHECK > 0 + // Currently implemented flags + static const int implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_RHS; +#endif int inner_boundary_flags; ///< Flags to set inner boundary condition int outer_boundary_flags; ///< Flags to set outer boundary condition }; - #endif // BOUT_HAS_PETSC #endif // __LAPLACEXZ_PETSC_H__ diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx index 3b27fee955..af46eb58c6 100644 --- a/src/invert/parderiv/impls/cyclic/cyclic.cxx +++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx @@ -40,36 +40,36 @@ #if not BOUT_USE_METRIC_3D -#include -#include -#include -#include -#include -#include -#include #include +#include +#include +#include +#include +#include +#include +#include #include #include -InvertParCR::InvertParCR(Options *opt, CELL_LOC location, Mesh *mesh_in) - : InvertPar(opt, location, mesh_in), A(1.0), B(0.0), C(0.0), D(0.0), E(0.0) { +InvertParCR::InvertParCR(Options* opt, CELL_LOC location, Mesh* mesh_in) + : InvertPar(opt, location, mesh_in), A(1.0), B(0.0), C(0.0), D(0.0), E(0.0) { // Number of k equations to solve for each x location - nsys = 1 + (localmesh->LocalNz)/2; + nsys = 1 + (localmesh->LocalNz) / 2; sg = sqrt(localmesh->getCoordinates(location)->g_22); sg = DDY(1. / sg) / sg; } -const Field3D InvertParCR::solve(const Field3D &f) { +const Field3D InvertParCR::solve(const Field3D& f) { TRACE("InvertParCR::solve(Field3D)"); ASSERT1(localmesh == f.getMesh()); ASSERT1(location == f.getLocation()); Field3D result = emptyFrom(f).setDirectionY(YDirectionType::Aligned); - - Coordinates *coord = f.getCoordinates(); + + Coordinates* coord = f.getCoordinates(); Field3D alignedField = toFieldAligned(f, "RGN_NOBNDRY"); @@ -95,8 +95,9 @@ const Field3D InvertParCR::solve(const Field3D &f) { n += localmesh->ystart; } - if (n > size) + if (n > size) { size = n; // Maximum size + } } } @@ -111,7 +112,7 @@ const Field3D InvertParCR::solve(const Field3D &f) { // Loop over flux-surfaces for (surf.first(); !surf.isDone(); surf.next()) { int x = surf.xpos; - + // Test if open or closed field-lines BoutReal ts; bool closed = surf.closed(ts); @@ -140,24 +141,24 @@ const Field3D InvertParCR::solve(const Field3D &f) { // Setup CyclicReduce object cr->setup(surf.communicator(), size); cr->setPeriodic(closed); - + // Take Fourier transform - for (int y = 0; y < localmesh->LocalNy - localmesh->ystart - local_ystart; y++) + for (int y = 0; y < localmesh->LocalNy - localmesh->ystart - local_ystart; y++) { rfft(alignedField(x, y + local_ystart), localmesh->LocalNz, &rhs(y + y0, 0)); + } // Set up tridiagonal system for (int k = 0; k < nsys; k++) { BoutReal kwave = k * 2.0 * PI / zlength; // wave number is 1/length for (int y = 0; y < localmesh->LocalNy - localmesh->ystart - local_ystart; y++) { - BoutReal acoef = A(x, y + local_ystart); // Constant + BoutReal acoef = A(x, y + local_ystart); // Constant BoutReal bcoef = B(x, y + local_ystart) / coord->g_22(x, y + local_ystart); // d2dy2 BoutReal ccoef = C(x, y + local_ystart); // d2dydz BoutReal dcoef = D(x, y + local_ystart); // d2dz2 - BoutReal ecoef = - E(x, y + local_ystart) - + sg(x, y + local_ystart)*B(x, y + local_ystart); // ddy + BoutReal ecoef = E(x, y + local_ystart) + + sg(x, y + local_ystart) * B(x, y + local_ystart); // ddy if (coord->non_uniform) { ecoef += bcoef * coord->d1_dy(x, y + local_ystart); @@ -169,9 +170,9 @@ const Field3D InvertParCR::solve(const Field3D &f) { // const d2dy2 d2dydz d2dz2 ddy // ----- ----- ------ ----- --- - a(k, y + y0) = bcoef - 0.5 * Im * kwave * ccoef - 0.5 * ecoef; - b(k, y + y0) = acoef - 2. * bcoef - SQ(kwave) * dcoef; - c(k, y + y0) = bcoef + 0.5 * Im * kwave * ccoef + 0.5 * ecoef; + a(k, y + y0) = bcoef - 0.5 * Im * kwave * ccoef - 0.5 * ecoef; + b(k, y + y0) = acoef - 2. * bcoef - SQ(kwave) * dcoef; + c(k, y + y0) = bcoef + 0.5 * Im * kwave * ccoef + 0.5 * ecoef; rhsk(k, y + y0) = rhs(y + y0, k); // Transpose } @@ -186,14 +187,14 @@ const Field3D InvertParCR::solve(const Field3D &f) { if (rank == 0) { for (int k = 0; k < nsys; k++) { BoutReal kwave = k * 2.0 * PI / zlength; // wave number is 1/[rad] - dcomplex phase(cos(kwave*ts) , -sin(kwave*ts)); + dcomplex phase(cos(kwave * ts), -sin(kwave * ts)); a(k, 0) *= phase; } } if (rank == np - 1) { for (int k = 0; k < nsys; k++) { BoutReal kwave = k * 2.0 * PI / zlength; // wave number is 1/[rad] - dcomplex phase(cos(kwave*ts) , sin(kwave*ts)); + dcomplex phase(cos(kwave * ts), sin(kwave * ts)); c(k, localmesh->LocalNy - 2 * localmesh->ystart - 1) *= phase; } } @@ -229,13 +230,15 @@ const Field3D InvertParCR::solve(const Field3D &f) { // Put back into rhs array for (int k = 0; k < nsys; k++) { - for (int y = 0; y < size; y++) + for (int y = 0; y < size; y++) { rhs(y, k) = xk(k, y); + } } // Inverse Fourier transform - for (int y = 0; y < size; y++) + for (int y = 0; y < size; y++) { irfft(&rhs(y, 0), localmesh->LocalNz, result(x, y + local_ystart - y0)); + } } return fromFieldAligned(result, "RGN_NOBNDRY"); diff --git a/src/invert/parderiv/impls/cyclic/cyclic.hxx b/src/invert/parderiv/impls/cyclic/cyclic.hxx index d7db822adb..8fae47a055 100644 --- a/src/invert/parderiv/impls/cyclic/cyclic.hxx +++ b/src/invert/parderiv/impls/cyclic/cyclic.hxx @@ -42,7 +42,7 @@ #ifndef __INV_PAR_CR_H__ #define __INV_PAR_CR_H__ -#include "invert_parderiv.hxx" +#include "bout/invert_parderiv.hxx" #include "bout/build_config.hxx" #if BOUT_USE_METRIC_3D @@ -54,9 +54,9 @@ RegisterUnavailableInvertPar registerinvertparcyclic{ #else -#include "dcomplex.hxx" -#include -#include "utils.hxx" +#include "bout/dcomplex.hxx" +#include "bout/utils.hxx" +#include class InvertParCR : public InvertPar { public: @@ -64,34 +64,34 @@ public: Mesh* mesh_in = bout::globals::mesh); using InvertPar::solve; - const Field3D solve(const Field3D &f) override; + const Field3D solve(const Field3D& f) override; using InvertPar::setCoefA; - void setCoefA(const Field2D &f) override { + void setCoefA(const Field2D& f) override { ASSERT1(localmesh == f.getMesh()); ASSERT1(location == f.getLocation()); A = f; } using InvertPar::setCoefB; - void setCoefB(const Field2D &f) override { + void setCoefB(const Field2D& f) override { ASSERT1(localmesh == f.getMesh()); ASSERT1(location == f.getLocation()); B = f; } using InvertPar::setCoefC; - void setCoefC(const Field2D &f) override { + void setCoefC(const Field2D& f) override { ASSERT1(localmesh == f.getMesh()); ASSERT1(location == f.getLocation()); C = f; } using InvertPar::setCoefD; - void setCoefD(const Field2D &f) override { + void setCoefD(const Field2D& f) override { ASSERT1(localmesh == f.getMesh()); ASSERT1(location == f.getLocation()); D = f; } using InvertPar::setCoefE; - void setCoefE(const Field2D &f) override { + void setCoefE(const Field2D& f) override { ASSERT1(localmesh == f.getMesh()); ASSERT1(location == f.getLocation()); E = f; @@ -100,7 +100,7 @@ public: private: Field2D A{0.0}, B{0.0}, C{0.0}, D{0.0}, E{0.0}; Field2D sg; // Coefficient of DDY contribution to Grad2_par2 - + int nsys; }; diff --git a/src/invert/parderiv/invert_parderiv.cxx b/src/invert/parderiv/invert_parderiv.cxx index 48245b53df..bc8ad8669f 100644 --- a/src/invert/parderiv/invert_parderiv.cxx +++ b/src/invert/parderiv/invert_parderiv.cxx @@ -27,12 +27,12 @@ * ************************************************************************/ -#include #include "impls/cyclic/cyclic.hxx" +#include -const Field2D InvertPar::solve(const Field2D &f) { +const Field2D InvertPar::solve(const Field2D& f) { Field3D var(f); - + var = solve(var); return DC(var); } diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx index 32cfea8306..a0db089713 100644 --- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx +++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx @@ -41,13 +41,13 @@ #if not BOUT_USE_METRIC_3D #include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include #include diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx index 2ce4f1acc9..13485d28de 100644 --- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx +++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx @@ -52,9 +52,9 @@ RegisterUnavailableInvertParDiv registerinvertpardivcyclic{ #else -#include "dcomplex.hxx" -#include "utils.hxx" -#include +#include "bout/dcomplex.hxx" +#include "bout/utils.hxx" +#include class InvertParDivCR : public InvertParDiv { public: diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx index 87f7835796..aa9363a816 100644 --- a/src/mesh/boundary_factory.cxx +++ b/src/mesh/boundary_factory.cxx @@ -1,20 +1,20 @@ -#include "parallel_boundary_op.hxx" -#include "parallel_boundary_region.hxx" -#include -#include -#include -#include -#include +#include "bout/parallel_boundary_op.hxx" +#include "bout/parallel_boundary_region.hxx" +#include +#include +#include +#include +#include #include -#include #include +#include using std::list; using std::string; -#include +#include -BoundaryFactory *BoundaryFactory::instance = nullptr; +BoundaryFactory* BoundaryFactory::instance = nullptr; BoundaryFactory::BoundaryFactory() { add(new BoundaryDirichlet(), "dirichlet"); @@ -36,7 +36,7 @@ BoundaryFactory::BoundaryFactory() { add(new BoundaryFree(), "free"); add(new BoundaryFree_O2(), "free_o2"); add(new BoundaryFree_O3(), "free_o3"); - + addMod(new BoundaryRelax(), "relax"); addMod(new BoundaryWidth(), "width"); addMod(new BoundaryToFieldAligned(), "toFieldAligned"); @@ -51,13 +51,13 @@ BoundaryFactory::BoundaryFactory() { BoundaryFactory::~BoundaryFactory() { // Free any boundaries - for (const auto &it : opmap) { + for (const auto& it : opmap) { delete it.second; } - for (const auto &it : modmap) { + for (const auto& it : modmap) { delete it.second; } - for (const auto &it : par_opmap) { + for (const auto& it : par_opmap) { delete it.second; } } @@ -71,15 +71,16 @@ BoundaryFactory* BoundaryFactory::getInstance() { } void BoundaryFactory::cleanup() { - if (instance == nullptr) + if (instance == nullptr) { return; + } // Just delete the instance delete instance; instance = nullptr; } -BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase *region) { +BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase* region) { // Search for a string of the form: modifier(operation) auto pos = name.find('('); @@ -87,14 +88,16 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * // No more (opening) brackets. Should be a boundary operation // Need to strip whitespace - if( (name == "null") || (name == "none") ) + if ((name == "null") || (name == "none")) { return nullptr; + } - if(region->isParallel) { + if (region->isParallel) { // Parallel boundary - BoundaryOpPar *pop = findBoundaryOpPar(trim(name)); - if (pop == nullptr) + BoundaryOpPar* pop = findBoundaryOpPar(trim(name)); + if (pop == nullptr) { throw BoutException("Could not find parallel boundary condition '{:s}'", name); + } // Clone the boundary operation, passing the region to operate over, // an empty args list and empty keyword map @@ -102,9 +105,10 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * return pop->clone(dynamic_cast(region), args, {}); } else { // Perpendicular boundary - BoundaryOp *op = findBoundaryOp(trim(name)); - if (op == nullptr) + BoundaryOp* op = findBoundaryOp(trim(name)); + if (op == nullptr) { throw BoutException("Could not find boundary condition '{:s}'", name); + } // Clone the boundary operation, passing the region to operate over, // an empty args list and empty keyword map @@ -114,14 +118,15 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * } // Contains a bracket. Find the last bracket and remove auto pos2 = name.rfind(')'); - if(pos2 == string::npos) { - output_warn << "\tWARNING: Unmatched brackets in boundary condition: " << name << endl; + if (pos2 == string::npos) { + output_warn << "\tWARNING: Unmatched brackets in boundary condition: " << name + << endl; } // Find the function name before the bracket - string func = trim(name.substr(0,pos)); + string func = trim(name.substr(0, pos)); // And the argument inside the bracket - string arg = trim(name.substr(pos+1, pos2-pos-1)); + string arg = trim(name.substr(pos + 1, pos2 - pos - 1)); // Split the argument on commas // NOTE: Commas could be part of sub-expressions, so // need to take account of brackets @@ -143,7 +148,7 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * break; case ',': { if (level == 0) { - string s = arg.substr(start, i-start); + string s = arg.substr(start, i - start); // Check if s contains '=', and if so treat as a keyword auto poseq = s.find('='); @@ -162,19 +167,20 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * std::string s = arg.substr(start); auto poseq = s.find('='); if (poseq != string::npos) { - keywords[trim(s.substr(0,poseq))] = trim(s.substr(poseq+1)); + keywords[trim(s.substr(0, poseq))] = trim(s.substr(poseq + 1)); } else { // No '=', so a positional argument arglist.push_back(trim(s)); } // Test if func is a modifier - BoundaryModifier *mod = findBoundaryMod(func); + BoundaryModifier* mod = findBoundaryMod(func); if (mod != nullptr) { // The first argument should be an operation auto* op = dynamic_cast(create(arglist.front(), region)); - if (op == nullptr) + if (op == nullptr) { return nullptr; + } // Remove the first element (name of operation) arglist.pop_front(); @@ -183,16 +189,16 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * return mod->cloneMod(op, arglist); } - if(region->isParallel) { + if (region->isParallel) { // Parallel boundary - BoundaryOpPar *pop = findBoundaryOpPar(trim(func)); + BoundaryOpPar* pop = findBoundaryOpPar(trim(func)); if (pop != nullptr) { // An operation with arguments return pop->clone(dynamic_cast(region), arglist, keywords); } } else { // Perpendicular boundary - BoundaryOp *op = findBoundaryOp(trim(func)); + BoundaryOp* op = findBoundaryOp(trim(func)); if (op != nullptr) { // An operation with arguments return op->clone(dynamic_cast(region), arglist, keywords); @@ -206,20 +212,22 @@ BoundaryOpBase* BoundaryFactory::create(const string &name, BoundaryRegionBase * return nullptr; } -BoundaryOpBase* BoundaryFactory::create(const char* name, BoundaryRegionBase *region) { +BoundaryOpBase* BoundaryFactory::create(const char* name, BoundaryRegionBase* region) { return create(string(name), region); } -BoundaryOpBase* BoundaryFactory::createFromOptions(const string &varname, BoundaryRegionBase *region) { - if (region == nullptr) +BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname, + BoundaryRegionBase* region) { + if (region == nullptr) { return nullptr; + } output_info << "\t" << region->label << " region: "; string prefix("bndry_"); string side; - switch(region->location) { + switch (region->location) { case BNDRY_XIN: { side = "xin"; break; @@ -259,33 +267,33 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string &varname, Bounda } // Get options - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); // Get variable options - Options *varOpts = options->getSection(varname); + Options* varOpts = options->getSection(varname); string set; /// First try looking for (var, region) - if(varOpts->isSet(prefix+region->label)) { - varOpts->get(prefix+region->label, set, ""); + if (varOpts->isSet(prefix + region->label)) { + varOpts->get(prefix + region->label, set, ""); return create(set, region); } /// Then (var, side) - if(varOpts->isSet(prefix+side)) { - varOpts->get(prefix+side, set, ""); + if (varOpts->isSet(prefix + side)) { + varOpts->get(prefix + side, set, ""); return create(set, region); } /// Then (var, all) - if(region->isParallel) { - if(varOpts->isSet(prefix+"par_all")) { - varOpts->get(prefix+"par_all", set, ""); + if (region->isParallel) { + if (varOpts->isSet(prefix + "par_all")) { + varOpts->get(prefix + "par_all", set, ""); return create(set, region); } } else { - if(varOpts->isSet(prefix+"all")) { - varOpts->get(prefix+"all", set, ""); + if (varOpts->isSet(prefix + "all")) { + varOpts->get(prefix + "all", set, ""); return create(set, region); } } @@ -294,34 +302,35 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string &varname, Bounda varOpts = options->getSection("all"); /// Then (all, region) - if(varOpts->isSet(prefix+region->label)) { - varOpts->get(prefix+region->label, set, ""); + if (varOpts->isSet(prefix + region->label)) { + varOpts->get(prefix + region->label, set, ""); return create(set, region); } /// Then (all, side) - if(varOpts->isSet(prefix+side)) { - varOpts->get(prefix+side, set, ""); + if (varOpts->isSet(prefix + side)) { + varOpts->get(prefix + side, set, ""); return create(set, region); } /// Then (all, all) - if(region->isParallel) { + if (region->isParallel) { // Different default for parallel boundary regions - varOpts->get(prefix+"par_all", set, "parallel_dirichlet"); + varOpts->get(prefix + "par_all", set, "parallel_dirichlet"); } else { - varOpts->get(prefix+"all", set, "dirichlet"); + varOpts->get(prefix + "all", set, "dirichlet"); } return create(set, region); // Defaults to Dirichlet conditions, to prevent undefined boundary // values. If a user want to override, specify "none" or "null" } -BoundaryOpBase* BoundaryFactory::createFromOptions(const char* varname, BoundaryRegionBase *region) { +BoundaryOpBase* BoundaryFactory::createFromOptions(const char* varname, + BoundaryRegionBase* region) { return createFromOptions(string(varname), region); } -void BoundaryFactory::add(BoundaryOp* bop, const string &name) { +void BoundaryFactory::add(BoundaryOp* bop, const string& name) { if ((findBoundaryMod(name) != nullptr) || (findBoundaryOp(name) != nullptr)) { // error - already exists output_error << "ERROR: Trying to add an already existing boundary: " << name << endl; @@ -330,11 +339,9 @@ void BoundaryFactory::add(BoundaryOp* bop, const string &name) { opmap[lowercase(name)] = bop; } -void BoundaryFactory::add(BoundaryOp* bop, const char *name) { - add(bop, string(name)); -} +void BoundaryFactory::add(BoundaryOp* bop, const char* name) { add(bop, string(name)); } -void BoundaryFactory::add(BoundaryOpPar* bop, const string &name) { +void BoundaryFactory::add(BoundaryOpPar* bop, const string& name) { if (findBoundaryOpPar(name) != nullptr) { // error - already exists output_error << "ERROR: Trying to add an already existing boundary: " << name << endl; @@ -343,40 +350,44 @@ void BoundaryFactory::add(BoundaryOpPar* bop, const string &name) { par_opmap[lowercase(name)] = bop; } -void BoundaryFactory::add(BoundaryOpPar* bop, const char *name) { +void BoundaryFactory::add(BoundaryOpPar* bop, const char* name) { add(bop, string(name)); } -void BoundaryFactory::addMod(BoundaryModifier* bmod, const string &name) { +void BoundaryFactory::addMod(BoundaryModifier* bmod, const string& name) { if ((findBoundaryMod(name) != nullptr) || (findBoundaryOp(name) != nullptr)) { // error - already exists - output_error << "ERROR: Trying to add an already existing boundary modifier: " << name << endl; + output_error << "ERROR: Trying to add an already existing boundary modifier: " << name + << endl; return; } modmap[lowercase(name)] = bmod; } -void BoundaryFactory::addMod(BoundaryModifier* bmod, const char *name) { +void BoundaryFactory::addMod(BoundaryModifier* bmod, const char* name) { addMod(bmod, string(name)); } -BoundaryOp* BoundaryFactory::findBoundaryOp(const string &s) { +BoundaryOp* BoundaryFactory::findBoundaryOp(const string& s) { auto it = opmap.find(lowercase(s)); - if(it == opmap.end()) + if (it == opmap.end()) { return nullptr; + } return it->second; } -BoundaryModifier* BoundaryFactory::findBoundaryMod(const string &s) { +BoundaryModifier* BoundaryFactory::findBoundaryMod(const string& s) { auto it = modmap.find(lowercase(s)); - if(it == modmap.end()) + if (it == modmap.end()) { return nullptr; + } return it->second; } -BoundaryOpPar* BoundaryFactory::findBoundaryOpPar(const string &s) { +BoundaryOpPar* BoundaryFactory::findBoundaryOpPar(const string& s) { auto it = par_opmap.find(lowercase(s)); - if(it == par_opmap.end()) + if (it == par_opmap.end()) { return nullptr; + } return it->second; } diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx index 1e884abc80..51b6c9043f 100644 --- a/src/mesh/boundary_region.cxx +++ b/src/mesh/boundary_region.cxx @@ -1,8 +1,8 @@ #include -#include -#include -#include +#include +#include +#include #include using std::swap; @@ -11,49 +11,46 @@ BoundaryRegionXIn::BoundaryRegionXIn(std::string name, int ymin, int ymax, Mesh* : BoundaryRegion(std::move(name), -1, 0, passmesh), ys(ymin), ye(ymax) { location = BNDRY_XIN; width = localmesh->xstart; - x = width-1; // First point inside the boundary - if(ye < ys) + x = width - 1; // First point inside the boundary + if (ye < ys) { swap(ys, ye); + } } -void BoundaryRegionXIn::first() -{ - x = width-1; +void BoundaryRegionXIn::first() { + x = width - 1; y = ys; } -void BoundaryRegionXIn::next() -{ +void BoundaryRegionXIn::next() { // Loop over all points, from inside out y++; - if(y > ye) { + if (y > ye) { y = ys; x--; // Going from inside out } } -void BoundaryRegionXIn::next1d() -{ +void BoundaryRegionXIn::next1d() { // Loop over the innermost points y++; } -void BoundaryRegionXIn::nextX() -{ +void BoundaryRegionXIn::nextX() { x--; - if(y > ye) + if (y > ye) { y = ys; + } } -void BoundaryRegionXIn::nextY() -{ +void BoundaryRegionXIn::nextY() { y++; - if(x < 0) - x = width-1; + if (x < 0) { + x = width - 1; + } } -bool BoundaryRegionXIn::isDone() -{ +bool BoundaryRegionXIn::isDone() { return (x < 0) || (y > ye); // Return true if gone out of the boundary } @@ -65,48 +62,45 @@ BoundaryRegionXOut::BoundaryRegionXOut(std::string name, int ymin, int ymax, location = BNDRY_XOUT; width = localmesh->LocalNx - localmesh->xend - 1; x = localmesh->LocalNx - width; // First point inside the boundary - if(ye < ys) + if (ye < ys) { swap(ys, ye); + } } -void BoundaryRegionXOut::first() -{ +void BoundaryRegionXOut::first() { x = localmesh->LocalNx - width; y = ys; } -void BoundaryRegionXOut::next() -{ +void BoundaryRegionXOut::next() { // Loop over all points, from inside out y++; - if(y > ye) { + if (y > ye) { y = ys; x++; // Going from inside out } } -void BoundaryRegionXOut::next1d() -{ +void BoundaryRegionXOut::next1d() { // Loop over the innermost points y++; } -void BoundaryRegionXOut::nextX() -{ +void BoundaryRegionXOut::nextX() { x++; - if(y > ye) + if (y > ye) { y = ys; + } } -void BoundaryRegionXOut::nextY() -{ +void BoundaryRegionXOut::nextY() { y++; - if(x >= localmesh->LocalNx) + if (x >= localmesh->LocalNx) { x = localmesh->LocalNx - width; + } } -bool BoundaryRegionXOut::isDone() -{ +bool BoundaryRegionXOut::isDone() { return (x >= localmesh->LocalNx) || (y > ye); // Return true if gone out of the boundary } @@ -117,53 +111,49 @@ BoundaryRegionYDown::BoundaryRegionYDown(std::string name, int xmin, int xmax, : BoundaryRegion(std::move(name), 0, -1, passmesh), xs(xmin), xe(xmax) { location = BNDRY_YDOWN; width = localmesh->ystart; - y = width-1; // First point inside the boundary - if(xe < xs) + y = width - 1; // First point inside the boundary + if (xe < xs) { swap(xs, xe); + } } -void BoundaryRegionYDown::first() -{ +void BoundaryRegionYDown::first() { x = xs; - y = width-1; + y = width - 1; } -void BoundaryRegionYDown::next() -{ +void BoundaryRegionYDown::next() { // Loop over all points, from inside out y--; - if(y < 0) { - y = width-1; + if (y < 0) { + y = width - 1; x++; } } -void BoundaryRegionYDown::next1d() -{ +void BoundaryRegionYDown::next1d() { // Loop over the innermost points x++; } -void BoundaryRegionYDown::nextX() -{ +void BoundaryRegionYDown::nextX() { x++; - if(y < 0) - y = width-1; + if (y < 0) { + y = width - 1; + } } -void BoundaryRegionYDown::nextY() -{ +void BoundaryRegionYDown::nextY() { y--; - if(x > xe) + if (x > xe) { x = xs; + } } -bool BoundaryRegionYDown::isDone() -{ +bool BoundaryRegionYDown::isDone() { return (x > xe) || (y < 0); // Return true if gone out of the boundary } - /////////////////////////////////////////////////////////////// BoundaryRegionYUp::BoundaryRegionYUp(std::string name, int xmin, int xmax, Mesh* passmesh) @@ -171,47 +161,44 @@ BoundaryRegionYUp::BoundaryRegionYUp(std::string name, int xmin, int xmax, Mesh* location = BNDRY_YUP; width = localmesh->LocalNy - localmesh->yend - 1; y = localmesh->LocalNy - width; // First point inside the boundary - if(xe < xs) + if (xe < xs) { swap(xs, xe); + } } -void BoundaryRegionYUp::first() -{ +void BoundaryRegionYUp::first() { x = xs; y = localmesh->LocalNy - width; } -void BoundaryRegionYUp::next() -{ +void BoundaryRegionYUp::next() { // Loop over all points, from inside out y++; - if(y >= localmesh->LocalNy) { + if (y >= localmesh->LocalNy) { y = localmesh->LocalNy - width; x++; } } -void BoundaryRegionYUp::next1d() -{ +void BoundaryRegionYUp::next1d() { // Loop over the innermost points x++; } -void BoundaryRegionYUp::nextX() -{ +void BoundaryRegionYUp::nextX() { x++; - if(y >= localmesh->LocalNy) + if (y >= localmesh->LocalNy) { y = localmesh->LocalNy - width; + } } -void BoundaryRegionYUp::nextY() -{ +void BoundaryRegionYUp::nextY() { y++; - if(x > xe) + if (x > xe) { x = xs; + } } -bool BoundaryRegionYUp::isDone() -{ +bool BoundaryRegionYUp::isDone() { return (x > xe) || (y >= localmesh->LocalNy); // Return true if gone out of the boundary } diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx index ad95a4ab6a..78e033b6e5 100644 --- a/src/mesh/boundary_standard.cxx +++ b/src/mesh/boundary_standard.cxx @@ -1,14 +1,14 @@ #include #include -#include -#include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include +#include +#include using bout::generator::Context; @@ -48,10 +48,12 @@ void verifyNumPoints(BoundaryRegion* region, int ptsRequired) { // Work out how many processor local points we have excluding boundaries // but including ghost/guard cells ptsAvailLocal = mesh->LocalNx; - if (mesh->firstX()) + if (mesh->firstX()) { ptsAvailLocal -= mesh->xstart; - if (mesh->lastX()) + } + if (mesh->lastX()) { ptsAvailLocal -= mesh->xstart; + } // Now decide if it's a local or global limit, prefer global if a tie if (ptsAvailGlobal <= ptsAvailLocal) { @@ -70,15 +72,17 @@ void verifyNumPoints(BoundaryRegion* region, int ptsRequired) { //Here mesh->numberOfYBoundaries()*mesh->ystart is the total number of guard/boundary //cells - ptsAvailGlobal = mesh->GlobalNy - mesh->numberOfYBoundaries()*2*mesh->ystart; + ptsAvailGlobal = mesh->GlobalNy - mesh->numberOfYBoundaries() * 2 * mesh->ystart; // Work out how many processor local points we have excluding boundaries // but including ghost/guard cells ptsAvailLocal = mesh->LocalNy; - if (mesh->firstY()) + if (mesh->firstY()) { ptsAvailLocal -= mesh->ystart; - if (mesh->lastY()) + } + if (mesh->lastY()) { ptsAvailLocal -= mesh->ystart; + } // Now decide if it's a local or global limit, prefer global if a tie if (ptsAvailGlobal <= ptsAvailLocal) { @@ -138,8 +142,9 @@ void BoundaryDirichlet::apply(Field2D& f, BoutReal t) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -269,19 +274,20 @@ void BoundaryDirichlet::apply(Field2D& f, BoutReal t) { } } else { // Non-staggered, standard case - for(; !bndry->isDone(); bndry->next1d()) { - - if(fg) { - val = fg->generate(Context(bndry, loc, t, mesh)); - } - - f(bndry->x,bndry->y) = 2*val - f(bndry->x-bndry->bx, bndry->y-bndry->by); - + for (; !bndry->isDone(); bndry->next1d()) { + + if (fg) { + val = fg->generate(Context(bndry, loc, t, mesh)); + } + + f(bndry->x, bndry->y) = 2 * val - f(bndry->x - bndry->bx, bndry->y - bndry->by); + // Need to set second guard cell, as may be used for interpolation or upwinding derivatives - for(int i=1;iwidth;i++) { - int xi = bndry->x + i*bndry->bx; - int yi = bndry->y + i*bndry->by; - f(xi, yi) = 2*f(xi - bndry->bx, yi - bndry->by) - f(xi - 2*bndry->bx, yi - 2*bndry->by); + for (int i = 1; i < bndry->width; i++) { + int xi = bndry->x + i * bndry->bx; + int yi = bndry->y + i * bndry->by; + f(xi, yi) = 2 * f(xi - bndry->bx, yi - bndry->by) + - f(xi - 2 * bndry->bx, yi - 2 * bndry->by); } } } @@ -299,8 +305,9 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -451,19 +458,23 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) { } else if (loc == CELL_ZLOW) { // Shifted in Z - for(; !bndry->isDone(); bndry->next1d()) { + for (; !bndry->isDone(); bndry->next1d()) { // Calculate the X and Y normalised values half-way between the guard cell and grid cell - BoutReal xnorm = 0.5*( mesh->GlobalX(bndry->x) // In the guard cell - + mesh->GlobalX(bndry->x - bndry->bx) ); // the grid cell + BoutReal xnorm = 0.5 + * (mesh->GlobalX(bndry->x) // In the guard cell + + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell - BoutReal ynorm = 0.5*( mesh->GlobalY(bndry->y) // In the guard cell - + mesh->GlobalY(bndry->y - bndry->by) ); // the grid cell + BoutReal ynorm = 0.5 + * (mesh->GlobalY(bndry->y) // In the guard cell + + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell - for(int zk=0;zkLocalNz;zk++) { - if(fg){ - val = fg->generate(xnorm,TWOPI*ynorm,TWOPI*(zk - 0.5)/(mesh->LocalNz), t); + for (int zk = 0; zk < mesh->LocalNz; zk++) { + if (fg) { + val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), + t); } - f(bndry->x,bndry->y,zk) = 2*val - f(bndry->x-bndry->bx, bndry->y-bndry->by, zk); + f(bndry->x, bndry->y, zk) = + 2 * val - f(bndry->x - bndry->bx, bndry->y - bndry->by, zk); // We've set the first boundary point using extrapolation in // the line above. The below block of code is attempting to @@ -497,13 +508,14 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) { // can help with the stability of higher order methods. for (int i = 1; i < bndry->width; i++) { // Set any other guard cells using the values on the cells - int xi = bndry->x + i*bndry->bx; - int yi = bndry->y + i*bndry->by; + int xi = bndry->x + i * bndry->bx; + int yi = bndry->y + i * bndry->by; xnorm = mesh->GlobalX(xi); ynorm = mesh->GlobalY(yi); - for(int zk=0;zkLocalNz;zk++) { - if(fg) { - val = fg->generate(xnorm,TWOPI*ynorm,TWOPI*(zk - 0.5)/(mesh->LocalNz), t); + for (int zk = 0; zk < mesh->LocalNz; zk++) { + if (fg) { + val = fg->generate(xnorm, TWOPI * ynorm, + TWOPI * (zk - 0.5) / (mesh->LocalNz), t); } f(xi, yi, zk) = val; } @@ -572,8 +584,9 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) { void BoundaryDirichlet::apply_ddt(Field2D& f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryDirichlet::apply_ddt(Field3D& f) { @@ -581,9 +594,11 @@ void BoundaryDirichlet::apply_ddt(Field3D& f) { ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -612,8 +627,9 @@ void BoundaryDirichlet_O3::apply(Field2D& f, BoutReal t) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -791,8 +807,9 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -946,26 +963,33 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) { } else if (loc == CELL_ZLOW) { // Shifted in Z - for(; !bndry->isDone(); bndry->next1d()) { + for (; !bndry->isDone(); bndry->next1d()) { // Calculate the X and Y normalised values half-way between the guard cell and grid cell - BoutReal xnorm = 0.5*( mesh->GlobalX(bndry->x) // In the guard cell - + mesh->GlobalX(bndry->x - bndry->bx) ); // the grid cell + BoutReal xnorm = 0.5 + * (mesh->GlobalX(bndry->x) // In the guard cell + + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell - BoutReal ynorm = 0.5*( mesh->GlobalY(bndry->y) // In the guard cell - + mesh->GlobalY(bndry->y - bndry->by) ); // the grid cell + BoutReal ynorm = 0.5 + * (mesh->GlobalY(bndry->y) // In the guard cell + + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell - for(int zk=0;zkLocalNz;zk++) { - if(fg) - val = fg->generate(xnorm,TWOPI*ynorm,TWOPI*(zk - 0.5)/(mesh->LocalNz), t); + for (int zk = 0; zk < mesh->LocalNz; zk++) { + if (fg) { + val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), + t); + } - f(bndry->x,bndry->y,zk) = (8./3)*val - 2.*f(bndry->x-bndry->bx, bndry->y-bndry->by,zk) + f(bndry->x-2*bndry->bx, bndry->y-2*bndry->by,zk)/3.; + f(bndry->x, bndry->y, zk) = + (8. / 3) * val - 2. * f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + + f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, zk) / 3.; // Need to set remaining guard cells, as may be used for interpolation or upwinding derivatives - for(int i=1;iwidth;i++) { - int xi = bndry->x + i*bndry->bx; - int yi = bndry->y + i*bndry->by; - f(xi, yi, zk) = 3.0*f(xi - bndry->bx, yi - bndry->by, zk) - 3.0*f(xi - 2*bndry->bx, yi - 2*bndry->by, zk) - + f(xi - 3*bndry->bx, yi - 3*bndry->by, zk); + for (int i = 1; i < bndry->width; i++) { + int xi = bndry->x + i * bndry->bx; + int yi = bndry->y + i * bndry->by; + f(xi, yi, zk) = 3.0 * f(xi - bndry->bx, yi - bndry->by, zk) + - 3.0 * f(xi - 2 * bndry->bx, yi - 2 * bndry->by, zk) + + f(xi - 3 * bndry->bx, yi - 3 * bndry->by, zk); } } } @@ -1000,8 +1024,9 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) { void BoundaryDirichlet_O3::apply_ddt(Field2D& f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryDirichlet_O3::apply_ddt(Field3D& f) { @@ -1044,8 +1069,9 @@ void BoundaryDirichlet_O4::apply(Field2D& f, BoutReal t) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -1238,8 +1264,9 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -1402,26 +1429,35 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) { } } else if (loc == CELL_ZLOW) { // Shifted in Z - for(; !bndry->isDone(); bndry->next1d()) { + for (; !bndry->isDone(); bndry->next1d()) { // Calculate the X and Y normalised values half-way between the guard cell and grid cell - BoutReal xnorm = 0.5*( mesh->GlobalX(bndry->x) // In the guard cell - + mesh->GlobalX(bndry->x - bndry->bx) ); // the grid cell + BoutReal xnorm = 0.5 + * (mesh->GlobalX(bndry->x) // In the guard cell + + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell - BoutReal ynorm = 0.5*( mesh->GlobalY(bndry->y) // In the guard cell - + mesh->GlobalY(bndry->y - bndry->by) ); // the grid cell + BoutReal ynorm = 0.5 + * (mesh->GlobalY(bndry->y) // In the guard cell + + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell - for(int zk=0;zkLocalNz;zk++) { - if(fg) - val = fg->generate(xnorm,TWOPI*ynorm,TWOPI*(zk - 0.5)/(mesh->LocalNz), t); + for (int zk = 0; zk < mesh->LocalNz; zk++) { + if (fg) { + val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), + t); + } - f(bndry->x,bndry->y,zk) = (16./5)*val - 3.*f(bndry->x-bndry->bx, bndry->y-bndry->by,zk) + f(bndry->x-2*bndry->bx, bndry->y-2*bndry->by,zk) - (1./5)*f(bndry->x-3*bndry->bx, bndry->y-3*bndry->by,zk); + f(bndry->x, bndry->y, zk) = + (16. / 5) * val - 3. * f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + + f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, zk) + - (1. / 5) * f(bndry->x - 3 * bndry->bx, bndry->y - 3 * bndry->by, zk); // Need to set remaining guard cells, as may be used for interpolation or upwinding derivatives - for(int i=1;iwidth;i++) { - int xi = bndry->x + i*bndry->bx; - int yi = bndry->y + i*bndry->by; - f(xi, yi, zk) = 4.0*f(xi - bndry->bx, yi - bndry->by, zk) - 6.0*f(xi - 2*bndry->bx, yi - 2*bndry->by, zk) - + 4.0*f(xi - 3*bndry->bx, yi - 3*bndry->by, zk) - f(xi - 4*bndry->bx, yi - 4*bndry->by, zk); + for (int i = 1; i < bndry->width; i++) { + int xi = bndry->x + i * bndry->bx; + int yi = bndry->y + i * bndry->by; + f(xi, yi, zk) = 4.0 * f(xi - bndry->bx, yi - bndry->by, zk) + - 6.0 * f(xi - 2 * bndry->bx, yi - 2 * bndry->by, zk) + + 4.0 * f(xi - 3 * bndry->bx, yi - 3 * bndry->by, zk) + - f(xi - 4 * bndry->bx, yi - 4 * bndry->by, zk); } } } @@ -1458,17 +1494,20 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) { void BoundaryDirichlet_O4::apply_ddt(Field2D& f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryDirichlet_O4::apply_ddt(Field3D& f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -1506,7 +1545,7 @@ void BoundaryDirichlet_4thOrder::apply(Field3D& f) { ASSERT1(mesh == f.getMesh()); // Set (at 4th order) the value at the mid-point between the guard cell and the grid // cell to be val - for (bndry->first(); !bndry->isDone(); bndry->next1d()) + for (bndry->first(); !bndry->isDone(); bndry->next1d()) { for (int z = 0; z < mesh->LocalNz; z++) { f(bndry->x, bndry->y, z) = 128. / 35. * val - 4. * f(bndry->x - bndry->bx, bndry->y - bndry->by, z) @@ -1519,21 +1558,25 @@ void BoundaryDirichlet_4thOrder::apply(Field3D& f) { - 4. * f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, z) + 3. / 5. * f(bndry->x - 3 * bndry->bx, bndry->y - 3 * bndry->by, z); } + } } void BoundaryDirichlet_4thOrder::apply_ddt(Field2D& f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryDirichlet_4thOrder::apply_ddt(Field3D& f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -1700,8 +1743,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -1887,8 +1931,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } } #else - throw BoutException("Applying boundary condition 'neumann' to Field2D " - "not compatible with 3D metrics in all cases."); + throw BoutException("Applying boundary condition 'neumann' to Field2D " + "not compatible with 3D metrics in all cases."); #endif } @@ -1903,8 +1947,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -2126,9 +2171,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk) + bndry->by * metric->dy(bndry->x, bndry->y, zk); #else - BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y) - + bndry->by * metric->dy(bndry->x, bndry->y); - for (int zk = 0; zk < mesh->LocalNz; zk++) { + BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y) + + bndry->by * metric->dy(bndry->x, bndry->y); + for (int zk = 0; zk < mesh->LocalNz; zk++) { #endif if (fg) { val = fg->generate(Context(bndry, zk, loc, t, mesh)); @@ -2147,17 +2192,20 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { void BoundaryNeumann::apply_ddt(Field2D & f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryNeumann::apply_ddt(Field3D & f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -2186,8 +2234,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -2223,8 +2272,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } } #else - throw BoutException("Applying boundary condition 'neumann_O4' to Field2D not " - "compatible with 3D metrics in all cases."); + throw BoutException("Applying boundary condition 'neumann_O4' to Field2D not " + "compatible with 3D metrics in all cases."); #endif } @@ -2237,8 +2286,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // Decide which generator to use std::shared_ptr fg = gen; - if (!fg) + if (!fg) { fg = f.getBndryGenerator(bndry->location); + } BoutReal val = 0.0; @@ -2275,17 +2325,20 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { void BoundaryNeumann_O4::apply_ddt(Field2D & f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryNeumann_O4::apply_ddt(Field3D & f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -2328,8 +2381,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // cell } #else - throw BoutException("void BoundaryNeumann_4thOrder::apply(Field2D& f) not " - "implemented with 3D metrics"); + throw BoutException("void BoundaryNeumann_4thOrder::apply(Field2D& f) not " + "implemented with 3D metrics"); #endif } @@ -2340,7 +2393,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // Set (at 4th order) the gradient at the mid-point between the guard cell and the // grid cell to be val This sets the value of the co-ordinate derivative, i.e. DDX/DDY // not Grad_par/Grad_perp.x - for (bndry->first(); !bndry->isDone(); bndry->next1d()) + for (bndry->first(); !bndry->isDone(); bndry->next1d()) { for (int z = 0; z < mesh->LocalNz; z++) { BoutReal delta = -(bndry->bx * metric->dx(bndry->x, bndry->y, z) + bndry->by * metric->dy(bndry->x, bndry->y, z)); @@ -2359,21 +2412,25 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // derivative at the point half way between the guard cell and the // grid cell } + } } void BoundaryNeumann_4thOrder::apply_ddt(Field2D & f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryNeumann_4thOrder::apply_ddt(Field3D & f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -2391,14 +2448,15 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { #if not(BOUT_USE_METRIC_3D) Coordinates* metric = f.getCoordinates(); // Loop over all elements and set equal to the next point in - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { f(bndry->x, bndry->y) = f(bndry->x - bndry->bx, bndry->y - bndry->by) * sqrt(metric->g_22(bndry->x, bndry->y) / metric->g_22(bndry->x - bndry->bx, bndry->y - bndry->by)); + } #else - throw BoutException("Applying boundary condition 'neumannpar' to Field2D not " - "compatible with 3D metrics in all cases."); + throw BoutException("Applying boundary condition 'neumannpar' to Field2D not " + "compatible with 3D metrics in all cases."); #endif } @@ -2406,12 +2464,14 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Coordinates* metric = f.getCoordinates(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { f(bndry->x, bndry->y, z) = f(bndry->x - bndry->bx, bndry->y - bndry->by, z) * sqrt(metric->g_22(bndry->x, bndry->y, z) / metric->g_22(bndry->x - bndry->bx, bndry->y - bndry->by, z)); + } + } } /////////////////////////////////////////////////////////////// @@ -2451,16 +2511,19 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { void BoundaryRobin::apply(Field2D & f) { if (fabs(bval) < 1.e-12) { // No derivative term so just constant value - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { f(bndry->x, bndry->y) = gval / aval; + } } else { BoutReal sign = 1.; - if ((bndry->bx < 0) || (bndry->by < 0)) + if ((bndry->bx < 0) || (bndry->by < 0)) { sign = -1.; - for (bndry->first(); !bndry->isDone(); bndry->next()) + } + for (bndry->first(); !bndry->isDone(); bndry->next()) { f(bndry->x, bndry->y) = f(bndry->x - bndry->bx, bndry->y - bndry->by) + sign * (gval - aval * f(bndry->x - bndry->bx, bndry->y - bndry->by)) / bval; + } } } @@ -2468,19 +2531,24 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); if (fabs(bval) < 1.e-12) { - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { f(bndry->x, bndry->y, z) = gval / aval; + } + } } else { BoutReal sign = 1.; - if ((bndry->bx < 0) || (bndry->by < 0)) + if ((bndry->bx < 0) || (bndry->by < 0)) { sign = -1.; - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + } + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { f(bndry->x, bndry->y, z) = f(bndry->x - bndry->bx, bndry->y - bndry->by, z) + sign * (gval - aval * f(bndry->x - bndry->bx, bndry->y - bndry->by, z)) / bval; + } + } } } @@ -2488,19 +2556,22 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { void BoundaryConstGradient::apply(Field2D & f) { // Loop over all elements and set equal to the next point in - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { f(bndry->x, bndry->y) = 2. * f(bndry->x - bndry->bx, bndry->y - bndry->by) - f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by); + } } void BoundaryConstGradient::apply(Field3D & f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { f(bndry->x, bndry->y, z) = 2. * f(bndry->x - bndry->bx, bndry->y - bndry->by, z) - f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, z); + } + } } /////////////////////////////////////////////////////////////// @@ -2549,8 +2620,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } while (!bndry->isDone()); } #else - throw BoutException("Applying boundary condition 'zerolaplace' to Field2D not " - "compatible with 3D metrics in all cases."); + throw BoutException("Applying boundary condition 'zerolaplace' to Field2D not " + "compatible with 3D metrics in all cases."); #endif } @@ -2610,9 +2681,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } while (!bndry->isDone()); } #else - throw BoutException( - "Applying boundary to Field3D not compatible with 3D metrics in " - "ZeroLaplace case."); + throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in " + "ZeroLaplace case."); #endif } @@ -2653,8 +2723,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } while (!bndry->isDone()); } #else - throw BoutException("Applying boundary condition 'zerolaplace2' to Field2D not " - "compatible with 3D metrics in all cases."); + throw BoutException("Applying boundary condition 'zerolaplace2' to Field2D not " + "compatible with 3D metrics in all cases."); #endif } @@ -2662,7 +2732,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { #if not(BOUT_USE_METRIC_3D) Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); - const int ncz = mesh->LocalNz; + const int ncz = mesh->LocalNz; ASSERT0(ncz % 2 == 0); // Allocation assumes even number @@ -2711,9 +2781,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } while (!bndry->isDone()); } #else - throw BoutException( - "Applying boundary to Field3D not compatible with 3D metrics in " - "ZeroLaplace2 case."); + throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in " + "ZeroLaplace2 case."); #endif } @@ -2751,8 +2820,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { laplace_tridag_coefs(x - bx, y, 0, la, lb, lc); if (bx < 0) { // Lower X f(x, y) = ((val - lb * f(x - bx, y) + lc * f(x - 2 * bx, y)) / la).real(); - } else // Upper X + } else { // Upper X f(x, y) = ((val - lb * f(x - bx, y) + la * f(x - 2 * bx, y)) / lc).real(); + } bndry->nextX(); x = bndry->x; @@ -2827,9 +2897,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { } while (!bndry->isDone()); } #else - throw BoutException( - "Applying boundary to Field3D not compatible with 3D metrics in " - "ConstLaplace case."); + throw BoutException("Applying boundary to Field3D not compatible with 3D metrics in " + "ConstLaplace case."); #endif } @@ -2883,9 +2952,10 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { var.y(jx, jy, jz) = var.y(jx - 2, jy, jz) + (metric->dx(jx - 2, jy) + metric->dx(jx - 1, jy)) * tmp; - if (mesh->xstart == 2) + if (mesh->xstart == 2) { // 4th order to get last point var.y(jx + 1, jy, jz) = var.y(jx - 3, jy, jz) + 4. * metric->dx(jx, jy) * tmp; + } // dB_z / dx = dB_x / dz @@ -2894,8 +2964,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { var.z(jx, jy, jz) = var.z(jx - 2, jy, jz) + (metric->dx(jx - 2, jy) + metric->dx(jx - 1, jy)) * tmp; - if (mesh->xstart == 2) + if (mesh->xstart == 2) { var.z(jx + 1, jy, jz) = var.z(jx - 3, jy, jz) + 4. * metric->dx(jx, jy) * tmp; + } // d/dx( Jmetric->g11 B_x ) = - d/dx( Jmetric->g12 B_y + Jmetric->g13 B_z) // - d/dy( JB^y ) - d/dz( JB^z ) @@ -2932,16 +3003,17 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { (metric->J(jx - 2, jy) * metric->g11(jx - 2, jy) * var.x(jx - 2, jy, jz) + (metric->dx(jx - 2, jy) + metric->dx(jx - 1, jy)) * tmp) / metric->J(jx, jy) * metric->g11(jx, jy); - if (mesh->xstart == 2) + if (mesh->xstart == 2) { var.x(jx + 1, jy, jz) = (metric->J(jx - 3, jy) * metric->g11(jx - 3, jy) * var.x(jx - 3, jy, jz) + 4. * metric->dx(jx, jy) * tmp) / metric->J(jx + 1, jy) * metric->g11(jx + 1, jy); + } } } #else - throw BoutException( - "Applying boundary to Vector3D not compatible with 3D metrics in DivCurl."); + throw BoutException( + "Applying boundary to Vector3D not compatible with 3D metrics in DivCurl."); #endif } @@ -3217,17 +3289,20 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { void BoundaryFree_O2::apply_ddt(Field2D & f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryFree_O2::apply_ddt(Field3D & f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } ////////////////////////////////// @@ -3483,17 +3558,20 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { void BoundaryFree_O3::apply_ddt(Field2D & f) { Field2D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero + } } void BoundaryFree_O3::apply_ddt(Field3D & f) { Mesh* mesh = bndry->localmesh; ASSERT1(mesh == f.getMesh()); Field3D* dt = f.timeDeriv(); - for (bndry->first(); !bndry->isDone(); bndry->next()) - for (int z = 0; z < mesh->LocalNz; z++) + for (bndry->first(); !bndry->isDone(); bndry->next()) { + for (int z = 0; z < mesh->LocalNz; z++) { (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero + } + } } /////////////////////////////////////////////////////////////// @@ -3549,11 +3627,12 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) { // Apply the boundary to g op->apply(g); // Set time-derivatives - for (bndry->first(); !bndry->isDone(); bndry->next()) + for (bndry->first(); !bndry->isDone(); bndry->next()) { for (int z = 0; z < mesh->LocalNz; z++) { ddt(f)(bndry->x, bndry->y, z) = r * (g(bndry->x, bndry->y, z) - f(bndry->x, bndry->y, z)); } + } } /////////////////////////////////////////////////////////////// diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx index ad1ed6fb6d..a468054dca 100644 --- a/src/mesh/coordinates.cxx +++ b/src/mesh/coordinates.cxx @@ -8,15 +8,15 @@ #include #include #include -#include -#include -#include +#include +#include +#include -#include -#include -#include +#include +#include +#include -#include +#include #include "parallel/fci.hxx" #include "parallel/shiftedmetricinterp.hxx" @@ -87,7 +87,9 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr ASSERT1(bndry->by == 0 or localmesh->ystart > 1); // note that either bx or by is >0 here result(bndry->x, bndry->y) = - (9. * (f(bndry->x - bndry->bx, bndry->y - bndry->by) + f(bndry->x, bndry->y)) + (9. + * (f(bndry->x - bndry->bx, bndry->y - bndry->by) + + f(bndry->x, bndry->y)) - f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by) - f(bndry->x + bndry->bx, bndry->y + bndry->by)) / 16.; @@ -97,8 +99,7 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr if ((bndry->bx != 0 && localmesh->GlobalNx - 2 * bndry->width >= 3) || (bndry->by != 0 && localmesh->GlobalNy - localmesh->numberOfYBoundaries() * bndry->width - >= 3)) - { + >= 3)) { if (bndry->bx != 0 && localmesh->LocalNx == 1 && bndry->width == 1) { throw BoutException( "Not enough points in the x-direction on this " @@ -132,16 +133,14 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr } } #if CHECK > 0 - if (not ( - // if include_corner_cells=true, then we extrapolate valid data into the - // corner cells if they are not already filled - localmesh->include_corner_cells - - // if we are not extrapolating at all, the corner cells should contain valid - // data - or (not extrapolate_x and not extrapolate_y) - ) - ) { + if (not( + // if include_corner_cells=true, then we extrapolate valid data into the + // corner cells if they are not already filled + localmesh->include_corner_cells + + // if we are not extrapolating at all, the corner cells should contain valid + // data + or (not extrapolate_x and not extrapolate_y))) { // Invalidate corner guard cells for (int i = 0; i < localmesh->xstart; i++) { for (int j = 0; j < localmesh->ystart; j++) { @@ -316,9 +315,9 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location, // If the CELL_CENTRE variable was read, the staggered version is required to // also exist for consistency void checkStaggeredGet(Mesh* mesh, const std::string& name, const std::string& suffix) { - if (mesh->sourceHasVar(name) != mesh->sourceHasVar(name+suffix)) { + if (mesh->sourceHasVar(name) != mesh->sourceHasVar(name + suffix)) { throw BoutException("Attempting to read staggered fields from grid, but " + name - + " is not present in both CELL_CENTRE and staggered versions."); + + " is not present in both CELL_CENTRE and staggered versions."); } } @@ -346,22 +345,23 @@ int getAtLocAndFillGuards(Mesh* mesh, Coordinates::FieldMetric& var, std::string getLocationSuffix(CELL_LOC location) { switch (location) { case CELL_CENTRE: { - return ""; - } + return ""; + } case CELL_XLOW: { - return "_xlow"; - } + return "_xlow"; + } case CELL_YLOW: { - return "_ylow"; - } + return "_ylow"; + } case CELL_ZLOW: { // in 2D metric, same as CELL_CENTRE return bout::build::use_metric_3d ? "_zlow" : ""; - } + } default: { - throw BoutException("Incorrect location passed to " - "Coordinates(Mesh*,const CELL_LOC,const Coordinates*) constructor."); - } + throw BoutException( + "Incorrect location passed to " + "Coordinates(Mesh*,const CELL_LOC,const Coordinates*) constructor."); + } } } } // anonymous namespace @@ -401,17 +401,19 @@ Coordinates::Coordinates(Mesh* mesh, Options* options) // 'interpolateAndExtrapolate' to set them. Ensures that derivatives are // smooth at all the boundaries. - const bool extrapolate_x = (*options)["extrapolate_x"].withDefault(not mesh->sourceHasXBoundaryGuards()); - const bool extrapolate_y = (*options)["extrapolate_y"].withDefault(not mesh->sourceHasYBoundaryGuards()); + const bool extrapolate_x = + (*options)["extrapolate_x"].withDefault(not mesh->sourceHasXBoundaryGuards()); + const bool extrapolate_y = + (*options)["extrapolate_y"].withDefault(not mesh->sourceHasYBoundaryGuards()); if (extrapolate_x) { output_warn.write(_("WARNING: extrapolating input mesh quantities into x-boundary " - "cells. Set option extrapolate_x=false to disable this.\n")); + "cells. Set option extrapolate_x=false to disable this.\n")); } if (extrapolate_y) { output_warn.write(_("WARNING: extrapolating input mesh quantities into y-boundary " - "cells. Set option extrapolate_y=false to disable this.\n")); + "cells. Set option extrapolate_y=false to disable this.\n")); } mesh->get(dx, "dx", 1.0, false); @@ -491,7 +493,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options) /// Find covariant metric components auto covariant_component_names = {"g_11", "g_22", "g_33", "g_12", "g_13", "g_23"}; - auto source_has_component = [&mesh] (const std::string& name) { + auto source_has_component = [&mesh](const std::string& name) { return mesh->sourceHasVar(name); }; // Check if any of the components are present @@ -554,8 +556,9 @@ Coordinates::Coordinates(Mesh* mesh, Options* options) bout::checkFinite(g_23, "g_23", "RGN_NOCORNERS"); /// Calculate Jacobian and Bxy - if (jacobian()) + if (jacobian()) { throw BoutException("Error in jacobian call"); + } // Attempt to read J from the grid file auto Jcalc = J; @@ -643,19 +646,19 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc, bool extrapolate_x = true; bool extrapolate_y = true; - if (!force_interpolate_from_centre && mesh->sourceHasVar("dx"+suffix)) { + if (!force_interpolate_from_centre && mesh->sourceHasVar("dx" + suffix)) { extrapolate_x = not mesh->sourceHasXBoundaryGuards(); extrapolate_y = not mesh->sourceHasYBoundaryGuards(); if (extrapolate_x) { output_warn.write(_("WARNING: extrapolating input mesh quantities into x-boundary " - "cells\n")); + "cells\n")); } if (extrapolate_y) { output_warn.write(_("WARNING: extrapolating input mesh quantities into y-boundary " - "cells\n")); + "cells\n")); } { @@ -714,7 +717,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc, /// Find covariant metric components auto covariant_component_names = {"g_11", "g_22", "g_33", "g_12", "g_13", "g_23"}; - auto source_has_component = [&suffix, &mesh] (const std::string& name) { + auto source_has_component = [&suffix, &mesh](const std::string& name) { return mesh->sourceHasVar(name + suffix); }; // Check if any of the components are present @@ -731,12 +734,14 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc, getAtLoc(mesh, g_13, "g_13", suffix, location); getAtLoc(mesh, g_23, "g_23", suffix, location); - output_warn.write("\tWARNING! Staggered covariant components of metric tensor set manually. " - "Contravariant components NOT recalculated\n"); + output_warn.write( + "\tWARNING! Staggered covariant components of metric tensor set manually. " + "Contravariant components NOT recalculated\n"); } else { - output_warn.write("Not all staggered covariant components of metric tensor found. " - "Calculating all from the contravariant tensor\n"); + output_warn.write( + "Not all staggered covariant components of metric tensor found. " + "Calculating all from the contravariant tensor\n"); /// Calculate contravariant metric components if not found if (calcCovariant("RGN_NOCORNERS")) { throw BoutException("Error in staggered calcCovariant call"); @@ -829,7 +834,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc, checkStaggeredGet(mesh, "ShiftTorsion", suffix); if (mesh->get(ShiftTorsion, "ShiftTorsion" + suffix, 0.0, false)) { - output_warn.write("\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n"); + output_warn.write( + "\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n"); ShiftTorsion = 0.0; } ShiftTorsion.setLocation(location); @@ -950,7 +956,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc, void Coordinates::outputVars(Options& output_options) { Timer time("io"); - const std::string loc_string = (location == CELL_CENTRE) ? "" : "_"+toString(location); + const std::string loc_string = + (location == CELL_CENTRE) ? "" : "_" + toString(location); output_options["dx" + loc_string].force(dx, "Coordinates"); output_options["dy" + loc_string].force(dy, "Coordinates"); @@ -996,21 +1003,24 @@ const Field2D& Coordinates::zlength() const { } int Coordinates::geometry(bool recalculate_staggered, - bool force_interpolate_from_centre) { + bool force_interpolate_from_centre) { TRACE("Coordinates::geometry"); communicate(dx, dy, dz, g11, g22, g33, g12, g13, g23, g_11, g_22, g_33, g_12, g_13, g_23, J, Bxy); output_progress.write("Calculating differential geometry terms\n"); - if (min(abs(dx)) < 1e-8) + if (min(abs(dx)) < 1e-8) { throw BoutException("dx magnitude less than 1e-8"); + } - if (min(abs(dy)) < 1e-8) + if (min(abs(dy)) < 1e-8) { throw BoutException("dy magnitude less than 1e-8"); + } - if (min(abs(dz)) < 1e-8) + if (min(abs(dz)) < 1e-8) { throw BoutException("dz magnitude less than 1e-8"); + } // Check input metrics // Diagonal metric components should be finite @@ -1162,8 +1172,8 @@ int Coordinates::geometry(bool recalculate_staggered, // Read correction for non-uniform meshes std::string suffix = getLocationSuffix(location); - if (location == CELL_CENTRE or (!force_interpolate_from_centre - and localmesh->sourceHasVar("dx"+suffix))) { + if (location == CELL_CENTRE + or (!force_interpolate_from_centre and localmesh->sourceHasVar("dx" + suffix))) { bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards(); bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards(); @@ -1316,7 +1326,8 @@ int Coordinates::calcCovariant(const std::string& region) { a(0, 2) = a(2, 0) = g13[i]; if (invert3x3(a)) { - output_error.write("\tERROR: metric tensor is singular at ({:d}, {:d})\n", i.x(), i.y()); + output_error.write("\tERROR: metric tensor is singular at ({:d}, {:d})\n", i.x(), + i.y()); return 1; } @@ -1371,7 +1382,8 @@ int Coordinates::calcContravariant(const std::string& region) { a(0, 2) = a(2, 0) = g_13[i]; if (invert3x3(a)) { - output_error.write("\tERROR: metric tensor is singular at ({:d}, {:d})\n", i.x(), i.y()); + output_error.write("\tERROR: metric tensor is singular at ({:d}, {:d})\n", i.x(), + i.y()); return 1; } @@ -1454,7 +1466,7 @@ void fixZShiftGuards(Field2D& zShift) { } } } -} +} // namespace void Coordinates::setParallelTransform(Options* options) { @@ -1466,10 +1478,10 @@ void Coordinates::setParallelTransform(Options* options) { // Convert to lower case for comparison ptstr = lowercase(ptstr); - if(ptstr == "identity") { + if (ptstr == "identity") { // Identity method i.e. no transform needed - transform = bout::utils::make_unique(*localmesh, - ptoptions); + transform = + bout::utils::make_unique(*localmesh, ptoptions); } else if (ptstr == "shifted" or ptstr == "shiftedinterp") { // Shifted metric method @@ -1478,14 +1490,14 @@ void Coordinates::setParallelTransform(Options* options) { // Read the zShift angle from the mesh std::string suffix = getLocationSuffix(location); - if (localmesh->sourceHasVar("dx"+suffix)) { + if (localmesh->sourceHasVar("dx" + suffix)) { // Grid file has variables at this location, so should be able to read checkStaggeredGet(localmesh, "zShift", suffix); if (localmesh->get(zShift, "zShift" + suffix, 0.0, false, location)) { // No zShift variable. Try qinty in BOUT grid files if (localmesh->get(zShift, "qinty" + suffix, 0.0, false, location)) { // Failed to find either variable, cannot use ShiftedMetric - throw BoutException("Could not read zShift"+suffix+" from grid file"); + throw BoutException("Could not read zShift" + suffix + " from grid file"); } } } else { @@ -1571,7 +1583,7 @@ Coordinates::FieldMetric Coordinates::DDY(const Field2D& f, CELL_LOC loc, Field3D Coordinates::DDY(const Field3D& f, CELL_LOC outloc, const std::string& method, const std::string& region) { #if BOUT_USE_METRIC_3D - if (! f.hasParallelSlices() and ! transform->canToFromFieldAligned()) { + if (!f.hasParallelSlices() and !transform->canToFromFieldAligned()) { Field3D f_parallel = f; transform->calcParallelSlices(f_parallel); f_parallel.applyParallelBoundary("parallel_neumann"); @@ -1610,7 +1622,7 @@ Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var, } Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc, - const std::string& method) { + const std::string& method) { TRACE("Coordinates::Grad_par( Field3D )"); ASSERT1(location == outloc || outloc == CELL_DEFAULT); @@ -1629,7 +1641,7 @@ Coordinates::FieldMetric Coordinates::Vpar_Grad_par(const Field2D& v, const Fiel } Field3D Coordinates::Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc, - const std::string& method) { + const std::string& method) { ASSERT1(location == outloc || outloc == CELL_DEFAULT); return VDDY(v, f, outloc, method) / sqrt(g_22); } @@ -1650,7 +1662,7 @@ Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc, } Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc, - const std::string& method) { + const std::string& method) { TRACE("Coordinates::Div_par( Field3D )"); ASSERT1(location == outloc || outloc == CELL_DEFAULT); @@ -1693,7 +1705,7 @@ Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outl } Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc, - const std::string& method) { + const std::string& method) { TRACE("Coordinates::Grad2_par2( Field3D )"); if (outloc == CELL_DEFAULT) { outloc = f.getLocation(); @@ -1719,7 +1731,7 @@ Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc, ///////////////////////////////////////////////////////// // perpendicular Laplacian operator -#include // Delp2 uses same coefficients as inversion code +#include // Delp2 uses same coefficients as inversion code Coordinates::FieldMetric Coordinates::Delp2(const Field2D& f, CELL_LOC outloc, bool UNUSED(useFFT)) { @@ -1763,8 +1775,9 @@ Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) { // Take forward FFT - for (int jx = 0; jx < localmesh->LocalNx; jx++) + for (int jx = 0; jx < localmesh->LocalNx; jx++) { rfft(&f(jx, jy, 0), ncz, &ft(jx, 0)); + } // Loop over kz for (int jz = 0; jz <= ncz / 2; jz++) { @@ -1825,8 +1838,9 @@ FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) { auto delft = Matrix(localmesh->LocalNx, ncz / 2 + 1); // Take forward FFT - for (int jx = 0; jx < localmesh->LocalNx; jx++) + for (int jx = 0; jx < localmesh->LocalNx; jx++) { rfft(&f(jx, 0), ncz, &ft(jx, 0)); + } // Loop over kz for (int jz = 0; jz <= ncz / 2; jz++) { @@ -1920,8 +1934,8 @@ Field2D Coordinates::Laplace_perpXY(MAYBE_UNUSED(const Field2D& A), const BoutReal outer_x_J = outer_x_avg(J); const BoutReal outer_x_g11 = outer_x_avg(g11); const BoutReal outer_x_dx = outer_x_avg(dx); - const BoutReal outer_x_value = outer_x_A * outer_x_J * outer_x_g11 / - (J[i] * outer_x_dx * dx[i]); + const BoutReal outer_x_value = + outer_x_A * outer_x_J * outer_x_g11 / (J[i] * outer_x_dx * dx[i]); result[i] += outer_x_value * (f[i.xp()] - f[i]); // inner x boundary @@ -1930,8 +1944,8 @@ Field2D Coordinates::Laplace_perpXY(MAYBE_UNUSED(const Field2D& A), const BoutReal inner_x_J = inner_x_avg(J); const BoutReal inner_x_g11 = inner_x_avg(g11); const BoutReal inner_x_dx = inner_x_avg(dx); - const BoutReal inner_x_value = inner_x_A * inner_x_J * inner_x_g11 / - (J[i] * inner_x_dx * dx[i]); + const BoutReal inner_x_value = + inner_x_A * inner_x_J * inner_x_g11 / (J[i] * inner_x_dx * dx[i]); result[i] += inner_x_value * (f[i.xm()] - f[i]); // upper y boundary @@ -1942,8 +1956,8 @@ Field2D Coordinates::Laplace_perpXY(MAYBE_UNUSED(const Field2D& A), const BoutReal upper_y_g23 = upper_y_avg(g23); const BoutReal upper_y_g_23 = upper_y_avg(g_23); const BoutReal upper_y_dy = upper_y_avg(dy); - const BoutReal upper_y_value = -upper_y_A * upper_y_J * upper_y_g23 *upper_y_g_23 / - (upper_y_g_22 * J[i] * upper_y_dy * dy[i]); + const BoutReal upper_y_value = -upper_y_A * upper_y_J * upper_y_g23 * upper_y_g_23 + / (upper_y_g_22 * J[i] * upper_y_dy * dy[i]); result[i] += upper_y_value * (f[i.yp()] - f[i]); // lower y boundary @@ -1954,8 +1968,8 @@ Field2D Coordinates::Laplace_perpXY(MAYBE_UNUSED(const Field2D& A), const BoutReal lower_y_g23 = lower_y_avg(g23); const BoutReal lower_y_g_23 = lower_y_avg(g_23); const BoutReal lower_y_dy = lower_y_avg(dy); - const BoutReal lower_y_value = -lower_y_A * lower_y_J * lower_y_g23 * lower_y_g_23 / - (lower_y_g_22 * J[i] * lower_y_dy * dy[i]); + const BoutReal lower_y_value = -lower_y_A * lower_y_J * lower_y_g23 * lower_y_g_23 + / (lower_y_g_22 * J[i] * lower_y_dy * dy[i]); result[i] += lower_y_value * (f[i.ym()] - f[i]); } diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index 85fa7c322f..f47d49a0b3 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -4,14 +4,14 @@ #include #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include #include -#include +#include GridFile::GridFile(std::string gridfilename) : GridDataSource(true), data(bout::OptionsNetCDF(gridfilename).read()), @@ -103,7 +103,8 @@ bool GridFile::get(Mesh* UNUSED(m), int& ival, const std::string& name, int def) * * */ -bool GridFile::get(Mesh *UNUSED(m), BoutReal &rval, const std::string &name, BoutReal def) { +bool GridFile::get(Mesh* UNUSED(m), BoutReal& rval, const std::string& name, + BoutReal def) { Timer timer("io"); TRACE("GridFile::get(BoutReal)"); const bool success = data.isSet(name); @@ -121,10 +122,12 @@ bool GridFile::get(Mesh *UNUSED(m), BoutReal &rval, const std::string &name, Bou * Successfully reads Field2D or FieldPerp if the variable in the file is 0-D or 2-D. * Successfully reads Field3D if the variable in the file is 0-D, 2-D or 3-D. */ -bool GridFile::get(Mesh *m, Field2D &var, const std::string &name, BoutReal def, CELL_LOC location) { +bool GridFile::get(Mesh* m, Field2D& var, const std::string& name, BoutReal def, + CELL_LOC location) { return getField(m, var, name, def, location); } -bool GridFile::get(Mesh *m, Field3D &var, const std::string &name, BoutReal def, CELL_LOC location) { +bool GridFile::get(Mesh* m, Field3D& var, const std::string& name, BoutReal def, + CELL_LOC location) { return getField(m, var, name, def, location); } @@ -162,7 +165,8 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, if (not data.isSet(name)) { // Variable not found - output_warn.write("\tWARNING: Could not read '{:s}' from grid. Setting to {:e}\n", name, def); + output_warn.write("\tWARNING: Could not read '{:s}' from grid. Setting to {:e}\n", + name, def); var = def; var.setLocation(location); return false; @@ -192,7 +196,9 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, case 3: { // Check size if getting Field3D if (bout::utils::is_Field2D::value or bout::utils::is_FieldPerp::value) { - output_warn.write("WARNING: Variable '{:s}' should be 2D, but has {:d} dimensions. Ignored\n", name, size.size()); + output_warn.write( + "WARNING: Variable '{:s}' should be 2D, but has {:d} dimensions. Ignored\n", + name, size.size()); var = def; var.setLocation(location); return false; @@ -200,7 +206,9 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, break; } default: { - output_warn.write("WARNING: Variable '{:s}' should be 2D or 3D, but has {:d} dimensions. Ignored\n", name, size.size()); + output_warn.write( + "WARNING: Variable '{:s}' should be 2D or 3D, but has {:d} dimensions. Ignored\n", + name, size.size()); var = def; var.setLocation(location); return false; @@ -222,7 +230,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, // Total number of y-boundary cells in grid file, used for check later. // Value depends on if we are double-null or not. - int total_grid_yguards = 2*grid_yguards; + int total_grid_yguards = 2 * grid_yguards; if (m->numberOfXPoints > 1) { ASSERT1(m->numberOfXPoints == 2); // Need to check if we are before or after the target in the middle of the @@ -230,11 +238,11 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, // target if we are after it. if (m->OffsetY >= ny_inner) { // Note: neither ny_inner nor OffsetY include guard cells - ys += 2*grid_yguards; + ys += 2 * grid_yguards; } // Add y-boundary guard cells at upper target - total_grid_yguards += 2*grid_yguards; + total_grid_yguards += 2 * grid_yguards; } // Index offsets into destination @@ -254,7 +262,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, xd = grid_xguards - mxg; ASSERT1(xd >= 0); } else if (grid_xguards == 0) { ///excluding ghostpoints - nx_to_read = m->LocalNx - 2*mxg; + nx_to_read = m->LocalNx - 2 * mxg; xd = mxg; } else { throw BoutException( @@ -275,7 +283,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, } else if (grid_yguards == 0) { // excluding ghostpoints ASSERT1(size[1] == m->GlobalNy - m->numberOfYBoundaries() * 2 * myg); - ny_to_read = m->LocalNy - 2*myg; + ny_to_read = m->LocalNy - 2 * myg; yd = myg; } else { throw BoutException( @@ -291,8 +299,8 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, if (location != CELL_DEFAULT and var.getLocation() != location) { throw BoutException("Incorrect location of field {:s} in grid file, expected {:s}, " - "got {:s}.", name, toString(location), - toString(var.getLocation())); + "got {:s}.", + name, toString(location), toString(var.getLocation())); } if (var.isAllocated()) { @@ -301,16 +309,16 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, // If field does not include ghost points in x-direction -> // Upper and lower X boundaries copied from nearest point if (size[0] == m->GlobalNx - 2 * mxg) { - for (int x=0; xxstart; x++) { - for (int y=0; yLocalNy; y++) { - for (int z=0; zxstart; x++) { + for (int y = 0; y < m->LocalNy; y++) { + for (int z = 0; z < var.getNz(); z++) { var(x, y, z) = var(m->xstart, y, z); } } } - for (int x=m->xend+1;xLocalNx;x++) { - for (int y=0; yLocalNy; y++) { - for (int z=0; zxend + 1; x < m->LocalNx; x++) { + for (int y = 0; y < m->LocalNy; y++) { + for (int z = 0; z < var.getNz(); z++) { var(x, y, z) = var(m->xend, y, z); } } @@ -321,14 +329,14 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, ///If field does not include ghost points in y-direction -> ///Upper and lower Y boundaries copied from nearest point if (grid_yguards == 0) { - for(int x=0; xLocalNx; x++) { - for(int y=0; yystart; y++) { - for (int z=0; zLocalNx; x++) { + for (int y = 0; y < m->ystart; y++) { + for (int z = 0; z < var.getNz(); z++) { var(x, y, z) = var(x, m->ystart, z); } } - for(int y=m->yend+1; yLocalNy; y++) { - for (int z=0; zyend + 1; y < m->LocalNy; y++) { + for (int z = 0; z < var.getNz(); z++) { var(x, y, z) = var(x, m->yend, z); } } @@ -376,9 +384,9 @@ void GridFile::readField(Mesh* UNUSED(m), const std::string& name, int ys, int y } } -void GridFile::readField(Mesh* m, const std::string& name, int ys, int yd, - int ny_to_read, int xs, int xd, int nx_to_read, const std::vector& size, - Field3D& var) { +void GridFile::readField(Mesh* m, const std::string& name, int ys, int yd, int ny_to_read, + int xs, int xd, int nx_to_read, const std::vector& size, + Field3D& var) { readFieldAttributes(data[name], var); @@ -393,26 +401,26 @@ void GridFile::readField(Mesh* m, const std::string& name, int ys, int yd, } if (!readgrid_3dvar_real(name, - ys,// Start reading at global y-index - yd,// Insert data starting from y=yd - ny_to_read,// Length of data in Y - xs,// Start reading at global x-index - xd,// Insert data starting from x=xd - nx_to_read, // Length of data in X - var) ) { + ys, // Start reading at global y-index + yd, // Insert data starting from y=yd + ny_to_read, // Length of data in Y + xs, // Start reading at global x-index + xd, // Insert data starting from x=xd + nx_to_read, // Length of data in X + var)) { throw BoutException("\tWARNING: Could not read '{:s}' from grid. Setting to zero\n", name); } } else { // No Z size specified in file. Assume FFT format if (!readgrid_3dvar_fft(m, name, - ys,// Start reading at global y-index - yd,// Insert data starting from y=yd - ny_to_read,// Length of data in Y - xs,// Start reading at global x-index - xd,// Insert data starting from x=xd - nx_to_read, // Length of data in X - var) ) { + ys, // Start reading at global y-index + yd, // Insert data starting from y=yd + ny_to_read, // Length of data in Y + xs, // Start reading at global x-index + xd, // Insert data starting from x=xd + nx_to_read, // Length of data in X + var)) { throw BoutException("\tWARNING: Could not read '{:s}' from grid. Setting to zero\n", name); } @@ -420,8 +428,8 @@ void GridFile::readField(Mesh* m, const std::string& name, int ys, int yd, } void GridFile::readField(Mesh* m, const std::string& name, int UNUSED(ys), int UNUSED(yd), - int UNUSED(ny_to_read), int xs, int xd, int nx_to_read, const std::vector& size, - FieldPerp& var) { + int UNUSED(ny_to_read), int xs, int xd, int nx_to_read, + const std::vector& size, FieldPerp& var) { readFieldAttributes(data[name], var); @@ -442,20 +450,20 @@ void GridFile::readField(Mesh* m, const std::string& name, int UNUSED(ys), int U } if (!readgrid_perpvar_real(name, - xs,// Start reading at global x-index - xd,// Insert data starting from x=xd - nx_to_read, // Length of data in X - var) ) { + xs, // Start reading at global x-index + xd, // Insert data starting from x=xd + nx_to_read, // Length of data in X + var)) { throw BoutException( "\tWARNING: Could not read '{:s}' from grid. Setting to zero\n", name); } } else { // No Z size specified in file. Assume FFT format if (!readgrid_perpvar_fft(m, name, - xs,// Start reading at global x-index - xd,// Insert data starting from x=xd - nx_to_read, // Length of data in X - var) ) { + xs, // Start reading at global x-index + xd, // Insert data starting from x=xd + nx_to_read, // Length of data in X + var)) { throw BoutException( "\tWARNING: Could not read '{:s}' from grid. Setting to zero\n", name); } @@ -472,7 +480,7 @@ bool GridFile::get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector& var), return false; } -bool GridFile::get(Mesh *UNUSED(m), std::vector &var, const std::string &name, +bool GridFile::get(Mesh* UNUSED(m), std::vector& var, const std::string& name, int len, int offset, GridDataSource::Direction UNUSED(dir)) { TRACE("GridFile::get(vector)"); @@ -517,15 +525,15 @@ bool GridFile::hasXBoundaryGuards(Mesh* m) { with the BoutReal and imaginary parts of each (positive) frequency up to the nyquist frequency. */ -bool GridFile::readgrid_3dvar_fft(Mesh *m, const std::string &name, - int yread, int ydest, int ysize, - int xread, int xdest, int xsize, Field3D &var) { +bool GridFile::readgrid_3dvar_fft(Mesh* m, const std::string& name, int yread, int ydest, + int ysize, int xread, int xdest, int xsize, + Field3D& var) { /// Check the arguments make sense if ((yread < 0) || (ydest < 0) || (ysize < 0) || (xread < 0) || (xdest < 0) || (xsize < 0)) { return false; } - + /// Check the size of the data Options option = data[name]; const std::vector size = bout::utils::visit(GetDimensions{}, option.value); @@ -535,7 +543,7 @@ bool GridFile::readgrid_3dvar_fft(Mesh *m, const std::string &name, return false; } - int maxmode = (size[2] - 1)/2; ///< Maximum mode-number n + int maxmode = (size[2] - 1) / 2; ///< Maximum mode-number n int ncz = m->LocalNz; @@ -551,13 +559,15 @@ bool GridFile::readgrid_3dvar_fft(Mesh *m, const std::string &name, // Print out which modes are going to be read in if (zperiod > maxmode) { // Domain is too small: Only DC - output_warn.write("zperiod ({:d}) > maxmode ({:d}) => Only reading n = 0 component\n", zperiod, maxmode); + output_warn.write("zperiod ({:d}) > maxmode ({:d}) => Only reading n = 0 component\n", + zperiod, maxmode); } else { // Get maximum mode in the input which is a multiple of zperiod int mm = (maxmode / zperiod) * zperiod; - if ( (ncz/2)*zperiod < mm ) - mm = (ncz/2)*zperiod; // Limited by Z resolution - + if ((ncz / 2) * zperiod < mm) { + mm = (ncz / 2) * zperiod; // Limited by Z resolution + } + if (mm == zperiod) { output_info.write(" => Reading n = 0, {:d}\n", zperiod); } else { @@ -571,9 +581,9 @@ bool GridFile::readgrid_3dvar_fft(Mesh *m, const std::string &name, const auto full_var = data[name].as>(); - for (int jx = xread; jx < xread+xsize; jx++) { + for (int jx = xread; jx < xread + xsize; jx++) { // jx is global x-index to start from - for (int jy = yread; jy < yread+ysize; jy++) { + for (int jy = yread; jy < yread + ysize; jy++) { // jy is global y-index to start from for (int jz = 0; jz < size[2]; ++jz) { zdata[jz] = full_var(jx, jy, jz); @@ -582,17 +592,17 @@ bool GridFile::readgrid_3dvar_fft(Mesh *m, const std::string &name, /// Load into dcomplex array fdata[0] = zdata[0]; // DC component - for(int i=1;i<=ncz/2;i++) { - int modenr = i*zperiod; // Z mode number + for (int i = 1; i <= ncz / 2; i++) { + int modenr = i * zperiod; // Z mode number if (modenr <= maxmode) { // Have data for this mode - fdata[i] = dcomplex(zdata[modenr*2 - 1], zdata[modenr*2]); + fdata[i] = dcomplex(zdata[modenr * 2 - 1], zdata[modenr * 2]); } else { fdata[i] = 0.0; } } - irfft(std::begin(fdata), ncz, &var(jx-xread+xdest, jy-yread+ydest, 0)); + irfft(std::begin(fdata), ncz, &var(jx - xread + xdest, jy - yread + ydest, 0)); } } @@ -647,8 +657,8 @@ bool GridFile::readgrid_3dvar_real(const std::string& name, int yread, int ydest with the BoutReal and imaginary parts of each (positive) frequency up to the nyquist frequency. */ -bool GridFile::readgrid_perpvar_fft(Mesh *m, const std::string &name, - int xread, int xdest, int xsize, FieldPerp &var) { +bool GridFile::readgrid_perpvar_fft(Mesh* m, const std::string& name, int xread, + int xdest, int xsize, FieldPerp& var) { /// Check the arguments make sense if ((xread < 0) || (xdest < 0) || (xsize < 0)) { return false; @@ -663,7 +673,7 @@ bool GridFile::readgrid_perpvar_fft(Mesh *m, const std::string &name, return false; } - int maxmode = (size[1] - 1)/2; ///< Maximum mode-number n + int maxmode = (size[1] - 1) / 2; ///< Maximum mode-number n int ncz = m->LocalNz; @@ -679,12 +689,14 @@ bool GridFile::readgrid_perpvar_fft(Mesh *m, const std::string &name, // Print out which modes are going to be read in if (zperiod > maxmode) { // Domain is too small: Only DC - output_warn.write("zperiod ({:d}) > maxmode ({:d}) => Only reading n = 0 component\n", zperiod, maxmode); + output_warn.write("zperiod ({:d}) > maxmode ({:d}) => Only reading n = 0 component\n", + zperiod, maxmode); } else { // Get maximum mode in the input which is a multiple of zperiod int mm = (maxmode / zperiod) * zperiod; - if ( (ncz/2)*zperiod < mm ) - mm = (ncz/2)*zperiod; // Limited by Z resolution + if ((ncz / 2) * zperiod < mm) { + mm = (ncz / 2) * zperiod; // Limited by Z resolution + } if (mm == zperiod) { output_info.write(" => Reading n = 0, {:d}\n", zperiod); @@ -699,7 +711,7 @@ bool GridFile::readgrid_perpvar_fft(Mesh *m, const std::string &name, const auto full_var = option.as>(); - for (int jx = xread; jx < xread+xsize; jx++) { + for (int jx = xread; jx < xread + xsize; jx++) { // jx is global x-index to start from for (int jz = 0; jz < size[1]; ++jz) { zdata[jz] = full_var(jx, jz); @@ -708,17 +720,17 @@ bool GridFile::readgrid_perpvar_fft(Mesh *m, const std::string &name, /// Load into dcomplex array fdata[0] = zdata[0]; // DC component - for(int i=1;i<=ncz/2;i++) { - int modenr = i*zperiod; // Z mode number + for (int i = 1; i <= ncz / 2; i++) { + int modenr = i * zperiod; // Z mode number if (modenr <= maxmode) { // Have data for this mode - fdata[i] = dcomplex(zdata[modenr*2 - 1], zdata[modenr*2]); + fdata[i] = dcomplex(zdata[modenr * 2 - 1], zdata[modenr * 2]); } else { fdata[i] = 0.0; } } - irfft(std::begin(fdata), ncz, &var(jx-xread+xdest, 0)); + irfft(std::begin(fdata), ncz, &var(jx - xread + xdest, 0)); } return true; @@ -728,8 +740,8 @@ bool GridFile::readgrid_perpvar_fft(Mesh *m, const std::string &name, * Reads a FieldPerp variable directly from the file, without * any processing */ -bool GridFile::readgrid_perpvar_real(const std::string &name, - int xread, int xdest, int xsize, FieldPerp &var) { +bool GridFile::readgrid_perpvar_real(const std::string& name, int xread, int xdest, + int xsize, FieldPerp& var) { /// Check the arguments make sense if ((xread < 0) || (xdest < 0) || (xsize < 0)) { return false; @@ -746,7 +758,7 @@ bool GridFile::readgrid_perpvar_real(const std::string &name, const auto full_var = option.as>(); - for (int jx = xread; jx < xread+xsize; jx++) { + for (int jx = xread; jx < xread + xsize; jx++) { // jx is global x-index to start from for (int jz = 0; jz < size[1]; ++jz) { var(jx - xread + xdest, jz) = full_var(jx, jz); @@ -755,4 +767,3 @@ bool GridFile::readgrid_perpvar_real(const std::string &name, return true; } - diff --git a/src/mesh/data/gridfromoptions.cxx b/src/mesh/data/gridfromoptions.cxx index 89ecf56316..311772ae2d 100644 --- a/src/mesh/data/gridfromoptions.cxx +++ b/src/mesh/data/gridfromoptions.cxx @@ -1,9 +1,9 @@ #include #include -#include -#include -#include -#include +#include +#include +#include +#include using bout::generator::Context; @@ -45,7 +45,8 @@ bool GridFromOptions::get(Mesh*, BoutReal& rval, const std::string& name, BoutRe return hasVar(name); } -bool GridFromOptions::get(Mesh* m, Field2D& var, const std::string& name, BoutReal def, CELL_LOC location) { +bool GridFromOptions::get(Mesh* m, Field2D& var, const std::string& name, BoutReal def, + CELL_LOC location) { if (!hasVar(name)) { output_warn.write("Variable '{:s}' not in mesh options. Setting to {:e}\n", name, def); @@ -57,7 +58,8 @@ bool GridFromOptions::get(Mesh* m, Field2D& var, const std::string& name, BoutRe return true; } -bool GridFromOptions::get(Mesh* m, Field3D& var, const std::string& name, BoutReal def, CELL_LOC location) { +bool GridFromOptions::get(Mesh* m, Field3D& var, const std::string& name, BoutReal def, + CELL_LOC location) { if (!hasVar(name)) { output_warn.write("Variable '{:s}' not in mesh options. Setting to {:e}\n", name, def); @@ -69,7 +71,8 @@ bool GridFromOptions::get(Mesh* m, Field3D& var, const std::string& name, BoutRe return true; } -bool GridFromOptions::get(Mesh* m, FieldPerp& var, const std::string& name, BoutReal def, CELL_LOC location) { +bool GridFromOptions::get(Mesh* m, FieldPerp& var, const std::string& name, BoutReal def, + CELL_LOC location) { // Cannot set attributes from options at the moment, so don't know what 'yindex' this // FieldPerp should have: just set to 0 for now, and create FieldPerp on all processors // (note: this is different to behaviour of GridFromFile which will only create the @@ -94,7 +97,8 @@ bool GridFromOptions::get(Mesh* m, std::vector& var, const std::string& nam GridDataSource::Direction UNUSED(dir)) { if (!hasVar(name)) { std::vector def{}; - output_warn.write("Variable '{:s}' not in mesh options. Setting to empty vector\n", name); + output_warn.write("Variable '{:s}' not in mesh options. Setting to empty vector\n", + name); var = def; return false; } @@ -112,7 +116,8 @@ bool GridFromOptions::get(Mesh* m, std::vector& var, const std::string int len, int offset, GridDataSource::Direction dir) { if (!hasVar(name)) { std::vector def{}; - output_warn.write("Variable '{:s}' not in mesh options. Setting to empty vector\n", name); + output_warn.write("Variable '{:s}' not in mesh options. Setting to empty vector\n", + name); var = def; return false; } @@ -122,7 +127,7 @@ bool GridFromOptions::get(Mesh* m, std::vector& var, const std::string var.resize(len); - Context pos(0,0,0,CELL_CENTRE, m, 0.0); + Context pos(0, 0, 0, CELL_CENTRE, m, 0.0); switch (dir) { case GridDataSource::X: { @@ -133,7 +138,7 @@ bool GridFromOptions::get(Mesh* m, std::vector& var, const std::string break; } case GridDataSource::Y: { - for (int y = 0; y < len; y++){ + for (int y = 0; y < len; y++) { pos.set("y", TWOPI * m->GlobalY(y - m->OffsetY + offset)); var[y] = gen->generate(pos); } @@ -141,12 +146,15 @@ bool GridFromOptions::get(Mesh* m, std::vector& var, const std::string } case GridDataSource::Z: { for (int z = 0; z < len; z++) { - pos.set("z", (TWOPI * (z - m->OffsetZ + offset)) / static_cast(m->LocalNz)); + pos.set("z", + (TWOPI * (z - m->OffsetZ + offset)) / static_cast(m->LocalNz)); var[z] = gen->generate(pos); } break; } - default: { throw BoutException("Invalid direction argument"); } + default: { + throw BoutException("Invalid direction argument"); + } } return true; } diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx index 758163b532..3ec3b0ca97 100644 --- a/src/mesh/difops.cxx +++ b/src/mesh/difops.cxx @@ -25,20 +25,20 @@ #include "bout/build_config.hxx" -#include -#include -#include -#include -#include -#include -#include -#include #include +#include +#include +#include +#include +#include +#include +#include +#include -#include // Delp2 uses same coefficients as inversion code +#include // Delp2 uses same coefficients as inversion code -#include -#include +#include +#include #include @@ -80,28 +80,30 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f) { ASSERT1_FIELDS_COMPATIBLE(apar, f); ASSERT1(f.hasParallelSlices()); - Mesh *mesh = apar.getMesh(); + Mesh* mesh = apar.getMesh(); Field3D result{emptyFrom(f)}; int ncz = mesh->LocalNz; - Coordinates *metric = apar.getCoordinates(); + Coordinates* metric = apar.getCoordinates(); Field3D gys{emptyFrom(f)}; // Need Y derivative everywhere - for(int x=1;x<=mesh->LocalNx-2;x++) - for(int y=1;y<=mesh->LocalNy-2;y++) - for(int z=0;zLocalNx - 2; x++) { + for (int y = 1; y <= mesh->LocalNy - 2; y++) { + for (int z = 0; z < ncz; z++) { gys(x, y, z) = (f.yup()(x, y + 1, z) - f.ydown()(x, y - 1, z)) / (0.5 * metric->dy(x, y + 1, z) + metric->dy(x, y, z) + 0.5 * metric->dy(x, y - 1, z)); } + } + } - for(int x=1;x<=mesh->LocalNx-2;x++) { - for(int y=mesh->ystart;y<=mesh->yend;y++) { - for(int z=0;zLocalNx - 2; x++) { + for (int y = mesh->ystart; y <= mesh->yend; y++) { + for (int z = 0; z < ncz; z++) { BoutReal by = 1. / sqrt(metric->g_22(x, y, z)); // Z indices zm and zp int zm = (z - 1 + ncz) % ncz; @@ -245,7 +247,7 @@ Field3D Div_par(const Field3D& f, const Field3D& v) { Coordinates* coord = f.getCoordinates(); - for (int i = mesh->xstart; i <= mesh->xend; i++) + for (int i = mesh->xstart; i <= mesh->xend; i++) { for (int j = mesh->ystart; j <= mesh->yend; j++) { for (int k = mesh->zstart; k <= mesh->zend; k++) { // Value of f and v at left cell face @@ -269,6 +271,7 @@ Field3D Div_par(const Field3D& f, const Field3D& v) { (fluxRight - fluxLeft) / (coord->dy(i, j, k) * coord->J(i, j, k)); } } + } return result; } @@ -277,12 +280,12 @@ Field3D Div_par(const Field3D& f, const Field3D& v) { Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc, const std::string& method) { - Coordinates *metric = f.getCoordinates(outloc); + Coordinates* metric = f.getCoordinates(outloc); auto Bxy_floc = f.getCoordinates()->Bxy; if (!f.hasParallelSlices()) { - return metric->Bxy*FDDY(v, f/Bxy_floc, outloc, method)/sqrt(metric->g_22); + return metric->Bxy * FDDY(v, f / Bxy_floc, outloc, method) / sqrt(metric->g_22); } // Need to modify yup and ydown fields @@ -291,12 +294,12 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc, f_B.splitParallelSlices(); f_B.yup() = f.yup() / Bxy_floc; f_B.ydown() = f.ydown() / Bxy_floc; - return metric->Bxy*FDDY(v, f_B, outloc, method)/sqrt(metric->g_22); + return metric->Bxy * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22); } Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& method, CELL_LOC outloc) { - return Div_par_flux(v,f, outloc, method); + return Div_par_flux(v, f, outloc, method); } /******************************************************************************* @@ -324,34 +327,44 @@ Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, const std::string& method) Coordinates::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f, CELL_LOC outloc) { - return kY*Grad2_par2(f, outloc); + return kY * Grad2_par2(f, outloc); } Field3D Div_par_K_Grad_par(BoutReal kY, const Field3D& f, CELL_LOC outloc) { - return kY*Grad2_par2(f, outloc); + return kY * Grad2_par2(f, outloc); } Coordinates::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f, CELL_LOC outloc) { - if (outloc == CELL_DEFAULT) outloc = f.getLocation(); - return interp_to(kY, outloc)*Grad2_par2(f, outloc) + Div_par(kY, outloc)*Grad_par(f, outloc); + if (outloc == CELL_DEFAULT) { + outloc = f.getLocation(); + } + return interp_to(kY, outloc) * Grad2_par2(f, outloc) + + Div_par(kY, outloc) * Grad_par(f, outloc); } Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3D& f, CELL_LOC outloc) { - if (outloc == CELL_DEFAULT) outloc = f.getLocation(); - return interp_to(kY, outloc)*Grad2_par2(f, outloc) + Div_par(kY, outloc)*Grad_par(f, outloc); + if (outloc == CELL_DEFAULT) { + outloc = f.getLocation(); + } + return interp_to(kY, outloc) * Grad2_par2(f, outloc) + + Div_par(kY, outloc) * Grad_par(f, outloc); } Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f, CELL_LOC outloc) { - if (outloc == CELL_DEFAULT) outloc = f.getLocation(); - return interp_to(kY, outloc)*Grad2_par2(f, outloc) + Div_par(kY, outloc)*Grad_par(f, outloc); + if (outloc == CELL_DEFAULT) { + outloc = f.getLocation(); + } + return interp_to(kY, outloc) * Grad2_par2(f, outloc) + + Div_par(kY, outloc) * Grad_par(f, outloc); } Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc) { if (outloc == CELL_DEFAULT) { outloc = f.getLocation(); } - return interp_to(kY, outloc)*Grad2_par2(f, outloc) + Div_par(kY, outloc)*Grad_par(f, outloc); + return interp_to(kY, outloc) * Grad2_par2(f, outloc) + + Div_par(kY, outloc) * Grad_par(f, outloc); } /******************************************************************************* @@ -447,11 +460,13 @@ Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A, TRACE("b0xGrad_dot_Grad( Field2D , Field2D )"); - if (outloc == CELL_DEFAULT) outloc = A.getLocation(); + if (outloc == CELL_DEFAULT) { + outloc = A.getLocation(); + } ASSERT1(phi.getMesh() == A.getMesh()); - Coordinates *metric = phi.getCoordinates(outloc); + Coordinates* metric = phi.getCoordinates(outloc); // Calculate phi derivatives Coordinates::FieldMetric dpdx = DDX(phi, outloc); @@ -463,12 +478,12 @@ Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A, // Upwind A using these velocities Coordinates::FieldMetric result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc); - result /= metric->J*sqrt(metric->g_22); + result /= metric->J * sqrt(metric->g_22); ASSERT1(result.getLocation() == outloc); #if BOUT_USE_TRACK - result.name = "b0xGrad_dot_Grad("+phi.name+","+A.name+")"; + result.name = "b0xGrad_dot_Grad(" + phi.name + "," + A.name + ")"; #endif return result; } @@ -476,13 +491,15 @@ Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A, Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc) { TRACE("b0xGrad_dot_Grad( Field2D , Field3D )"); - if (outloc == CELL_DEFAULT) outloc = A.getLocation(); + if (outloc == CELL_DEFAULT) { + outloc = A.getLocation(); + } ASSERT1(phi.getMesh() == A.getMesh()); - Mesh *mesh = phi.getMesh(); + Mesh* mesh = phi.getMesh(); - Coordinates *metric = phi.getCoordinates(outloc); + Coordinates* metric = phi.getCoordinates(outloc); // Calculate phi derivatives Coordinates::FieldMetric dpdx = DDX(phi, outloc); @@ -493,7 +510,7 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc) Coordinates::FieldMetric vy = metric->g_23 * dpdx; Coordinates::FieldMetric vz = metric->g_12 * dpdy - metric->g_22 * dpdx; - if(mesh->IncIntShear) { + if (mesh->IncIntShear) { // BOUT-06 style differencing vz += metric->IntShiftTorsion * vx; } @@ -502,10 +519,10 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc) Field3D result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc) + VDDZ(vz, A, outloc); - result /= (metric->J*sqrt(metric->g_22)); + result /= (metric->J * sqrt(metric->g_22)); #if BOUT_USE_TRACK - result.name = "b0xGrad_dot_Grad("+phi.name+","+A.name+")"; + result.name = "b0xGrad_dot_Grad(" + phi.name + "," + A.name + ")"; #endif ASSERT2(result.getLocation() == outloc); @@ -516,11 +533,13 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc) Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) { TRACE("b0xGrad_dot_Grad( Field3D , Field2D )"); - if (outloc == CELL_DEFAULT) outloc = A.getLocation(); + if (outloc == CELL_DEFAULT) { + outloc = A.getLocation(); + } ASSERT1(p.getMesh() == A.getMesh()); - Coordinates *metric = p.getCoordinates(outloc); + Coordinates* metric = p.getCoordinates(outloc); // Calculate phi derivatives Field3D dpdx = DDX(p, outloc); @@ -535,10 +554,10 @@ Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) { Field3D result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc); - result /= (metric->J*sqrt(metric->g_22)); + result /= (metric->J * sqrt(metric->g_22)); #if BOUT_USE_TRACK - result.name = "b0xGrad_dot_Grad("+p.name+","+A.name+")"; + result.name = "b0xGrad_dot_Grad(" + p.name + "," + A.name + ")"; #endif ASSERT2(result.getLocation() == outloc); @@ -549,13 +568,15 @@ Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) { Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc) { TRACE("b0xGrad_dot_Grad( Field3D , Field3D )"); - if (outloc == CELL_DEFAULT) outloc = A.getLocation(); + if (outloc == CELL_DEFAULT) { + outloc = A.getLocation(); + } ASSERT1(phi.getMesh() == A.getMesh()); - Mesh * mesh = phi.getMesh(); + Mesh* mesh = phi.getMesh(); - Coordinates *metric = phi.getCoordinates(outloc); + Coordinates* metric = phi.getCoordinates(outloc); // Calculate phi derivatives Field3D dpdx = DDX(phi, outloc); @@ -567,17 +588,17 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc) Field3D vy = metric->g_23 * dpdx - metric->g_12 * dpdz; Field3D vz = metric->g_12 * dpdy - metric->g_22 * dpdx; - if(mesh->IncIntShear) { + if (mesh->IncIntShear) { // BOUT-06 style differencing vz += metric->IntShiftTorsion * vx; } Field3D result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc) + VDDZ(vz, A, outloc); - result /= (metric->J*sqrt(metric->g_22)); + result /= (metric->J * sqrt(metric->g_22)); #if BOUT_USE_TRACK - result.name = "b0xGrad_dot_Grad("+phi.name+","+A.name+")"; + result.name = "b0xGrad_dot_Grad(" + phi.name + "," + A.name + ")"; #endif ASSERT2(result.getLocation() == outloc); @@ -603,11 +624,11 @@ Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g, Coordinates::FieldMetric result{emptyFrom(f)}; - if( (method == BRACKET_SIMPLE) || (method == BRACKET_ARAKAWA)) { + if ((method == BRACKET_SIMPLE) || (method == BRACKET_ARAKAWA)) { // Use a subset of terms for comparison to BOUT-06 result = 0.0; result.setLocation(outloc); - }else { + } else { // Use full expression with all terms result = b0xGrad_dot_Grad(f, g, outloc) / f.getCoordinates(outloc)->Bxy; } @@ -628,21 +649,22 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, Field3D result{emptyFrom(f).setLocation(outloc)}; - Coordinates *metric = f.getCoordinates(outloc); + Coordinates* metric = f.getCoordinates(outloc); - switch(method) { + switch (method) { case BRACKET_CTU: { // First order Corner Transport Upwind method // P.Collela JCP 87, 171-200 (1990) - if(!solver) + if (!solver) { throw BoutException("CTU method requires access to the solver"); + } #if not(BOUT_USE_METRIC_3D) const int ncz = mesh->LocalNz; - for(int x=mesh->xstart;x<=mesh->xend;x++) - for(int y=mesh->ystart;y<=mesh->yend;y++) { + for (int x = mesh->xstart; x <= mesh->xend; x++) { + for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = 0; z < ncz; z++) { int zm = (z - 1 + ncz) % ncz; int zp = (z + 1) % ncz; @@ -656,20 +678,21 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, solver->setMaxTimestep(metric->dx(x, y, z) / (fabs(vx) + 1e-16)); // X differencing - if(vx > 0.0) { - gp = g(x,y); + if (vx > 0.0) { + gp = g(x, y); - gm = g(x-1,y); + gm = g(x - 1, y); - }else { - gp = g(x+1,y); + } else { + gp = g(x + 1, y); - gm = g(x,y); + gm = g(x, y); } result(x, y, z) = vx * (gp - gm) / metric->dx(x, y, z); } } + } #else throw BoutException("BRACKET_CTU not valid with 3D metrics yet."); #endif @@ -681,7 +704,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, #if not(BOUT_USE_METRIC_3D) const int ncz = mesh->LocalNz; - BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) { + BOUT_FOR (j2D, result.getRegion2D("RGN_NOBNDRY")) { // Get constants for this iteration const BoutReal spacingFactor = 1.0 / (12 * metric->dz[j2D] * metric->dx[j2D]); const int jy = j2D.y(), jx = j2D.x(); @@ -706,8 +729,8 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, const BoutReal Jpp = 2 * (fc[jzp] - fc[jzm]) * (gxp - gxm); // J+x - const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm]) + - gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]); + const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm]) + + gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]); result(jx, jy, 0) = (Jpp + Jpx) * spacingFactor; } @@ -721,8 +744,8 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, const BoutReal Jpp = 2 * (fc[jzp] - fc[jzm]) * (gxp - gxm); // J+x - const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm]) + - gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]); + const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm]) + + gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]); result(jx, jy, jz) = (Jpp + Jpx) * spacingFactor; } @@ -736,8 +759,8 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, const BoutReal Jpp = 2 * (fc[jzp] - fc[jzm]) * (gxp - gxm); // J+x - const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm]) + - gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]); + const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm]) + + gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]); result(jx, jy, ncz - 1) = (Jpp + Jpx) * spacingFactor; } @@ -752,12 +775,12 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, #if not(BOUT_USE_METRIC_3D) const int ncz = mesh->LocalNz; BOUT_OMP(parallel for) - for(int jx=mesh->xstart;jx<=mesh->xend;jx++){ - for(int jy=mesh->ystart;jy<=mesh->yend;jy++){ + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = mesh->ystart; jy <= mesh->yend; jy++) { const BoutReal partialFactor = 1.0 / (12 * metric->dz(jx, jy)); const BoutReal spacingFactor = partialFactor / metric->dx(jx, jy); for (int jz = 0; jz < mesh->LocalNz; jz++) { - const int jzp = jz+1 < ncz ? jz + 1 : 0; + const int jzp = jz + 1 < ncz ? jz + 1 : 0; // Above is alternative to const int jzp = (jz + 1) % ncz; const int jzm = jz - 1 >= 0 ? jz - 1 : ncz - 1; // Above is alternative to const int jzmTmp = (jz - 1 + ncz) % ncz; @@ -779,7 +802,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, - g(jx - 1, jy) * (f(jx, jy, jzp) - f(jx - 1, jy, jz)) + g(jx + 1, jy) * (f(jx + 1, jy, jz) - f(jx, jy, jzm))); - result(jx,jy,jz) = (Jpp + Jpx + Jxp) * spacingFactor; + result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor; } } } @@ -811,17 +834,17 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method, } ASSERT1(outloc == g.getLocation()) - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); Field3D result(mesh); - switch(method) { + switch (method) { case BRACKET_CTU: throw BoutException("Bracket method CTU is not yet implemented for [2d,3d] fields."); break; case BRACKET_ARAKAWA: // It is symmetric, therefore we can return -[3d,2d] - return -bracket(g,f,method,outloc,solver); + return -bracket(g, f, method, outloc, solver); break; case BRACKET_SIMPLE: { // Use a subset of terms for comparison to BOUT-06 @@ -830,7 +853,7 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method, } default: { // Use full expression with all terms - Coordinates *metric = f.getCoordinates(outloc); + Coordinates* metric = f.getCoordinates(outloc); result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy; } } @@ -848,25 +871,26 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, } ASSERT1(outloc == g.getLocation()); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f).setLocation(outloc)}; - Coordinates *metric = f.getCoordinates(outloc); + Coordinates* metric = f.getCoordinates(outloc); if (mesh->GlobalNx == 1 || mesh->GlobalNz == 1) { - result=0; + result = 0; result.setLocation(outloc); return result; } - switch(method) { + switch (method) { case BRACKET_CTU: { // First order Corner Transport Upwind method // P.Collela JCP 87, 171-200 (1990) #if not(BOUT_USE_METRIC_3D) - if(!solver) + if (!solver) { throw BoutException("CTU method requires access to the solver"); + } // Get current timestep BoutReal dt = solver->getCurrentTimestep(); @@ -878,8 +902,8 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, vz.setLocation(outloc); int ncz = mesh->LocalNz; - for(int y=mesh->ystart;y<=mesh->yend;y++) { - for(int x=1;x<=mesh->LocalNx-2;x++) { + for (int y = mesh->ystart; y <= mesh->yend; y++) { + for (int x = 1; x <= mesh->LocalNx - 2; x++) { for (int z = 0; z < mesh->LocalNz; z++) { int zm = (z - 1 + ncz) % ncz; int zp = (z + 1) % ncz; @@ -887,17 +911,19 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, // Vx = DDZ(f) vx(x, z) = (f(x, y, zp) - f(x, y, zm)) / (2. * metric->dz(x, y, z)); // Vz = -DDX(f) - vz(x,z) = (f(x-1,y,z) - f(x+1,y,z))/(0.5*metric->dx(x-1,y) + metric->dx(x,y) + 0.5*metric->dx(x+1,y)); + vz(x, z) = (f(x - 1, y, z) - f(x + 1, y, z)) + / (0.5 * metric->dx(x - 1, y) + metric->dx(x, y) + + 0.5 * metric->dx(x + 1, y)); // Set stability condition - solver->setMaxTimestep(fabs(metric->dx(x,y)) / (fabs(vx(x,z)) + 1e-16)); + solver->setMaxTimestep(fabs(metric->dx(x, y)) / (fabs(vx(x, z)) + 1e-16)); solver->setMaxTimestep(metric->dz(x, y) / (fabs(vz(x, z)) + 1e-16)); } } // Simplest form: use cell-centered velocities (no divergence included so not flux conservative) - for(int x=mesh->xstart;x<=mesh->xend;x++) + for (int x = mesh->xstart; x <= mesh->xend; x++) { for (int z = 0; z < ncz; z++) { int zm = (z - 1 + ncz) % ncz; int zp = (z + 1) % ncz; @@ -932,29 +958,30 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, // Z differencing if (vz(x, z) > 0.0) { - gp = g(x, y, z) + - (0.5 * dt / metric->dx(x, y)) * - ((vx[x][z] > 0) ? vx[x][z] * (g(x - 1, y, z) - g(x, y, z)) - : vx[x][z] * (g(x, y, z) - g(x + 1, y, z))); - - gm = g(x, y, zm) + - (0.5 * dt / metric->dx(x, y)) * - ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zm) - g(x, y, zm)) - : vx(x, z) * (g(x, y, zm) - g(x + 1, y, zm))); + gp = g(x, y, z) + + (0.5 * dt / metric->dx(x, y)) + * ((vx[x][z] > 0) ? vx[x][z] * (g(x - 1, y, z) - g(x, y, z)) + : vx[x][z] * (g(x, y, z) - g(x + 1, y, z))); + + gm = g(x, y, zm) + + (0.5 * dt / metric->dx(x, y)) + * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zm) - g(x, y, zm)) + : vx(x, z) * (g(x, y, zm) - g(x + 1, y, zm))); } else { - gp = g(x, y, zp) + - (0.5 * dt / metric->dx(x, y)) * - ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zp) - g(x, y, zp)) - : vx(x, z) * (g(x, y, zp) - g(x + 1, y, zp))); - - gm = g(x, y, z) + - (0.5 * dt / metric->dx(x, y)) * - ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, z) - g(x, y, z)) - : vx(x, z) * (g(x, y, z) - g(x + 1, y, z))); + gp = g(x, y, zp) + + (0.5 * dt / metric->dx(x, y)) + * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zp) - g(x, y, zp)) + : vx(x, z) * (g(x, y, zp) - g(x + 1, y, zp))); + + gm = g(x, y, z) + + (0.5 * dt / metric->dx(x, y)) + * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, z) - g(x, y, z)) + : vx(x, z) * (g(x, y, z) - g(x + 1, y, z))); } result(x, y, z) += vz(x, z) * (gp - gm) / metric->dz(x, y); } + } } #else throw BoutException("BRACKET_CTU not valid with 3D metrics yet."); @@ -970,7 +997,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, Field3D f_temp = f; Field3D g_temp = g; - BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) { + BOUT_FOR (j2D, result.getRegion2D("RGN_NOBNDRY")) { #if not(BOUT_USE_METRIC_3D) const BoutReal spacingFactor = 1.0 / (12 * metric->dz[j2D] * metric->dx[j2D]); #endif @@ -994,18 +1021,18 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, #endif // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g) - const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]) - - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])); + const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]) + - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])); // J+x const BoutReal Jpx = - (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm]) - - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm])); + (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm]) + - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm])); // Jx+ const BoutReal Jxp = - (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm]) - - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm])); + (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm]) + - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm])); result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor; } @@ -1019,18 +1046,18 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, const int jzm = jz - 1; // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g) - const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]) - - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])); + const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]) + - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])); // J+x const BoutReal Jpx = - (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm]) - - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm])); + (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm]) + - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm])); // Jx+ const BoutReal Jxp = - (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm]) - - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm])); + (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm]) + - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm])); result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor; } @@ -1045,18 +1072,18 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, #endif // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g) - const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]) - - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])); + const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]) + - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])); // J+x const BoutReal Jpx = - (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm]) - - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm])); + (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm]) + - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm])); // Jx+ const BoutReal Jxp = - (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm]) - - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm])); + (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm]) + - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm])); result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor; } @@ -1074,24 +1101,24 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, Field3D g_temp = g; BOUT_OMP(parallel for) - for(int jx=mesh->xstart;jx<=mesh->xend;jx++){ - for(int jy=mesh->ystart;jy<=mesh->yend;jy++){ + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = mesh->ystart; jy <= mesh->yend; jy++) { #if not(BOUT_USE_METRIC_3D) const BoutReal spacingFactor = 1.0 / (12 * metric->dz(jx, jy) * metric->dx(jx, jy)); #endif - const BoutReal *Fxm = f_temp(jx-1, jy); - const BoutReal *Fx = f_temp(jx, jy); - const BoutReal *Fxp = f_temp(jx+1, jy); - const BoutReal *Gxm = g_temp(jx-1, jy); - const BoutReal *Gx = g_temp(jx, jy); - const BoutReal *Gxp = g_temp(jx+1, jy); + const BoutReal* Fxm = f_temp(jx - 1, jy); + const BoutReal* Fx = f_temp(jx, jy); + const BoutReal* Fxp = f_temp(jx + 1, jy); + const BoutReal* Gxm = g_temp(jx - 1, jy); + const BoutReal* Gx = g_temp(jx, jy); + const BoutReal* Gxp = g_temp(jx + 1, jy); for (int jz = 0; jz < mesh->LocalNz; jz++) { #if BOUT_USE_METRIC_3D const BoutReal spacingFactor = 1.0 / (12 * metric->dz(jx, jy, jz) * metric->dx(jx, jy, jz)); #endif - const int jzp = jz+1 < ncz ? jz + 1 : 0; + const int jzp = jz + 1 < ncz ? jz + 1 : 0; // Above is alternative to const int jzp = (jz + 1) % ncz; const int jzm = jz - 1 >= 0 ? jz - 1 : ncz - 1; // Above is alternative to const int jzm = (jz - 1 + ncz) % ncz; diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx index ffcee3ed31..28094840a2 100644 --- a/src/mesh/fv_ops.cxx +++ b/src/mesh/fv_ops.cxx @@ -1,10 +1,10 @@ #include -#include -#include -#include +#include +#include +#include -#include +#include namespace FV { @@ -225,383 +225,388 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) { return result; } - const Field3D Div_par_K_Grad_par(const Field3D &Kin, const Field3D &fin, bool bndry_flux) { - TRACE("FV::Div_par_K_Grad_par"); +const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, + bool bndry_flux) { + TRACE("FV::Div_par_K_Grad_par"); - ASSERT2(Kin.getLocation() == fin.getLocation()); + ASSERT2(Kin.getLocation() == fin.getLocation()); - Mesh *mesh = Kin.getMesh(); + Mesh* mesh = Kin.getMesh(); - bool use_parallel_slices = (Kin.hasParallelSlices() && fin.hasParallelSlices()); + bool use_parallel_slices = (Kin.hasParallelSlices() && fin.hasParallelSlices()); - const auto& K = use_parallel_slices ? Kin : toFieldAligned(Kin, "RGN_NOX"); - const auto& f = use_parallel_slices ? fin : toFieldAligned(fin, "RGN_NOX"); + const auto& K = use_parallel_slices ? Kin : toFieldAligned(Kin, "RGN_NOX"); + const auto& f = use_parallel_slices ? fin : toFieldAligned(fin, "RGN_NOX"); - Field3D result{zeroFrom(f)}; + Field3D result{zeroFrom(f)}; - // K and f fields in yup and ydown directions - const auto& Kup = use_parallel_slices ? Kin.yup() : K; - const auto& Kdown = use_parallel_slices ? Kin.ydown() : K; - const auto& fup = use_parallel_slices ? fin.yup() : f; - const auto& fdown = use_parallel_slices ? fin.ydown() : f; - - Coordinates *coord = fin.getCoordinates(); + // K and f fields in yup and ydown directions + const auto& Kup = use_parallel_slices ? Kin.yup() : K; + const auto& Kdown = use_parallel_slices ? Kin.ydown() : K; + const auto& fup = use_parallel_slices ? fin.yup() : f; + const auto& fdown = use_parallel_slices ? fin.ydown() : f; - BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { - // Calculate flux at upper surface - - const auto iyp = i.yp(); - const auto iym = i.ym(); + Coordinates* coord = fin.getCoordinates(); - if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x()) - || (i.y() != mesh->yend)) { + BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + // Calculate flux at upper surface - BoutReal c = 0.5*(K[i] + Kup[iyp]); // K at the upper boundary - BoutReal J = 0.5*(coord->J[i] + coord->J[iyp]); // Jacobian at boundary - BoutReal g_22 = 0.5*(coord->g_22[i] + coord->g_22[iyp]); - - BoutReal gradient = 2.*(fup[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]); - - BoutReal flux = c * J * gradient / g_22; - - result[i] += flux / (coord->dy[i] * coord->J[i]); - } + const auto iyp = i.yp(); + const auto iym = i.ym(); - // Calculate flux at lower surface - if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x()) - || (i.y() != mesh->ystart)) { - BoutReal c = 0.5*(K[i] + Kdown[iym]); // K at the lower boundary - BoutReal J = 0.5*(coord->J[i] + coord->J[iym]); // Jacobian at boundary - - BoutReal g_22 = 0.5*(coord->g_22[i] + coord->g_22[iym]); - - BoutReal gradient = 2.*(f[i] - fdown[iym]) / (coord->dy[i] + coord->dy[iym]); - - BoutReal flux = c * J * gradient / g_22; - - result[i] -= flux / (coord->dy[i] * coord->J[i]); - } + if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x()) + || (i.y() != mesh->yend)) { + + BoutReal c = 0.5 * (K[i] + Kup[iyp]); // K at the upper boundary + BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary + BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]); + + BoutReal gradient = 2. * (fup[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]); + + BoutReal flux = c * J * gradient / g_22; + + result[i] += flux / (coord->dy[i] * coord->J[i]); } - - if (!use_parallel_slices) { - // Shifted to field aligned coordinates, so need to shift back - result = fromFieldAligned(result, "RGN_NOBNDRY"); + + // Calculate flux at lower surface + if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x()) + || (i.y() != mesh->ystart)) { + BoutReal c = 0.5 * (K[i] + Kdown[iym]); // K at the lower boundary + BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary + + BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]); + + BoutReal gradient = 2. * (f[i] - fdown[iym]) / (coord->dy[i] + coord->dy[iym]); + + BoutReal flux = c * J * gradient / g_22; + + result[i] -= flux / (coord->dy[i] * coord->J[i]); } - - return result; } - const Field3D D4DY4(const Field3D &d_in, const Field3D &f_in) { - ASSERT1_FIELDS_COMPATIBLE(d_in, f_in); + if (!use_parallel_slices) { + // Shifted to field aligned coordinates, so need to shift back + result = fromFieldAligned(result, "RGN_NOBNDRY"); + } - Mesh* mesh = d_in.getMesh(); + return result; +} - Coordinates *coord = f_in.getCoordinates(); - - ASSERT2(d_in.getDirectionY() == f_in.getDirectionY()); - const bool are_unaligned = ((d_in.getDirectionY() == YDirectionType::Standard) - and (f_in.getDirectionY() == YDirectionType::Standard)); +const Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) { + ASSERT1_FIELDS_COMPATIBLE(d_in, f_in); - // Convert to field aligned coordinates - Field3D d = are_unaligned ? toFieldAligned(d_in, "RGN_NOX") : d_in; - Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in; + Mesh* mesh = d_in.getMesh(); - Field3D result{zeroFrom(f)}; + Coordinates* coord = f_in.getCoordinates(); - for (int i = mesh->xstart; i <= mesh->xend; i++) { - // Check for boundaries - bool yperiodic = mesh->periodicY(i); - bool has_upper_boundary = !yperiodic && mesh->lastY(i); - bool has_lower_boundary = !yperiodic && mesh->firstY(i); + ASSERT2(d_in.getDirectionY() == f_in.getDirectionY()); + const bool are_unaligned = ((d_in.getDirectionY() == YDirectionType::Standard) + and (f_in.getDirectionY() == YDirectionType::Standard)); - // Always calculate fluxes at upper Y cell boundary - const int ystart = - has_lower_boundary - ? mesh->ystart - : // Don't calculate flux from boundary mesh->ystart-1 into domain - mesh->ystart - 1; // Calculate flux from last guard cell into domain + // Convert to field aligned coordinates + Field3D d = are_unaligned ? toFieldAligned(d_in, "RGN_NOX") : d_in; + Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in; - const int yend = has_upper_boundary - ? mesh->yend - 1 - : // Don't calculate flux from mesh->yend into boundary - mesh->yend; + Field3D result{zeroFrom(f)}; - for (int j = ystart; j <= yend; j++) { - for(int k=0;kLocalNz;k++) { - BoutReal dy3 = SQ(coord->dy(i, j, k)) * coord->dy(i, j, k); - // 3rd derivative at upper boundary + for (int i = mesh->xstart; i <= mesh->xend; i++) { + // Check for boundaries + bool yperiodic = mesh->periodicY(i); + bool has_upper_boundary = !yperiodic && mesh->lastY(i); + bool has_lower_boundary = !yperiodic && mesh->firstY(i); + + // Always calculate fluxes at upper Y cell boundary + const int ystart = + has_lower_boundary + ? mesh->ystart + : // Don't calculate flux from boundary mesh->ystart-1 into domain + mesh->ystart - 1; // Calculate flux from last guard cell into domain + + const int yend = has_upper_boundary + ? mesh->yend - 1 + : // Don't calculate flux from mesh->yend into boundary + mesh->yend; + + for (int j = ystart; j <= yend; j++) { + for (int k = 0; k < mesh->LocalNz; k++) { + BoutReal dy3 = SQ(coord->dy(i, j, k)) * coord->dy(i, j, k); + // 3rd derivative at upper boundary - BoutReal d3fdy3 = - (f(i, j + 2, k) - 3. * f(i, j + 1, k) + 3. * f(i, j, k) - f(i, j - 1, k)) - / dy3; + BoutReal d3fdy3 = + (f(i, j + 2, k) - 3. * f(i, j + 1, k) + 3. * f(i, j, k) - f(i, j - 1, k)) + / dy3; - BoutReal flux = 0.5 * (d(i, j, k) + d(i, j + 1, k)) - * (coord->J(i, j, k) + coord->J(i, j + 1, k)) * d3fdy3; + BoutReal flux = 0.5 * (d(i, j, k) + d(i, j + 1, k)) + * (coord->J(i, j, k) + coord->J(i, j + 1, k)) * d3fdy3; - result(i, j, k) += flux / (coord->J(i, j, k) * coord->dy(i, j, k)); - result(i, j + 1, k) -= flux / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k)); - } + result(i, j, k) += flux / (coord->J(i, j, k) * coord->dy(i, j, k)); + result(i, j + 1, k) -= flux / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k)); } } - - // Convert result back to non-aligned coordinates - return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result; } - const Field3D D4DY4_Index(const Field3D &f_in, bool bndry_flux) { - Mesh* mesh = f_in.getMesh(); - - // Convert to field aligned coordinates - const bool is_unaligned = (f_in.getDirectionY() == YDirectionType::Standard); - Field3D f = is_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in; - - Field3D result{zeroFrom(f)}; - - Coordinates *coord = f_in.getCoordinates(); - - for(int i=mesh->xstart;i<=mesh->xend;i++) { - bool yperiodic = mesh->periodicY(i); - - bool has_upper_boundary = !yperiodic && mesh->lastY(i); - bool has_lower_boundary = !yperiodic && mesh->firstY(i); - - for(int j=mesh->ystart;j<=mesh->yend;j++) { - - // Right boundary - - if (bndry_flux || (j != mesh->yend) || !has_upper_boundary) { - // Calculate the fluxes - - if (j != mesh->yend || !has_upper_boundary) { - - for (int k = 0; k < mesh->LocalNz; k++) { - // Right boundary common factors - const BoutReal common_factor = - 0.25 * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) - * (coord->J(i, j, j) + coord->J(i, j + 1, k)); - - const BoutReal factor_rc = - common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); - const BoutReal factor_rp = - common_factor / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k)); - - // Not on domain boundary - // 3rd derivative at right cell boundary - - const BoutReal d3fdx3 = (f(i, j + 2, k) - 3. * f(i, j + 1, k) - + 3. * f(i, j, k) - f(i, j - 1, k)); - - result(i,j, k) += d3fdx3 * factor_rc; - result(i, j + 1, k) -= d3fdx3 * factor_rp; - } - } else { - // At a domain boundary - // Use a one-sided difference formula - - for(int k=0;kLocalNz;k++) { - // Right boundary common factors - const BoutReal common_factor = - 0.25 * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) - * (coord->J(i, j, j) + coord->J(i, j + 1, k)); - - const BoutReal factor_rc = - common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); - const BoutReal factor_rp = - common_factor / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k)); - - const BoutReal d3fdx3 = - -((16. / 5) * 0.5 * (f(i, j + 1, k) + f(i, j, k)) // Boundary value f_b - - 6. * f(i, j, k) // f_0 - + 4. * f(i, j - 1, k) // f_1 - - (6. / 5) * f(i, j - 2, k) // f_2 - ); - - result(i,j, k) += d3fdx3 * factor_rc; - result(i,j+1,k) -= d3fdx3 * factor_rp; - } + // Convert result back to non-aligned coordinates + return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result; +} + +const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) { + Mesh* mesh = f_in.getMesh(); + + // Convert to field aligned coordinates + const bool is_unaligned = (f_in.getDirectionY() == YDirectionType::Standard); + Field3D f = is_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in; + + Field3D result{zeroFrom(f)}; + + Coordinates* coord = f_in.getCoordinates(); + + for (int i = mesh->xstart; i <= mesh->xend; i++) { + bool yperiodic = mesh->periodicY(i); + + bool has_upper_boundary = !yperiodic && mesh->lastY(i); + bool has_lower_boundary = !yperiodic && mesh->firstY(i); + + for (int j = mesh->ystart; j <= mesh->yend; j++) { + + // Right boundary + + if (bndry_flux || (j != mesh->yend) || !has_upper_boundary) { + // Calculate the fluxes + + if (j != mesh->yend || !has_upper_boundary) { + + for (int k = 0; k < mesh->LocalNz; k++) { + // Right boundary common factors + const BoutReal common_factor = 0.25 + * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) + * (coord->J(i, j, j) + coord->J(i, j + 1, k)); + + const BoutReal factor_rc = + common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); + const BoutReal factor_rp = + common_factor / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k)); + + // Not on domain boundary + // 3rd derivative at right cell boundary + + const BoutReal d3fdx3 = + (f(i, j + 2, k) - 3. * f(i, j + 1, k) + 3. * f(i, j, k) - f(i, j - 1, k)); + + result(i, j, k) += d3fdx3 * factor_rc; + result(i, j + 1, k) -= d3fdx3 * factor_rp; + } + } else { + // At a domain boundary + // Use a one-sided difference formula + + for (int k = 0; k < mesh->LocalNz; k++) { + // Right boundary common factors + const BoutReal common_factor = 0.25 + * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) + * (coord->J(i, j, j) + coord->J(i, j + 1, k)); + + const BoutReal factor_rc = + common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); + const BoutReal factor_rp = + common_factor / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k)); + + const BoutReal d3fdx3 = + -((16. / 5) * 0.5 * (f(i, j + 1, k) + f(i, j, k)) // Boundary value f_b + - 6. * f(i, j, k) // f_0 + + 4. * f(i, j - 1, k) // f_1 + - (6. / 5) * f(i, j - 2, k) // f_2 + ); + + result(i, j, k) += d3fdx3 * factor_rc; + result(i, j + 1, k) -= d3fdx3 * factor_rp; } } + } + + // Left cell boundary + + if (bndry_flux || (j != mesh->ystart) || !has_lower_boundary) { + // Calculate the fluxes - // Left cell boundary - - if (bndry_flux || (j != mesh->ystart) || !has_lower_boundary) { - // Calculate the fluxes - - - if ( j != mesh->ystart || !has_lower_boundary ) { - for(int k=0;kLocalNz;k++) { - const BoutReal common_factor = - 0.25 * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) - * (coord->J(i, j, k) + coord->J(i, j - 1, k)); - - const BoutReal factor_lc = - common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); - const BoutReal factor_lm = - common_factor / (coord->J(i, j - 1, k) * coord->dy(i, j - 1, k)); - - // Not on a domain boundary - const BoutReal d3fdx3 = (f(i, j + 1, k) - 3. * f(i, j, k) - + 3. * f(i, j - 1, k) - f(i, j - 2, k)); - - result(i, j , k) -= d3fdx3 * factor_lc; - result(i, j - 1, k) += d3fdx3 * factor_lm; - } - } else { - // On a domain (Y) boundary - for(int k=0;kLocalNz;k++) { - const BoutReal common_factor = - 0.25 * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) - * (coord->J(i, j, k) + coord->J(i, j - 1, k)); - - const BoutReal factor_lc = - common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); - const BoutReal factor_lm = - common_factor / (coord->J(i, j - 1, k) * coord->dy(i, j - 1, k)); - const BoutReal d3fdx3 = - -(-(16. / 5) * 0.5 * (f(i, j - 1, k) + f(i, j, k)) // Boundary value f_b - + 6. * f(i, j, k) // f_0 - - 4. * f(i, j + 1, k) // f_1 - + (6. / 5) * f(i, j + 2, k) // f_2 - ); - - result(i, j , k) -= d3fdx3 * factor_lc; - result(i, j - 1, k) += d3fdx3 * factor_lm; - } + if (j != mesh->ystart || !has_lower_boundary) { + for (int k = 0; k < mesh->LocalNz; k++) { + const BoutReal common_factor = 0.25 + * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) + * (coord->J(i, j, k) + coord->J(i, j - 1, k)); + + const BoutReal factor_lc = + common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); + const BoutReal factor_lm = + common_factor / (coord->J(i, j - 1, k) * coord->dy(i, j - 1, k)); + + // Not on a domain boundary + const BoutReal d3fdx3 = + (f(i, j + 1, k) - 3. * f(i, j, k) + 3. * f(i, j - 1, k) - f(i, j - 2, k)); + + result(i, j, k) -= d3fdx3 * factor_lc; + result(i, j - 1, k) += d3fdx3 * factor_lm; + } + } else { + // On a domain (Y) boundary + for (int k = 0; k < mesh->LocalNz; k++) { + const BoutReal common_factor = 0.25 + * (coord->dy(i, j, k) + coord->dy(i, j + 1, k)) + * (coord->J(i, j, k) + coord->J(i, j - 1, k)); + + const BoutReal factor_lc = + common_factor / (coord->J(i, j, k) * coord->dy(i, j, k)); + const BoutReal factor_lm = + common_factor / (coord->J(i, j - 1, k) * coord->dy(i, j - 1, k)); + const BoutReal d3fdx3 = + -(-(16. / 5) * 0.5 * (f(i, j - 1, k) + f(i, j, k)) // Boundary value f_b + + 6. * f(i, j, k) // f_0 + - 4. * f(i, j + 1, k) // f_1 + + (6. / 5) * f(i, j + 2, k) // f_2 + ); + + result(i, j, k) -= d3fdx3 * factor_lc; + result(i, j - 1, k) += d3fdx3 * factor_lm; } } } } - - // Convert result back to non-aligned coordinates - return is_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result; } - void communicateFluxes(Field3D &f) { - Mesh* mesh = f.getMesh(); - - // Use X=0 as temporary buffer - if (mesh->xstart != 2) - throw BoutException("communicateFluxes: Sorry!"); - - int size = mesh->LocalNy * mesh->LocalNz; - comm_handle xin, xout; - // Cache results to silence spurious compiler warning about xin, - // xout possibly being uninitialised when used - bool not_first = !mesh->firstX(); - bool not_last = !mesh->lastX(); - if (not_first) { - xin = mesh->irecvXIn(f(0, 0), size, 0); - } - if (not_last) { - xout = mesh->irecvXOut(f(mesh->LocalNx - 1, 0), size, 1); - } - // Send X=1 values - if (not_first) { - mesh->sendXIn(f(1, 0), size, 1); - } - if (not_last) { - mesh->sendXOut(f(mesh->LocalNx - 2, 0), size, 0); - } - // Wait - if (not_first) { - mesh->wait(xin); - // Add to cells - for (int y = mesh->ystart; y <= mesh->yend; y++) - for (int z = 0; z < mesh->LocalNz; z++) { - f(2, y, z) += f(0, y, z); - } + // Convert result back to non-aligned coordinates + return is_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result; +} + +void communicateFluxes(Field3D& f) { + Mesh* mesh = f.getMesh(); + + // Use X=0 as temporary buffer + if (mesh->xstart != 2) { + throw BoutException("communicateFluxes: Sorry!"); + } + + int size = mesh->LocalNy * mesh->LocalNz; + comm_handle xin, xout; + // Cache results to silence spurious compiler warning about xin, + // xout possibly being uninitialised when used + bool not_first = !mesh->firstX(); + bool not_last = !mesh->lastX(); + if (not_first) { + xin = mesh->irecvXIn(f(0, 0), size, 0); + } + if (not_last) { + xout = mesh->irecvXOut(f(mesh->LocalNx - 1, 0), size, 1); + } + // Send X=1 values + if (not_first) { + mesh->sendXIn(f(1, 0), size, 1); + } + if (not_last) { + mesh->sendXOut(f(mesh->LocalNx - 2, 0), size, 0); + } + // Wait + if (not_first) { + mesh->wait(xin); + // Add to cells + for (int y = mesh->ystart; y <= mesh->yend; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + f(2, y, z) += f(0, y, z); + } } - if (not_last) { - mesh->wait(xout); - // Add to cells - for (int y = mesh->ystart; y <= mesh->yend; y++) - for (int z = 0; z < mesh->LocalNz; z++) { - f(mesh->LocalNx - 3, y, z) += f(mesh->LocalNx - 1, y, z); - } + } + if (not_last) { + mesh->wait(xout); + // Add to cells + for (int y = mesh->ystart; y <= mesh->yend; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + f(mesh->LocalNx - 3, y, z) += f(mesh->LocalNx - 1, y, z); + } } } +} - Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc) { - - Field3D result = 0.0; - - ////////////////////////////////////////// - // X-Z diffusion - // - // Z - // | - // - // o --- gU --- o - // | nU | - // | | - // gL nL nR gR -> X - // | | - // | nD | - // o --- gD --- o - // - Coordinates* coords = a.getCoordinates(outloc); - Mesh* mesh = f.getMesh(); - - for (int i = mesh->xstart; i <= mesh->xend; i++) - for (int j = mesh->ystart; j <= mesh->yend; j++) - for (int k = 0; k < mesh->LocalNz; k++) { - - // wrap k-index around as Z is (currently) periodic. - int kp = (k + 1) % (mesh->LocalNz); - int km = (k - 1 + mesh->LocalNz) % (mesh->LocalNz); - - // Calculate gradients on cell faces -- assumes constant grid spacing - - BoutReal gR = - (coords->g11(i, j, k) + coords->g11(i + 1, j, k)) - * (f(i + 1, j, k) - f(i, j, k)) - / (coords->dx(i + 1, j, k) + coords->dx(i, j, k)) - + 0.5 * (coords->g13(i, j, k) + coords->g13(i + 1, j, k)) - * (f(i + 1, j, kp) - f(i + 1, j, km) + f(i, j, kp) - f(i, j, km)) - / (4. * coords->dz(i, j, k)); - - BoutReal gL = - (coords->g11(i - 1, j, k) + coords->g11(i, j, k)) - * (f(i, j, k) - f(i - 1, j, k)) - / (coords->dx(i - 1, j, k) + coords->dx(i, j, k)) - + 0.5 * (coords->g13(i - 1, j, k) + coords->g13(i, j, k)) - * (f(i - 1, j, kp) - f(i - 1, j, km) + f(i, j, kp) - f(i, j, km)) - / (4 * coords->dz(i, j, k)); - - BoutReal gD = - coords->g13(i, j, k) - * (f(i + 1, j, km) - f(i - 1, j, km) + f(i + 1, j, k) - f(i - 1, j, k)) - / (4. * coords->dx(i, j, k)) - + coords->g33(i, j, k) * (f(i, j, k) - f(i, j, km)) / coords->dz(i, j, k); - - BoutReal gU = - coords->g13(i, j, k) - * (f(i + 1, j, kp) - f(i - 1, j, kp) + f(i + 1, j, k) - f(i - 1, j, k)) - / (4. * coords->dx(i, j, k)) - + coords->g33(i, j, k) * (f(i, j, kp) - f(i, j, k)) / coords->dz(i, j, k); - - // Flow right - BoutReal flux = gR * 0.25 * (coords->J(i + 1, j, k) + coords->J(i, j, k)) - * (a(i + 1, j, k) + a(i, j, k)); - result(i, j, k) += flux / (coords->dx(i, j, k) * coords->J(i, j, k)); - - // Flow left - flux = gL * 0.25 * (coords->J(i - 1, j, k) + coords->J(i, j, k)) - * (a(i - 1, j, k) + a(i, j, k)); - result(i, j, k) -= flux / (coords->dx(i, j, k) * coords->J(i, j, k)); - - // Flow up - flux = gU * 0.25 * (coords->J(i, j, k) + coords->J(i, j, kp)) - * (a(i, j, k) + a(i, j, kp)); - result(i, j, k) += flux / (coords->dz(i, j, k) * coords->J(i, j, k)); - - // Flow down - flux = gD * 0.25 * (coords->J(i, j, km) + coords->J(i, j, k)) - * (a(i, j, km) + a(i, j, k)); - result(i, j, k) += flux / (coords->dz(i, j, k) * coords->J(i, j, k)); - } +Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc) { + + Field3D result = 0.0; + + ////////////////////////////////////////// + // X-Z diffusion + // + // Z + // | + // + // o --- gU --- o + // | nU | + // | | + // gL nL nR gR -> X + // | | + // | nD | + // o --- gD --- o + // + Coordinates* coords = a.getCoordinates(outloc); + Mesh* mesh = f.getMesh(); - return result; + for (int i = mesh->xstart; i <= mesh->xend; i++) { + for (int j = mesh->ystart; j <= mesh->yend; j++) { + for (int k = 0; k < mesh->LocalNz; k++) { + + // wrap k-index around as Z is (currently) periodic. + int kp = (k + 1) % (mesh->LocalNz); + int km = (k - 1 + mesh->LocalNz) % (mesh->LocalNz); + + // Calculate gradients on cell faces -- assumes constant grid spacing + + BoutReal gR = + (coords->g11(i, j, k) + coords->g11(i + 1, j, k)) + * (f(i + 1, j, k) - f(i, j, k)) + / (coords->dx(i + 1, j, k) + coords->dx(i, j, k)) + + 0.5 * (coords->g13(i, j, k) + coords->g13(i + 1, j, k)) + * (f(i + 1, j, kp) - f(i + 1, j, km) + f(i, j, kp) - f(i, j, km)) + / (4. * coords->dz(i, j, k)); + + BoutReal gL = + (coords->g11(i - 1, j, k) + coords->g11(i, j, k)) + * (f(i, j, k) - f(i - 1, j, k)) + / (coords->dx(i - 1, j, k) + coords->dx(i, j, k)) + + 0.5 * (coords->g13(i - 1, j, k) + coords->g13(i, j, k)) + * (f(i - 1, j, kp) - f(i - 1, j, km) + f(i, j, kp) - f(i, j, km)) + / (4 * coords->dz(i, j, k)); + + BoutReal gD = + coords->g13(i, j, k) + * (f(i + 1, j, km) - f(i - 1, j, km) + f(i + 1, j, k) - f(i - 1, j, k)) + / (4. * coords->dx(i, j, k)) + + coords->g33(i, j, k) * (f(i, j, k) - f(i, j, km)) / coords->dz(i, j, k); + + BoutReal gU = + coords->g13(i, j, k) + * (f(i + 1, j, kp) - f(i - 1, j, kp) + f(i + 1, j, k) - f(i - 1, j, k)) + / (4. * coords->dx(i, j, k)) + + coords->g33(i, j, k) * (f(i, j, kp) - f(i, j, k)) / coords->dz(i, j, k); + + // Flow right + BoutReal flux = gR * 0.25 * (coords->J(i + 1, j, k) + coords->J(i, j, k)) + * (a(i + 1, j, k) + a(i, j, k)); + result(i, j, k) += flux / (coords->dx(i, j, k) * coords->J(i, j, k)); + + // Flow left + flux = gL * 0.25 * (coords->J(i - 1, j, k) + coords->J(i, j, k)) + * (a(i - 1, j, k) + a(i, j, k)); + result(i, j, k) -= flux / (coords->dx(i, j, k) * coords->J(i, j, k)); + + // Flow up + flux = gU * 0.25 * (coords->J(i, j, k) + coords->J(i, j, kp)) + * (a(i, j, k) + a(i, j, kp)); + result(i, j, k) += flux / (coords->dz(i, j, k) * coords->J(i, j, k)); + + // Flow down + flux = gD * 0.25 * (coords->J(i, j, km) + coords->J(i, j, k)) + * (a(i, j, km) + a(i, j, k)); + result(i, j, k) += flux / (coords->dz(i, j, k) * coords->J(i, j, k)); + } + } } + return result; +} + } // Namespace FV diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index a052c304f8..f2854b6b01 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -37,17 +37,17 @@ #include #include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include #include #include @@ -56,7 +56,7 @@ /// MPI type of BoutReal for communications #define PVEC_REAL_MPI_TYPE MPI_DOUBLE -BoutMesh::BoutMesh(GridDataSource *s, Options *opt) : Mesh(s, opt) { +BoutMesh::BoutMesh(GridDataSource* s, Options* opt) : Mesh(s, opt) { OPTION(options, symmetricGlobalX, true); if (!options->isSet("symmetricGlobalY")) { std::string optionfile = Options::root()["optionfile"].withDefault("BOUT.inp"); @@ -348,7 +348,7 @@ void BoutMesh::setDerivedGridSizes() { } // Set global grid sizes, excluding boundary points - GlobalNxNoBoundaries = nx - 2*MXG; + GlobalNxNoBoundaries = nx - 2 * MXG; GlobalNyNoBoundaries = ny; GlobalNzNoBoundaries = nz; @@ -535,7 +535,7 @@ int BoutMesh::load() { output_info.write("Applying Twist-Shift condition. Interpolation: FFT\n"); if (ShiftAngle.empty()) { throw BoutException("ERROR: Twist-shift angle 'ShiftAngle' not found. " - "Required when TwistShift==true."); + "Required when TwistShift==true."); } } @@ -562,7 +562,7 @@ int BoutMesh::load() { if (!boundary.empty()) { output_info << _("Boundary regions in this processor: "); - for (const auto &bndry : boundary) { + for (const auto& bndry : boundary) { output_info << bndry->label << ", "; } output_info << endl; @@ -1001,32 +1001,47 @@ std::set BoutMesh::getPossibleBoundaries() const { WithQuietOutput quiet_warn(output_warn); // Lambda that modifies `all_boundaries` - const auto get_boundaries_on_different_rank = [mesh = this, &all_boundaries]( - int x_rank, int y_rank) { - // Don't try to check boundaries on unphysical processors - if (x_rank < 0 or x_rank >= mesh->NXPE) { - return; - } - if (y_rank < 0 or y_rank >= mesh->NYPE) { - return; - } - - // Make a copy of this mesh, EXCEPT we change the (X, Y) rank of the processor - BoutMesh mesh_copy{mesh->GlobalNx, mesh->GlobalNyNoBoundaries, mesh->GlobalNz, - mesh->MXG, mesh->MYG, mesh->NXPE, mesh->NYPE, x_rank, y_rank, - mesh->symmetricGlobalX, mesh->symmetricGlobalY, mesh->periodicX, - mesh->ixseps1, mesh->ixseps2, mesh->jyseps1_1, mesh->jyseps2_1, - mesh->jyseps1_2, mesh->jyseps2_2, mesh->ny_inner, false}; - // We need to create the boundaries - mesh_copy.createXBoundaries(); - mesh_copy.createYBoundaries(); - - // Get the boundaries and shove their names into the set - auto boundaries = mesh_copy.getBoundaries(); - std::transform(boundaries.begin(), boundaries.end(), - std::inserter(all_boundaries, all_boundaries.begin()), - [](BoundaryRegionBase* boundary) { return boundary->label; }); - }; + const auto get_boundaries_on_different_rank = + [mesh = this, &all_boundaries](int x_rank, int y_rank) { + // Don't try to check boundaries on unphysical processors + if (x_rank < 0 or x_rank >= mesh->NXPE) { + return; + } + if (y_rank < 0 or y_rank >= mesh->NYPE) { + return; + } + + // Make a copy of this mesh, EXCEPT we change the (X, Y) rank of the processor + BoutMesh mesh_copy{mesh->GlobalNx, + mesh->GlobalNyNoBoundaries, + mesh->GlobalNz, + mesh->MXG, + mesh->MYG, + mesh->NXPE, + mesh->NYPE, + x_rank, + y_rank, + mesh->symmetricGlobalX, + mesh->symmetricGlobalY, + mesh->periodicX, + mesh->ixseps1, + mesh->ixseps2, + mesh->jyseps1_1, + mesh->jyseps2_1, + mesh->jyseps1_2, + mesh->jyseps2_2, + mesh->ny_inner, + false}; + // We need to create the boundaries + mesh_copy.createXBoundaries(); + mesh_copy.createYBoundaries(); + + // Get the boundaries and shove their names into the set + auto boundaries = mesh_copy.getBoundaries(); + std::transform(boundaries.begin(), boundaries.end(), + std::inserter(all_boundaries, all_boundaries.begin()), + [](BoundaryRegionBase* boundary) { return boundary->label; }); + }; // This is sufficient to get the SOL boundary, if it exists get_boundaries_on_different_rank(NXPE - 1, 0); @@ -1064,30 +1079,28 @@ const int OUT_SENT_DOWN = 3; ///< Data higher in X than branch-cut, at lower bou const int IN_SENT_OUT = 4; ///< Data going in positive X direction (in to out) const int OUT_SENT_IN = 5; ///< Data going in negative X direction (out to in) -void BoutMesh::post_receiveX(CommHandle &ch) { +void BoutMesh::post_receiveX(CommHandle& ch) { /// Post receive data from left (x-1) if (IDATA_DEST != -1) { - mpi->MPI_Irecv(std::begin(ch.imsg_recvbuff), - msg_len(ch.var_list.get(), 0, MXG, 0, - ch.include_x_corners ? LocalNy : MYSUB), - PVEC_REAL_MPI_TYPE, IDATA_DEST, OUT_SENT_IN, BoutComm::get(), - &ch.request[4]); + mpi->MPI_Irecv( + std::begin(ch.imsg_recvbuff), + msg_len(ch.var_list.get(), 0, MXG, 0, ch.include_x_corners ? LocalNy : MYSUB), + PVEC_REAL_MPI_TYPE, IDATA_DEST, OUT_SENT_IN, BoutComm::get(), &ch.request[4]); } // Post receive data from right (x+1) if (ODATA_DEST != -1) { - mpi->MPI_Irecv(std::begin(ch.omsg_recvbuff), - msg_len(ch.var_list.get(), 0, MXG, 0, - ch.include_x_corners ? LocalNy : MYSUB), - PVEC_REAL_MPI_TYPE, ODATA_DEST, IN_SENT_OUT, BoutComm::get(), - &ch.request[5]); + mpi->MPI_Irecv( + std::begin(ch.omsg_recvbuff), + msg_len(ch.var_list.get(), 0, MXG, 0, ch.include_x_corners ? LocalNy : MYSUB), + PVEC_REAL_MPI_TYPE, ODATA_DEST, IN_SENT_OUT, BoutComm::get(), &ch.request[5]); } } -void BoutMesh::post_receiveY(CommHandle &ch) { - BoutReal *inbuff; +void BoutMesh::post_receiveY(CommHandle& ch) { + BoutReal* inbuff; int len; /// Post receive data from above (y+1) @@ -1122,7 +1135,7 @@ void BoutMesh::post_receiveY(CommHandle &ch) { } } -comm_handle BoutMesh::send(FieldGroup &g) { +comm_handle BoutMesh::send(FieldGroup& g) { /// Start timer Timer timer("comms"); @@ -1137,16 +1150,16 @@ comm_handle BoutMesh::send(FieldGroup &g) { int ylen = msg_len(g.get(), 0, LocalNx, 0, MYG); /// Get a communications handle of (at least) the needed size - CommHandle *ch = get_handle(xlen, ylen); + CommHandle* ch = get_handle(xlen, ylen); ch->var_list = g; // Group of fields to send sendX(g, ch, true); sendY(g, ch); - return static_cast(ch); + return static_cast(ch); } -comm_handle BoutMesh::sendX(FieldGroup &g, comm_handle handle, bool disable_corners) { +comm_handle BoutMesh::sendX(FieldGroup& g, comm_handle handle, bool disable_corners) { /// Start timer Timer timer("comms"); @@ -1189,9 +1202,9 @@ comm_handle BoutMesh::sendX(FieldGroup &g, comm_handle handle, bool disable_corn /// Send to the right (x+1) if (ODATA_DEST != -1) { - int len = pack_data(ch->var_list.get(), MXSUB, MXSUB + MXG, ch->include_x_corners ? 0 : - MYG, ch->include_x_corners ? LocalNy : MYG + MYSUB, - std::begin(ch->omsg_sendbuff)); + int len = pack_data( + ch->var_list.get(), MXSUB, MXSUB + MXG, ch->include_x_corners ? 0 : MYG, + ch->include_x_corners ? LocalNy : MYG + MYSUB, std::begin(ch->omsg_sendbuff)); if (async_send) { mpi->MPI_Isend(std::begin(ch->omsg_sendbuff), len, PVEC_REAL_MPI_TYPE, ODATA_DEST, OUT_SENT_IN, BoutComm::get(), &(ch->sendreq[5])); @@ -1204,10 +1217,10 @@ comm_handle BoutMesh::sendX(FieldGroup &g, comm_handle handle, bool disable_corn /// Mark communication handle as in progress ch->in_progress = true; - return static_cast(ch); + return static_cast(ch); } -comm_handle BoutMesh::sendY(FieldGroup &g, comm_handle handle) { +comm_handle BoutMesh::sendY(FieldGroup& g, comm_handle handle) { /// Start timer Timer timer("comms"); @@ -1301,7 +1314,7 @@ comm_handle BoutMesh::sendY(FieldGroup &g, comm_handle handle) { /// Mark as y-communication ch->has_y_communication = true; - return static_cast(ch); + return static_cast(ch); } int BoutMesh::wait(comm_handle handle) { @@ -1455,8 +1468,9 @@ int BoutMesh::wait(comm_handle handle) { #if CHECK > 0 // Keeping track of whether communications have been done - for (const auto &var : ch->var_list) + for (const auto& var : ch->var_list) { var->doneComms(); + } #endif free_handle(ch); @@ -1512,14 +1526,15 @@ int BoutMesh::sendXIn(BoutReal* buffer, int size, int tag) { return 0; } -comm_handle BoutMesh::irecvXOut(BoutReal *buffer, int size, int tag) { - if (PE_XIND == NXPE - 1) +comm_handle BoutMesh::irecvXOut(BoutReal* buffer, int size, int tag) { + if (PE_XIND == NXPE - 1) { return nullptr; + } Timer timer("comms"); // Get a communications handle. Not fussy about size of arrays - CommHandle *ch = get_handle(0, 0); + CommHandle* ch = get_handle(0, 0); mpi->MPI_Irecv(buffer, size, PVEC_REAL_MPI_TYPE, PROC_NUM(PE_XIND + 1, PE_YIND), tag, BoutComm::get(), ch->request); @@ -1609,7 +1624,7 @@ int BoutMesh::PROC_NUM(int xind, int yind) const { } /// Returns the global X index given a local index -int BoutMesh::XGLOBAL(BoutReal xloc, BoutReal &xglo) const { +int BoutMesh::XGLOBAL(BoutReal xloc, BoutReal& xglo) const { xglo = xloc + PE_XIND * MXSUB; return static_cast(xglo); } @@ -1626,16 +1641,16 @@ int BoutMesh::getLocalXIndexNoBoundaries(int xglobal) const { return xglobal - PE_XIND * MXSUB + MXG; } -int BoutMesh::YGLOBAL(BoutReal yloc, BoutReal &yglo) const { +int BoutMesh::YGLOBAL(BoutReal yloc, BoutReal& yglo) const { yglo = yloc + PE_YIND * MYSUB - MYG; return static_cast(yglo); } int BoutMesh::getGlobalYIndex(int ylocal) const { - int yglobal = ylocal + PE_YIND * MYSUB; - if (jyseps1_2 > jyseps2_1 and PE_YIND*MYSUB + 2*MYG + 1 > ny_inner) { + int yglobal = ylocal + PE_YIND * MYSUB; + if (jyseps1_2 > jyseps2_1 and PE_YIND * MYSUB + 2 * MYG + 1 > ny_inner) { // Double null, and we are past the upper target - yglobal += 2*MYG; + yglobal += 2 * MYG; } return yglobal; } @@ -1825,9 +1840,9 @@ void BoutMesh::set_connection(int ypos1, int ypos2, int xge, int xlt, bool ts) { ypos1, ypos2, xge, xlt); } - output_info.write( - "Connection between top of Y processor {:d} and bottom of {:d} in range {:d} <= x < {:d}\n", - ypeup, ypedown, xge, xlt); + output_info.write("Connection between top of Y processor {:d} and bottom of {:d} in " + "range {:d} <= x < {:d}\n", + ypeup, ypedown, xge, xlt); // Convert X coordinates into local indices @@ -1923,8 +1938,8 @@ void BoutMesh::add_target(int ypos, int xge, int xlt) { } output_info.write( - "Target at top of Y processor {:d} and bottom of {:d} in range {:d} <= x < {:d}\n", ypeup, - ypedown, xge, xlt); + "Target at top of Y processor {:d} and bottom of {:d} in range {:d} <= x < {:d}\n", + ypeup, ypedown, xge, xlt); // Convert X coordinates into local indices xge = getLocalXIndex(xge); @@ -2110,7 +2125,7 @@ void BoutMesh::topology() { * Communication handles ****************************************************************/ -BoutMesh::CommHandle *BoutMesh::get_handle(int xlen, int ylen) { +BoutMesh::CommHandle* BoutMesh::get_handle(int xlen, int ylen) { if (comm_list.empty()) { // Allocate a new CommHandle @@ -2142,7 +2157,7 @@ BoutMesh::CommHandle *BoutMesh::get_handle(int xlen, int ylen) { } // Pop first pointer off the list - CommHandle *ch = comm_list.front(); + CommHandle* ch = comm_list.front(); comm_list.pop_front(); // Check that the buffers are big enough (NOTE: Could search list for bigger buffers) @@ -2172,14 +2187,14 @@ BoutMesh::CommHandle *BoutMesh::get_handle(int xlen, int ylen) { return ch; } -void BoutMesh::free_handle(CommHandle *h) { +void BoutMesh::free_handle(CommHandle* h) { h->var_list.clear(); comm_list.push_front(h); } void BoutMesh::clear_handles() { while (!comm_list.empty()) { - CommHandle *ch = comm_list.front(); + CommHandle* ch = comm_list.front(); delete ch; @@ -2239,13 +2254,13 @@ void BoutMesh::overlapHandleMemory(BoutMesh* yup, BoutMesh* ydown, BoutMesh* xin * Communication utilities ****************************************************************/ -int BoutMesh::pack_data(const std::vector &var_list, int xge, int xlt, int yge, - int ylt, BoutReal *buffer) { +int BoutMesh::pack_data(const std::vector& var_list, int xge, int xlt, + int yge, int ylt, BoutReal* buffer) { int len = 0; /// Loop over variables - for (const auto &var : var_list) { + for (const auto& var : var_list) { if (var->is3D()) { // 3D variable auto& var3d_ref = *dynamic_cast(var); @@ -2272,13 +2287,13 @@ int BoutMesh::pack_data(const std::vector &var_list, int xge, int x return (len); } -int BoutMesh::unpack_data(const std::vector &var_list, int xge, int xlt, int yge, - int ylt, BoutReal *buffer) { +int BoutMesh::unpack_data(const std::vector& var_list, int xge, int xlt, + int yge, int ylt, BoutReal* buffer) { int len = 0; /// Loop over variables - for (const auto &var : var_list) { + for (const auto& var : var_list) { if (var->is3D()) { // 3D variable auto& var3d_ref = *dynamic_cast(var); @@ -2331,8 +2346,8 @@ int BoutMesh::numberOfYBoundaries() const { } std::pair BoutMesh::hasBranchCutLower(int jx) const { - if ( (TS_down_in and DDATA_INDEST != -1 and jx < DDATA_XSPLIT) - or (TS_down_out and DDATA_OUTDEST != -1 and jx >= DDATA_XSPLIT) ) { + if ((TS_down_in and DDATA_INDEST != -1 and jx < DDATA_XSPLIT) + or (TS_down_out and DDATA_OUTDEST != -1 and jx >= DDATA_XSPLIT)) { // this processor has branch cut at lower boundary for jx if (ShiftAngle.empty()) { // This function should only be called during initialization, so always check @@ -2344,10 +2359,9 @@ std::pair BoutMesh::hasBranchCutLower(int jx) const { return std::make_pair(false, 0.); } - std::pair BoutMesh::hasBranchCutUpper(int jx) const { - if ( (TS_up_in and UDATA_INDEST != -1 and jx < UDATA_XSPLIT) - or (TS_up_out and UDATA_OUTDEST != -1 and jx >= UDATA_XSPLIT) ) { + if ((TS_up_in and UDATA_INDEST != -1 and jx < UDATA_XSPLIT) + or (TS_up_out and UDATA_OUTDEST != -1 and jx >= UDATA_XSPLIT)) { // this processor has branch cut at upper boundary for jx if (ShiftAngle.empty()) { // This function should only be called during initialization, so always check @@ -2367,8 +2381,8 @@ int BoutMesh::ySize(int xpos) const { // Lower PF region return (jyseps1_1 + 1) + (ny - jyseps2_2); - } else if ((xglobal < ixseps_upper) && (yglobal > jyseps2_1) && - (yglobal >= jyseps1_2)) { + } else if ((xglobal < ixseps_upper) && (yglobal > jyseps2_1) + && (yglobal >= jyseps1_2)) { // Upper PF region return jyseps1_2 - jyseps2_1; @@ -2415,7 +2429,7 @@ MPI_Comm BoutMesh::getYcomm(int xpos) const { void BoutMesh::addBoundaryRegions() { std::list all_boundaries; ///< Keep track of all boundary regions - + // Lower Inner Y int xs = 0; int xe = LocalNx - 1; @@ -2447,16 +2461,16 @@ void BoutMesh::addBoundaryRegions() { xe = LocalNx - 1; } } - - addRegion3D("RGN_LOWER_INNER_Y", Region(xs, xe, 0, ystart-1, 0, LocalNz-1, + + addRegion3D("RGN_LOWER_INNER_Y", Region(xs, xe, 0, ystart - 1, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_LOWER_INNER_Y", Region(xs, xe, 0, ystart-1, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion2D("RGN_LOWER_INNER_Y", + Region(xs, xe, 0, ystart - 1, 0, 0, LocalNy, 1, maxregionblocksize)); all_boundaries.emplace_back("RGN_LOWER_INNER_Y"); // Lower Outer Y - + xs = 0; xe = LocalNx - 1; if (!firstY()) { @@ -2487,12 +2501,12 @@ void BoutMesh::addBoundaryRegions() { xe = -2; } - addRegion3D("RGN_LOWER_OUTER_Y", Region(xs, xe, 0, ystart-1, 0, LocalNz-1, + addRegion3D("RGN_LOWER_OUTER_Y", Region(xs, xe, 0, ystart - 1, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_LOWER_OUTER_Y", Region(xs, xe, 0, ystart-1, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion2D("RGN_LOWER_OUTER_Y", + Region(xs, xe, 0, ystart - 1, 0, 0, LocalNy, 1, maxregionblocksize)); all_boundaries.emplace_back("RGN_LOWER_OUTER_Y"); - + // Lower Y xs = 0; @@ -2520,12 +2534,12 @@ void BoutMesh::addBoundaryRegions() { xe = LocalNx - 1; } - addRegion3D("RGN_LOWER_Y", Region(xs, xe, 0, ystart-1, 0, LocalNz-1, - LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_LOWER_Y", Region(xs, xe, 0, ystart-1, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion3D("RGN_LOWER_Y", Region(xs, xe, 0, ystart - 1, 0, LocalNz - 1, LocalNy, + LocalNz, maxregionblocksize)); + addRegion2D("RGN_LOWER_Y", + Region(xs, xe, 0, ystart - 1, 0, 0, LocalNy, 1, maxregionblocksize)); all_boundaries.emplace_back("RGN_LOWER_Y"); - + // Upper Inner Y xs = 0; @@ -2558,15 +2572,16 @@ void BoutMesh::addBoundaryRegions() { // Include corner cells on x-boundary xe = LocalNx - 1; } - - addRegion3D("RGN_UPPER_INNER_Y", Region(xs, xe, yend+1, LocalNy-1, 0, LocalNz-1, - LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_UPPER_INNER_Y", Region(xs, xe, yend+1, LocalNy-1, 0, 0, + + addRegion3D("RGN_UPPER_INNER_Y", + Region(xs, xe, yend + 1, LocalNy - 1, 0, LocalNz - 1, LocalNy, + LocalNz, maxregionblocksize)); + addRegion2D("RGN_UPPER_INNER_Y", Region(xs, xe, yend + 1, LocalNy - 1, 0, 0, LocalNy, 1, maxregionblocksize)); all_boundaries.emplace_back("RGN_UPPER_INNER_Y"); // Upper Outer Y - + xs = 0; xe = LocalNx - 1; @@ -2598,9 +2613,10 @@ void BoutMesh::addBoundaryRegions() { } } - addRegion3D("RGN_UPPER_OUTER_Y", Region(xs, xe, yend+1, LocalNy-1, 0, LocalNz-1, - LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_UPPER_OUTER_Y", Region(xs, xe, yend+1, LocalNy-1, 0, 0, + addRegion3D("RGN_UPPER_OUTER_Y", + Region(xs, xe, yend + 1, LocalNy - 1, 0, LocalNz - 1, LocalNy, + LocalNz, maxregionblocksize)); + addRegion2D("RGN_UPPER_OUTER_Y", Region(xs, xe, yend + 1, LocalNy - 1, 0, 0, LocalNy, 1, maxregionblocksize)); all_boundaries.emplace_back("RGN_UPPER_OUTER_Y"); @@ -2631,14 +2647,14 @@ void BoutMesh::addBoundaryRegions() { xe = LocalNx - 1; } - addRegion3D("RGN_UPPER_Y", Region(xs, xe, yend+1, LocalNy-1, 0, LocalNz-1, + addRegion3D("RGN_UPPER_Y", Region(xs, xe, yend + 1, LocalNy - 1, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_UPPER_Y", Region(xs, xe, yend+1, LocalNy-1, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion2D("RGN_UPPER_Y", Region(xs, xe, yend + 1, LocalNy - 1, 0, 0, LocalNy, + 1, maxregionblocksize)); all_boundaries.emplace_back("RGN_UPPER_Y"); - + // Inner X - if(firstX() && !periodicX) { + if (firstX() && !periodicX) { addRegion3D("RGN_INNER_X_THIN", Region(xstart - 1, xstart - 1, ystart, yend, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); @@ -2647,14 +2663,14 @@ void BoutMesh::addBoundaryRegions() { addRegionPerp("RGN_INNER_X_THIN", Region(xstart - 1, xstart - 1, 0, 0, 0, LocalNz - 1, 1, LocalNz, maxregionblocksize)); - addRegion3D("RGN_INNER_X", Region(0, xstart-1, ystart, yend, 0, LocalNz-1, + addRegion3D("RGN_INNER_X", Region(0, xstart - 1, ystart, yend, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_INNER_X", Region(0, xstart-1, ystart, yend, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion2D("RGN_INNER_X", Region(0, xstart - 1, ystart, yend, 0, 0, LocalNy, + 1, maxregionblocksize)); addRegionPerp("RGN_INNER_X", Region(0, xstart - 1, 0, 0, 0, LocalNz - 1, 1, LocalNz, maxregionblocksize)); all_boundaries.emplace_back("RGN_INNER_X"); - + output_info.write("\tBoundary region inner X\n"); } else { // Empty region @@ -2664,16 +2680,16 @@ void BoutMesh::addBoundaryRegions() { Region(0, -1, 0, 0, 0, 0, LocalNy, 1, maxregionblocksize)); addRegionPerp("RGN_INNER_X_THIN", Region(0, -1, 0, 0, 0, 0, 1, LocalNz, maxregionblocksize)); - addRegion3D("RGN_INNER_X", Region(0, -1, 0, 0, 0, 0, - LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_INNER_X", Region(0, -1, 0, 0, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion3D("RGN_INNER_X", + Region(0, -1, 0, 0, 0, 0, LocalNy, LocalNz, maxregionblocksize)); + addRegion2D("RGN_INNER_X", + Region(0, -1, 0, 0, 0, 0, LocalNy, 1, maxregionblocksize)); addRegionPerp("RGN_INNER_X", Region(0, -1, 0, 0, 0, 0, 1, LocalNz, maxregionblocksize)); } // Outer X - if(lastX() && !periodicX) { + if (lastX() && !periodicX) { addRegion3D("RGN_OUTER_X_THIN", Region(xend + 1, xend + 1, ystart, yend, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); @@ -2682,15 +2698,16 @@ void BoutMesh::addBoundaryRegions() { addRegionPerp("RGN_OUTER_X_THIN", Region(xend + 1, xend + 1, 0, 0, 0, LocalNz - 1, 1, LocalNz, maxregionblocksize)); - addRegion3D("RGN_OUTER_X", Region(xend+1, LocalNx-1, ystart, yend, 0, LocalNz-1, - LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_OUTER_X", Region(xend+1, LocalNx-1, ystart, yend, 0, 0, + addRegion3D("RGN_OUTER_X", + Region(xend + 1, LocalNx - 1, ystart, yend, 0, LocalNz - 1, + LocalNy, LocalNz, maxregionblocksize)); + addRegion2D("RGN_OUTER_X", Region(xend + 1, LocalNx - 1, ystart, yend, 0, 0, LocalNy, 1, maxregionblocksize)); addRegionPerp("RGN_OUTER_X", Region(xend + 1, LocalNx - 1, 0, 0, 0, LocalNz - 1, 1, LocalNz, maxregionblocksize)); all_boundaries.emplace_back("RGN_OUTER_X"); - + output_info.write("\tBoundary region outer X\n"); } else { // Empty region @@ -2700,18 +2717,18 @@ void BoutMesh::addBoundaryRegions() { Region(0, -1, 0, 0, 0, 0, LocalNy, 1, maxregionblocksize)); addRegionPerp("RGN_OUTER_X_THIN", Region(0, -1, 0, 0, 0, 0, 1, LocalNz, maxregionblocksize)); - addRegion3D("RGN_OUTER_X", Region(0, -1, 0, 0, 0, 0, - LocalNy, LocalNz, maxregionblocksize)); - addRegion2D("RGN_OUTER_X", Region(0, -1, 0, 0, 0, 0, - LocalNy, 1, maxregionblocksize)); + addRegion3D("RGN_OUTER_X", + Region(0, -1, 0, 0, 0, 0, LocalNy, LocalNz, maxregionblocksize)); + addRegion2D("RGN_OUTER_X", + Region(0, -1, 0, 0, 0, 0, LocalNy, 1, maxregionblocksize)); addRegionPerp("RGN_OUTER_X", Region(0, -1, 0, 0, 0, 0, 1, LocalNz, maxregionblocksize)); } // Join boundary regions together - + Region bndry3d; // Empty - for (const auto ®ion_name : all_boundaries) { + for (const auto& region_name : all_boundaries) { bndry3d += getRegion3D(region_name); } bndry3d.unique(); // Ensure that the points are unique @@ -2737,7 +2754,7 @@ void BoutMesh::addBoundaryRegions() { addRegion3D("RGN_WITH_BNDRIES", bndry3d); Region bndry2d; // Empty - for (const auto ®ion_name : all_boundaries) { + for (const auto& region_name : all_boundaries) { bndry2d += getRegion2D(region_name); } bndry2d.unique(); // Ensure that the points are unique @@ -2958,7 +2975,7 @@ RangeIterator BoutMesh::iterateBndryUpperY() const { return RangeIterator(xs, xe); } -std::vector BoutMesh::getBoundaries() { return boundary; } +std::vector BoutMesh::getBoundaries() { return boundary; } std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { return par_boundary[static_cast(type)]; diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx index 384f40e076..6c9ec5ec40 100644 --- a/src/mesh/impls/bout/boutmesh.hxx +++ b/src/mesh/impls/bout/boutmesh.hxx @@ -4,8 +4,8 @@ #include "mpi.h" +#include "bout/unused.hxx" #include -#include "unused.hxx" #include #include @@ -18,8 +18,8 @@ /// Topology and communications compatible with BOUT /// conventions. class BoutMesh : public Mesh { - public: - BoutMesh(GridDataSource *s, Options *options = nullptr); +public: + BoutMesh(GridDataSource* s, Options* options = nullptr); ~BoutMesh() override; /// Read in the mesh from data sources @@ -66,10 +66,12 @@ class BoutMesh : public Mesh { ///////////////////////////////////////////// // X communications - bool firstX() const override; ///< Is this processor the first in X? i.e. is there a boundary - ///< to the left in X? - bool lastX() const override; ///< Is this processor last in X? i.e. is there a boundary to the - ///< right in X? + bool + firstX() const override; ///< Is this processor the first in X? i.e. is there a boundary + ///< to the left in X? + bool lastX() + const override; ///< Is this processor last in X? i.e. is there a boundary to the + ///< right in X? /// Send a buffer of data to processor at X index +1 /// @@ -135,7 +137,8 @@ class BoutMesh : public Mesh { /// poloidal circuit if there is a branch cut std::pair hasBranchCutUpper(int jx) const override; - int ySize(int xpos) const override; ///< The number of points in Y at fixed X index \p jx + int ySize( + int xpos) const override; ///< The number of points in Y at fixed X index \p jx ///////////////////////////////////////////// // Y communications @@ -202,7 +205,7 @@ protected: BoutMesh(int input_nx, int input_ny, int input_nz, int mxg, int myg, int nxpe, int nype, int pe_xind, int pe_yind, bool symmetric_X, bool symmetric_Y, bool periodic_X, int ixseps1_, int ixseps2_, int jyseps1_1_, int jyseps2_1_, int jyseps1_2_, - int jyseps2_2_, int ny_inner_, bool create_regions=true); + int jyseps2_2_, int ny_inner_, bool create_regions = true); /// Very basic initialisation, only suitable for testing BoutMesh(int input_nx, int input_ny, int input_nz, int mxg, int myg, int input_npes) @@ -214,8 +217,7 @@ protected: /// the send and receive buffers share memory. This allows for /// communications to be faked between meshes as though they were on /// different processors. - void overlapHandleMemory(BoutMesh* yup, BoutMesh* ydown, BoutMesh* xin, - BoutMesh* xout); + void overlapHandleMemory(BoutMesh* yup, BoutMesh* ydown, BoutMesh* xin, BoutMesh* xout); /// Set the various y-decomposition indices, enforcing the following invariants: /// @@ -279,6 +281,7 @@ protected: /// Set the shift angle and enable twist shift. Should only be used for testing! void setShiftAngle(const std::vector& shift_angle); + private: std::string gridname; int nx, ny, nz; ///< Size of the grid in the input file @@ -390,7 +393,7 @@ protected: void addBoundaryRegions(); private: - std::vector boundary; // Vector of boundary regions + std::vector boundary; // Vector of boundary regions std::vector> par_boundary; // Vector of parallel boundary regions diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx index 6e015c7a19..c87a956749 100644 --- a/src/mesh/index_derivs.cxx +++ b/src/mesh/index_derivs.cxx @@ -25,8 +25,8 @@ #include "bout/traits.hxx" #include #include -#include -#include +#include +#include /******************************************************************************* * Helper routines @@ -49,8 +49,9 @@ STAGGER Mesh::getStagger(const CELL_LOC inloc, const CELL_LOC outloc, ASSERT1(outloc == inloc || (outloc == CELL_CENTRE && inloc == allowedStaggerLoc) || (outloc == allowedStaggerLoc && inloc == CELL_CENTRE)); - if ((!StaggerGrids) || outloc == inloc) + if ((!StaggerGrids) || outloc == inloc) { return STAGGER::None; + } if (outloc == allowedStaggerLoc) { return STAGGER::C2L; } else { @@ -223,17 +224,21 @@ REGISTER_STANDARD_DERIVATIVE(DDX_CWENO3, "W3", 2, DERIV::Standard) { BoutReal a, ma = fabs(f.c); // Split flux a = fabs(f.m); - if (a > ma) + if (a > ma) { ma = a; + } a = fabs(f.p); - if (a > ma) + if (a > ma) { ma = a; + } a = fabs(f.mm); - if (a > ma) + if (a > ma) { ma = a; + } a = fabs(f.pp); - if (a > ma) + if (a > ma) { ma = a; + } stencil sp, sm; @@ -282,11 +287,12 @@ REGISTER_FLUX_DERIVATIVE(FDDX_U2, "U2", 2, DERIV::Flux) { // No vec // Velocity at lower end BoutReal vs = 0.5 * (v.m + v.c); - BoutReal result = (vs >= 0.0) ? vs * (1.5*f.m - 0.5*f.mm) : vs * (1.5*f.c - 0.5*f.p); + BoutReal result = + (vs >= 0.0) ? vs * (1.5 * f.m - 0.5 * f.mm) : vs * (1.5 * f.c - 0.5 * f.p); // and at upper vs = 0.5 * (v.c + v.p); // Existing form doesn't vectorise due to branching - result -= (vs >= 0.0) ? vs * (1.5*f.c - 0.5*f.m) : vs * (1.5*f.p - 0.5*f.pp); + result -= (vs >= 0.0) ? vs * (1.5 * f.c - 0.5 * f.m) : vs * (1.5 * f.p - 0.5 * f.pp); return -result; } @@ -422,7 +428,8 @@ class FFTDerivativeType { ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); ASSERT2(direction == DIRECTION::Z); // Only in Z for now ASSERT2(stagger == STAGGER::None); // Staggering not currently supported - ASSERT2(bout::utils::is_Field3D::value); // Should never need to call this with Field2D + ASSERT2( + bout::utils::is_Field3D::value); // Should never need to call this with Field2D auto* theMesh = var.getMesh(); @@ -431,10 +438,12 @@ class FFTDerivativeType { int kfilter = static_cast(theMesh->fft_derivs_filter * ncz / 2); // truncates, rounding down - if (kfilter < 0) + if (kfilter < 0) { kfilter = 0; - if (kfilter > (ncz / 2)) + } + if (kfilter > (ncz / 2)) { kfilter = ncz / 2; + } const int kmax = ncz / 2 - kfilter; // Up to and including this wavenumber index BOUT_OMP(parallel) { @@ -486,7 +495,8 @@ class FFT2ndDerivativeType { ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); ASSERT2(direction == DIRECTION::Z); // Only in Z for now ASSERT2(stagger == STAGGER::None); // Staggering not currently supported - ASSERT2(bout::utils::is_Field3D::value); // Should never need to call this with Field2D + ASSERT2( + bout::utils::is_Field3D::value); // Should never need to call this with Field2D auto* theMesh = var.getMesh(); @@ -549,7 +559,8 @@ class SplitFluxDerivativeType { } template - void upwindOrFlux(const T& vel, const T& var, T& result, const std::string region) const { + void upwindOrFlux(const T& vel, const T& var, T& result, + const std::string region) const { AUTO_TRACE(); // Split into an upwind and a central differencing part // d/dx(v*f) = v*d/dx(f) + f*d/dx(v) @@ -563,10 +574,9 @@ class SplitFluxDerivativeType { }; constexpr metaData SplitFluxDerivativeType::meta; -produceCombinations, - Set, - Set, TypeContainer>, - Set> +produceCombinations< + Set, + Set, + Set, TypeContainer>, Set> registerSplitDerivative(registerMethod{}); diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx index 7819fafe6f..584c8d8d29 100644 --- a/src/mesh/interpolation/bilinear_xz.cxx +++ b/src/mesh/interpolation/bilinear_xz.cxx @@ -20,16 +20,16 @@ * **************************************************************************/ +#include "bout/globals.hxx" +#include "bout/interpolation_xz.hxx" #include "bout/mesh.hxx" -#include "globals.hxx" -#include "interpolation_xz.hxx" #include #include -XZBilinear::XZBilinear(int y_offset, Mesh *mesh) - : XZInterpolation(y_offset, mesh), - w0(localmesh), w1(localmesh), w2(localmesh), w3(localmesh) { +XZBilinear::XZBilinear(int y_offset, Mesh* mesh) + : XZInterpolation(y_offset, mesh), w0(localmesh), w1(localmesh), w2(localmesh), + w3(localmesh) { // Index arrays contain guard cells in order to get subscripts right i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz); @@ -45,13 +45,14 @@ XZBilinear::XZBilinear(int y_offset, Mesh *mesh) void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, delta_x.getRegion(region)) { + BOUT_FOR (i, delta_x.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } // The integer part of xt_prime, zt_prime are the indices of the cell // containing the field line end-point @@ -95,13 +96,14 @@ Field3D XZBilinear::interpolate(const Field3D& f, const std::string& region) con ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR (i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } const int y_next = y + y_offset; // Due to lack of guard cells in z-direction, we need to ensure z-index diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx index f5ce3357cb..97639c7ee8 100644 --- a/src/mesh/interpolation/hermite_spline_xz.cxx +++ b/src/mesh/interpolation/hermite_spline_xz.cxx @@ -20,17 +20,17 @@ * **************************************************************************/ -#include "globals.hxx" -#include "interpolation_xz.hxx" +#include "bout/globals.hxx" +#include "bout/interpolation_xz.hxx" #include "bout/index_derivs_interface.hxx" #include "bout/mesh.hxx" #include -XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh) - : XZInterpolation(y_offset, mesh), - h00_x(localmesh), h01_x(localmesh), h10_x(localmesh), h11_x(localmesh), - h00_z(localmesh), h01_z(localmesh), h10_z(localmesh), h11_z(localmesh) { +XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh) + : XZInterpolation(y_offset, mesh), h00_x(localmesh), h01_x(localmesh), + h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh), + h10_z(localmesh), h11_z(localmesh) { // Index arrays contain guard cells in order to get subscripts right i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz); @@ -55,13 +55,14 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh) void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, delta_x.getRegion(region)) { + BOUT_FOR (i, delta_x.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } // The integer part of xt_prime, zt_prime are the indices of the cell // containing the field line end-point @@ -141,7 +142,7 @@ XZHermiteSpline::getWeightsForYApproximation(int i, int j, int k, int yoffset) { const int k_mod_p2 = (k_mod + 2) % ncz; return {{i, j + yoffset, k_mod_m1, -0.5 * h10_z(i, j, k)}, - {i, j + yoffset, k_mod, h00_z(i, j, k) - 0.5 * h11_z(i, j, k)}, + {i, j + yoffset, k_mod, h00_z(i, j, k) - 0.5 * h11_z(i, j, k)}, {i, j + yoffset, k_mod_p1, h01_z(i, j, k) + 0.5 * h10_z(i, j, k)}, {i, j + yoffset, k_mod_p2, 0.5 * h11_z(i, j, k)}}; } @@ -175,13 +176,14 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region localmesh->wait(h); } - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR (i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } // Due to lack of guard cells in z-direction, we need to ensure z-index // wraps around diff --git a/src/mesh/interpolation/hermite_spline_z.cxx b/src/mesh/interpolation/hermite_spline_z.cxx index c43287a4f1..5d98ff5ed5 100644 --- a/src/mesh/interpolation/hermite_spline_z.cxx +++ b/src/mesh/interpolation/hermite_spline_z.cxx @@ -20,8 +20,8 @@ * **************************************************************************/ -#include "globals.hxx" -#include "interpolation_z.hxx" +#include "bout/globals.hxx" +#include "bout/interpolation_z.hxx" #include "bout/index_derivs_interface.hxx" #include "bout/mesh.hxx" @@ -30,7 +30,8 @@ ZHermiteSpline::ZHermiteSpline(int y_offset, Mesh* mesh, Region region_in) : ZInterpolation(y_offset, mesh, region_in), fz_region(region_in.size() != 0 ? "RGN_ALL" - : y_offset == 0 ? "RGN_NOBNDRY" : "RGN_NOX"), + : y_offset == 0 ? "RGN_NOBNDRY" + : "RGN_NOX"), h00(localmesh), h01(localmesh), h10(localmesh), h11(localmesh) { if (region_in.size() != 0) { @@ -40,7 +41,7 @@ ZHermiteSpline::ZHermiteSpline(int y_offset, Mesh* mesh, Region region_in } // Index arrays contain guard cells in order to get subscripts right - const int n_total = localmesh->LocalNx*localmesh->LocalNy*localmesh->LocalNz; + const int n_total = localmesh->LocalNx * localmesh->LocalNy * localmesh->LocalNz; k_corner.reallocate(n_total); // Initialise in order to avoid 'uninitialized value' errors from Valgrind when using @@ -62,9 +63,10 @@ void ZHermiteSpline::calcWeights(const Field3D& delta_z) { // Calculate weights for all points if y_offset==0 in case they are needed, otherwise // only calculate weights for RGN_NOY, which should be a superset of 'region' - const auto& local_region = (y_offset == 0) ? delta_z.getRegion("RGN_ALL") : delta_z.getRegion("RGN_NOY"); + const auto& local_region = + (y_offset == 0) ? delta_z.getRegion("RGN_ALL") : delta_z.getRegion("RGN_NOY"); - BOUT_FOR(i, local_region) { + BOUT_FOR (i, local_region) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -83,7 +85,7 @@ void ZHermiteSpline::calcWeights(const Field3D& delta_z) { corner_zind = ((corner_zind % ncz) + ncz) % ncz; // Convert z-index to Ind3D - k_corner[i.ind] = Ind3D((x*ncy + y)*ncz + corner_zind, ncy, ncz); + k_corner[i.ind] = Ind3D((x * ncy + y) * ncz + corner_zind, ncy, ncz); // Check that t_z is in range if ((t_z < 0.0) || (t_z > 1.0)) { @@ -132,19 +134,20 @@ ZHermiteSpline::getWeightsForYApproximation(int i, int j, int k, int yoffset) co ASSERT3(k <= localmesh->LocalNz); const int ncz = localmesh->LocalNz; - const auto corner = k_corner[(i*localmesh->LocalNy + j)*ncz + k]; + const auto corner = k_corner[(i * localmesh->LocalNy + j) * ncz + k]; const int k_mod = corner.z(); const int k_mod_m1 = corner.zm().z(); const int k_mod_p1 = corner.zp().z(); const int k_mod_p2 = corner.zpp().z(); return {{i, j + yoffset, k_mod_m1, -0.5 * h10(i, j, k)}, - {i, j + yoffset, k_mod, h00(i, j, k) - 0.5 * h11(i, j, k)}, + {i, j + yoffset, k_mod, h00(i, j, k) - 0.5 * h11(i, j, k)}, {i, j + yoffset, k_mod_p1, h01(i, j, k) + 0.5 * h10(i, j, k)}, {i, j + yoffset, k_mod_p2, 0.5 * h11(i, j, k)}}; } -Field3D ZHermiteSpline::interpolate(const Field3D& f, const std::string& region_str) const { +Field3D ZHermiteSpline::interpolate(const Field3D& f, + const std::string& region_str) const { ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; @@ -164,7 +167,7 @@ Field3D ZHermiteSpline::interpolate(const Field3D& f, const std::string& region_ // coordinates Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", local_fz_region); - BOUT_FOR(i, local_region) { + BOUT_FOR (i, local_region) { const auto corner = k_corner[i.ind].yp(y_offset); const auto corner_zp1 = corner.zp(); @@ -191,8 +194,8 @@ RegisterZInterpolation registerzinterphermitespline{"hermitespli } // namespace constexpr decltype(ZInterpolationFactory::type_name) ZInterpolationFactory::type_name; -constexpr decltype( - ZInterpolationFactory::section_name) ZInterpolationFactory::section_name; +constexpr decltype(ZInterpolationFactory::section_name) + ZInterpolationFactory::section_name; constexpr decltype(ZInterpolationFactory::option_name) ZInterpolationFactory::option_name; -constexpr decltype( - ZInterpolationFactory::default_type) ZInterpolationFactory::default_type; +constexpr decltype(ZInterpolationFactory::default_type) + ZInterpolationFactory::default_type; diff --git a/src/mesh/interpolation/interpolation_z.cxx b/src/mesh/interpolation/interpolation_z.cxx index 9b15e9ea81..6162129965 100644 --- a/src/mesh/interpolation/interpolation_z.cxx +++ b/src/mesh/interpolation/interpolation_z.cxx @@ -21,11 +21,11 @@ **************************************************************************/ #include -#include +#include ZInterpolation::ZInterpolation(int y_offset, Mesh* mesh, Region region_in) - : localmesh(mesh == nullptr ? bout::globals::mesh : mesh), - region(region_in), y_offset(y_offset) { + : localmesh(mesh == nullptr ? bout::globals::mesh : mesh), region(region_in), + y_offset(y_offset) { if (region.size() == 0) { // Construct region that skips calculating interpolation in y-boundary regions that // should be filled by boundary conditions @@ -37,16 +37,15 @@ ZInterpolation::ZInterpolation(int y_offset, Mesh* mesh, Region region_in auto mask_region = Region(0, -1, 0, -1, 0, 0, ny, nz); if (y_offset > 0) { for (auto it = localmesh->iterateBndryUpperY(); not it.isDone(); it.next()) { - mask_region += Region(it.ind, it.ind, localmesh->yend - y_offset + 1, - localmesh->yend, localmesh->zstart, localmesh->zend, - ny, nz); + mask_region += + Region(it.ind, it.ind, localmesh->yend - y_offset + 1, localmesh->yend, + localmesh->zstart, localmesh->zend, ny, nz); } - } - else if (y_offset < 0) { + } else if (y_offset < 0) { for (auto it = localmesh->iterateBndryLowerY(); not it.isDone(); it.next()) { - mask_region += Region(it.ind, it.ind, - localmesh->ystart, localmesh->ystart - y_offset - 1, - localmesh->zstart, localmesh->zend, ny, nz); + mask_region += Region(it.ind, it.ind, localmesh->ystart, + localmesh->ystart - y_offset - 1, localmesh->zstart, + localmesh->zend, ny, nz); } } diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx index 3a5de28e59..00f6752b2a 100644 --- a/src/mesh/interpolation/lagrange_4pt_xz.cxx +++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx @@ -20,13 +20,13 @@ * **************************************************************************/ +#include "bout/globals.hxx" +#include "bout/interpolation_xz.hxx" #include "bout/mesh.hxx" -#include "globals.hxx" -#include "interpolation_xz.hxx" #include -XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh *mesh) +XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh* mesh) : XZInterpolation(y_offset, mesh), t_x(localmesh), t_z(localmesh) { // Index arrays contain guard cells in order to get subscripts right @@ -40,13 +40,14 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh *mesh) void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR(i, delta_x.getRegion(region)) { + BOUT_FOR (i, delta_x.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } // The integer part of xt_prime, zt_prime are the indices of the cell // containing the field line end-point @@ -89,13 +90,14 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const std::string& region) ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR (i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } const int jx = i_corner(x, y, z); const int jx2mnew = (jx == 0) ? 0 : (jx - 1); @@ -155,10 +157,10 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const Field3D& delta_x, BoutReal XZLagrange4pt::lagrange_4pt(const BoutReal v2m, const BoutReal vm, const BoutReal vp, const BoutReal v2p, const BoutReal offset) const { - return -offset * (offset - 1.0) * (offset - 2.0) * v2m / 6.0 + - 0.5 * (offset * offset - 1.0) * (offset - 2.0) * vm - - 0.5 * offset * (offset + 1.0) * (offset - 2.0) * vp + - offset * (offset * offset - 1.0) * v2p / 6.0; + return -offset * (offset - 1.0) * (offset - 2.0) * v2m / 6.0 + + 0.5 * (offset * offset - 1.0) * (offset - 2.0) * vm + - 0.5 * offset * (offset + 1.0) * (offset - 2.0) * vp + + offset * (offset * offset - 1.0) * v2p / 6.0; } BoutReal XZLagrange4pt::lagrange_4pt(const BoutReal v[], const BoutReal offset) const { diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx index bcf402231b..d753812da0 100644 --- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx +++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx @@ -20,9 +20,9 @@ * **************************************************************************/ -#include "globals.hxx" -#include "interpolation_xz.hxx" -#include "output.hxx" +#include "bout/globals.hxx" +#include "bout/interpolation_xz.hxx" +#include "bout/output.hxx" #include "bout/index_derivs_interface.hxx" #include "bout/mesh.hxx" @@ -58,13 +58,14 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f, localmesh->wait(h); } - BOUT_FOR(i, f.getRegion(region)) { + BOUT_FOR (i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); - if (skip_mask(x, y, z)) + if (skip_mask(x, y, z)) { continue; + } // Due to lack of guard cells in z-direction, we need to ensure z-index // wraps around diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx index 2a684d4cd7..11dbdc215d 100644 --- a/src/mesh/interpolation_xz.cxx +++ b/src/mesh/interpolation_xz.cxx @@ -23,37 +23,33 @@ * **************************************************************************/ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include -void printLocation(const Field3D& var) { - output << toString(var.getLocation()); -} -void printLocation(const Field2D& var) { - output << toString(var.getLocation()); -} +void printLocation(const Field3D& var) { output << toString(var.getLocation()); } +void printLocation(const Field2D& var) { output << toString(var.getLocation()); } const char* strLocation(CELL_LOC loc) { return toString(loc).c_str(); } -const Field3D interpolate(const Field3D &f, const Field3D &delta_x, - const Field3D &delta_z) { +const Field3D interpolate(const Field3D& f, const Field3D& delta_x, + const Field3D& delta_z) { TRACE("Interpolating 3D field"); XZLagrange4pt interpolateMethod{f.getMesh()}; return interpolateMethod.interpolate(f, delta_x, delta_z); } -const Field3D interpolate(const Field2D &f, const Field3D &delta_x, - const Field3D &UNUSED(delta_z)) { +const Field3D interpolate(const Field2D& f, const Field3D& delta_x, + const Field3D& UNUSED(delta_z)) { return interpolate(f, delta_x); } -const Field3D interpolate(const Field2D &f, const Field3D &delta_x) { +const Field3D interpolate(const Field2D& f, const Field3D& delta_x) { TRACE("interpolate(Field2D, Field3D)"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); ASSERT1(mesh == delta_x.getMesh()); Field3D result{emptyFrom(delta_x)}; @@ -99,6 +95,9 @@ RegisterXZInterpolation registerinterpbilinear{"bilinear"}; } // namespace constexpr decltype(XZInterpolationFactory::type_name) XZInterpolationFactory::type_name; -constexpr decltype(XZInterpolationFactory::section_name) XZInterpolationFactory::section_name; -constexpr decltype(XZInterpolationFactory::option_name) XZInterpolationFactory::option_name; -constexpr decltype(XZInterpolationFactory::default_type) XZInterpolationFactory::default_type; +constexpr decltype(XZInterpolationFactory::section_name) + XZInterpolationFactory::section_name; +constexpr decltype(XZInterpolationFactory::option_name) + XZInterpolationFactory::option_name; +constexpr decltype(XZInterpolationFactory::default_type) + XZInterpolationFactory::default_type; diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 8063b9ebfc..acfd090cdd 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -1,14 +1,14 @@ -#include -#include #include -#include -#include -#include +#include +#include +#include +#include +#include #include -#include -#include +#include +#include #include "impls/bout/boutmesh.hxx" @@ -47,11 +47,11 @@ MeshFactory::ReturnType MeshFactory::create(const std::string& type, Options* op return Factory::create(type, source, options); } -Mesh* Mesh::create(GridDataSource *s, Options *opt) { +Mesh* Mesh::create(GridDataSource* s, Options* opt) { return MeshFactory::getInstance().create(opt, s).release(); } -Mesh *Mesh::create(Options *opt) { return create(nullptr, opt); } +Mesh* Mesh::create(Options* opt) { return create(nullptr, opt); } Mesh::Mesh(GridDataSource* s, Options* opt) : source(s), options(opt == nullptr ? Options::getRoot()->getSection("mesh") : opt), @@ -114,7 +114,7 @@ int Mesh::get(std::string& sval, const std::string& name, const std::string& def return !source->get(this, sval, name, def); } -int Mesh::get(int &ival, const std::string &name, int def) { +int Mesh::get(int& ival, const std::string& name, int def) { TRACE("Mesh::get(ival, {:s})", name); if (source == nullptr) { @@ -138,7 +138,7 @@ int Mesh::get(BoutReal& rval, const std::string& name, BoutReal def) { return !source->get(this, rval, name, def); } -int Mesh::get(bool &bval, const std::string &name, bool def) { +int Mesh::get(bool& bval, const std::string& name, bool def) { TRACE("Mesh::get(bval, {:s})", name); if (source == nullptr) { @@ -175,8 +175,8 @@ int Mesh::get(Field2D& var, const std::string& name, BoutReal def, bool communic return 0; } -int Mesh::get(Field3D &var, const std::string &name, BoutReal def, - bool communicate, CELL_LOC location) { +int Mesh::get(Field3D& var, const std::string& name, BoutReal def, bool communicate, + CELL_LOC location) { TRACE("Loading 3D field: Mesh::get(Field3D, {:s})", name); if (source == nullptr or !source->get(this, var, name, def, location)) { @@ -187,7 +187,7 @@ int Mesh::get(Field3D &var, const std::string &name, BoutReal def, } // Communicate to get guard cell data - if(communicate) { + if (communicate) { Mesh::communicate(var); } @@ -197,8 +197,8 @@ int Mesh::get(Field3D &var, const std::string &name, BoutReal def, return 0; } -int Mesh::get(FieldPerp &var, const std::string &name, BoutReal def, - bool UNUSED(communicate), CELL_LOC location) { +int Mesh::get(FieldPerp& var, const std::string& name, BoutReal def, + bool UNUSED(communicate), CELL_LOC location) { TRACE("Loading FieldPerp: Mesh::get(FieldPerp, {:s})", name); if (source == nullptr or !source->get(this, var, name, def, location)) { @@ -227,14 +227,14 @@ int Mesh::get(FieldPerp &var, const std::string &name, BoutReal def, int Mesh::get(Vector2D& var, const std::string& name, BoutReal def, bool communicate) { TRACE("Loading 2D vector: Mesh::get(Vector2D, {:s})", name); - if(var.covariant) { + if (var.covariant) { output << _("\tReading covariant vector ") << name << endl; get(var.x, name + "_x", def, communicate); get(var.y, name + "_y", def, communicate); get(var.z, name + "_z", def, communicate); - }else { + } else { output << _("\tReading contravariant vector ") << name << endl; get(var.x, name + "x", def, communicate); @@ -248,14 +248,14 @@ int Mesh::get(Vector2D& var, const std::string& name, BoutReal def, bool communi int Mesh::get(Vector3D& var, const std::string& name, BoutReal def, bool communicate) { TRACE("Loading 3D vector: Mesh::get(Vector3D, {:s})", name); - if(var.covariant) { + if (var.covariant) { output << _("\tReading covariant vector ") << name << endl; get(var.x, name + "_x", def, communicate); get(var.y, name + "_y", def, communicate); get(var.z, name + "_z", def, communicate); - }else { + } else { output << ("\tReading contravariant vector ") << name << endl; get(var.x, name + "x", def, communicate); @@ -266,32 +266,27 @@ int Mesh::get(Vector3D& var, const std::string& name, BoutReal def, bool communi return 0; } -bool Mesh::isDataSourceGridFile() const { - return source != nullptr and source->is_file; -} +bool Mesh::isDataSourceGridFile() const { return source != nullptr and source->is_file; } -bool Mesh::sourceHasVar(const std::string &name) { +bool Mesh::sourceHasVar(const std::string& name) { TRACE("Mesh::sourceHasVar({:s})", name); - if (source == nullptr) + if (source == nullptr) { return false; + } return source->hasVar(name); } /// Wrapper for GridDataSource::hasXBoundaryGuards -bool Mesh::sourceHasXBoundaryGuards() { - return source->hasXBoundaryGuards(this); -} +bool Mesh::sourceHasXBoundaryGuards() { return source->hasXBoundaryGuards(this); } /// Wrapper for GridDataSource::hasYBoundaryGuards -bool Mesh::sourceHasYBoundaryGuards() { - return source->hasYBoundaryGuards(); -} +bool Mesh::sourceHasYBoundaryGuards() { return source->hasYBoundaryGuards(); } /************************************************************************** * Communications **************************************************************************/ -void Mesh::communicateXZ(FieldGroup &g) { +void Mesh::communicateXZ(FieldGroup& g) { TRACE("Mesh::communicate(FieldGroup&)"); // Send data @@ -301,7 +296,7 @@ void Mesh::communicateXZ(FieldGroup &g) { wait(h); } -void Mesh::communicateYZ(FieldGroup &g) { +void Mesh::communicateYZ(FieldGroup& g) { TRACE("Mesh::communicate(FieldGroup&)"); // Send data @@ -312,13 +307,13 @@ void Mesh::communicateYZ(FieldGroup &g) { // Calculate yup and ydown fields for 3D fields if (calcParallelSlices_on_communicate) { - for(const auto& fptr : g.field3d()) { + for (const auto& fptr : g.field3d()) { fptr->calcParallelSlices(); } } } -void Mesh::communicate(FieldGroup &g) { +void Mesh::communicate(FieldGroup& g) { TRACE("Mesh::communicate(FieldGroup&)"); if (include_corner_cells) { @@ -343,7 +338,7 @@ void Mesh::communicate(FieldGroup &g) { // Calculate yup and ydown fields for 3D fields if (calcParallelSlices_on_communicate) { - for(const auto& fptr : g.field3d()) { + for (const auto& fptr : g.field3d()) { fptr->calcParallelSlices(); } } @@ -351,32 +346,33 @@ void Mesh::communicate(FieldGroup &g) { /// This is a bit of a hack for now to get FieldPerp communications /// The FieldData class needs to be changed to accomodate FieldPerp objects -void Mesh::communicate(FieldPerp &f) { +void Mesh::communicate(FieldPerp& f) { comm_handle recv[2]; - - int nin = xstart; // Number of x points in inner guard cell - int nout = LocalNx-xend-1; // Number of x points in outer guard cell + + int nin = xstart; // Number of x points in inner guard cell + int nout = LocalNx - xend - 1; // Number of x points in outer guard cell // Post receives for guard cell regions - recv[0] = irecvXIn(f[0], nin*LocalNz, 0); - recv[1] = irecvXOut(f[xend+1], nout*LocalNz, 1); - + recv[0] = irecvXIn(f[0], nin * LocalNz, 0); + recv[1] = irecvXOut(f[xend + 1], nout * LocalNz, 1); + // Send data - sendXIn(f[xstart], nin*LocalNz, 1); - sendXOut(f[xend-nout+1], nout*LocalNz, 0); - + sendXIn(f[xstart], nin * LocalNz, 1); + sendXOut(f[xend - nout + 1], nout * LocalNz, 0); + // Wait for receive wait(recv[0]); wait(recv[1]); } -int Mesh::msg_len(const std::vector &var_list, int xge, int xlt, int yge, int ylt) { +int Mesh::msg_len(const std::vector& var_list, int xge, int xlt, int yge, + int ylt) { int len = 0; /// Loop over variables - for(const auto& var : var_list) { - if(var->is3D()) { + for (const auto& var : var_list) { + if (var->is3D()) { len += (xlt - xge) * (ylt - yge) * LocalNz * var->elementSize(); } else { len += (xlt - xge) * (ylt - yge) * var->elementSize(); @@ -387,7 +383,8 @@ int Mesh::msg_len(const std::vector &var_list, int xge, int xlt, int } bool Mesh::periodicY(int jx) const { - BoutReal ts; return periodicY(jx, ts); + BoutReal ts; + return periodicY(jx, ts); } int Mesh::ySize(int jx) const { @@ -519,7 +516,7 @@ int Mesh::globalStartIndexPerp() { return cumulativeSize - localSize; } -const std::vector Mesh::readInts(const std::string &name, int n) { +const std::vector Mesh::readInts(const std::string& name, int n) { TRACE("Mesh::readInts({:s})", name); if (source == nullptr) { @@ -529,12 +526,12 @@ const std::vector Mesh::readInts(const std::string &name, int n) { std::vector result; - if(source->hasVar(name)) { - if(!source->get(this, result, name, n, 0)) { + if (source->hasVar(name)) { + if (!source->get(this, result, name, n, 0)) { // Error reading throw BoutException(_("Could not read integer array '{:s}'\n"), name.c_str()); } - }else { + } else { // Not found throw BoutException(_("Missing integer array {:s}\n"), name.c_str()); } @@ -542,8 +539,9 @@ const std::vector Mesh::readInts(const std::string &name, int n) { return result; } -std::shared_ptr Mesh::createDefaultCoordinates(const CELL_LOC location, - bool force_interpolate_from_centre) { +std::shared_ptr +Mesh::createDefaultCoordinates(const CELL_LOC location, + bool force_interpolate_from_centre) { if (location == CELL_CENTRE || location == CELL_DEFAULT) { // Initialize coordinates from input @@ -551,7 +549,8 @@ std::shared_ptr Mesh::createDefaultCoordinates(const CELL_LOC locat } else { // Interpolate coordinates from CELL_CENTRE version return std::make_shared(this, options, location, - getCoordinates(CELL_CENTRE), force_interpolate_from_centre); + getCoordinates(CELL_CENTRE), + force_interpolate_from_centre); } } @@ -591,37 +590,37 @@ bool Mesh::hasRegionPerp(const std::string& region_name) const { return regionMapPerp.find(region_name) != std::end(regionMapPerp); } -void Mesh::addRegion3D(const std::string ®ion_name, const Region<> ®ion) { +void Mesh::addRegion3D(const std::string& region_name, const Region<>& region) { if (regionMap3D.count(region_name)) { throw BoutException(_("Trying to add an already existing region {:s} to regionMap3D"), region_name); } regionMap3D[region_name] = region; - output_verbose.write(_("Registered region 3D {:s}"),region_name); + output_verbose.write(_("Registered region 3D {:s}"), region_name); output_verbose << "\n:\t" << region.getStats() << "\n"; } -void Mesh::addRegion2D(const std::string ®ion_name, const Region ®ion) { +void Mesh::addRegion2D(const std::string& region_name, const Region& region) { if (regionMap2D.count(region_name)) { throw BoutException(_("Trying to add an already existing region {:s} to regionMap2D"), region_name); } regionMap2D[region_name] = region; - output_verbose.write(_("Registered region 2D {:s}"),region_name); + output_verbose.write(_("Registered region 2D {:s}"), region_name); output_verbose << "\n:\t" << region.getStats() << "\n"; } -void Mesh::addRegionPerp(const std::string ®ion_name, const Region ®ion) { +void Mesh::addRegionPerp(const std::string& region_name, const Region& region) { if (regionMapPerp.count(region_name)) { throw BoutException( _("Trying to add an already existing region {:s} to regionMapPerp"), region_name); } regionMapPerp[region_name] = region; - output_verbose.write(_("Registered region Perp {:s}"),region_name); + output_verbose.write(_("Registered region Perp {:s}"), region_name); output_verbose << "\n:\t" << region.getStats() << "\n"; } -void Mesh::createDefaultRegions(){ +void Mesh::createDefaultRegions() { //3D regions addRegion3D("RGN_ALL", Region(0, LocalNx - 1, 0, LocalNy - 1, 0, LocalNz - 1, LocalNy, LocalNz, maxregionblocksize)); @@ -634,21 +633,24 @@ void Mesh::createDefaultRegions(){ addRegion3D("RGN_NOZ", Region(0, LocalNx - 1, 0, LocalNy - 1, zstart, zend, LocalNy, LocalNz, maxregionblocksize)); addRegion3D("RGN_GUARDS", mask(getRegion3D("RGN_ALL"), getRegion3D("RGN_NOBNDRY"))); - addRegion3D("RGN_XGUARDS", Region(0, xstart - 1, ystart, yend, zstart, zend, - LocalNy, LocalNz, maxregionblocksize) - + Region(xend + 1, LocalNx - 1, ystart, yend, zstart, zend, - LocalNy, LocalNz, maxregionblocksize)); - addRegion3D("RGN_YGUARDS", Region(xstart, xend, 0, ystart - 1, zstart, zend, - LocalNy, LocalNz, maxregionblocksize) - + Region(xstart, xend, yend + 1, LocalNy - 1, zstart, zend, - LocalNy, LocalNz, maxregionblocksize)); - addRegion3D("RGN_ZGUARDS", Region(xstart, xend, ystart, yend, 0, zstart - 1, - LocalNy, LocalNz, maxregionblocksize) - + Region(xstart, xend, ystart, yend, zend + 1, LocalNz - 1, - LocalNy, LocalNz, maxregionblocksize)); - addRegion3D("RGN_NOCORNERS", - (getRegion3D("RGN_NOBNDRY") + getRegion3D("RGN_XGUARDS") + - getRegion3D("RGN_YGUARDS") + getRegion3D("RGN_ZGUARDS")).unique()); + addRegion3D("RGN_XGUARDS", + Region(0, xstart - 1, ystart, yend, zstart, zend, LocalNy, LocalNz, + maxregionblocksize) + + Region(xend + 1, LocalNx - 1, ystart, yend, zstart, zend, + LocalNy, LocalNz, maxregionblocksize)); + addRegion3D("RGN_YGUARDS", + Region(xstart, xend, 0, ystart - 1, zstart, zend, LocalNy, LocalNz, + maxregionblocksize) + + Region(xstart, xend, yend + 1, LocalNy - 1, zstart, zend, + LocalNy, LocalNz, maxregionblocksize)); + addRegion3D("RGN_ZGUARDS", + Region(xstart, xend, ystart, yend, 0, zstart - 1, LocalNy, LocalNz, + maxregionblocksize) + + Region(xstart, xend, ystart, yend, zend + 1, LocalNz - 1, + LocalNy, LocalNz, maxregionblocksize)); + addRegion3D("RGN_NOCORNERS", (getRegion3D("RGN_NOBNDRY") + getRegion3D("RGN_XGUARDS") + + getRegion3D("RGN_YGUARDS") + getRegion3D("RGN_ZGUARDS")) + .unique()); //2D regions addRegion2D("RGN_ALL", Region(0, LocalNx - 1, 0, LocalNy - 1, 0, 0, LocalNy, 1, @@ -663,20 +665,20 @@ void Mesh::createDefaultRegions(){ maxregionblocksize)); addRegion2D("RGN_GUARDS", mask(getRegion2D("RGN_ALL"), getRegion2D("RGN_NOBNDRY"))); addRegion2D("RGN_XGUARDS", Region(0, xstart - 1, ystart, yend, 0, 0, LocalNy, 1, - maxregionblocksize) - + Region(xend + 1, LocalNx - 1, ystart, yend, 0, 0, LocalNy, 1, - maxregionblocksize)); + maxregionblocksize) + + Region(xend + 1, LocalNx - 1, ystart, yend, 0, + 0, LocalNy, 1, maxregionblocksize)); addRegion2D("RGN_YGUARDS", Region(xstart, xend, 0, ystart - 1, 0, 0, LocalNy, 1, - maxregionblocksize) - + Region(xstart, xend, yend + 1, LocalNy - 1, 0, 0, LocalNy, 1, - maxregionblocksize)); + maxregionblocksize) + + Region(xstart, xend, yend + 1, LocalNy - 1, 0, + 0, LocalNy, 1, maxregionblocksize)); addRegion2D("RGN_ZGUARDS", Region(xstart, xend, ystart, yend, 0, -1, LocalNy, 1, - maxregionblocksize) - + Region(xstart, xend, ystart, yend, 0, -1, LocalNy, 1, - maxregionblocksize)); - addRegion2D("RGN_NOCORNERS", - (getRegion2D("RGN_NOBNDRY") + getRegion2D("RGN_XGUARDS") + - getRegion2D("RGN_YGUARDS") + getRegion2D("RGN_ZGUARDS")).unique()); + maxregionblocksize) + + Region(xstart, xend, ystart, yend, 0, -1, + LocalNy, 1, maxregionblocksize)); + addRegion2D("RGN_NOCORNERS", (getRegion2D("RGN_NOBNDRY") + getRegion2D("RGN_XGUARDS") + + getRegion2D("RGN_YGUARDS") + getRegion2D("RGN_ZGUARDS")) + .unique()); // Perp regions addRegionPerp("RGN_ALL", Region(0, LocalNx - 1, 0, 0, 0, LocalNz - 1, 1, @@ -690,32 +692,36 @@ void Mesh::createDefaultRegions(){ addRegionPerp("RGN_NOZ", Region(0, LocalNx - 1, 0, 0, zstart, zend, 1, LocalNz, maxregionblocksize)); - addRegionPerp("RGN_GUARDS", mask(getRegionPerp("RGN_ALL"), getRegionPerp("RGN_NOBNDRY"))); - addRegionPerp("RGN_XGUARDS", Region(0, xstart - 1, 0, 0, zstart, zend, 1, - LocalNz, maxregionblocksize) - + Region(xend + 1, LocalNx - 1, 0, 0, zstart, zend, 1, - LocalNz, maxregionblocksize)); + addRegionPerp("RGN_GUARDS", + mask(getRegionPerp("RGN_ALL"), getRegionPerp("RGN_NOBNDRY"))); + addRegionPerp( + "RGN_XGUARDS", + Region(0, xstart - 1, 0, 0, zstart, zend, 1, LocalNz, maxregionblocksize) + + Region(xend + 1, LocalNx - 1, 0, 0, zstart, zend, 1, LocalNz, + maxregionblocksize)); addRegionPerp("RGN_YGUARDS", Region(xstart, xend, 0, -1, zstart, zend, 1, - LocalNz, maxregionblocksize) - + Region(xstart, xend, 0, -1, zstart, zend, 1, - LocalNz, maxregionblocksize)); - addRegionPerp("RGN_ZGUARDS", Region(xstart, xend, 0, 0, 0, zstart - 1, 1, - LocalNz, maxregionblocksize) - + Region(xstart, xend, 0, 0, zend + 1, LocalNz - 1, 1, - LocalNz, maxregionblocksize)); + LocalNz, maxregionblocksize) + + Region(xstart, xend, 0, -1, zstart, zend, 1, + LocalNz, maxregionblocksize)); + addRegionPerp( + "RGN_ZGUARDS", + Region(xstart, xend, 0, 0, 0, zstart - 1, 1, LocalNz, maxregionblocksize) + + Region(xstart, xend, 0, 0, zend + 1, LocalNz - 1, 1, LocalNz, + maxregionblocksize)); addRegionPerp("RGN_NOCORNERS", - (getRegionPerp("RGN_NOBNDRY") + getRegionPerp("RGN_XGUARDS") + - getRegionPerp("RGN_YGUARDS") + getRegionPerp("RGN_ZGUARDS")).unique()); + (getRegionPerp("RGN_NOBNDRY") + getRegionPerp("RGN_XGUARDS") + + getRegionPerp("RGN_YGUARDS") + getRegionPerp("RGN_ZGUARDS")) + .unique()); // Construct index lookup for 3D-->2D - indexLookup3Dto2D = Array(LocalNx*LocalNy*LocalNz); - BOUT_FOR(ind3D, getRegion3D("RGN_ALL")) { + indexLookup3Dto2D = Array(LocalNx * LocalNy * LocalNz); + BOUT_FOR (ind3D, getRegion3D("RGN_ALL")) { indexLookup3Dto2D[ind3D.ind] = ind3Dto2D(ind3D).ind; } } void Mesh::recalculateStaggeredCoordinates() { - for (auto &i : coords_map) { + for (auto& i : coords_map) { CELL_LOC location = i.first; if (location == CELL_CENTRE) { diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index c25765852e..f991bde1f1 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -37,13 +37,13 @@ **************************************************************************/ #include "fci.hxx" -#include "parallel_boundary_op.hxx" -#include "parallel_boundary_region.hxx" +#include "bout/parallel_boundary_op.hxx" +#include "bout/parallel_boundary_region.hxx" #include #include -#include -#include -#include +#include +#include +#include #include @@ -118,7 +118,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, Field3D xt_prime_corner{emptyFrom(xt_prime)}; Field3D zt_prime_corner{emptyFrom(zt_prime)}; - BOUT_FOR(i, xt_prime_corner.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, xt_prime_corner.getRegion("RGN_NOBNDRY")) { // Point interpolated from (x+1/2, z+1/2) // Cache the offsets @@ -135,10 +135,12 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, zt_prime_corner[i] = -1.0; } else { xt_prime_corner[i] = - 0.25 * (xt_prime[i] + xt_prime[i_xplus] + xt_prime[i_zplus] + xt_prime[i_xzplus]); + 0.25 + * (xt_prime[i] + xt_prime[i_xplus] + xt_prime[i_zplus] + xt_prime[i_xzplus]); zt_prime_corner[i] = - 0.25 * (zt_prime[i] + zt_prime[i_xplus] + zt_prime[i_zplus] + zt_prime[i_xzplus]); + 0.25 + * (zt_prime[i] + zt_prime[i_xplus] + zt_prime[i_zplus] + zt_prime[i_xzplus]); } } @@ -245,7 +247,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, interp->setMask(boundary_mask); } -Field3D FCIMap::integrate(Field3D &f) const { +Field3D FCIMap::integrate(Field3D& f) const { TRACE("FCIMap::integrate"); ASSERT1(f.getDirectionY() == YDirectionType::Standard); @@ -265,25 +267,26 @@ Field3D FCIMap::integrate(Field3D &f) const { int nz = map_mesh.LocalNz; - for(int x = map_mesh.xstart; x <= map_mesh.xend; x++) { - for(int y = map_mesh.ystart; y <= map_mesh.yend; y++) { + for (int x = map_mesh.xstart; x <= map_mesh.xend; x++) { + for (int y = map_mesh.ystart; y <= map_mesh.yend; y++) { - int ynext = y+offset; + int ynext = y + offset; - for(int z = 0; z < nz; z++) { - if (boundary_mask(x,y,z)) + for (int z = 0; z < nz; z++) { + if (boundary_mask(x, y, z)) { continue; + } int zm = z - 1; if (z == 0) { - zm = nz-1; + zm = nz - 1; } - BoutReal f_c = centre(x,ynext,z); + BoutReal f_c = centre(x, ynext, z); - if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z) || - corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm) || - (x == map_mesh.xstart)) { + if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z) + || corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm) + || (x == map_mesh.xstart)) { // One of the corners leaves the domain. // Use the cell centre value, since boundary conditions are not // currently applied to corners. @@ -300,7 +303,7 @@ Field3D FCIMap::integrate(Field3D &f) const { // which would include cell edges and corners result(x, ynext, z) = 0.5 * (f_c + 0.25 * (f_pp + f_mp + f_pm + f_mm)); - ASSERT2(std::isfinite(result(x,ynext,z))); + ASSERT2(std::isfinite(result(x, ynext, z))); } } } @@ -310,10 +313,13 @@ Field3D FCIMap::integrate(Field3D &f) const { void FCITransform::checkInputGrid() { std::string parallel_transform; - if (mesh.isDataSourceGridFile() && !mesh.get(parallel_transform, "parallel_transform")) { + if (mesh.isDataSourceGridFile() + && !mesh.get(parallel_transform, "parallel_transform")) { if (parallel_transform != "fci") { - throw BoutException("Incorrect parallel transform type '"+parallel_transform+"' used " - "to generate metric components for FCITransform. Should be 'fci'."); + throw BoutException( + "Incorrect parallel transform type '" + parallel_transform + + "' used " + "to generate metric components for FCITransform. Should be 'fci'."); } } // else: parallel_transform variable not found in grid input, indicates older input // file or grid from options so must rely on the user having ensured the type is diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 663e20c635..4e7802b0c8 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -27,15 +27,14 @@ #define __FCITRANSFORM_H__ #include -#include -#include -#include -#include +#include +#include +#include +#include #include #include - /// Field line map - contains the coefficients for interpolation class FCIMap { /// Interpolation objects @@ -58,16 +57,15 @@ public: BoutMask boundary_mask; /// If any of the integration area has left the domain BoutMask corner_boundary_mask; - + Field3D interpolate(Field3D& f) const { ASSERT1(&map_mesh == f.getMesh()); return interp->interpolate(f); } - Field3D integrate(Field3D &f) const; + Field3D integrate(Field3D& f) const; }; - /// Flux Coordinate Independent method for parallel derivatives class FCITransform : public ParallelTransform { public: @@ -103,9 +101,9 @@ public: } } - void calcParallelSlices(Field3D &f) override; - - void integrateParallelSlices(Field3D &f) override; + void calcParallelSlices(Field3D& f) override; + + void integrateParallelSlices(Field3D& f) override; Field3D toFieldAligned(const Field3D& UNUSED(f), const std::string& UNUSED(region) = "RGN_ALL") override { @@ -127,7 +125,8 @@ public: bool canToFromFieldAligned() override { return false; } - bool requiresTwistShift(bool UNUSED(twist_shift_enabled), MAYBE_UNUSED(YDirectionType ytype)) override { + bool requiresTwistShift(bool UNUSED(twist_shift_enabled), + MAYBE_UNUSED(YDirectionType ytype)) override { // No Field3Ds require twist-shift, because they cannot be field-aligned ASSERT1(ytype == YDirectionType::Standard); @@ -137,7 +136,6 @@ public: protected: void checkInputGrid() override; - private: /// FCI maps for each of the parallel slices std::vector field_line_maps; diff --git a/src/mesh/parallel/identity.cxx b/src/mesh/parallel/identity.cxx index abd3c97396..90fcaef45e 100644 --- a/src/mesh/parallel/identity.cxx +++ b/src/mesh/parallel/identity.cxx @@ -30,11 +30,14 @@ void ParallelTransformIdentity::calcParallelSlices(Field3D& f) { void ParallelTransformIdentity::checkInputGrid() { std::string parallel_transform; - if (mesh.isDataSourceGridFile() and !mesh.get(parallel_transform, "parallel_transform")) { + if (mesh.isDataSourceGridFile() + and !mesh.get(parallel_transform, "parallel_transform")) { if (parallel_transform != "identity") { - throw BoutException("Incorrect parallel transform type '"+parallel_transform+"' used " - "to generate metric components for ParallelTransformIdentity. Should be " - "'identity'."); + throw BoutException( + "Incorrect parallel transform type '" + parallel_transform + + "' used " + "to generate metric components for ParallelTransformIdentity. Should be " + "'identity'."); } } // else: parallel_transform variable not found in grid input, indicates older input // file or grid from options so must rely on the user having ensured the type is diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index 9c686b801f..2284237701 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -10,14 +10,14 @@ #include #include #include -#include -#include -#include +#include +#include +#include #include ShiftedMetric::ShiftedMetric(Mesh& m, CELL_LOC location_in, Field2D zShift_, - BoutReal zlength_in, Options* opt) + BoutReal zlength_in, Options* opt) : ParallelTransform(m, opt), location(location_in), zShift(std::move(zShift_)), zlength(zlength_in) { ASSERT1(zShift.getLocation() == location); @@ -29,7 +29,8 @@ ShiftedMetric::ShiftedMetric(Mesh& m, CELL_LOC location_in, Field2D zShift_, void ShiftedMetric::checkInputGrid() { std::string parallel_transform; - if (mesh.isDataSourceGridFile() and !mesh.get(parallel_transform, "parallel_transform")) { + if (mesh.isDataSourceGridFile() + and !mesh.get(parallel_transform, "parallel_transform")) { if (parallel_transform != "shiftedmetric") { throw BoutException("Incorrect parallel transform type '" + parallel_transform + "' used to generate metric components for ShiftedMetric. " @@ -42,7 +43,8 @@ void ShiftedMetric::checkInputGrid() { void ShiftedMetric::outputVars(Options& output_options) { Timer time("io"); - const std::string loc_string = (location == CELL_CENTRE) ? "" : "_"+toString(location); + const std::string loc_string = + (location == CELL_CENTRE) ? "" : "_" + toString(location); output_options["zShift" + loc_string].force(zShift, "ShiftedMetric"); } @@ -64,7 +66,7 @@ void ShiftedMetric::cachePhases() { toAlignedPhs = Tensor(mesh.LocalNx, mesh.LocalNy, nmodes); // To/From field aligned phases - BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) { + BOUT_FOR (i, mesh.getRegion2D("RGN_ALL")) { int ix = i.x(); int iy = i.y(); for (int jz = 0; jz < nmodes; jz++) { @@ -102,7 +104,7 @@ void ShiftedMetric::cachePhases() { // Parallel slice phases -- note we don't shift in the boundaries/guards for (auto& slice : parallel_slice_phases) { - BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) { + BOUT_FOR (i, mesh.getRegion2D("RGN_NOY")) { int ix = i.x(); int iy = i.y(); @@ -163,7 +165,7 @@ Field3D ShiftedMetric::shiftZ(const Field3D& f, const Tensor& phs, Field3D result{emptyFrom(f).setDirectionY(y_direction_out)}; - BOUT_FOR(i, mesh.getRegion2D(toString(region))) { + BOUT_FOR (i, mesh.getRegion2D(toString(region))) { shiftZ(&f(i, 0), &phs(i.x(), i.y(), 0), &result(i, 0)); } @@ -186,7 +188,7 @@ FieldPerp ShiftedMetric::shiftZ(const FieldPerp& f, const Tensor& phs, int y = f.getIndex(); // Note that this loop is essentially hardcoded to be RGN_NOX - for (int i=mesh.xstart; i<=mesh.xend; ++i) { + for (int i = mesh.xstart; i <= mesh.xend; ++i) { shiftZ(&f(i, 0), &phs(i, y, 0), &result(i, 0)); } @@ -231,7 +233,7 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) { for (const auto& phase : parallel_slice_phases) { auto& f_slice = f.ynext(phase.y_offset); f_slice.allocate(); - BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) { + BOUT_FOR (i, mesh.getRegion2D("RGN_NOY")) { const int ix = i.x(); const int iy = i.y(); const int iy_offset = iy + phase.y_offset; @@ -254,7 +256,7 @@ ShiftedMetric::shiftZ(const Field3D& f, Matrix> f_fft(mesh.LocalNx, mesh.LocalNy); f_fft = Array(nmodes); - BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) { + BOUT_FOR (i, mesh.getRegion2D("RGN_ALL")) { int ix = i.x(); int iy = i.y(); f_fft(ix, iy).ensureUnique(); @@ -271,7 +273,7 @@ ShiftedMetric::shiftZ(const Field3D& f, current_result.allocate(); current_result.setLocation(f.getLocation()); - BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) { + BOUT_FOR (i, mesh.getRegion2D("RGN_NOY")) { // Deep copy the FFT'd field int ix = i.x(); int iy = i.y(); diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 58e2a59191..517d0c8bf3 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -28,10 +28,10 @@ **************************************************************************/ #include "shiftedmetricinterp.hxx" -#include "mask.hxx" +#include "bout/mask.hxx" #include "bout/constants.hxx" -#include -#include +#include +#include ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, Field2D zShift_in, BoutReal zlength_in, @@ -55,9 +55,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, // offset, so we don't need to faff about after this for (int y_offset = 0; y_offset < mesh.ystart; ++y_offset) { parallel_slice_interpolators[yup_index + y_offset] = - ZInterpolationFactory::getInstance().create(&interp_options, y_offset + 1, &mesh); + ZInterpolationFactory::getInstance().create(&interp_options, y_offset + 1, &mesh); parallel_slice_interpolators[ydown_index + y_offset] = - ZInterpolationFactory::getInstance().create(&interp_options, -y_offset - 1, &mesh); + ZInterpolationFactory::getInstance().create(&interp_options, -y_offset - 1, + &mesh); // Find the index positions where the magnetic field line intersects the x-z plane // y_offset points up @@ -87,7 +88,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, } // Set up interpolation to/from field-aligned coordinates - interp_to_aligned = ZInterpolationFactory::getInstance().create(&interp_options, 0, &mesh); + interp_to_aligned = + ZInterpolationFactory::getInstance().create(&interp_options, 0, &mesh); interp_from_aligned = ZInterpolationFactory::getInstance().create(&interp_options, 0, &mesh); diff --git a/src/mesh/parallel/shiftedmetricinterp.hxx b/src/mesh/parallel/shiftedmetricinterp.hxx index 9a2c65b3d2..29e5a80091 100644 --- a/src/mesh/parallel/shiftedmetricinterp.hxx +++ b/src/mesh/parallel/shiftedmetricinterp.hxx @@ -28,7 +28,7 @@ #define __SHIFTEDINTERP_H__ #include -#include +#include /*! * Shifted metric method diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index 4e46687369..08fa3b9bc7 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -1,9 +1,9 @@ +#include "bout/parallel_boundary_op.hxx" +#include "bout/field_factory.hxx" +#include "bout/globals.hxx" +#include "bout/output.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" -#include "field_factory.hxx" -#include "globals.hxx" -#include "output.hxx" -#include "parallel_boundary_op.hxx" using bout::generator::Context; @@ -20,17 +20,16 @@ BoutReal BoundaryOpPar::getValue(int x, int y, int z, BoutReal t) { // answer. This instead generates the value at the gridpoint return gen_values->generate(Context(x, y, z, CELL_CENTRE, mesh, t)); case ValueType::FIELD: - value = (*field_values)(x,y,z); + value = (*field_values)(x, y, z); return value; case ValueType::REAL: return real_value; default: throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue"); } - } -BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar &bndry, BoutReal t) { +BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) { Mesh* mesh = bndry.localmesh; @@ -38,24 +37,25 @@ BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar &bndry, BoutReal t) { switch (value_type) { case ValueType::GEN: - return gen_values->generate(Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); + return gen_values->generate( + Context(bndry.s_x, bndry.s_y, bndry.s_z, CELL_CENTRE, mesh, t)); case ValueType::FIELD: // FIXME: Interpolate to s_x, s_y, s_z... - value = (*field_values)(bndry.x,bndry.y,bndry.z); + value = (*field_values)(bndry.x, bndry.y, bndry.z); return value; case ValueType::REAL: return real_value; default: throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue"); } - } ////////////////////////////////////////// // Dirichlet boundary -BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { +BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar* region, + const std::list& args) { + if (!args.empty()) { try { real_value = stringToReal(args.front()); return new BoundaryOpPar_dirichlet(region, real_value); @@ -69,11 +69,11 @@ BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar *region, const s return new BoundaryOpPar_dirichlet(region); } -BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar *region, Field3D *f) { +BoundaryOpPar* BoundaryOpPar_dirichlet::clone(BoundaryRegionPar* region, Field3D* f) { return new BoundaryOpPar_dirichlet(region, f); } -void BoundaryOpPar_dirichlet::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_dirichlet::apply(Field3D& f, BoutReal t) { Field3D& f_next = f.ynext(bndry->dir); Coordinates& coord = *(f.getCoordinates()); @@ -82,7 +82,9 @@ void BoundaryOpPar_dirichlet::apply(Field3D &f, BoutReal t) { // f_next such that the field would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convenience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal value = getValue(*bndry, t); @@ -91,15 +93,16 @@ void BoundaryOpPar_dirichlet::apply(Field3D &f, BoutReal t) { BoutReal y_prime = bndry->length; BoutReal f2 = (f(x, y, z) - value) * (coord.dy(x, y, z) - y_prime) / y_prime; - f_next(x, y+bndry->dir, z) = value - f2; + f_next(x, y + bndry->dir, z) = value - f2; } } ////////////////////////////////////////// // Dirichlet boundary - Third order -BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { +BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar* region, + const std::list& args) { + if (!args.empty()) { try { real_value = stringToReal(args.front()); return new BoundaryOpPar_dirichlet_O3(region, real_value); @@ -113,11 +116,11 @@ BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar *region, cons return new BoundaryOpPar_dirichlet_O3(region); } -BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar *region, Field3D *f) { +BoundaryOpPar* BoundaryOpPar_dirichlet_O3::clone(BoundaryRegionPar* region, Field3D* f) { return new BoundaryOpPar_dirichlet_O3(region, f); } -void BoundaryOpPar_dirichlet_O3::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_dirichlet_O3::apply(Field3D& f, BoutReal t) { Field3D& f_next = f.ynext(bndry->dir); Field3D& f_prev = f.ynext(-bndry->dir); @@ -128,30 +131,33 @@ void BoundaryOpPar_dirichlet_O3::apply(Field3D &f, BoutReal t) { // f_next such that the field would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convenience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal fb = getValue(*bndry, t); - BoutReal f1 = f_prev(x, y-bndry->dir, z); - BoutReal f2 = f(x,y,z); + BoutReal f1 = f_prev(x, y - bndry->dir, z); + BoutReal f2 = f(x, y, z); BoutReal l1 = coord.dy(x, y, z); BoutReal l2 = bndry->length; BoutReal l3 = coord.dy(x, y, z) - l2; - BoutReal denom = (l1*l1*l2 + l1*l2*l2); - BoutReal term1 = (l2*l2*l3 + l2*l3*l3); - BoutReal term2 = l1*(l1+l2+l3)*(l2+l3); - BoutReal term3 = l3*((l1+l2)*l3 + (l1+l2)*(l1+l2)); + BoutReal denom = (l1 * l1 * l2 + l1 * l2 * l2); + BoutReal term1 = (l2 * l2 * l3 + l2 * l3 * l3); + BoutReal term2 = l1 * (l1 + l2 + l3) * (l2 + l3); + BoutReal term3 = l3 * ((l1 + l2) * l3 + (l1 + l2) * (l1 + l2)); - f_next(x, y+bndry->dir, z) = (term1*f1 + term2*fb - term3*f2)/denom; + f_next(x, y + bndry->dir, z) = (term1 * f1 + term2 * fb - term3 * f2) / denom; } } ////////////////////////////////////////// // Dirichlet with interpolation -BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { +BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar* region, + const std::list& args) { + if (!args.empty()) { try { real_value = stringToReal(args.front()); return new BoundaryOpPar_dirichlet_interp(region, real_value); @@ -165,11 +171,12 @@ BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar *region, return new BoundaryOpPar_dirichlet_interp(region); } -BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar *region, Field3D *f) { +BoundaryOpPar* BoundaryOpPar_dirichlet_interp::clone(BoundaryRegionPar* region, + Field3D* f) { return new BoundaryOpPar_dirichlet_interp(region, f); } -void BoundaryOpPar_dirichlet_interp::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_dirichlet_interp::apply(Field3D& f, BoutReal t) { Field3D& f_next = f.ynext(bndry->dir); Field3D& f_prev = f.ynext(-bndry->dir); @@ -180,27 +187,29 @@ void BoundaryOpPar_dirichlet_interp::apply(Field3D &f, BoutReal t) { // f_next such that the field would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convenience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal fs = getValue(*bndry, t); // Scale the field and normalise to the desired value BoutReal dy = coord.dy(x, y, z); - BoutReal s = bndry->length*dy; + BoutReal s = bndry->length * dy; - f_next(x, y+bndry->dir, z) = f_prev(x, y-bndry->dir, z)*(1.-(2.*s/(dy+s))) - + 2.*f(x, y, z)*((s-dy)/s) - + fs*(dy/s - (2./s + 1.)); + f_next(x, y + bndry->dir, z) = + f_prev(x, y - bndry->dir, z) * (1. - (2. * s / (dy + s))) + + 2. * f(x, y, z) * ((s - dy) / s) + fs * (dy / s - (2. / s + 1.)); } - } ////////////////////////////////////////// // Neumann boundary -BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar *region, const std::list &args) { - if(!args.empty()) { +BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar* region, + const std::list& args) { + if (!args.empty()) { try { real_value = stringToReal(args.front()); return new BoundaryOpPar_neumann(region, real_value); @@ -214,29 +223,30 @@ BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar *region, const std return new BoundaryOpPar_neumann(region); } -BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar *region, Field3D *f) { +BoundaryOpPar* BoundaryOpPar_neumann::clone(BoundaryRegionPar* region, Field3D* f) { return new BoundaryOpPar_neumann(region, f); } -void BoundaryOpPar_neumann::apply(Field3D &f, BoutReal t) { +void BoundaryOpPar_neumann::apply(Field3D& f, BoutReal t) { TRACE("BoundaryOpPar_neumann::apply"); - + Field3D& f_next = f.ynext(bndry->dir); f_next.allocate(); // Ensure unique before modifying - + Coordinates& coord = *(f.getCoordinates()); // If point is in boundary, then fill in f_next such that the derivative // would be VALUE on the boundary for (bndry->first(); !bndry->isDone(); bndry->next()) { // temp variables for convience - int x = bndry->x; int y = bndry->y; int z = bndry->z; + int x = bndry->x; + int y = bndry->y; + int z = bndry->z; // Generate the boundary value BoutReal value = getValue(x, y, z, t); BoutReal dy = coord.dy(x, y, z); - f_next(x, y+bndry->dir, z) = f(x, y, z) + bndry->dir*value*dy; + f_next(x, y + bndry->dir, z) = f(x, y, z) + bndry->dir * value * dy; } - } diff --git a/src/mesh/parallel_boundary_region.cxx b/src/mesh/parallel_boundary_region.cxx index 510286e27a..3f77d96737 100644 --- a/src/mesh/parallel_boundary_region.cxx +++ b/src/mesh/parallel_boundary_region.cxx @@ -1,4 +1,4 @@ -#include "parallel_boundary_region.hxx" +#include "bout/parallel_boundary_region.hxx" void BoundaryRegionPar::add_point(const int jx, const int jy, const int jz, const BoutReal x, const BoutReal y, const BoutReal z, @@ -9,32 +9,29 @@ void BoundaryRegionPar::add_point(const int jx, const int jy, const int jz, void BoundaryRegionPar::first() { bndry_position = begin(bndry_points); if (!isDone()) { - x = bndry_position->index.jx; - y = bndry_position->index.jy; - z = bndry_position->index.jz; - s_x = bndry_position->intersection.s_x; - s_y = bndry_position->intersection.s_y; - s_z = bndry_position->intersection.s_z; + x = bndry_position->index.jx; + y = bndry_position->index.jy; + z = bndry_position->index.jz; + s_x = bndry_position->intersection.s_x; + s_y = bndry_position->intersection.s_y; + s_z = bndry_position->intersection.s_z; length = bndry_position->length; - angle = bndry_position->angle; + angle = bndry_position->angle; } } void BoundaryRegionPar::next() { ++bndry_position; if (!isDone()) { - x = bndry_position->index.jx; - y = bndry_position->index.jy; - z = bndry_position->index.jz; - s_x = bndry_position->intersection.s_x; - s_y = bndry_position->intersection.s_y; - s_z = bndry_position->intersection.s_z; + x = bndry_position->index.jx; + y = bndry_position->index.jy; + z = bndry_position->index.jz; + s_x = bndry_position->intersection.s_x; + s_y = bndry_position->intersection.s_y; + s_z = bndry_position->intersection.s_z; length = bndry_position->length; - angle = bndry_position->angle; + angle = bndry_position->angle; } } -bool BoundaryRegionPar::isDone() { - return (bndry_position == end(bndry_points)); -} - +bool BoundaryRegionPar::isDone() { return (bndry_position == end(bndry_points)); } diff --git a/src/mesh/surfaceiter.cxx b/src/mesh/surfaceiter.cxx index e966fd3200..d687ccd68e 100644 --- a/src/mesh/surfaceiter.cxx +++ b/src/mesh/surfaceiter.cxx @@ -1,29 +1,21 @@ #include -#include -#include +#include +#include -int SurfaceIter::ySize() { - return m->ySize(xpos); -} +int SurfaceIter::ySize() { return m->ySize(xpos); } -bool SurfaceIter::closed() { - return m->periodicY(xpos); -} +bool SurfaceIter::closed() { return m->periodicY(xpos); } -bool SurfaceIter::closed(BoutReal &ts) { - return m->periodicY(xpos, ts); -} +bool SurfaceIter::closed(BoutReal& ts) { return m->periodicY(xpos, ts); } -MPI_Comm SurfaceIter::communicator() { - return m->getYcomm(xpos); -} +MPI_Comm SurfaceIter::communicator() { return m->getYcomm(xpos); } int SurfaceIter::yGlobal(int UNUSED(yloc)) { // Communicator for this surface MPI_Comm comm = communicator(); - + // Get number of processors and processor rank int np; bout::globals::mpi->MPI_Comm_size(comm, &np); @@ -33,17 +25,18 @@ int SurfaceIter::yGlobal(int UNUSED(yloc)) { // Need a generic method throw BoutException("SurfaceIter::yGlobal not implemented"); - + return 0; } bool SurfaceIter::firstY() { ///< Is this processor at the lower end? - if(closed()) + if (closed()) { return false; - + } + // Communicator for this surface MPI_Comm comm = communicator(); - + // Get processor rank int myp; bout::globals::mpi->MPI_Comm_rank(comm, &myp); @@ -52,34 +45,33 @@ bool SurfaceIter::firstY() { ///< Is this processor at the lower end? } bool SurfaceIter::lastY() { - if(closed()) + if (closed()) { return false; - + } + // Communicator for this surface MPI_Comm comm = communicator(); - + // Get number of processors and processor rank int np; bout::globals::mpi->MPI_Comm_size(comm, &np); int myp; bout::globals::mpi->MPI_Comm_rank(comm, &myp); - return myp == np-1; + return myp == np - 1; } -void SurfaceIter::first() { - xpos = firstpos; -} +void SurfaceIter::first() { xpos = firstpos; } void SurfaceIter::next() { - if(xpos < 0) + if (xpos < 0) { return; - + } + xpos++; - if(xpos > lastpos) + if (xpos > lastpos) { xpos = -1; + } } -bool SurfaceIter::isDone() { - return xpos < 0; -} +bool SurfaceIter::isDone() { return xpos < 0; } diff --git a/src/physics/gyro_average.cxx b/src/physics/gyro_average.cxx index b952b0c282..75df9e3338 100644 --- a/src/physics/gyro_average.cxx +++ b/src/physics/gyro_average.cxx @@ -29,16 +29,17 @@ #include #include -#include -#include -#include -#include +#include +#include +#include +#include Field3D gyroTaylor0(const Field3D& f, const Field3D& rho) { return f + SQ(rho) * Delp2(f); } -Field3D gyroPade0(const Field3D& f, BoutReal rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade0(const Field3D& f, BoutReal rho, int inner_boundary_flags, + int outer_boundary_flags) { const Field2D a = 1.0; const Field2D d = -rho * rho; @@ -57,7 +58,8 @@ Field3D gyroPade0(const Field3D& f, BoutReal rho, int inner_boundary_flags, int return lap->solve(f).setLocation(f.getLocation()); } -Field3D gyroPade0(const Field3D& f, const Field2D& rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade0(const Field3D& f, const Field2D& rho, int inner_boundary_flags, + int outer_boundary_flags) { const Field2D a = 1.0; const Field2D d = -rho * rho; @@ -75,12 +77,14 @@ Field3D gyroPade0(const Field3D& f, const Field2D& rho, int inner_boundary_flags return lap->solve(f).setLocation(f.getLocation()); } -Field3D gyroPade0(const Field3D& f, const Field3D& rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade0(const Field3D& f, const Field3D& rho, int inner_boundary_flags, + int outer_boundary_flags) { // Have to use Z average of rho for efficient inversion return gyroPade0(f, DC(rho), inner_boundary_flags, outer_boundary_flags); } -Field3D gyroPade1(const Field3D& f, BoutReal rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade1(const Field3D& f, BoutReal rho, int inner_boundary_flags, + int outer_boundary_flags) { const Field2D a = 1.0; const Field2D d = -0.5 * rho * rho; @@ -98,7 +102,8 @@ Field3D gyroPade1(const Field3D& f, BoutReal rho, int inner_boundary_flags, int return lap->solve(f).setLocation(f.getLocation()); } -Field3D gyroPade1(const Field3D& f, const Field2D& rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade1(const Field3D& f, const Field2D& rho, int inner_boundary_flags, + int outer_boundary_flags) { const Field2D a = 1.0; const Field2D d = -0.5 * rho * rho; @@ -116,20 +121,24 @@ Field3D gyroPade1(const Field3D& f, const Field2D& rho, int inner_boundary_flags return lap->solve(f).setLocation(f.getLocation()); } -Field3D gyroPade1(const Field3D& f, const Field3D& rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade1(const Field3D& f, const Field3D& rho, int inner_boundary_flags, + int outer_boundary_flags) { return gyroPade1(f, DC(rho), inner_boundary_flags, outer_boundary_flags); } -Field2D gyroPade1(const Field2D& f, const Field2D& rho, int inner_boundary_flags, int outer_boundary_flags) { +Field2D gyroPade1(const Field2D& f, const Field2D& rho, int inner_boundary_flags, + int outer_boundary_flags) { // Very inefficient implementation Field3D tmp = f; tmp = gyroPade1(tmp, rho, inner_boundary_flags, outer_boundary_flags); return DC(tmp); } -Field3D gyroPade2(const Field3D& f, BoutReal rho, int inner_boundary_flags, int outer_boundary_flags) { - Field3D result = gyroPade1(gyroPade1(f, rho, inner_boundary_flags, outer_boundary_flags), - rho, inner_boundary_flags, outer_boundary_flags); +Field3D gyroPade2(const Field3D& f, BoutReal rho, int inner_boundary_flags, + int outer_boundary_flags) { + Field3D result = + gyroPade1(gyroPade1(f, rho, inner_boundary_flags, outer_boundary_flags), rho, + inner_boundary_flags, outer_boundary_flags); result.getMesh()->communicate(result); result = 0.5 * rho * rho * Delp2(result); @@ -137,16 +146,19 @@ Field3D gyroPade2(const Field3D& f, BoutReal rho, int inner_boundary_flags, int return result; } -Field3D gyroPade2(const Field3D& f, const Field2D& rho, int inner_boundary_flags, int outer_boundary_flags) { - Field3D result = gyroPade1(gyroPade1(f, rho, inner_boundary_flags, outer_boundary_flags), - rho, inner_boundary_flags, outer_boundary_flags); +Field3D gyroPade2(const Field3D& f, const Field2D& rho, int inner_boundary_flags, + int outer_boundary_flags) { + Field3D result = + gyroPade1(gyroPade1(f, rho, inner_boundary_flags, outer_boundary_flags), rho, + inner_boundary_flags, outer_boundary_flags); result.getMesh()->communicate(result); result = 0.5 * rho * rho * Delp2(result); result.applyBoundary("dirichlet"); return result; } -Field3D gyroPade2(const Field3D& f, const Field3D& rho, int inner_boundary_flags, int outer_boundary_flags) { +Field3D gyroPade2(const Field3D& f, const Field3D& rho, int inner_boundary_flags, + int outer_boundary_flags) { // Have to use Z average of rho for efficient inversion return gyroPade2(f, DC(rho), inner_boundary_flags, outer_boundary_flags); } diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx index 1ba2d4289f..94ee9832f4 100644 --- a/src/physics/physicsmodel.cxx +++ b/src/physics/physicsmodel.cxx @@ -105,13 +105,9 @@ void PhysicsModel::initialise(Solver* s) { } } -int PhysicsModel::runRHS(BoutReal time, bool linear) { - return rhs(time, linear); -} +int PhysicsModel::runRHS(BoutReal time, bool linear) { return rhs(time, linear); } -bool PhysicsModel::splitOperator() { - return splitop; -} +bool PhysicsModel::splitOperator() { return splitop; } int PhysicsModel::runConvective(BoutReal time, bool linear) { return convective(time, linear); @@ -124,36 +120,38 @@ int PhysicsModel::runDiffusive(BoutReal time, bool linear) { bool PhysicsModel::hasPrecon() { return (userprecon != nullptr); } int PhysicsModel::runPrecon(BoutReal t, BoutReal gamma, BoutReal delta) { - if(!userprecon) + if (!userprecon) { return 1; + } return (*this.*userprecon)(t, gamma, delta); } bool PhysicsModel::hasJacobian() { return (userjacobian != nullptr); } int PhysicsModel::runJacobian(BoutReal t) { - if (!userjacobian) + if (!userjacobian) { return 1; + } return (*this.*userjacobian)(t); } -void PhysicsModel::bout_solve(Field2D &var, const char *name, +void PhysicsModel::bout_solve(Field2D& var, const char* name, const std::string& description) { // Add to solver solver->add(var, name, description); } -void PhysicsModel::bout_solve(Field3D &var, const char *name, +void PhysicsModel::bout_solve(Field3D& var, const char* name, const std::string& description) { solver->add(var, name, description); } -void PhysicsModel::bout_solve(Vector2D &var, const char *name, +void PhysicsModel::bout_solve(Vector2D& var, const char* name, const std::string& description) { solver->add(var, name, description); } -void PhysicsModel::bout_solve(Vector3D &var, const char *name, +void PhysicsModel::bout_solve(Vector3D& var, const char* name, const std::string& description) { solver->add(var, name, description); } diff --git a/src/physics/smoothing.cxx b/src/physics/smoothing.cxx index 465cedcce6..bae428897e 100644 --- a/src/physics/smoothing.cxx +++ b/src/physics/smoothing.cxx @@ -35,35 +35,39 @@ #include "bout/build_config.hxx" #include -#include -#include -#include -#include +#include +#include +#include +#include #include #include -#include +#include // Smooth using simple 1-2-1 filter -const Field3D smooth_x(const Field3D &f) { +const Field3D smooth_x(const Field3D& f) { TRACE("smooth_x"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f)}; - + // Copy boundary region - for(int jy=0;jyLocalNy;jy++) - for(int jz=0;jzLocalNz;jz++) { - result(0,jy,jz) = f(0,jy,jz); - result(mesh->LocalNx-1,jy,jz) = f(mesh->LocalNx-1,jy,jz); + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + result(0, jy, jz) = f(0, jy, jz); + result(mesh->LocalNx - 1, jy, jz) = f(mesh->LocalNx - 1, jy, jz); } + } // Smooth using simple 1-2-1 filter - for(int jx=1;jxLocalNx-1;jx++) - for(int jy=0;jyLocalNy;jy++) - for(int jz=0;jzLocalNz;jz++) { - result(jx,jy,jz) = 0.5*f(jx,jy,jz) + 0.25*( f(jx-1,jy,jz) + f(jx+1,jy,jz) ); + for (int jx = 1; jx < mesh->LocalNx - 1; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + result(jx, jy, jz) = + 0.5 * f(jx, jy, jz) + 0.25 * (f(jx - 1, jy, jz) + f(jx + 1, jy, jz)); } + } + } // Need to communicate boundaries mesh->communicate(result); @@ -71,30 +75,34 @@ const Field3D smooth_x(const Field3D &f) { return result; } - -const Field3D smooth_y(const Field3D &f) { +const Field3D smooth_y(const Field3D& f) { TRACE("smooth_y"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f)}; - + // Copy boundary region - for(int jx=0;jxLocalNx;jx++) - for(int jz=0;jzLocalNz;jz++) { - result(jx,0,jz) = f(jx,0,jz); - result(jx,mesh->LocalNy-1,jz) = f(jx,mesh->LocalNy-1,jz); + for (int jx = 0; jx < mesh->LocalNx; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + result(jx, 0, jz) = f(jx, 0, jz); + result(jx, mesh->LocalNy - 1, jz) = f(jx, mesh->LocalNy - 1, jz); } - + } + // Smooth using simple 1-2-1 filter - for(int jx=0;jxLocalNx;jx++) - for(int jy=1;jyLocalNy-1;jy++) - for(int jz=0;jzLocalNz;jz++) { - result(jx,jy,jz) = 0.5*f(jx,jy,jz) + 0.25*( f.ydown()(jx,jy-1,jz) + f.yup()(jx,jy+1,jz) ); + for (int jx = 0; jx < mesh->LocalNx; jx++) { + for (int jy = 1; jy < mesh->LocalNy - 1; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + result(jx, jy, jz) = + 0.5 * f(jx, jy, jz) + + 0.25 * (f.ydown()(jx, jy - 1, jz) + f.yup()(jx, jy + 1, jz)); } + } + } // Need to communicate boundaries mesh->communicate(result); - + return result; } @@ -108,21 +116,21 @@ const Field3D smooth_y(const Field3D &f) { Will only work if X communicator is constant in Y so no processor/branch cuts in X */ -const Field2D averageX(const Field2D &f) { +const Field2D averageX(const Field2D& f) { TRACE("averageX(Field2D)"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); int ngx = mesh->LocalNx; int ngy = mesh->LocalNy; Array input(ngy), result(ngy); - + // Average on this processor - for(int y=0;yxstart;x<=mesh->xend;x++) { - input[y] += f(x,y); + for (int x = mesh->xstart; x <= mesh->xend; x++) { + input[y] += f(x, y); } input[y] /= (mesh->xend - mesh->xstart + 1); } @@ -133,18 +141,22 @@ const Field2D averageX(const Field2D &f) { int np; MPI_Comm_size(comm_x, &np); - - if(np == 1) { - for(int x=0;x(np); + for (int x = 0; x < ngx; x++) { + for (int y = 0; y < ngy; y++) { + r(x, y) = result[y] / static_cast(np); + } + } } - + return r; } @@ -163,10 +175,10 @@ const Field2D averageX(const Field2D &f) { so no processor/branch cuts in X */ -const Field3D averageX(const Field3D &f) { +const Field3D averageX(const Field3D& f) { TRACE("averageX(Field3D)"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); int ngx = mesh->LocalNx; int ngy = mesh->LocalNy; @@ -176,56 +188,62 @@ const Field3D averageX(const Field3D &f) { auto result = Matrix(ngy, ngz); // Average on this processor - for(int y=0;yxstart;x<=mesh->xend;x++) { + for (int x = mesh->xstart; x <= mesh->xend; x++) { input(y, z) += f(x, y, z); } input(y, z) /= (mesh->xend - mesh->xstart + 1); } + } Field3D r{emptyFrom(f)}; - + MPI_Comm comm_x = mesh->getXcomm(); - + int np; MPI_Comm_size(comm_x, &np); - if(np > 1) { - MPI_Allreduce(std::begin(input), std::begin(result), ngy*ngz, MPI_DOUBLE, MPI_SUM, comm_x); - - for(int x=0;x 1) { + MPI_Allreduce(std::begin(input), std::begin(result), ngy * ngz, MPI_DOUBLE, MPI_SUM, + comm_x); + + for (int x = 0; x < ngx; x++) { + for (int y = 0; y < ngy; y++) { + for (int z = 0; z < ngz; z++) { r(x, y, z) = result(y, z) / static_cast(np); } - }else { - for(int x=0;xLocalNx; int ngy = mesh->LocalNy; Array input(ngx), result(ngx); - + // Average on this processor - for(int x=0;xystart;y<=mesh->yend;y++) { - input[x] += f(x,y); + for (int y = mesh->ystart; y <= mesh->yend; y++) { + input[x] += f(x, y); } input[x] /= (mesh->yend - mesh->ystart + 1); } @@ -234,28 +252,32 @@ const Field2D averageY(const Field2D &f) { /// NOTE: This only works if there are no branch-cuts MPI_Comm comm_inner = mesh->getYcomm(0); - + int np; MPI_Comm_size(comm_inner, &np); - - if(np == 1) { - for(int x=0;x(np); + for (int x = 0; x < ngx; x++) { + for (int y = 0; y < ngy; y++) { + r(x, y) = result[x] / static_cast(np); + } + } } return r; } -const Field3D averageY(const Field3D &f) { +const Field3D averageY(const Field3D& f) { TRACE("averageY(Field3D)"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); int ngx = mesh->LocalNx; int ngy = mesh->LocalNy; @@ -265,45 +287,50 @@ const Field3D averageY(const Field3D &f) { auto result = Matrix(ngx, ngz); // Average on this processor - for(int x=0;xystart;y<=mesh->yend;y++) { + for (int y = mesh->ystart; y <= mesh->yend; y++) { input(x, z) += f(x, y, z); } input(x, z) /= (mesh->yend - mesh->ystart + 1); } + } Field3D r{emptyFrom(f)}; /// NOTE: This only works if there are no branch-cuts MPI_Comm comm_inner = mesh->getYcomm(0); - + int np; MPI_Comm_size(comm_inner, &np); - if(np > 1) { - MPI_Allreduce(std::begin(input), std::begin(result), ngx*ngz, MPI_DOUBLE, MPI_SUM, comm_inner); - - for(int x=0;x 1) { + MPI_Allreduce(std::begin(input), std::begin(result), ngx * ngz, MPI_DOUBLE, MPI_SUM, + comm_inner); + + for (int x = 0; x < ngx; x++) { + for (int y = 0; y < ngy; y++) { + for (int z = 0; z < ngz; z++) { r(x, y, z) = result(x, z) / static_cast(np); } - }else { - for(int x=0;xxstart;i<=mesh->xend;i++) - Vol_Loc += result(i,0); + for (i = mesh->xstart; i <= mesh->xend; i++) { + Vol_Loc += result(i, 0); + } MPI_Comm comm_x = mesh->getXcomm(); - MPI_Allreduce(&Vol_Loc,&Vol_Glb,1,MPI_DOUBLE,MPI_SUM,comm_x); - Vol_Glb /= static_cast(mesh->GlobalNx-2*mesh->xstart); + MPI_Allreduce(&Vol_Loc, &Vol_Glb, 1, MPI_DOUBLE, MPI_SUM, comm_x); + Vol_Glb /= static_cast(mesh->GlobalNx - 2 * mesh->xstart); return Vol_Glb; } -BoutReal Vol_Integral(const Field2D &var) { +BoutReal Vol_Integral(const Field2D& var) { #if BOUT_USE_METRIC_3D AUTO_TRACE(); throw BoutException("Vol_Intregral currently incompatible with 3D metrics"); #else - Mesh *mesh = var.getMesh(); + Mesh* mesh = var.getMesh(); BoutReal Int_Glb; - Coordinates *metric = var.getCoordinates(); + Coordinates* metric = var.getCoordinates(); auto result = metric->J * var * metric->dx * metric->dy; Int_Glb = Average_XY(result); Int_Glb *= static_cast( - (mesh->GlobalNx-2*mesh->xstart) - * (mesh->GlobalNy-mesh->numberOfYBoundaries()*2*mesh->ystart)) * PI * 2.; + (mesh->GlobalNx - 2 * mesh->xstart) + * (mesh->GlobalNy - mesh->numberOfYBoundaries() * 2 * mesh->ystart)) + * PI * 2.; return Int_Glb; #endif } -const Field3D smoothXY(const Field3D &f) { - Mesh *mesh = f.getMesh(); +const Field3D smoothXY(const Field3D& f) { + Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f)}; - for(int x=2;xLocalNx-2;x++) - for(int y=2;yLocalNy-2;y++) - for(int z=0;zLocalNz;z++) { - result(x,y,z) = 0.5*f(x,y,z) + 0.125*( 0.5*f(x+1,y,z) + 0.125*(f(x+2,y,z) + f(x,y,z) + f(x+1,y-1,z) + f(x+1,y+1,z)) + - 0.5*f(x-1,y,z) + 0.125*(f(x,y,z) + f(x-2,y,z) + f(x-1,y-1,z) + f(x-1,y+1,z)) + - 0.5*f(x,y-1,z) + 0.125*(f(x+1,y-1,z) + f(x-1,y-1,z) + f(x,y-2,z) + f(x,y,z)) + - 0.5*f(x,y+1,z) + 0.125*(f(x+1,y+1,z) + f(x-1,y+1,z) + f(x,y,z) + f(x,y+2,z))); + for (int x = 2; x < mesh->LocalNx - 2; x++) { + for (int y = 2; y < mesh->LocalNy - 2; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + result(x, y, z) = 0.5 * f(x, y, z) + + 0.125 + * (0.5 * f(x + 1, y, z) + + 0.125 + * (f(x + 2, y, z) + f(x, y, z) + + f(x + 1, y - 1, z) + f(x + 1, y + 1, z)) + + 0.5 * f(x - 1, y, z) + + 0.125 + * (f(x, y, z) + f(x - 2, y, z) + + f(x - 1, y - 1, z) + f(x - 1, y + 1, z)) + + 0.5 * f(x, y - 1, z) + + 0.125 + * (f(x + 1, y - 1, z) + f(x - 1, y - 1, z) + + f(x, y - 2, z) + f(x, y, z)) + + 0.5 * f(x, y + 1, z) + + 0.125 + * (f(x + 1, y + 1, z) + f(x - 1, y + 1, z) + + f(x, y, z) + f(x, y + 2, z))); } - + } + } + return result; } +void nl_filter(rvec& f, BoutReal w) { + for (size_t i = 1; i < f.size() - 1; i++) { -void nl_filter(rvec &f, BoutReal w) { - for(size_t i=1; i 0.) { + BoutReal dp = f[i + 1] - f[i]; + BoutReal dm = f[i - 1] - f[i]; + if (dp * dm > 0.) { // Local extrema - adjust BoutReal ep, em, e; // Amount to adjust by - if(fabs(dp) > fabs(dm)) { - ep = w*0.5*dp; - em = w*dm; - e = (fabs(ep) < fabs(em)) ? ep : em; // Pick smallest absolute - // Adjust - f[i+1] -= e; - f[i] += e; - }else { - ep = w*0.5*dm; - em = w*dp; - e = (fabs(ep) < fabs(em)) ? ep : em; // Pick smallest absolute - // Adjust - f[i-1] -= e; - f[i] += e; + if (fabs(dp) > fabs(dm)) { + ep = w * 0.5 * dp; + em = w * dm; + e = (fabs(ep) < fabs(em)) ? ep : em; // Pick smallest absolute + // Adjust + f[i + 1] -= e; + f[i] += e; + } else { + ep = w * 0.5 * dm; + em = w * dp; + e = (fabs(ep) < fabs(em)) ? ep : em; // Pick smallest absolute + // Adjust + f[i - 1] -= e; + f[i] += e; } } } } -const Field3D nl_filter_x(const Field3D &f, BoutReal w) { +const Field3D nl_filter_x(const Field3D& f, BoutReal w) { TRACE("nl_filter_x( Field3D )"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f)}; rvec v(mesh->LocalNx); - - for (int jy=0;jyLocalNy;jy++) { - for (int jz=0;jzLocalNz;jz++) { - for (int jx=0;jxLocalNx;jx++) { - v[jx] = f(jx,jy,jz); + + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + for (int jx = 0; jx < mesh->LocalNx; jx++) { + v[jx] = f(jx, jy, jz); } nl_filter(v, w); - for (int jx=0;jxLocalNx;jx++) { - result(jx,jy,jz) = v[jx]; + for (int jx = 0; jx < mesh->LocalNx; jx++) { + result(jx, jy, jz) = v[jx]; } } } - + return result; } -const Field3D nl_filter_y(const Field3D &f, BoutReal w) { +const Field3D nl_filter_y(const Field3D& f, BoutReal w) { TRACE("nl_filter_x( Field3D )"); - Mesh *mesh = f.getMesh(); + Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f)}; rvec v(mesh->LocalNy); // Temporary array - + // Transform into field-aligned coordinates Field3D fs = toFieldAligned(f); - for (int jx=0;jxLocalNx;jx++) { - for (int jz=0;jzLocalNz;jz++) { - for (int jy=0;jyLocalNy;jy++) { - v[jy] = fs(jx,jy,jz); + for (int jx = 0; jx < mesh->LocalNx; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + v[jy] = fs(jx, jy, jz); } nl_filter(v, w); - for (int jy=0;jyLocalNy;jy++) { - result(jx,jy,jz) = v[jy]; + for (int jy = 0; jy < mesh->LocalNy; jy++) { + result(jx, jy, jz) = v[jy]; } } } - + // Tranform the field back from field aligned coordinates return fromFieldAligned(result); } -const Field3D nl_filter_z(const Field3D &fs, BoutReal w) { +const Field3D nl_filter_z(const Field3D& fs, BoutReal w) { TRACE("nl_filter_z( Field3D )"); - Mesh *mesh = fs.getMesh(); + Mesh* mesh = fs.getMesh(); Field3D result{emptyFrom(fs)}; - + rvec v(mesh->LocalNz); - - for (int jx=0;jxLocalNx;jx++) { - for (int jy=0;jyLocalNy;jy++) { - for (int jz=0;jzLocalNz;jz++) { - v[jz] = fs(jx,jy,jz); + + for (int jx = 0; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + v[jz] = fs(jx, jy, jz); } nl_filter(v, w); - for (int jz=0;jzLocalNz;jz++) { - result(jx,jy,jz) = v[jz]; + for (int jz = 0; jz < mesh->LocalNz; jz++) { + result(jx, jy, jz) = v[jz]; } } } - + return result; } -const Field3D nl_filter(const Field3D &f, BoutReal w) { +const Field3D nl_filter(const Field3D& f, BoutReal w) { /// Perform filtering in Z, Y then X Field3D result = nl_filter_x(nl_filter_y(nl_filter_z(f, w), w), w); /// Communicate boundaries diff --git a/src/physics/snb.cxx b/src/physics/snb.cxx index 2c805bfa02..2e495818d8 100644 --- a/src/physics/snb.cxx +++ b/src/physics/snb.cxx @@ -2,7 +2,7 @@ /// #include "bout/snb.hxx" -#include "derivs.hxx" +#include "bout/derivs.hxx" #include "bout/constants.hxx" #include "bout/fv_ops.hxx" diff --git a/src/physics/sourcex.cxx b/src/physics/sourcex.cxx index 82b23de367..ccfc20750e 100644 --- a/src/physics/sourcex.cxx +++ b/src/physics/sourcex.cxx @@ -2,15 +2,15 @@ * radial source and mask operators **************************************************************/ -#include #include +#include #include -#include -#include -#include +#include +#include +#include -#include "unused.hxx" +#include "bout/unused.hxx" BoutReal TanH(BoutReal a) { BoutReal temp = exp(a); @@ -18,13 +18,13 @@ BoutReal TanH(BoutReal a) { } // create radial buffer zones to set jpar zero near radial boundaries -const Field2D source_tanhx(const Field2D &f, BoutReal swidth, BoutReal slength) { +const Field2D source_tanhx(const Field2D& f, BoutReal swidth, BoutReal slength) { Mesh* localmesh = f.getMesh(); Field2D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()) - slength; BoutReal dampl = TanH(lx / swidth); result[i] = 0.5 * (1.0 - dampl); @@ -37,13 +37,13 @@ const Field2D source_tanhx(const Field2D &f, BoutReal swidth, BoutReal slength) } // create radial buffer zones to set jpar zero near radial boundaries -const Field2D source_expx2(const Field2D &f, BoutReal swidth, BoutReal slength) { +const Field2D source_expx2(const Field2D& f, BoutReal swidth, BoutReal slength) { Mesh* localmesh = f.getMesh(); Field2D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()) - slength; BoutReal dampl = exp(-lx * lx / swidth / swidth); result[i] = dampl; @@ -56,14 +56,14 @@ const Field2D source_expx2(const Field2D &f, BoutReal swidth, BoutReal slength) } // create radial buffer zones to set jpar zero near radial boundaries -const Field3D sink_tanhx(const Field2D &UNUSED(f0), const Field3D &f, BoutReal swidth, +const Field3D sink_tanhx(const Field2D& UNUSED(f0), const Field3D& f, BoutReal swidth, BoutReal slength, bool UNUSED(BoutRealspace)) { Mesh* localmesh = f.getMesh(); Field3D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal rlx = 1. - localmesh->GlobalX(i.x()) - slength; BoutReal dampr = TanH(rlx / swidth); result[i] = 0.5 * (1.0 - dampr) * f[i]; @@ -76,7 +76,7 @@ const Field3D sink_tanhx(const Field2D &UNUSED(f0), const Field3D &f, BoutReal s } // create radial buffer zones to set jpar zero near radial boundaries -const Field3D mask_x(const Field3D &f, bool UNUSED(BoutRealspace)) { +const Field3D mask_x(const Field3D& f, bool UNUSED(BoutRealspace)) { TRACE("mask_x"); Mesh* localmesh = f.getMesh(); @@ -84,7 +84,7 @@ const Field3D mask_x(const Field3D &f, bool UNUSED(BoutRealspace)) { Field3D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()); BoutReal dampl = TanH(lx / 40.0); BoutReal dampr = TanH((1. - lx) / 40.0); @@ -99,7 +99,7 @@ const Field3D mask_x(const Field3D &f, bool UNUSED(BoutRealspace)) { } // create radial buffer zones to set jpar zero near radial boundaries -const Field3D sink_tanhxl(const Field2D &UNUSED(f0), const Field3D &f, BoutReal swidth, +const Field3D sink_tanhxl(const Field2D& UNUSED(f0), const Field3D& f, BoutReal swidth, BoutReal slength, bool UNUSED(BoutRealspace)) { TRACE("sink_tanhx"); @@ -107,7 +107,7 @@ const Field3D sink_tanhxl(const Field2D &UNUSED(f0), const Field3D &f, BoutReal Field3D result{emptyFrom(f)}; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()) - slength; BoutReal dampl = TanH(lx / swidth); @@ -121,7 +121,7 @@ const Field3D sink_tanhxl(const Field2D &UNUSED(f0), const Field3D &f, BoutReal } // create radial buffer zones to set jpar zero near radial boundaries -const Field3D sink_tanhxr(const Field2D &UNUSED(f0), const Field3D &f, BoutReal swidth, +const Field3D sink_tanhxr(const Field2D& UNUSED(f0), const Field3D& f, BoutReal swidth, BoutReal slength, bool UNUSED(BoutRealspace)) { TRACE("sink_tanhxr"); @@ -129,7 +129,7 @@ const Field3D sink_tanhxr(const Field2D &UNUSED(f0), const Field3D &f, BoutReal Field3D result{emptyFrom(f)}; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal rlx = 1. - localmesh->GlobalX(i.x()) - slength; BoutReal dampr = TanH(rlx / swidth); @@ -143,7 +143,7 @@ const Field3D sink_tanhxr(const Field2D &UNUSED(f0), const Field3D &f, BoutReal } // create radial buffer zones to damp Psi to zero near radial boundaries -const Field3D buff_x(const Field3D &f, bool UNUSED(BoutRealspace)) { +const Field3D buff_x(const Field3D& f, bool UNUSED(BoutRealspace)) { TRACE("buff_x"); Mesh* localmesh = f.getMesh(); @@ -155,13 +155,13 @@ const Field3D buff_x(const Field3D &f, bool UNUSED(BoutRealspace)) { const BoutReal deltal = 0.05; const BoutReal deltar = 0.05; - BOUT_FOR(i, result.getRegion("RGN_ALL")) { + BOUT_FOR (i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()); BoutReal rlx = 1. - lx; - result[i] = (dampl * exp(-(lx * lx) / (deltal * deltal)) + - dampr * exp(-(rlx * rlx) / (deltar * deltar))) * - f[i]; + result[i] = (dampl * exp(-(lx * lx) / (deltal * deltal)) + + dampr * exp(-(rlx * rlx) / (deltar * deltar))) + * f[i]; } // Need to communicate boundaries diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx index a654ad09a1..c2cb561737 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx @@ -2,12 +2,12 @@ #include -#include -#include -#include -#include +#include +#include +#include +#include -#include +#include namespace { BoutReal lagrange_at_position_denominator(const std::deque& grid, diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.hxx b/src/solver/impls/adams_bashforth/adams_bashforth.hxx index 07b49e959e..fa10353db5 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.hxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.hxx @@ -29,7 +29,7 @@ class AdamsBashforthSolver; #define __ADAMSBASHFORTH_SOLVER_H__ #include -#include +#include #include @@ -57,8 +57,8 @@ public: private: // Take a single timestep of specified order. If adaptive also calculates // and returns an error estimate. - BoutReal take_step(BoutReal timeIn, BoutReal dt, int order, - Array& current, Array& result); + BoutReal take_step(BoutReal timeIn, BoutReal dt, int order, Array& current, + Array& result); // Holds the current/next state Array state, nextState; @@ -92,8 +92,8 @@ private: BoutReal timestep; // Internal vars - int current_order; // The current order of the scheme - int nlocal, neq; // Number of variables on local processor and in total + int current_order; // The current order of the scheme + int nlocal, neq; // Number of variables on local processor and in total }; #endif // __ADAMSBASHFORTH_SOLVER_H__ diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 55595a6dee..acf9fa1c62 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -31,15 +31,15 @@ #if BOUT_HAS_ARKODE -#include "boutcomm.hxx" -#include "boutexception.hxx" -#include "field3d.hxx" -#include "msg_stack.hxx" -#include "options.hxx" -#include "output.hxx" -#include "unused.hxx" +#include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" +#include "bout/field3d.hxx" +#include "bout/msg_stack.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/mesh.hxx" -#include "utils.hxx" #if SUNDIALS_VERSION_MAJOR >= 4 #include @@ -110,10 +110,12 @@ inline int ARKStepSetJacTimes(void* arkode_mem, std::nullptr_t, void* ARKStepCreate(ARKRhsFn fe, ARKRhsFn fi, BoutReal t0, N_Vector y0) { auto arkode_mem = ARKodeCreate(); - if (arkode_mem == nullptr) + if (arkode_mem == nullptr) { throw BoutException("ARKodeCreate failed\n"); - if (ARKodeInit(arkode_mem, fe, fi, t0, y0) != ARK_SUCCESS) + } + if (ARKodeInit(arkode_mem, fe, fi, t0, y0) != ARK_SUCCESS) { throw BoutException("ARKodeInit failed\n"); + } return arkode_mem; } @@ -303,33 +305,39 @@ int ArkodeSolver::init() { if (imex and solve_explicit and solve_implicit) { output_info.write("\tUsing ARKode ImEx solver \n"); - if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) + if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImEx failed\n"); + } } else if (solve_explicit) { output_info.write("\tUsing ARKStep Explicit solver \n"); - if (ARKStepSetExplicit(arkode_mem) != ARK_SUCCESS) + if (ARKStepSetExplicit(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetExplicit failed\n"); + } } else { output_info.write("\tUsing ARKStep Implicit solver \n"); - if (ARKStepSetImplicit(arkode_mem) != ARK_SUCCESS) + if (ARKStepSetImplicit(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImplicit failed\n"); + } } // For callbacks, need pointer to solver object - if (ARKStepSetUserData(arkode_mem, this) != ARK_SUCCESS) + if (ARKStepSetUserData(arkode_mem, this) != ARK_SUCCESS) { throw BoutException("ARKStepSetUserData failed\n"); + } if (set_linear) { output.write("\tSetting ARKStep implicit solver to Linear\n"); - if (ARKStepSetLinear(arkode_mem, 1) != ARK_SUCCESS) + if (ARKStepSetLinear(arkode_mem, 1) != ARK_SUCCESS) { throw BoutException("ARKStepSetLinear failed\n"); + } } if (fixed_step) { // If not given, default to adaptive timestepping const auto fixed_timestep = (*options)["timestep"].withDefault(0.0); - if (ARKStepSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) + if (ARKStepSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) { throw BoutException("ARKStepSetFixedStep failed\n"); + } } if (ARKStepSetOrder(arkode_mem, order) != ARK_SUCCESS) { @@ -367,36 +375,43 @@ int ArkodeSolver::init() { }); N_Vector abstolvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext); - if (abstolvec == nullptr) + if (abstolvec == nullptr) { throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n"); + } set_abstol_values(NV_DATA_P(abstolvec), f2dtols, f3dtols); - if (ARKStepSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) + if (ARKStepSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) { throw BoutException("ARKStepSVtolerances failed\n"); + } N_VDestroy_Parallel(abstolvec); } else { - if (ARKStepSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) + if (ARKStepSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) { throw BoutException("ARKStepSStolerances failed\n"); + } } - if (ARKStepSetMaxNumSteps(arkode_mem, mxsteps) != ARK_SUCCESS) + if (ARKStepSetMaxNumSteps(arkode_mem, mxsteps) != ARK_SUCCESS) { throw BoutException("ARKStepSetMaxNumSteps failed\n"); + } if (max_timestep > 0.0) { - if (ARKStepSetMaxStep(arkode_mem, max_timestep) != ARK_SUCCESS) + if (ARKStepSetMaxStep(arkode_mem, max_timestep) != ARK_SUCCESS) { throw BoutException("ARKStepSetMaxStep failed\n"); + } } if (min_timestep > 0.0) { - if (ARKStepSetMinStep(arkode_mem, min_timestep) != ARK_SUCCESS) + if (ARKStepSetMinStep(arkode_mem, min_timestep) != ARK_SUCCESS) { throw BoutException("ARKStepSetMinStep failed\n"); + } } if (start_timestep > 0.0) { - if (ARKStepSetInitStep(arkode_mem, start_timestep) != ARK_SUCCESS) + if (ARKStepSetInitStep(arkode_mem, start_timestep) != ARK_SUCCESS) { throw BoutException("ARKStepSetInitStep failed"); + } } // ARKStepSetPredictorMethod(arkode_mem,4); @@ -404,12 +419,14 @@ int ArkodeSolver::init() { #if SUNDIALS_VERSION_MAJOR < 4 if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); - if (ARKodeSetFixedPoint(arkode_mem, 3.0)) + if (ARKodeSetFixedPoint(arkode_mem, 3.0)) { throw BoutException("ARKodeSetFixedPoint failed\n"); + } } else { output.write("\tUsing Newton iteration\n"); - if (ARKodeSetNewton(arkode_mem)) + if (ARKodeSetNewton(arkode_mem)) { throw BoutException("ARKodeSetNewton failed\n"); + } } #else if (fixed_point) { @@ -423,8 +440,9 @@ int ArkodeSolver::init() { throw BoutException("Creating SUNDIALS Newton nonlinear solver failed\n"); } } - if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) + if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { throw BoutException("ARKStepSetNonlinearSolver failed\n"); + } #endif /// Set Preconditioner @@ -435,11 +453,13 @@ int ArkodeSolver::init() { if ((sun_solver = SUNLinSol_SPGMR(uvec, prectype, maxl, suncontext)) == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } - if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) + if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) { throw BoutException("ARKStepSetLinearSolver failed\n"); + } #else - if (ARKSpgmr(arkode_mem, prectype, maxl) != ARKSPILS_SUCCESS) + if (ARKSpgmr(arkode_mem, prectype, maxl) != ARKSPILS_SUCCESS) { throw BoutException("ARKSpgmr failed\n"); + } #endif if (!hasPreconditioner()) { @@ -477,14 +497,16 @@ int ArkodeSolver::init() { if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, ZERO, arkode_bbd_rhs, nullptr) - != ARK_SUCCESS) + != ARK_SUCCESS) { throw BoutException("ARKBBDPrecInit failed\n"); + } } else { output.write("\tUsing user-supplied preconditioner\n"); - if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre_shim) != ARK_SUCCESS) + if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre_shim) != ARK_SUCCESS) { throw BoutException("ARKStepSetPreconditioner failed\n"); + } } } else { // Not using preconditioning @@ -496,11 +518,13 @@ int ArkodeSolver::init() { == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } - if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) + if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) { throw BoutException("ARKStepSetLinearSolver failed\n"); + } #else - if (ARKSpgmr(arkode_mem, SUN_PREC_NONE, maxl) != ARKSPILS_SUCCESS) + if (ARKSpgmr(arkode_mem, SUN_PREC_NONE, maxl) != ARKSPILS_SUCCESS) { throw BoutException("ARKSpgmr failed\n"); + } #endif } @@ -509,15 +533,18 @@ int ArkodeSolver::init() { if (use_jacobian and hasJacobian()) { output.write("\tUsing user-supplied Jacobian function\n"); - if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARK_SUCCESS) + if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARK_SUCCESS) { throw BoutException("ARKStepSetJacTimesVecFn failed\n"); - } else + } + } else { output.write("\tUsing difference quotient approximation for Jacobian\n"); + } if (optimize) { output.write("\tUsing ARKode inbuilt optimization\n"); - if (ARKStepSetOptimalParams(arkode_mem) != ARK_SUCCESS) + if (ARKStepSetOptimalParams(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetOptimalParams failed"); + } } return 0; } @@ -529,8 +556,9 @@ int ArkodeSolver::init() { int ArkodeSolver::run() { TRACE("ArkodeSolver::run()"); - if (!initialised) + if (!initialised) { throw BoutException("ArkodeSolver not initialised\n"); + } for (int i = 0; i < getNumberOutputSteps(); i++) { @@ -623,7 +651,8 @@ BoutReal ArkodeSolver::run(BoutReal tout) { run_rhs(simtime); // run_diffusive(simtime); if (flag != ARK_SUCCESS) { - output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n", simtime, flag); + output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n", simtime, + flag); return -1.0; } @@ -846,8 +875,9 @@ void ArkodeSolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_ std::vector& f3dtols, bool bndry) { // Loop over 2D variables for (std::vector::size_type i = 0; i < f2dtols.size(); i++) { - if (bndry && !f2d[i].evolve_bndry) + if (bndry && !f2d[i].evolve_bndry) { continue; + } abstolvec_data[p] = f2dtols[i]; p++; } @@ -855,8 +885,9 @@ void ArkodeSolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_ for (int jz = 0; jz < bout::globals::mesh->LocalNz; jz++) { // Loop over 3D variables for (std::vector::size_type i = 0; i < f3dtols.size(); i++) { - if (bndry && !f3d[i].evolve_bndry) + if (bndry && !f3d[i].evolve_bndry) { continue; + } abstolvec_data[p] = f3dtols[i]; p++; } diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index 75cd862c3b..afdce0b701 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -35,17 +35,17 @@ #if not BOUT_HAS_ARKODE namespace { -RegisterUnavailableSolver registerunavailablearkode("arkode", - "BOUT++ was not configured with ARKODE/SUNDIALS"); +RegisterUnavailableSolver + registerunavailablearkode("arkode", "BOUT++ was not configured with ARKODE/SUNDIALS"); } #else -#include "bout_types.hxx" +#include "bout/bout_types.hxx" #include "bout/sundials_backports.hxx" -#include #include +#include #include diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index b190d196db..4da9d0c149 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -30,16 +30,16 @@ #if BOUT_HAS_CVODE -#include "boutcomm.hxx" -#include "boutexception.hxx" -#include "field3d.hxx" -#include "msg_stack.hxx" -#include "options.hxx" -#include "output.hxx" -#include "unused.hxx" +#include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" +#include "bout/field3d.hxx" +#include "bout/msg_stack.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/bout_enum_class.hxx" #include "bout/mesh.hxx" -#include "utils.hxx" #include "fmt/core.h" @@ -255,20 +255,24 @@ int CvodeSolver::init() { } // For callbacks, need pointer to solver object - if (CVodeSetUserData(cvode_mem, this) < 0) + if (CVodeSetUserData(cvode_mem, this) < 0) { throw BoutException("CVodeSetUserData failed\n"); + } - if (CVodeInit(cvode_mem, cvode_rhs, simtime, uvec) < 0) + if (CVodeInit(cvode_mem, cvode_rhs, simtime, uvec) < 0) { throw BoutException("CVodeInit failed\n"); + } if (max_order > 0) { - if (CVodeSetMaxOrd(cvode_mem, max_order) < 0) + if (CVodeSetMaxOrd(cvode_mem, max_order) < 0) { throw BoutException("CVodeSetMaxOrder failed\n"); + } } if (stablimdet) { - if (CVodeSetStabLimDet(cvode_mem, stablimdet) < 0) + if (CVodeSetStabLimDet(cvode_mem, stablimdet) < 0) { throw BoutException("CVodeSetStabLimDet failed\n"); + } } if (use_vector_abstol) { @@ -294,18 +298,21 @@ int CvodeSolver::init() { }); N_Vector abstolvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext); - if (abstolvec == nullptr) + if (abstolvec == nullptr) { throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n"); + } set_vector_option_values(NV_DATA_P(abstolvec), f2dtols, f3dtols); - if (CVodeSVtolerances(cvode_mem, reltol, abstolvec) < 0) + if (CVodeSVtolerances(cvode_mem, reltol, abstolvec) < 0) { throw BoutException("CVodeSVtolerances failed\n"); + } N_VDestroy_Parallel(abstolvec); } else { - if (CVodeSStolerances(cvode_mem, reltol, abstol) < 0) + if (CVodeSStolerances(cvode_mem, reltol, abstol) < 0) { throw BoutException("CVodeSStolerances failed\n"); + } } CVodeSetMaxNumSteps(cvode_mem, mxsteps); @@ -341,15 +348,17 @@ int CvodeSolver::init() { auto f3d_constraints = create_constraints(f3d); N_Vector constraints_vec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext); - if (constraints_vec == nullptr) + if (constraints_vec == nullptr) { throw BoutException("SUNDIALS memory allocation (positivity constraints vector) " "failed\n"); + } set_vector_option_values(NV_DATA_P(constraints_vec), f2d_constraints, f3d_constraints); - if (CVodeSetConstraints(cvode_mem, constraints_vec) < 0) + if (CVodeSetConstraints(cvode_mem, constraints_vec) < 0) { throw BoutException("CVodeSetConstraints failed\n"); + } N_VDestroy_Parallel(constraints_vec); } @@ -366,11 +375,13 @@ int CvodeSolver::init() { if ((sun_solver = SUNLinSol_SPGMR(uvec, prectype, maxl, suncontext)) == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } - if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) + if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) { throw BoutException("CVSpilsSetLinearSolver failed\n"); + } #else - if (CVSpgmr(cvode_mem, prectype, maxl) != CVSPILS_SUCCESS) + if (CVSpgmr(cvode_mem, prectype, maxl) != CVSPILS_SUCCESS) { throw BoutException("CVSpgmr failed\n"); + } #endif if (!hasPreconditioner()) { @@ -395,14 +406,16 @@ int CvodeSolver::init() { const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars()); if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, ZERO, - cvode_bbd_rhs, nullptr)) + cvode_bbd_rhs, nullptr)) { throw BoutException("CVBBDPrecInit failed\n"); + } } else { output_info.write("\tUsing user-supplied preconditioner\n"); - if (CVSpilsSetPreconditioner(cvode_mem, nullptr, cvode_pre_shim)) + if (CVSpilsSetPreconditioner(cvode_mem, nullptr, cvode_pre_shim)) { throw BoutException("CVSpilsSetPreconditioner failed\n"); + } } } else { output_info.write("\tNo preconditioning\n"); @@ -412,11 +425,13 @@ int CvodeSolver::init() { == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } - if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) + if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) { throw BoutException("CVSpilsSetLinearSolver failed\n"); + } #else - if (CVSpgmr(cvode_mem, SUN_PREC_NONE, maxl) != CVSPILS_SUCCESS) + if (CVSpgmr(cvode_mem, SUN_PREC_NONE, maxl) != CVSPILS_SUCCESS) { throw BoutException("CVSpgmr failed\n"); + } #endif } @@ -424,10 +439,12 @@ int CvodeSolver::init() { if (use_jacobian and hasJacobian()) { output_info.write("\tUsing user-supplied Jacobian function\n"); - if (CVSpilsSetJacTimes(cvode_mem, nullptr, cvode_jac) != CV_SUCCESS) + if (CVSpilsSetJacTimes(cvode_mem, nullptr, cvode_jac) != CV_SUCCESS) { throw BoutException("CVSpilsSetJacTimesVecFn failed\n"); - } else + } + } else { output_info.write("\tUsing difference quotient approximation for Jacobian\n"); + } } else { output_info.write("\tUsing Functional iteration\n"); #if SUNDIALS_VERSION_MAJOR >= 4 @@ -435,8 +452,9 @@ int CvodeSolver::init() { throw BoutException("SUNNonlinSol_FixedPoint failed\n"); } - if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver)) + if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver)) { throw BoutException("CVodeSetNonlinearSolver failed\n"); + } #endif } @@ -445,37 +463,43 @@ int CvodeSolver::init() { return 0; } -template -std::vector CvodeSolver::create_constraints( - const std::vector>& fields) { +template +std::vector +CvodeSolver::create_constraints(const std::vector>& fields) { std::vector constraints; constraints.reserve(fields.size()); std::transform(begin(fields), end(fields), std::back_inserter(constraints), [](const VarStr& f) { auto f_options = Options::root()[f.name]; - const auto value = f_options["positivity_constraint"] - .doc(fmt::format( - "Constraint to apply to {} if " - "solver:apply_positivity_constraint=true. " - "Possible values are: none (default), " - "positive, non_negative, negative, or " - "non_positive.", f.name)) - .withDefault(positivity_constraint::none); + const auto value = + f_options["positivity_constraint"] + .doc(fmt::format("Constraint to apply to {} if " + "solver:apply_positivity_constraint=true. " + "Possible values are: none (default), " + "positive, non_negative, negative, or " + "non_positive.", + f.name)) + .withDefault(positivity_constraint::none); switch (value) { - case positivity_constraint::none: return 0.0; - case positivity_constraint::positive: return 2.0; - case positivity_constraint::non_negative: return 1.0; - case positivity_constraint::negative: return -2.0; - case positivity_constraint::non_positive: return -1.0; - default: throw BoutException("Incorrect value for " - "positivity_constraint"); + case positivity_constraint::none: + return 0.0; + case positivity_constraint::positive: + return 2.0; + case positivity_constraint::non_negative: + return 1.0; + case positivity_constraint::negative: + return -2.0; + case positivity_constraint::non_positive: + return -1.0; + default: + throw BoutException("Incorrect value for " + "positivity_constraint"); } }); return constraints; } - /************************************************************************** * Run - Advance time **************************************************************************/ @@ -483,8 +507,9 @@ std::vector CvodeSolver::create_constraints( int CvodeSolver::run() { TRACE("CvodeSolver::run()"); - if (!cvode_initialised) + if (!cvode_initialised) { throw BoutException("CvodeSolver not initialised\n"); + } for (int i = 0; i < getNumberOutputSteps(); i++) { @@ -531,9 +556,9 @@ int CvodeSolver::run() { if (diagnose) { // Print additional diagnostics - output.write( - "\nCVODE: nsteps {:d}, nfevals {:d}, nniters {:d}, npevals {:d}, nliters {:d}\n", - nsteps, nfevals, nniters, npevals, nliters); + output.write("\nCVODE: nsteps {:d}, nfevals {:d}, nniters {:d}, npevals {:d}, " + "nliters {:d}\n", + nsteps, nfevals, nniters, npevals, nliters); output.write(" -> Newton iterations per step: {:e}\n", static_cast(nniters) / static_cast(nsteps)); @@ -644,8 +669,9 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udat if (!hasPreconditioner()) { // Identity (but should never happen) - for (int i = 0; i < N; i++) + for (int i = 0; i < N; i++) { zvec[i] = rvec[i]; + } return; } @@ -765,8 +791,8 @@ void CvodeSolver::set_vector_option_values(BoutReal* option_data, void CvodeSolver::loop_vector_option_values_op(Ind2D UNUSED(i2d), BoutReal* option_data, int& p, std::vector& f2dtols, - std::vector& f3dtols, bool bndry) -{ + std::vector& f3dtols, + bool bndry) { // Loop over 2D variables for (std::vector::size_type i = 0; i < f2dtols.size(); i++) { if (bndry && !f2d[i].evolve_bndry) { @@ -792,8 +818,9 @@ void CvodeSolver::resetInternalFields() { TRACE("CvodeSolver::resetInternalFields"); save_vars(NV_DATA_P(uvec)); - if (CVodeReInit(cvode_mem, simtime, uvec) < 0) + if (CVodeReInit(cvode_mem, simtime, uvec) < 0) { throw BoutException("CVodeReInit failed\n"); + } } #endif diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx index a6d728f01d..b2ed83568b 100644 --- a/src/solver/impls/cvode/cvode.hxx +++ b/src/solver/impls/cvode/cvode.hxx @@ -40,11 +40,11 @@ RegisterUnavailableSolver #else -#include "bout_types.hxx" +#include "bout/bout_types.hxx" #include "bout/sundials_backports.hxx" -#include #include +#include #include diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx index d010514991..6abf50e918 100644 --- a/src/solver/impls/euler/euler.cxx +++ b/src/solver/impls/euler/euler.cxx @@ -1,15 +1,15 @@ #include "euler.hxx" -#include -#include -#include -#include #include +#include +#include +#include +#include #include -#include +#include EulerSolver::EulerSolver(Options* options) : Solver(options), mxstep((*options)["mxstep"] @@ -23,10 +23,12 @@ EulerSolver::EulerSolver(Options* options) .withDefault(getOutputTimestep())) {} void EulerSolver::setMaxTimestep(BoutReal dt) { - if(dt >= cfl_factor*timestep) + if (dt >= cfl_factor * timestep) { return; // Already less than this - - timestep = dt*0.99 / cfl_factor; // Slightly below to avoid re-setting to same value over again + } + + timestep = dt * 0.99 + / cfl_factor; // Slightly below to avoid re-setting to same value over again timestep_reduced = true; } @@ -39,17 +41,17 @@ int EulerSolver::init() { // Calculate number of variables nlocal = getLocalN(); - + // Get total problem size int neq; if (bout::globals::mpi->MPI_Allreduce(&nlocal, &neq, 1, MPI_INT, MPI_SUM, BoutComm::get())) { throw BoutException("MPI_Allreduce failed in EulerSolver::init"); } - - output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", - n3Dvars(), n2Dvars(), neq, nlocal); - + + output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(), + n2Dvars(), neq, nlocal); + // Allocate memory f0.reallocate(nlocal); f1.reallocate(nlocal); @@ -71,24 +73,25 @@ int EulerSolver::run() { do { // Take a step BoutReal dt_limit = timestep; // Store the timestep - - if((simtime + timestep) >= target) { - // Make sure the last timestep is on the output - timestep = target - simtime; + + if ((simtime + timestep) >= target) { + // Make sure the last timestep is on the output + timestep = target - simtime; running = false; } - + BoutReal old_timestep = timestep; - + timestep_reduced = false; take_step(simtime, timestep, f0, f1); - + // Check with all processors if timestep was reduced - - BoutReal newdt_local = 10.*old_timestep; // Signal no change - if(timestep_reduced) + + BoutReal newdt_local = 10. * old_timestep; // Signal no change + if (timestep_reduced) { newdt_local = timestep; - + } + BoutReal newdt; if (bout::globals::mpi->MPI_Allreduce(&newdt_local, &newdt, 1, MPI_DOUBLE, MPI_MIN, BoutComm::get())) { @@ -96,34 +99,35 @@ int EulerSolver::run() { } // If timestep_reduced re-run - if(newdt < old_timestep) { // At least one processor reduced the timestep + if (newdt < old_timestep) { // At least one processor reduced the timestep timestep = newdt; take_step(simtime, timestep, f0, f1); dt_limit = timestep; // This becomes the new limit - running = true; // Need another step + running = true; // Need another step } - + // Taken a step, swap buffers swap(f1, f0); simtime += timestep; internal_steps++; - if(internal_steps > mxstep) + if (internal_steps > mxstep) { throw BoutException("ERROR: MXSTEP exceeded. simtime={:e}, timestep = {:e}\n", simtime, timestep); + } // Call timestep monitors call_timestep_monitors(simtime, timestep); - + timestep = dt_limit; // Change back to limiting timestep - }while(running); + } while (running); load_vars(std::begin(f0)); // Put result into variables // Call rhs function to get extra variables at this time run_rhs(simtime); - + iteration++; // Advance iteration number - + /// Call the monitor function if (call_monitors(simtime, s, getNumberOutputSteps())) { @@ -135,14 +139,15 @@ int EulerSolver::run() { return 0; } -void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array &start, - Array &result) { +void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array& start, + Array& result) { load_vars(std::begin(start)); run_rhs(curtime); save_derivs(std::begin(result)); BOUT_OMP(parallel for) - for(int i=0;i #include +#include -namespace{ +namespace { RegisterSolver registersolvereuler("euler"); } @@ -67,4 +67,3 @@ private: }; #endif // __KARNIADAKIS_SOLVER_H__ - diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 38106614b8..e60f1fb127 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -33,11 +33,11 @@ #if BOUT_HAS_IDA -#include "boutcomm.hxx" -#include "boutexception.hxx" -#include "msg_stack.hxx" -#include "output.hxx" -#include "unused.hxx" +#include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" +#include "bout/msg_stack.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" #include @@ -167,8 +167,9 @@ int IdaSolver::init() { set_id(NV_DATA_P(id)); // Call IDACreate to initialise - if ((idamem = IDACreate(suncontext)) == nullptr) + if ((idamem = IDACreate(suncontext)) == nullptr) { throw BoutException("IDACreate failed\n"); + } // For callbacks, need pointer to solver object if (IDASetUserData(idamem, this) < 0) { @@ -192,13 +193,16 @@ int IdaSolver::init() { // Call IDASpgmr to specify the IDA linear solver IDASPGMR const auto maxl = (*options)["maxl"].withDefault(6 * n3d); #if SUNDIALS_VERSION_MAJOR >= 3 - if ((sun_solver = SUNLinSol_SPGMR(uvec, SUN_PREC_NONE, maxl, suncontext)) == nullptr) + if ((sun_solver = SUNLinSol_SPGMR(uvec, SUN_PREC_NONE, maxl, suncontext)) == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); - if (IDASpilsSetLinearSolver(idamem, sun_solver) != IDA_SUCCESS) + } + if (IDASpilsSetLinearSolver(idamem, sun_solver) != IDA_SUCCESS) { throw BoutException("IDASpilsSetLinearSolver failed\n"); + } #else - if (IDASpgmr(idamem, maxl)) + if (IDASpgmr(idamem, maxl)) { throw BoutException("IDASpgmr failed\n"); + } #endif if (use_precon) { @@ -222,19 +226,22 @@ int IdaSolver::init() { const auto mukeep = (*options)["mukeep"].withDefault(n3d); const auto mlkeep = (*options)["mlkeep"].withDefault(n3d); if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, ZERO, ida_bbd_res, - nullptr)) + nullptr)) { throw BoutException("IDABBDPrecInit failed\n"); + } } else { output.write("\tUsing user-supplied preconditioner\n"); - if (IDASpilsSetPreconditioner(idamem, nullptr, ida_pre_shim)) + if (IDASpilsSetPreconditioner(idamem, nullptr, ida_pre_shim)) { throw BoutException("IDASpilsSetPreconditioner failed\n"); + } } } // Call IDACalcIC (with default options) to correct the initial values if (correct_start) { - if (IDACalcIC(idamem, IDA_YA_YDP_INIT, 1e-6)) + if (IDACalcIC(idamem, IDA_YA_YDP_INIT, 1e-6)) { throw BoutException("IDACalcIC failed\n"); + } } return 0; @@ -247,8 +254,9 @@ int IdaSolver::init() { int IdaSolver::run() { TRACE("IDA IdaSolver::run()"); - if (!initialised) + if (!initialised) { throw BoutException("IdaSolver not initialised\n"); + } for (int i = 0; i < getNumberOutputSteps(); i++) { @@ -274,8 +282,9 @@ int IdaSolver::run() { BoutReal IdaSolver::run(BoutReal tout) { TRACE("Running solver: solver::run({:e})", tout); - if (!initialised) + if (!initialised) { throw BoutException("Running IDA solver without initialisation\n"); + } pre_Wtime = 0.0; pre_ncalls = 0; @@ -289,7 +298,8 @@ BoutReal IdaSolver::run(BoutReal tout) { run_rhs(simtime); if (flag < 0) { - output_error.write("ERROR IDA solve failed at t = {:e}, flag = {:d}\n", simtime, flag); + output_error.write("ERROR IDA solve failed at t = {:e}, flag = {:d}\n", simtime, + flag); return -1.0; } @@ -316,8 +326,9 @@ void IdaSolver::res(BoutReal t, BoutReal* udata, BoutReal* dudata, BoutReal* rda const int N = NV_LOCLENGTH_P(id); const BoutReal* idd = NV_DATA_P(id); for (int i = 0; i < N; i++) { - if (idd[i] > 0.5) // 1 -> differential, 0 -> algebraic + if (idd[i] > 0.5) { // 1 -> differential, 0 -> algebraic rdata[i] -= dudata[i]; + } } } diff --git a/src/solver/impls/ida/ida.hxx b/src/solver/impls/ida/ida.hxx index d134f92d1e..83ee4d83e6 100644 --- a/src/solver/impls/ida/ida.hxx +++ b/src/solver/impls/ida/ida.hxx @@ -42,7 +42,7 @@ RegisterUnavailableSolver #else -#include "bout_types.hxx" +#include "bout/bout_types.hxx" #include "bout/sundials_backports.hxx" #include diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx index 6835089b97..e78ba2ac0d 100644 --- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx +++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx @@ -6,14 +6,14 @@ #include #include -#include -#include -#include -#include +#include +#include +#include +#include #include -#include +#include #include "petscmat.h" #include "petscsnes.h" @@ -338,12 +338,14 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { ASSERT2((localIndex >= 0) && (localIndex < localN)); if (z == 0) { // All 2D and 3D fields - for (int i = 0; i < n2d + n3d; i++) + for (int i = 0; i < n2d + n3d; i++) { d_nnz[localIndex + i] -= (n3d + n2d); + } } else { // Only 3D fields - for (int i = 0; i < n3d; i++) + for (int i = 0; i < n3d; i++) { d_nnz[localIndex + i] -= (n3d + n2d); + } } } } @@ -378,12 +380,14 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { ASSERT2((localIndex >= 0) && (localIndex < localN)); if (z == 0) { // All 2D and 3D fields - for (int i = 0; i < n2d + n3d; i++) + for (int i = 0; i < n2d + n3d; i++) { d_nnz[localIndex + i] -= (n3d + n2d); + } } else { // Only 3D fields - for (int i = 0; i < n3d; i++) + for (int i = 0; i < n3d; i++) { d_nnz[localIndex + i] -= (n3d + n2d); + } } } } @@ -535,15 +539,16 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { int xi = x + xoffset[c]; int yi = y + yoffset[c]; - if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) { + if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) + || (yi >= mesh->LocalNy)) { continue; - } + } int ind2 = ROUND(index(xi, yi, 0)); if (ind2 < 0) { continue; // A boundary point - } + } // Depends on all variables on this cell for (int j = 0; j < n2d; j++) { @@ -564,7 +569,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { PetscInt row = ind + i; if (z == 0) { row += n2d; - } + } // Depends on 2D fields for (int j = 0; j < n2d; j++) { @@ -581,16 +586,16 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) { continue; - } + } int ind2 = ROUND(index(xi, yi, z)); if (ind2 < 0) { continue; // Boundary point - } + } if (z == 0) { ind2 += n2d; - } + } // 3D fields on this cell for (int j = 0; j < n3d; j++) { @@ -609,7 +614,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { int ind2 = ROUND(index(x, y, zp)); if (zp == 0) { ind2 += n2d; - } + } for (int j = 0; j < n3d; j++) { PetscInt col = ind2 + j; // output.write("SETTING 4: {:d}, {:d}\n", row, col); @@ -620,7 +625,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) { ind2 = ROUND(index(x, y, zm)); if (zm == 0) { ind2 += n2d; - } + } for (int j = 0; j < n3d; j++) { PetscInt col = ind2 + j; // output.write("SETTING 5: {:d}, {:d}\n", row, col); @@ -790,11 +795,11 @@ int IMEXBDF2::run() { // Validate our desired next timestep if (dtNext < dtMinFatal) { - // Don't allow the timestep to go below requested fatal min + // Don't allow the timestep to go below requested fatal min throw BoutException( "Aborting: Timestep ({:f}) tried to go below minimum allowed", dtNext); } - if (dtNext < dtMin) { // Don't allow timestep below requested min + if (dtNext < dtMin) { // Don't allow timestep below requested min dtNext = dtMin; } else if (dtNext > dtMax) { // Don't allow timestep above request max dtNext = dtMax; @@ -837,7 +842,7 @@ int IMEXBDF2::run() { // An error occurred. If adaptive, reduce timestep if (!adaptive) { throw; - } + } failCounter++; if (failCounter > 10) { @@ -872,7 +877,7 @@ int IMEXBDF2::run() { // An error occurred. If adaptive, reduce timestep if (!adaptive) { throw; - } + } failCounter++; if (failCounter > 10) { @@ -1251,8 +1256,9 @@ PetscErrorCode IMEXBDF2::solve_implicit(BoutReal curtime, BoutReal gamma) { ierr = VecGetArray(snes_x, &xdata); CHKERRQ(ierr); - for (int i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) { u[i] = xdata[i]; + } ierr = VecRestoreArray(snes_x, &xdata); CHKERRQ(ierr); @@ -1369,20 +1375,22 @@ void IMEXBDF2::loopVars(BoutReal* u) { // Inner X if (mesh->firstX() && !mesh->periodicX) { - for (int jx = 0; jx < mesh->xstart; ++jx) + for (int jx = 0; jx < mesh->xstart; ++jx) { for (int jy = mesh->ystart; jy <= mesh->yend; ++jy) { op.run(jx, jy, u); ++u; } + } } // Outer X if (mesh->lastX() && !mesh->periodicX) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; ++jx) + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; ++jx) { for (int jy = mesh->ystart; jy <= mesh->yend; ++jy) { op.run(jx, jy, u); ++u; } + } } // Lower Y for (RangeIterator xi = mesh->iterateBndryLowerY(); !xi.isDone(); ++xi) { @@ -1402,11 +1410,12 @@ void IMEXBDF2::loopVars(BoutReal* u) { } // Bulk of points - for (int jx = mesh->xstart; jx <= mesh->xend; ++jx) + for (int jx = mesh->xstart; jx <= mesh->xend; ++jx) { for (int jy = mesh->ystart; jy <= mesh->yend; ++jy) { op.run(jx, jy, u); ++u; } + } } // Loop over 3D variables diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.hxx b/src/solver/impls/imex-bdf2/imex-bdf2.hxx index fc610b4753..abda07606f 100644 --- a/src/solver/impls/imex-bdf2/imex-bdf2.hxx +++ b/src/solver/impls/imex-bdf2/imex-bdf2.hxx @@ -52,7 +52,7 @@ class IMEXBDF2; #include "mpi.h" #include -#include +#include #include #include @@ -105,14 +105,15 @@ public: /// @param[in] x The vector to be operated on /// @param[out] f The result of the operation PetscErrorCode precon(Vec x, Vec f); + private: static constexpr int MAX_SUPPORTED_ORDER = 4; // Should this be #defined instead? int maxOrder; ///< Specify the maximum order of the scheme to use (1/2/3) - BoutReal timestep; ///< The internal timestep - int ninternal; ///< Number of internal steps per output - int mxstep; ///< Maximum number of internal steps between outputs + BoutReal timestep; ///< The internal timestep + int ninternal; ///< Number of internal steps per output + int mxstep; ///< Maximum number of internal steps between outputs // Adaptivity diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx index 4d65008c03..ad8e99dd38 100644 --- a/src/solver/impls/petsc/petsc.cxx +++ b/src/solver/impls/petsc/petsc.cxx @@ -32,31 +32,35 @@ //#include #include -#include +#include #include -#include // Cell interpolation -#include -#include +#include // Cell interpolation +#include +#include -extern PetscErrorCode solver_f(TS ts, BoutReal t, Vec globalin, Vec globalout, void *f_data); +extern PetscErrorCode solver_f(TS ts, BoutReal t, Vec globalin, Vec globalout, + void* f_data); -#if PETSC_VERSION_GE(3,5,0) -extern PetscErrorCode solver_rhsjacobian(TS ts,BoutReal t,Vec globalin,Mat J,Mat Jpre,void *f_data); -extern PetscErrorCode solver_ijacobianfd(TS,PetscReal,Vec,Vec,PetscReal,Mat,Mat,void*); +#if PETSC_VERSION_GE(3, 5, 0) +extern PetscErrorCode solver_rhsjacobian(TS ts, BoutReal t, Vec globalin, Mat J, Mat Jpre, + void* f_data); +extern PetscErrorCode solver_ijacobianfd(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat, + void*); #else -extern PetscErrorCode solver_rhsjacobian(TS ts,BoutReal t,Vec globalin,Mat *J,Mat *Jpre,MatStructure *str,void *f_data); -extern PetscErrorCode solver_ijacobianfd(TS,PetscReal,Vec,Vec,PetscReal,Mat*,Mat*,MatStructure*,void*); +extern PetscErrorCode solver_rhsjacobian(TS ts, BoutReal t, Vec globalin, Mat* J, + Mat* Jpre, MatStructure* str, void* f_data); +extern PetscErrorCode solver_ijacobianfd(TS, PetscReal, Vec, Vec, PetscReal, Mat*, Mat*, + MatStructure*, void*); #endif -extern PetscErrorCode solver_if(TS,BoutReal,Vec,Vec,Vec,void*); - +extern PetscErrorCode solver_if(TS, BoutReal, Vec, Vec, Vec, void*); /// KSP preconditioner PCShell routines for physics preconditioners -extern PetscErrorCode PhysicsPCApply(PC,Vec x,Vec y); +extern PetscErrorCode PhysicsPCApply(PC, Vec x, Vec y); extern PetscErrorCode PhysicsJacobianApply(Mat J, Vec x, Vec y); -extern PetscErrorCode PhysicsSNESApply(SNES,Vec); +extern PetscErrorCode PhysicsSNESApply(SNES, Vec); PetscSolver::PetscSolver(Options* opts) : Solver(opts), @@ -95,21 +99,22 @@ PetscSolver::~PetscSolver() { **************************************************************************/ int PetscSolver::init() { - PetscErrorCode ierr; - int neq; - MPI_Comm comm = PETSC_COMM_WORLD; - PetscMPIInt rank; + PetscErrorCode ierr; + int neq; + MPI_Comm comm = PETSC_COMM_WORLD; + PetscMPIInt rank; TRACE("Initialising PETSc-dev solver"); PetscFunctionBegin; - PetscLogEventRegister("PetscSolver::init",PETSC_VIEWER_CLASSID,&init_event); - PetscLogEventRegister("loop_vars",PETSC_VIEWER_CLASSID,&loop_event); - PetscLogEventRegister("solver_f",PETSC_VIEWER_CLASSID,&solver_event); + PetscLogEventRegister("PetscSolver::init", PETSC_VIEWER_CLASSID, &init_event); + PetscLogEventRegister("loop_vars", PETSC_VIEWER_CLASSID, &loop_event); + PetscLogEventRegister("solver_f", PETSC_VIEWER_CLASSID, &solver_event); Solver::init(); - ierr = PetscLogEventBegin(init_event,0,0,0,0);CHKERRQ(ierr); + ierr = PetscLogEventBegin(init_event, 0, 0, 0, 0); + CHKERRQ(ierr); output.write("Initialising PETSc-dev solver\n"); ierr = bout::globals::mpi->MPI_Comm_rank(comm, &rank); CHKERRQ(ierr); @@ -120,80 +125,105 @@ int PetscSolver::init() { if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM, BoutComm::get())) { output_error.write("\tERROR: MPI_Allreduce failed!\n"); - ierr = PetscLogEventEnd(init_event,0,0,0,0);CHKERRQ(ierr); + ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0); + CHKERRQ(ierr); PetscFunctionReturn(1); } - ierr = VecCreate(BoutComm::get(), &u);CHKERRQ(ierr); - ierr = VecSetSizes(u, local_N, PETSC_DECIDE);CHKERRQ(ierr); - ierr = VecSetFromOptions(u);CHKERRQ(ierr); + ierr = VecCreate(BoutComm::get(), &u); + CHKERRQ(ierr); + ierr = VecSetSizes(u, local_N, PETSC_DECIDE); + CHKERRQ(ierr); + ierr = VecSetFromOptions(u); + CHKERRQ(ierr); ////////// SAVE INITIAL STATE TO PETSc VECTOR /////////// // Set pointer to data array in vector u. - BoutReal *udata; + BoutReal* udata; - ierr = VecGetArray(u,&udata);CHKERRQ(ierr); + ierr = VecGetArray(u, &udata); + CHKERRQ(ierr); save_vars(udata); - ierr = VecRestoreArray(u,&udata);CHKERRQ(ierr); + ierr = VecRestoreArray(u, &udata); + CHKERRQ(ierr); PetscReal norm; - ierr = VecNorm(u,NORM_1,&norm);CHKERRQ(ierr); + ierr = VecNorm(u, NORM_1, &norm); + CHKERRQ(ierr); output_info << "initial |u| = " << norm << "\n"; - PetscBool J_load; - char load_file[PETSC_MAX_PATH_LEN]; /* jacobian input file name */ - PetscBool J_write=PETSC_FALSE,J_slowfd=PETSC_FALSE; + PetscBool J_load; + char load_file[PETSC_MAX_PATH_LEN]; /* jacobian input file name */ + PetscBool J_write = PETSC_FALSE, J_slowfd = PETSC_FALSE; // Create timestepper - ierr = TSCreate(BoutComm::get(),&ts);CHKERRQ(ierr); - ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); + ierr = TSCreate(BoutComm::get(), &ts); + CHKERRQ(ierr); + ierr = TSSetProblemType(ts, TS_NONLINEAR); + CHKERRQ(ierr); #if PETSC_HAS_SUNDIALS - ierr = TSSetType(ts,TSSUNDIALS);CHKERRQ(ierr); + ierr = TSSetType(ts, TSSUNDIALS); + CHKERRQ(ierr); #else - ierr = TSSetType(ts,TSRK);CHKERRQ(ierr); + ierr = TSSetType(ts, TSRK); + CHKERRQ(ierr); #endif - ierr = TSSetApplicationContext(ts, this);CHKERRQ(ierr); + ierr = TSSetApplicationContext(ts, this); + CHKERRQ(ierr); // Set user provided RHSFunction // Need to duplicate the solution vector for the residual Vec rhs_vec; - ierr = VecDuplicate(u,&rhs_vec);CHKERRQ(ierr); - ierr = TSSetRHSFunction(ts,rhs_vec,solver_f,this);CHKERRQ(ierr); - ierr = VecDestroy(&rhs_vec);CHKERRQ(ierr); + ierr = VecDuplicate(u, &rhs_vec); + CHKERRQ(ierr); + ierr = TSSetRHSFunction(ts, rhs_vec, solver_f, this); + CHKERRQ(ierr); + ierr = VecDestroy(&rhs_vec); + CHKERRQ(ierr); // Set up adaptive time-stepping TSAdapt adapt; - ierr = TSGetAdapt(ts, &adapt);CHKERRQ(ierr); + ierr = TSGetAdapt(ts, &adapt); + CHKERRQ(ierr); if (adaptive) { - ierr = TSAdaptSetType(adapt, TSADAPTBASIC);CHKERRQ(ierr); + ierr = TSAdaptSetType(adapt, TSADAPTBASIC); + CHKERRQ(ierr); } else { - ierr = TSAdaptSetType(adapt, TSADAPTNONE);CHKERRQ(ierr); + ierr = TSAdaptSetType(adapt, TSADAPTNONE); + CHKERRQ(ierr); } // Set default absolute/relative tolerances - ierr = TSSetTolerances(ts, abstol, nullptr, reltol, nullptr);CHKERRQ(ierr); + ierr = TSSetTolerances(ts, abstol, nullptr, reltol, nullptr); + CHKERRQ(ierr); -#if PETSC_VERSION_LT(3,5,0) - ierr = TSRKSetTolerance(ts, reltol); CHKERRQ(ierr); +#if PETSC_VERSION_LT(3, 5, 0) + ierr = TSRKSetTolerance(ts, reltol); + CHKERRQ(ierr); #endif #if PETSC_HAS_SUNDIALS // Set Sundials tolerances - ierr = TSSundialsSetTolerance(ts, abstol, reltol);CHKERRQ(ierr); + ierr = TSSundialsSetTolerance(ts, abstol, reltol); + CHKERRQ(ierr); // Select Sundials Adams-Moulton or BDF method if (adams_moulton) { output.write("\tUsing Adams-Moulton implicit multistep method\n"); - ierr = TSSundialsSetType(ts, SUNDIALS_ADAMS);CHKERRQ(ierr); + ierr = TSSundialsSetType(ts, SUNDIALS_ADAMS); + CHKERRQ(ierr); } else { output.write("\tUsing BDF method\n"); - ierr = TSSundialsSetType(ts, SUNDIALS_BDF);CHKERRQ(ierr); + ierr = TSSundialsSetType(ts, SUNDIALS_BDF); + CHKERRQ(ierr); } #endif // Initial time and timestep - ierr = TSSetTime(ts, simtime); CHKERRQ(ierr); - ierr = TSSetTimeStep(ts, start_timestep); CHKERRQ(ierr); + ierr = TSSetTime(ts, simtime); + CHKERRQ(ierr); + ierr = TSSetTimeStep(ts, start_timestep); + CHKERRQ(ierr); next_output = simtime; // Total number of steps @@ -203,185 +233,254 @@ int PetscSolver::init() { output.write("\tSet total_steps {:d}, tfinal {:g}, simtime {:g}\n", total_steps, tfinal, simtime); -#if PETSC_VERSION_GE(3,8,0) +#if PETSC_VERSION_GE(3, 8, 0) ierr = TSSetMaxSteps(ts, total_steps); CHKERRQ(ierr); - ierr = TSSetMaxTime(ts, tfinal); CHKERRQ(ierr); + ierr = TSSetMaxTime(ts, tfinal); + CHKERRQ(ierr); #else ierr = TSSetDuration(ts, total_steps, tfinal); CHKERRQ(ierr); #endif // Set the current solution - ierr = TSSetSolution(ts,u);CHKERRQ(ierr); + ierr = TSSetSolution(ts, u); + CHKERRQ(ierr); // Create RHSJacobian J - SNES snes, psnes; - KSP ksp, nksp; - PC pc, npc; - PCType pctype; - TSType tstype; - PetscBool pcnone=PETSC_TRUE; - - ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); - ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_INTERPOLATE);CHKERRQ(ierr); - -#if PETSC_VERSION_GE(3,7,0) - ierr = PetscOptionsGetBool(PETSC_NULL, PETSC_NULL,"-interpolate",&interpolate,PETSC_NULL);CHKERRQ(ierr); + SNES snes, psnes; + KSP ksp, nksp; + PC pc, npc; + PCType pctype; + TSType tstype; + PetscBool pcnone = PETSC_TRUE; + + ierr = TSGetSNES(ts, &snes); + CHKERRQ(ierr); + ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_INTERPOLATE); + CHKERRQ(ierr); + +#if PETSC_VERSION_GE(3, 7, 0) + ierr = PetscOptionsGetBool(PETSC_NULL, PETSC_NULL, "-interpolate", &interpolate, + PETSC_NULL); + CHKERRQ(ierr); #else - ierr = PetscOptionsGetBool(PETSC_NULL,"-interpolate",&interpolate,PETSC_NULL);CHKERRQ(ierr); + ierr = PetscOptionsGetBool(PETSC_NULL, "-interpolate", &interpolate, PETSC_NULL); + CHKERRQ(ierr); #endif // Check for -output_name to see if user specified a "performance" // run, if they didn't then use the standard monitor function. TODO: // use PetscFList -#if PETSC_VERSION_GE(3,7,0) - ierr = PetscOptionsGetString(PETSC_NULL, PETSC_NULL,"-output_name",this->output_name, sizeof this->output_name,&output_flag);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 7, 0) + ierr = PetscOptionsGetString(PETSC_NULL, PETSC_NULL, "-output_name", this->output_name, + sizeof this->output_name, &output_flag); + CHKERRQ(ierr); #else - ierr = PetscOptionsGetString(PETSC_NULL,"-output_name",this->output_name, sizeof this->output_name,&output_flag);CHKERRQ(ierr); + ierr = PetscOptionsGetString(PETSC_NULL, "-output_name", this->output_name, + sizeof this->output_name, &output_flag); + CHKERRQ(ierr); #endif // If the output_name is not specified then use the standard monitor function - if(output_flag) { - ierr = SNESMonitorSet(snes,PetscSNESMonitor,this,PETSC_NULL);CHKERRQ(ierr); + if (output_flag) { + ierr = SNESMonitorSet(snes, PetscSNESMonitor, this, PETSC_NULL); + CHKERRQ(ierr); } else { - ierr = TSMonitorSet(ts,PetscMonitor,this,PETSC_NULL);CHKERRQ(ierr); + ierr = TSMonitorSet(ts, PetscMonitor, this, PETSC_NULL); + CHKERRQ(ierr); } - ierr = SNESSetTolerances(snes,abstol,reltol,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(ierr); + ierr = SNESSetTolerances(snes, abstol, reltol, PETSC_DEFAULT, PETSC_DEFAULT, + PETSC_DEFAULT); + CHKERRQ(ierr); // Matrix free Jacobian if (use_jacobian and hasJacobian()) { // Use a user-supplied Jacobian function - ierr = MatCreateShell(comm, local_N, local_N, neq, neq, this, &Jmf); CHKERRQ(ierr); - ierr = MatShellSetOperation(Jmf, MATOP_MULT, reinterpret_cast(PhysicsJacobianApply)); CHKERRQ(ierr); - ierr = TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this); CHKERRQ(ierr); + ierr = MatCreateShell(comm, local_N, local_N, neq, neq, this, &Jmf); + CHKERRQ(ierr); + ierr = MatShellSetOperation(Jmf, MATOP_MULT, + reinterpret_cast(PhysicsJacobianApply)); + CHKERRQ(ierr); + ierr = TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this); + CHKERRQ(ierr); } else { // Use finite difference approximation - ierr = MatCreateSNESMF(snes,&Jmf);CHKERRQ(ierr); - ierr = SNESSetJacobian(snes,Jmf,Jmf,MatMFFDComputeJacobian,this);CHKERRQ(ierr); + ierr = MatCreateSNESMF(snes, &Jmf); + CHKERRQ(ierr); + ierr = SNESSetJacobian(snes, Jmf, Jmf, MatMFFDComputeJacobian, this); + CHKERRQ(ierr); } - ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr); + ierr = SNESGetKSP(snes, &ksp); + CHKERRQ(ierr); - ierr = KSPSetTolerances(ksp, reltol, abstol, PETSC_DEFAULT, PETSC_DEFAULT); CHKERRQ(ierr); + ierr = KSPSetTolerances(ksp, reltol, abstol, PETSC_DEFAULT, PETSC_DEFAULT); + CHKERRQ(ierr); - ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); + ierr = KSPGetPC(ksp, &pc); + CHKERRQ(ierr); if (use_precon and hasPreconditioner()) { -#if PETSC_VERSION_GE(3,5,0) - ierr = SNESGetNPC(snes,&psnes);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 5, 0) + ierr = SNESGetNPC(snes, &psnes); + CHKERRQ(ierr); #else - ierr = SNESGetPC(snes,&psnes);CHKERRQ(ierr); + ierr = SNESGetPC(snes, &psnes); + CHKERRQ(ierr); #endif - ierr = SNESGetKSP(psnes,&nksp);CHKERRQ(ierr); - ierr = KSPGetPC(nksp,&npc);CHKERRQ(ierr); - ierr = SNESSetType(psnes,SNESSHELL);CHKERRQ(ierr); - ierr = SNESShellSetSolve(psnes,PhysicsSNESApply);CHKERRQ(ierr); + ierr = SNESGetKSP(psnes, &nksp); + CHKERRQ(ierr); + ierr = KSPGetPC(nksp, &npc); + CHKERRQ(ierr); + ierr = SNESSetType(psnes, SNESSHELL); + CHKERRQ(ierr); + ierr = SNESShellSetSolve(psnes, PhysicsSNESApply); + CHKERRQ(ierr); // Use a user-supplied preconditioner // Tell PETSc we're using a "shell" preconditioner - ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr); + ierr = PCSetType(pc, PCSHELL); + CHKERRQ(ierr); // Set routine for applying preconditioner - ierr = PCShellSetApply(pc,PhysicsPCApply);CHKERRQ(ierr); + ierr = PCShellSetApply(pc, PhysicsPCApply); + CHKERRQ(ierr); // Set context to this solver object - ierr = PCShellSetContext(pc,this);CHKERRQ(ierr); + ierr = PCShellSetContext(pc, this); + CHKERRQ(ierr); // Set name of preconditioner - ierr = PCShellSetName(pc,"PhysicsPreconditioner");CHKERRQ(ierr); + ierr = PCShellSetName(pc, "PhysicsPreconditioner"); + CHKERRQ(ierr); // Need a callback for IJacobian to get shift 'alpha' - ierr = TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this);CHKERRQ(ierr); + ierr = TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this); + CHKERRQ(ierr); // Use right preconditioner - ierr = KSPSetPCSide(ksp, PC_RIGHT);CHKERRQ(ierr); + ierr = KSPSetPCSide(ksp, PC_RIGHT); + CHKERRQ(ierr); } else { // Default to no preconditioner - ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr); + ierr = PCSetType(pc, PCNONE); + CHKERRQ(ierr); } - ierr = TSSetFromOptions(ts);CHKERRQ(ierr); // enable PETSc runtime options + ierr = TSSetFromOptions(ts); + CHKERRQ(ierr); // enable PETSc runtime options - ierr = PCGetType(pc,&pctype);CHKERRQ(ierr); - ierr = TSGetType(ts,&tstype);CHKERRQ(ierr); - output.write("\tTS type {:s}, PC type {:s}\n",tstype,pctype); + ierr = PCGetType(pc, &pctype); + CHKERRQ(ierr); + ierr = TSGetType(ts, &tstype); + CHKERRQ(ierr); + output.write("\tTS type {:s}, PC type {:s}\n", tstype, pctype); - ierr = PetscObjectTypeCompare(reinterpret_cast(pc),PCNONE,&pcnone);CHKERRQ(ierr); + ierr = PetscObjectTypeCompare(reinterpret_cast(pc), PCNONE, &pcnone); + CHKERRQ(ierr); if (pcnone) { - ierr = PetscLogEventEnd(init_event,0,0,0,0);CHKERRQ(ierr); + ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0); + CHKERRQ(ierr); PetscFunctionReturn(0); } - ierr = PetscObjectTypeCompare(reinterpret_cast(pc),PCSHELL,&pcnone);CHKERRQ(ierr); + ierr = PetscObjectTypeCompare(reinterpret_cast(pc), PCSHELL, &pcnone); + CHKERRQ(ierr); if (pcnone) { - ierr = PetscLogEventEnd(init_event,0,0,0,0);CHKERRQ(ierr); + ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0); + CHKERRQ(ierr); PetscFunctionReturn(0); } // Create Jacobian matrix to be used by preconditioner output_info << " Get Jacobian matrix at simtime " << simtime << "\n"; -#if PETSC_VERSION_GE(3,7,0) - ierr = PetscOptionsGetString(PETSC_NULL, PETSC_NULL,"-J_load",load_file,PETSC_MAX_PATH_LEN-1,&J_load);CHKERRQ(ierr); -#else - ierr = PetscOptionsGetString(PETSC_NULL,"-J_load",load_file,PETSC_MAX_PATH_LEN-1,&J_load);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 7, 0) + ierr = PetscOptionsGetString(PETSC_NULL, PETSC_NULL, "-J_load", load_file, + PETSC_MAX_PATH_LEN - 1, &J_load); + CHKERRQ(ierr); +#else + ierr = PetscOptionsGetString(PETSC_NULL, "-J_load", load_file, PETSC_MAX_PATH_LEN - 1, + &J_load); + CHKERRQ(ierr); #endif - if(J_load) { - PetscViewer fd; + if (J_load) { + PetscViewer fd; output_info << " Load Jmat ...local_N " << local_N << " neq " << neq << "\n"; - ierr = PetscViewerBinaryOpen(comm,load_file,FILE_MODE_READ,&fd);CHKERRQ(ierr); - ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr); + ierr = PetscViewerBinaryOpen(comm, load_file, FILE_MODE_READ, &fd); + CHKERRQ(ierr); + ierr = MatCreate(PETSC_COMM_WORLD, &J); + CHKERRQ(ierr); //ierr = MatSetType(J, MATBAIJ);CHKERRQ(ierr); - ierr = MatSetSizes(J,local_N,local_N,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); - ierr = MatSetFromOptions(J);CHKERRQ(ierr); - ierr = MatLoad(J, fd);CHKERRQ(ierr); - ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); + ierr = MatSetSizes(J, local_N, local_N, PETSC_DECIDE, PETSC_DECIDE); + CHKERRQ(ierr); + ierr = MatSetFromOptions(J); + CHKERRQ(ierr); + ierr = MatLoad(J, fd); + CHKERRQ(ierr); + ierr = PetscViewerDestroy(&fd); + CHKERRQ(ierr); } else { // create Jacobian matrix /* number of degrees (variables) at each grid point */ PetscInt dof = n3Dvars(); // Maximum allowable size of stencil in x is the number of guard cells - PetscInt stencil_width_estimate = options->operator[]("stencil_width_estimate").withDefault(bout::globals::mesh->xstart); + PetscInt stencil_width_estimate = options->operator[]("stencil_width_estimate") + .withDefault(bout::globals::mesh->xstart); // This is the stencil in each direction (*2) along each dimension // (*3), plus the point itself. Not sure if this is correct // though, on several levels: // 1. Ignores corner points used in e.g. brackets // 2. Could have different stencil widths in each dimension // 3. FFTs couple every single point together - PetscInt cols = stencil_width_estimate*2*3+1; + PetscInt cols = stencil_width_estimate * 2 * 3 + 1; PetscInt prealloc; // = cols*dof; - ierr = MatCreate(comm,&J);CHKERRQ(ierr); - ierr = MatSetType(J, MATBAIJ);CHKERRQ(ierr); - ierr = MatSetSizes(J,local_N, local_N, neq,neq);CHKERRQ(ierr); - ierr = MatSetFromOptions(J);CHKERRQ(ierr); + ierr = MatCreate(comm, &J); + CHKERRQ(ierr); + ierr = MatSetType(J, MATBAIJ); + CHKERRQ(ierr); + ierr = MatSetSizes(J, local_N, local_N, neq, neq); + CHKERRQ(ierr); + ierr = MatSetFromOptions(J); + CHKERRQ(ierr); // Get nonzero pattern of J - color_none !!! - prealloc = cols*dof*dof; - ierr = MatSeqAIJSetPreallocation(J,prealloc,PETSC_NULL);CHKERRQ(ierr); - ierr = MatMPIAIJSetPreallocation(J,prealloc,PETSC_NULL,prealloc,PETSC_NULL);CHKERRQ(ierr); - - prealloc = cols; // why nonzeros=295900, allocated nonzeros=2816000/12800000 (*dof*dof), number of mallocs used during MatSetValues calls =256? - ierr = MatSeqBAIJSetPreallocation(J,dof,prealloc,PETSC_NULL);CHKERRQ(ierr); - ierr = MatMPIBAIJSetPreallocation(J,dof,prealloc,PETSC_NULL,prealloc,PETSC_NULL);CHKERRQ(ierr); -#if PETSC_VERSION_GE(3,7,0) - ierr = PetscOptionsHasName(PETSC_NULL, PETSC_NULL,"-J_slowfd",&J_slowfd);CHKERRQ(ierr); + prealloc = cols * dof * dof; + ierr = MatSeqAIJSetPreallocation(J, prealloc, PETSC_NULL); + CHKERRQ(ierr); + ierr = MatMPIAIJSetPreallocation(J, prealloc, PETSC_NULL, prealloc, PETSC_NULL); + CHKERRQ(ierr); + + prealloc = + cols; // why nonzeros=295900, allocated nonzeros=2816000/12800000 (*dof*dof), number of mallocs used during MatSetValues calls =256? + ierr = MatSeqBAIJSetPreallocation(J, dof, prealloc, PETSC_NULL); + CHKERRQ(ierr); + ierr = MatMPIBAIJSetPreallocation(J, dof, prealloc, PETSC_NULL, prealloc, PETSC_NULL); + CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 7, 0) + ierr = PetscOptionsHasName(PETSC_NULL, PETSC_NULL, "-J_slowfd", &J_slowfd); + CHKERRQ(ierr); #else - ierr = PetscOptionsHasName(PETSC_NULL,"-J_slowfd",&J_slowfd);CHKERRQ(ierr); + ierr = PetscOptionsHasName(PETSC_NULL, "-J_slowfd", &J_slowfd); + CHKERRQ(ierr); #endif if (J_slowfd) { // create Jacobian matrix by slow fd - ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,PETSC_NULL);CHKERRQ(ierr); + ierr = SNESSetJacobian(snes, J, J, SNESComputeJacobianDefault, PETSC_NULL); + CHKERRQ(ierr); output_info << "SNESComputeJacobian J by slow fd...\n"; -#if PETSC_VERSION_GE(3,5,0) - ierr = TSComputeRHSJacobian(ts,simtime,u,J,J);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 5, 0) + ierr = TSComputeRHSJacobian(ts, simtime, u, J, J); + CHKERRQ(ierr); #else MatStructure flg; - ierr = TSComputeRHSJacobian(ts,simtime,u,&J,&J,&flg);CHKERRQ(ierr); + ierr = TSComputeRHSJacobian(ts, simtime, u, &J, &J, &flg); + CHKERRQ(ierr); #endif output_info << "compute J by slow fd is done.\n"; } else { // get sparse pattern of the Jacobian @@ -394,11 +493,11 @@ int PetscSolver::init() { } // Create coloring context of J to be used during time stepping - + output_info << " Create coloring ...\n"; - + ISColoring iscoloring; -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) MatColoring coloring; MatColoringCreate(Jmf, &coloring); MatColoringSetType(coloring, MATCOLORINGSL); @@ -407,50 +506,70 @@ int PetscSolver::init() { MatColoringApply(coloring, &iscoloring); MatColoringDestroy(&coloring); #else - ierr = MatGetColoring(J,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr); + ierr = MatGetColoring(J, MATCOLORINGSL, &iscoloring); + CHKERRQ(ierr); #endif - ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); - - ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); - ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); - ierr = MatFDColoringSetFunction(matfdcoloring, reinterpret_cast(solver_f), this);CHKERRQ(ierr); - ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); + ierr = MatFDColoringCreate(J, iscoloring, &matfdcoloring); + CHKERRQ(ierr); + + ierr = MatFDColoringSetFromOptions(matfdcoloring); + CHKERRQ(ierr); + ierr = ISColoringDestroy(&iscoloring); + CHKERRQ(ierr); + ierr = MatFDColoringSetFunction(matfdcoloring, + reinterpret_cast(solver_f), this); + CHKERRQ(ierr); + ierr = SNESSetJacobian(snes, J, J, SNESComputeJacobianDefaultColor, matfdcoloring); + CHKERRQ(ierr); // Write J in binary for study - see ~petsc/src/mat/examples/tests/ex124.c -#if PETSC_VERSION_GE(3,7,0) - ierr = PetscOptionsHasName(PETSC_NULL, PETSC_NULL,"-J_write",&J_write);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 7, 0) + ierr = PetscOptionsHasName(PETSC_NULL, PETSC_NULL, "-J_write", &J_write); + CHKERRQ(ierr); #else - ierr = PetscOptionsHasName(PETSC_NULL,"-J_write",&J_write);CHKERRQ(ierr); + ierr = PetscOptionsHasName(PETSC_NULL, "-J_write", &J_write); + CHKERRQ(ierr); #endif - if (J_write){ - PetscViewer viewer; + if (J_write) { + PetscViewer viewer; output_info << "\n[" << rank << "] Test TSComputeRHSJacobian() ...\n"; -#if PETSC_VERSION_GE(3,5,0) - ierr = TSComputeRHSJacobian(ts,simtime,u,J,J);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 5, 0) + ierr = TSComputeRHSJacobian(ts, simtime, u, J, J); + CHKERRQ(ierr); #else MatStructure J_structure; - ierr = TSComputeRHSJacobian(ts,simtime,u,&J,&J,&J_structure);CHKERRQ(ierr); + ierr = TSComputeRHSJacobian(ts, simtime, u, &J, &J, &J_structure); + CHKERRQ(ierr); #endif - ierr = PetscSynchronizedPrintf(comm, "[{:d}] TSComputeRHSJacobian is done\n",rank);CHKERRQ(ierr); + ierr = PetscSynchronizedPrintf(comm, "[{:d}] TSComputeRHSJacobian is done\n", rank); + CHKERRQ(ierr); -#if PETSC_VERSION_GE(3,5,0) - ierr = PetscSynchronizedFlush(comm,PETSC_STDOUT);CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 5, 0) + ierr = PetscSynchronizedFlush(comm, PETSC_STDOUT); + CHKERRQ(ierr); #else - ierr = PetscSynchronizedFlush(comm);CHKERRQ(ierr); + ierr = PetscSynchronizedFlush(comm); + CHKERRQ(ierr); #endif if (J_slowfd) { output_info << "[" << rank << "] writing J in binary to data/Jrhs_dense.dat...\n"; - ierr = PetscViewerBinaryOpen(comm,"data/Jrhs_dense.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); + ierr = PetscViewerBinaryOpen(comm, "data/Jrhs_dense.dat", FILE_MODE_WRITE, &viewer); + CHKERRQ(ierr); } else { output_info << "[" << rank << "] writing J in binary to data/Jrhs_sparse.dat...\n"; - ierr = PetscViewerBinaryOpen(comm,"data/Jrhs_sparse.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); + ierr = + PetscViewerBinaryOpen(comm, "data/Jrhs_sparse.dat", FILE_MODE_WRITE, &viewer); + CHKERRQ(ierr); } - ierr = MatView(J,viewer);CHKERRQ(ierr); - ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); + ierr = MatView(J, viewer); + CHKERRQ(ierr); + ierr = PetscViewerDestroy(&viewer); + CHKERRQ(ierr); } - ierr = PetscLogEventEnd(init_event,0,0,0,0);CHKERRQ(ierr); + ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0); + CHKERRQ(ierr); PetscFunctionReturn(0); } @@ -461,30 +580,35 @@ int PetscSolver::init() { PetscErrorCode PetscSolver::run() { PetscErrorCode ierr; - FILE *fp = nullptr; + FILE* fp = nullptr; // Set when the next call to monitor is desired next_output = simtime + getOutputTimestep(); PetscFunctionBegin; - if(this->output_flag) { + if (this->output_flag) { prev_linear_its = 0; bout_snes_time = bout::globals::mpi->MPI_Wtime(); } - ierr = TSSolve(ts,u);CHKERRQ(ierr); + ierr = TSSolve(ts, u); + CHKERRQ(ierr); // Gawd, everything is a hack - if(this->output_flag) { - ierr = PetscFOpen(PETSC_COMM_WORLD, this->output_name, "w", &fp);CHKERRQ(ierr); - ierr = PetscFPrintf(PETSC_COMM_WORLD, fp, "SNES Iteration, KSP Iterations, Wall Time, Norm\n");CHKERRQ(ierr); - for (const auto &info : snes_list) { + if (this->output_flag) { + ierr = PetscFOpen(PETSC_COMM_WORLD, this->output_name, "w", &fp); + CHKERRQ(ierr); + ierr = PetscFPrintf(PETSC_COMM_WORLD, fp, + "SNES Iteration, KSP Iterations, Wall Time, Norm\n"); + CHKERRQ(ierr); + for (const auto& info : snes_list) { ierr = PetscFPrintf(PETSC_COMM_WORLD, fp, "{:d}, {:d}, {:e}, {:e}\n", info.it, info.linear_its, info.time, info.norm); CHKERRQ(ierr); } - ierr = PetscFClose(PETSC_COMM_WORLD, fp);CHKERRQ(ierr); + ierr = PetscFClose(PETSC_COMM_WORLD, fp); + CHKERRQ(ierr); } PetscFunctionReturn(0); @@ -497,14 +621,14 @@ PetscErrorCode PetscSolver::run() { PetscErrorCode PetscSolver::rhs(TS UNUSED(ts), BoutReal t, Vec udata, Vec dudata) { TRACE("Running RHS: PetscSolver::rhs({:e})", t); - const BoutReal *udata_array; - BoutReal *dudata_array; + const BoutReal* udata_array; + BoutReal* dudata_array; PetscFunctionBegin; // Load state from PETSc VecGetArrayRead(udata, &udata_array); - load_vars(const_cast(udata_array)); + load_vars(const_cast(udata_array)); VecRestoreArrayRead(udata, &udata_array); // Call RHS function @@ -525,10 +649,11 @@ PetscErrorCode PetscSolver::rhs(TS UNUSED(ts), BoutReal t, Vec udata, Vec dudata PetscErrorCode PetscSolver::pre(PC UNUSED(pc), Vec x, Vec y) { TRACE("PetscSolver::pre()"); - BoutReal *data; + BoutReal* data; - if(diagnose) + if (diagnose) { output << "Preconditioning" << endl; + } // Load state VecGetArray(state, &data); @@ -549,7 +674,8 @@ PetscErrorCode PetscSolver::pre(PC UNUSED(pc), Vec x, Vec y) { VecRestoreArray(y, &data); // Petsc's definition of Jacobian differs by a factor from Sundials' - PetscErrorCode ierr = VecScale(y, shift); CHKERRQ(ierr); + PetscErrorCode ierr = VecScale(y, shift); + CHKERRQ(ierr); return 0; } @@ -561,10 +687,11 @@ PetscErrorCode PetscSolver::pre(PC UNUSED(pc), Vec x, Vec y) { PetscErrorCode PetscSolver::jac(Vec x, Vec y) { TRACE("PetscSolver::jac()"); - BoutReal *data; + BoutReal* data; - if(diagnose) + if (diagnose) { output << "Jacobian evaluation\n"; + } // Load state VecGetArray(state, &data); @@ -585,7 +712,8 @@ PetscErrorCode PetscSolver::jac(Vec x, Vec y) { VecRestoreArray(y, &data); // y = a * x - y - PetscErrorCode ierr = VecAXPBY(y, shift, -1.0, x);CHKERRQ(ierr); + PetscErrorCode ierr = VecAXPBY(y, shift, -1.0, x); + CHKERRQ(ierr); return 0; } @@ -594,55 +722,66 @@ PetscErrorCode PetscSolver::jac(Vec x, Vec y) { * Static functions which can be used for PETSc callbacks **************************************************************************/ -PetscErrorCode solver_f(TS ts, BoutReal t, Vec globalin, Vec globalout, void *f_data) { +PetscErrorCode solver_f(TS ts, BoutReal t, Vec globalin, Vec globalout, void* f_data) { PetscFunctionBegin; auto* s = static_cast(f_data); - PetscLogEventBegin(s->solver_event,0,0,0,0); + PetscLogEventBegin(s->solver_event, 0, 0, 0, 0); s->rhs(ts, t, globalin, globalout); - PetscLogEventEnd(s->solver_event,0,0,0,0); + PetscLogEventEnd(s->solver_event, 0, 0, 0, 0); PetscFunctionReturn(0); } /* FormIFunction = Udot - RHSFunction */ -PetscErrorCode solver_if(TS ts, BoutReal t, Vec globalin,Vec globalindot, Vec globalout, void *f_data) { +PetscErrorCode solver_if(TS ts, BoutReal t, Vec globalin, Vec globalindot, Vec globalout, + void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = solver_f(ts, t, globalin, globalout, f_data); CHKERRQ(ierr); + ierr = solver_f(ts, t, globalin, globalout, f_data); + CHKERRQ(ierr); - ierr = VecAYPX(globalout,-1.0,globalindot);CHKERRQ(ierr); // globalout = globalindot + (-1)globalout + ierr = VecAYPX(globalout, -1.0, globalindot); + CHKERRQ(ierr); // globalout = globalindot + (-1)globalout PetscFunctionReturn(0); } -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) PetscErrorCode solver_rhsjacobian(TS UNUSED(ts), BoutReal UNUSED(t), Vec UNUSED(globalin), - Mat J, Mat Jpre, void *UNUSED(f_data)) { + Mat J, Mat Jpre, void* UNUSED(f_data)) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = MatAssemblyBegin(Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); - ierr = MatAssemblyEnd(Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); - if (J != Jpre){ - ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); - ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); + ierr = MatAssemblyBegin(Jpre, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); + ierr = MatAssemblyEnd(Jpre, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); + if (J != Jpre) { + ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); + ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); } PetscFunctionReturn(0); } #else PetscErrorCode solver_rhsjacobian(MAYBE_UNUSED(TS ts), MAYBE_UNUSED(BoutReal t), - MAYBE_UNUSED(Vec globalin), Mat *J, Mat *Jpre, - MAYBE_UNUSED(MatStructure *str), - MAYBE_UNUSED(void *f_data)) { + MAYBE_UNUSED(Vec globalin), Mat* J, Mat* Jpre, + MAYBE_UNUSED(MatStructure* str), + MAYBE_UNUSED(void* f_data)) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = MatAssemblyBegin(*Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); - ierr = MatAssemblyEnd(*Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); + ierr = MatAssemblyBegin(*Jpre, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); + ierr = MatAssemblyEnd(*Jpre, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); if (*J != *Jpre) { - ierr = MatAssemblyBegin(*J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); - ierr = MatAssemblyEnd(*J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); + ierr = MatAssemblyBegin(*J, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); + ierr = MatAssemblyEnd(*J, MAT_FINAL_ASSEMBLY); + CHKERRQ(ierr); } PetscFunctionReturn(0); } @@ -651,22 +790,24 @@ PetscErrorCode solver_rhsjacobian(MAYBE_UNUSED(TS ts), MAYBE_UNUSED(BoutReal t), /* solver_ijacobian - Compute IJacobian = dF/dU + a dF/dUdot - a dummy matrix used for pc=none */ -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, Vec UNUSED(globalindot), - PetscReal a, Mat J, Mat Jpre, void *f_data) { + PetscReal a, Mat J, Mat Jpre, void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, f_data); CHKERRQ(ierr); + ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, f_data); + CHKERRQ(ierr); ////// Save data for preconditioner auto* solver = static_cast(f_data); - if(solver->diagnose) + if (solver->diagnose) { output << "Saving state, t = " << t << ", a = " << a << endl; + } - solver->shift = a; // Save the shift 'a' - solver->state = globalin; // Save system state + solver->shift = a; // Save the shift 'a' + solver->state = globalin; // Save system state solver->ts_time = t; PetscFunctionReturn(0); @@ -674,17 +815,19 @@ PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, Vec UNUSED(glob #else PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, MAYBE_UNUSED(Vec globalindot), MAYBE_UNUSED(PetscReal a), - Mat *J, Mat *Jpre, MatStructure *str, void *f_data) { + Mat* J, Mat* Jpre, MatStructure* str, void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, str, (void *)f_data);CHKERRQ(ierr); + ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, str, (void*)f_data); + CHKERRQ(ierr); ////// Save data for preconditioner - PetscSolver *solver = (PetscSolver *)f_data; + PetscSolver* solver = (PetscSolver*)f_data; - if (solver->diagnose) + if (solver->diagnose) { output << "Saving state, t = " << t << ", a = " << a << endl; + } solver->shift = a; // Save the shift 'a' solver->state = globalin; // Save system state @@ -697,23 +840,27 @@ PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, /* solver_ijacobianfd - Compute IJacobian = dF/dU + a dF/dUdot using finite deference - not implemented yet */ -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) PetscErrorCode solver_ijacobianfd(TS ts, BoutReal t, Vec globalin, - Vec UNUSED(globalindot), PetscReal UNUSED(a), Mat J, Mat Jpre, - void *f_data) { + Vec UNUSED(globalindot), PetscReal UNUSED(a), Mat J, + Mat Jpre, void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, f_data); CHKERRQ(ierr); + ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, f_data); + CHKERRQ(ierr); //*Jpre + a PetscFunctionReturn(0); } #else -PetscErrorCode solver_ijacobianfd(TS ts,BoutReal t,Vec globalin,Vec globalindot,PetscReal a,Mat *J,Mat *Jpre,MatStructure *str,void *f_data) { +PetscErrorCode solver_ijacobianfd(TS ts, BoutReal t, Vec globalin, Vec globalindot, + PetscReal a, Mat* J, Mat* Jpre, MatStructure* str, + void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; - ierr = solver_rhsjacobian(ts,t,globalin,J,Jpre,str,(void *)f_data);CHKERRQ(ierr); + ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, str, (void*)f_data); + CHKERRQ(ierr); //*Jpre + a PetscFunctionReturn(0); } @@ -722,91 +869,118 @@ PetscErrorCode solver_ijacobianfd(TS ts,BoutReal t,Vec globalin,Vec globalindot, PetscErrorCode PhysicsSNESApply(SNES snes, Vec x) { PetscErrorCode ierr; - Vec F,Fout; - PetscReal fnorm = 0., foutnorm = 0., dot=0.; + Vec F, Fout; + PetscReal fnorm = 0., foutnorm = 0., dot = 0.; KSP ksp; PC pc; - Mat A,B; + Mat A, B; PetscFunctionBegin; - ierr = SNESGetJacobian(snes, &A, &B, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr); -#if PETSC_VERSION_GE(3,5,0) - ierr = SNESComputeJacobian(snes, x, A, B);CHKERRQ(ierr); + ierr = SNESGetJacobian(snes, &A, &B, PETSC_NULL, PETSC_NULL); + CHKERRQ(ierr); +#if PETSC_VERSION_GE(3, 5, 0) + ierr = SNESComputeJacobian(snes, x, A, B); + CHKERRQ(ierr); #else MatStructure diff = DIFFERENT_NONZERO_PATTERN; - ierr = SNESComputeJacobian(snes, x, &A, &B, &diff);CHKERRQ(ierr); + ierr = SNESComputeJacobian(snes, x, &A, &B, &diff); + CHKERRQ(ierr); #endif - ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); - ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); - ierr = SNESGetFunction(snes,&F,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr); - ierr = SNESComputeFunction(snes, x, F);CHKERRQ(ierr); - ierr = SNESGetSolutionUpdate(snes, &Fout);CHKERRQ(ierr); - - ierr = PCApply(pc,F,Fout);CHKERRQ(ierr); - ierr = VecNorm(Fout, NORM_2, &foutnorm);CHKERRQ(ierr); - ierr = VecAXPY(x, -1., Fout);CHKERRQ(ierr); - ierr = SNESComputeFunction(snes, x, F);CHKERRQ(ierr); - ierr = VecNorm(F,NORM_2,&fnorm);CHKERRQ(ierr); - ierr = VecDot(F,Fout,&dot);CHKERRQ(ierr); + ierr = SNESGetKSP(snes, &ksp); + CHKERRQ(ierr); + ierr = KSPGetPC(ksp, &pc); + CHKERRQ(ierr); + ierr = SNESGetFunction(snes, &F, PETSC_NULL, PETSC_NULL); + CHKERRQ(ierr); + ierr = SNESComputeFunction(snes, x, F); + CHKERRQ(ierr); + ierr = SNESGetSolutionUpdate(snes, &Fout); + CHKERRQ(ierr); + + ierr = PCApply(pc, F, Fout); + CHKERRQ(ierr); + ierr = VecNorm(Fout, NORM_2, &foutnorm); + CHKERRQ(ierr); + ierr = VecAXPY(x, -1., Fout); + CHKERRQ(ierr); + ierr = SNESComputeFunction(snes, x, F); + CHKERRQ(ierr); + ierr = VecNorm(F, NORM_2, &fnorm); + CHKERRQ(ierr); + ierr = VecDot(F, Fout, &dot); + CHKERRQ(ierr); output_info << " (Debug) function norm: " << fnorm << ", P(f) norm " << foutnorm << ", F \\cdot Fout " << dot << " "; -#if PETSC_VERSION_GE(3,5,0) +#if PETSC_VERSION_GE(3, 5, 0) Vec func; - ierr = SNESGetFunction(snes,&func,PETSC_NULL,PETSC_NULL); CHKERRQ(ierr); - ierr = VecNorm(func,NORM_2,&fnorm); CHKERRQ(ierr); + ierr = SNESGetFunction(snes, &func, PETSC_NULL, PETSC_NULL); + CHKERRQ(ierr); + ierr = VecNorm(func, NORM_2, &fnorm); + CHKERRQ(ierr); #else - ierr = SNESSetFunctionNorm(snes, fnorm);CHKERRQ(ierr); + ierr = SNESSetFunctionNorm(snes, fnorm); + CHKERRQ(ierr); #endif - ierr = SNESMonitor(snes,0,fnorm);CHKERRQ(ierr); + ierr = SNESMonitor(snes, 0, fnorm); + CHKERRQ(ierr); PetscFunctionReturn(0); } -PetscErrorCode PhysicsPCApply(PC pc,Vec x,Vec y) { +PetscErrorCode PhysicsPCApply(PC pc, Vec x, Vec y) { int ierr; // Get the context - PetscSolver *s; - ierr = PCShellGetContext(pc, reinterpret_cast(&s)); CHKERRQ(ierr); + PetscSolver* s; + ierr = PCShellGetContext(pc, reinterpret_cast(&s)); + CHKERRQ(ierr); PetscFunctionReturn(s->pre(pc, x, y)); } PetscErrorCode PhysicsJacobianApply(Mat J, Vec x, Vec y) { // Get the context - PetscSolver *s; - int ierr = MatShellGetContext(J, reinterpret_cast(&s)); CHKERRQ(ierr); + PetscSolver* s; + int ierr = MatShellGetContext(J, reinterpret_cast(&s)); + CHKERRQ(ierr); PetscFunctionReturn(s->jac(x, y)); } -PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, void *ctx) { +PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, void* ctx) { PetscErrorCode ierr; auto* s = static_cast(ctx); PetscReal tfinal, dt; Vec interpolatedX; - const PetscScalar *x; + const PetscScalar* x; static int i = 0; PetscFunctionBegin; - ierr = TSGetTimeStep(ts, &dt);CHKERRQ(ierr); + ierr = TSGetTimeStep(ts, &dt); + CHKERRQ(ierr); #if PETSC_VERSION_GE(3, 8, 0) - ierr = TSGetMaxTime(ts, &tfinal); CHKERRQ(ierr); + ierr = TSGetMaxTime(ts, &tfinal); + CHKERRQ(ierr); #else - ierr = TSGetDuration(ts, PETSC_NULL, &tfinal);CHKERRQ(ierr); + ierr = TSGetDuration(ts, PETSC_NULL, &tfinal); + CHKERRQ(ierr); #endif /* Duplicate the solution vector X into a work vector */ - ierr = VecDuplicate(X,&interpolatedX);CHKERRQ(ierr); + ierr = VecDuplicate(X, &interpolatedX); + CHKERRQ(ierr); while (s->next_output <= t && s->next_output <= tfinal) { - if (s->interpolate){ - ierr = TSInterpolate(ts,s->next_output,interpolatedX);CHKERRQ(ierr); + if (s->interpolate) { + ierr = TSInterpolate(ts, s->next_output, interpolatedX); + CHKERRQ(ierr); } /* Place the interpolated values into the global variables */ - ierr = VecGetArrayRead(interpolatedX,&x);CHKERRQ(ierr); - s->load_vars(const_cast(x)); - ierr = VecRestoreArrayRead(interpolatedX,&x);CHKERRQ(ierr); + ierr = VecGetArrayRead(interpolatedX, &x); + CHKERRQ(ierr); + s->load_vars(const_cast(x)); + ierr = VecRestoreArrayRead(interpolatedX, &x); + CHKERRQ(ierr); if (s->call_monitors(simtime, i++, s->getNumberOutputSteps())) { PetscFunctionReturn(1); @@ -817,28 +991,31 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo } /* Done with vector, so destroy it */ - ierr = VecDestroy(&interpolatedX);CHKERRQ(ierr); + ierr = VecDestroy(&interpolatedX); + CHKERRQ(ierr); PetscFunctionReturn(0); } -PetscErrorCode PetscSNESMonitor(SNES snes, PetscInt its, PetscReal norm, void *ctx) -{ +PetscErrorCode PetscSNESMonitor(SNES snes, PetscInt its, PetscReal norm, void* ctx) { PetscErrorCode ierr; - PetscInt linear_its=0; + PetscInt linear_its = 0; BoutReal tmp = .0; snes_info row; - auto *s = static_cast(ctx); + auto* s = static_cast(ctx); PetscFunctionBegin; - if(!its) s->prev_linear_its = 0; - ierr = SNESGetLinearSolveIterations(snes, &linear_its);CHKERRQ(ierr); + if (!its) { + s->prev_linear_its = 0; + } + ierr = SNESGetLinearSolveIterations(snes, &linear_its); + CHKERRQ(ierr); tmp = bout::globals::mpi->MPI_Wtime(); row.it = its; - s->prev_linear_its = row.linear_its = linear_its-s->prev_linear_its; - row.time = tmp-s->bout_snes_time; + s->prev_linear_its = row.linear_its = linear_its - s->prev_linear_its; + row.time = tmp - s->bout_snes_time; row.norm = norm; s->snes_list.push_back(row); diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx index 25e11541a2..cbae641f9a 100644 --- a/src/solver/impls/petsc/petsc.hxx +++ b/src/solver/impls/petsc/petsc.hxx @@ -33,18 +33,18 @@ #if not BOUT_HAS_PETSC namespace { -RegisterUnavailableSolver registerunavailablepetsc("petsc", - "BOUT++ was not configured with PETSc"); +RegisterUnavailableSolver + registerunavailablepetsc("petsc", "BOUT++ was not configured with PETSc"); } #else class PetscSolver; -#include -#include -#include -#include +#include +#include +#include +#include #include // PETSc creates macros for MPI calls, which interfere with the MpiWrapper class @@ -66,17 +66,17 @@ using rhsfunc = int (*)(BoutReal); extern BoutReal simtime; /// Monitor function called on every internal timestep -extern PetscErrorCode PetscMonitor(TS, PetscInt, PetscReal, Vec, void *ctx); +extern PetscErrorCode PetscMonitor(TS, PetscInt, PetscReal, Vec, void* ctx); /// Monitor function for SNES -extern PetscErrorCode PetscSNESMonitor(SNES, PetscInt, PetscReal, void *ctx); +extern PetscErrorCode PetscSNESMonitor(SNES, PetscInt, PetscReal, void* ctx); /// Compute IJacobian = dF/dU + a dF/dUdot - a dummy matrix used for pc=none #if PETSC_VERSION_GE(3, 5, 0) extern PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat, - void *); + void*); #else -extern PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat *, Mat *, - MatStructure *, void *); +extern PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat*, Mat*, + MatStructure*, void*); #endif /// Data for SNES @@ -89,7 +89,7 @@ struct snes_info { class PetscSolver : public Solver { public: - PetscSolver(Options *opts = nullptr); + PetscSolver(Options* opts = nullptr); ~PetscSolver(); int init() override; @@ -105,14 +105,14 @@ public: PetscErrorCode jac(Vec x, Vec y); // Call back functions that need to access internal state - friend PetscErrorCode PetscMonitor(TS, PetscInt, PetscReal, Vec, void *ctx); - friend PetscErrorCode PetscSNESMonitor(SNES, PetscInt, PetscReal, void *ctx); + friend PetscErrorCode PetscMonitor(TS, PetscInt, PetscReal, Vec, void* ctx); + friend PetscErrorCode PetscSNESMonitor(SNES, PetscInt, PetscReal, void* ctx); #if PETSC_VERSION_GE(3, 5, 0) friend PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat, - void *); + void*); #else - friend PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat *, Mat *, - MatStructure *, void *); + friend PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat*, Mat*, + MatStructure*, void*); #endif PetscLogEvent solver_event, loop_event, init_event; diff --git a/src/solver/impls/power/power.cxx b/src/solver/impls/power/power.cxx index 39eb3c049c..f8a4e27b32 100644 --- a/src/solver/impls/power/power.cxx +++ b/src/solver/impls/power/power.cxx @@ -3,12 +3,12 @@ #include "power.hxx" #include -#include -#include +#include +#include #include -#include +#include PowerSolver::PowerSolver(Options* opts) : Solver(opts), @@ -22,21 +22,21 @@ int PowerSolver::init() { // Calculate number of variables nlocal = getLocalN(); - + // Get total problem size if (bout::globals::mpi->MPI_Allreduce(&nlocal, &nglobal, 1, MPI_INT, MPI_SUM, BoutComm::get())) { throw BoutException("MPI_Allreduce failed in EulerSolver::init"); } - - output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", - n3Dvars(), n2Dvars(), nglobal, nlocal); - + + output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(), + n2Dvars(), nglobal, nlocal); + // Allocate memory f0.reallocate(nlocal); eigenvalue = 0.0; - + // Put starting values into f0 save_vars(std::begin(f0)); @@ -84,11 +84,12 @@ void PowerSolver::outputVars(Options& output_options, bool save_repeat) { output_options["eigenvalue"].assignRepeat(eigenvalue, "t", save_repeat, "Solver"); } -BoutReal PowerSolver::norm(Array &state) { +BoutReal PowerSolver::norm(Array& state) { BoutReal total = 0.0, result; - - for(int i=0;i(nglobal); @@ -98,7 +99,8 @@ BoutReal PowerSolver::norm(Array &state) { return sqrt(result); } -void PowerSolver::divide(Array &in, BoutReal value) { - for(int i=0;i& in, BoutReal value) { + for (int i = 0; i < nlocal; i++) { in[i] /= value; + } } diff --git a/src/solver/impls/power/power.hxx b/src/solver/impls/power/power.hxx index 75e0967de6..a9ec754f73 100644 --- a/src/solver/impls/power/power.hxx +++ b/src/solver/impls/power/power.hxx @@ -29,8 +29,8 @@ class PowerSolver; #ifndef __POWER_SOLVER_H__ #define __POWER_SOLVER_H__ -#include #include +#include namespace { RegisterSolver registersolverpower("power"); @@ -61,4 +61,3 @@ private: }; #endif // __KARNIADAKIS_SOLVER_H__ - diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx index e9ad3bd171..78b21c796f 100644 --- a/src/solver/impls/pvode/pvode.cxx +++ b/src/solver/impls/pvode/pvode.cxx @@ -30,23 +30,23 @@ #if BOUT_HAS_PVODE #include -#include -#include -#include #include -#include +#include +#include +#include +#include -#include "unused.hxx" +#include "bout/unused.hxx" -#include // contains the enum for types of preconditioning -#include // use CVSPGMR linear solver each internal step -#include // band preconditioner function prototypes +#include // use CVSPGMR linear solver each internal step +#include // contains the enum for types of preconditioning +#include // band preconditioner function prototypes using namespace pvode; -void solver_f(integer N, BoutReal t, N_Vector u, N_Vector udot, void *f_data); -void solver_gloc(integer N, BoutReal t, BoutReal* u, BoutReal* udot, void *f_data); -void solver_cfn(integer N, BoutReal t, N_Vector u, void *f_data); +void solver_f(integer N, BoutReal t, N_Vector u, N_Vector udot, void* f_data); +void solver_gloc(integer N, BoutReal t, BoutReal* u, BoutReal* udot, void* f_data); +void solver_cfn(integer N, BoutReal t, N_Vector u, void* f_data); const BoutReal ZERO = 0.0; @@ -70,9 +70,9 @@ PvodeSolver::PvodeSolver(Options* opts) } PvodeSolver::~PvodeSolver() { - if(pvode_initialised) { + if (pvode_initialised) { // Free CVODE memory - + N_VFree(u); PVBBDFree(pdata); CVodeFree(cvode_mem); @@ -104,22 +104,23 @@ int PvodeSolver::init() { int local_N = getLocalN(); - if(local_N == 0) { + if (local_N == 0) { throw BoutException("No local evolving variables"); } - + // Get total problem size int neq; if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM, BoutComm::get())) { throw BoutException("\tERROR: MPI_Allreduce failed!\n"); } - - output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", - n3d, n2d, neq, local_N); + + output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3d, n2d, + neq, local_N); // Set machEnv block - machEnv = static_cast(PVecInitMPI(BoutComm::get(), local_N, neq, pargc, pargv)); + machEnv = + static_cast(PVecInitMPI(BoutComm::get(), local_N, neq, pargc, pargv)); if (machEnv == nullptr) { throw BoutException("\tError: PVecInitMPI failed\n"); @@ -147,8 +148,8 @@ int PvodeSolver::init() { options->get("mukeep", mukeep, 0); options->get("mlkeep", mlkeep, 0); - pdata = PVBBDAlloc(local_N, mudq, mldq, mukeep, mlkeep, ZERO, - solver_gloc, solver_cfn, static_cast(this)); + pdata = PVBBDAlloc(local_N, mudq, mldq, mukeep, mlkeep, ZERO, solver_gloc, solver_cfn, + static_cast(this)); if (pdata == nullptr) { throw BoutException("\tError: PVBBDAlloc failed.\n"); @@ -157,9 +158,9 @@ int PvodeSolver::init() { ////////// SAVE DATA TO CVODE /////////// // Set pointer to data array in vector u. - BoutReal *udata = N_VDATA(u); + BoutReal* udata = N_VDATA(u); save_vars(udata); - + /* Call CVodeMalloc to initialize CVODE: neq is the problem size = number of equations @@ -208,8 +209,8 @@ int PvodeSolver::init() { // PvodeSolver is now initialised fully pvode_initialised = true; - - return(0); + + return (0); } /************************************************************************** @@ -218,9 +219,10 @@ int PvodeSolver::init() { int PvodeSolver::run() { TRACE("PvodeSolver::run()"); - - if(!pvode_initialised) + + if (!pvode_initialised) { throw BoutException("PvodeSolver not initialised\n"); + } for (int i = 0; i < getNumberOutputSteps(); i++) { @@ -229,13 +231,13 @@ int PvodeSolver::run() { iteration++; /// Check if the run succeeded - if(simtime < 0.0) { + if (simtime < 0.0) { // Step failed output.write("Timestep failed. Aborting\n"); - + throw BoutException("PVODE timestep failed\n"); } - + /// Call the monitor function if (call_monitors(simtime, i, getNumberOutputSteps())) { @@ -250,30 +252,31 @@ int PvodeSolver::run() { BoutReal PvodeSolver::run(BoutReal tout) { TRACE("Running solver: solver::run({})", tout); - BoutReal *udata; - + BoutReal* udata; + // Set pointer to data array in vector u. udata = N_VDATA(u); // Run CVODE int flag; - if(!monitor_timestep) { + if (!monitor_timestep) { // Run in normal mode flag = CVode(cvode_mem, tout, u, &simtime, NORMAL); - }else { + } else { // Run in single step mode, to call timestep monitors BoutReal internal_time = static_cast(cvode_mem)->cv_tn; //CvodeGetCurrentTime(cvode_mem, &internal_time); - - while(internal_time < tout) { + + while (internal_time < tout) { // Run another step BoutReal last_time = internal_time; flag = CVode(cvode_mem, tout, u, &internal_time, ONE_STEP); - if(flag < 0) { - output_error.write("ERROR CVODE solve failed at t = {:e}, flag = {:d}\n", internal_time, flag); + if (flag < 0) { + output_error.write("ERROR CVODE solve failed at t = {:e}, flag = {:d}\n", + internal_time, flag); return -1.0; } - + // Call timestep monitor call_timestep_monitors(internal_time, internal_time - last_time); } @@ -284,14 +287,14 @@ BoutReal PvodeSolver::run(BoutReal tout) { // Copy variables load_vars(udata); - + // Call rhs function to get extra variables at this time run_rhs(simtime); // Check return flag - if(flag != SUCCESS) { + if (flag != SUCCESS) { output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag); - return(-1.0); + return (-1.0); } return simtime; @@ -301,7 +304,7 @@ BoutReal PvodeSolver::run(BoutReal tout) { * RHS function **************************************************************************/ -void PvodeSolver::rhs(int UNUSED(N), BoutReal t, BoutReal *udata, BoutReal *dudata) { +void PvodeSolver::rhs(int UNUSED(N), BoutReal t, BoutReal* udata, BoutReal* dudata) { TRACE("Running RHS: PvodeSolver::rhs({})", t); // Get current timestep @@ -317,7 +320,7 @@ void PvodeSolver::rhs(int UNUSED(N), BoutReal t, BoutReal *udata, BoutReal *duda save_derivs(dudata); } -void PvodeSolver::gloc(int UNUSED(N), BoutReal t, BoutReal *udata, BoutReal *dudata) { +void PvodeSolver::gloc(int UNUSED(N), BoutReal t, BoutReal* udata, BoutReal* dudata) { TRACE("Running RHS: PvodeSolver::gloc({})", t); Timer timer("rhs"); @@ -336,31 +339,31 @@ void PvodeSolver::gloc(int UNUSED(N), BoutReal t, BoutReal *udata, BoutReal *dud * CVODE rhs function **************************************************************************/ -void solver_f(integer N, BoutReal t, N_Vector u, N_Vector udot, void *f_data) { +void solver_f(integer N, BoutReal t, N_Vector u, N_Vector udot, void* f_data) { BoutReal *udata, *dudata; - PvodeSolver *s; + PvodeSolver* s; udata = N_VDATA(u); dudata = N_VDATA(udot); - s = static_cast(f_data); + s = static_cast(f_data); s->rhs(N, t, udata, dudata); } // Preconditioner RHS -void solver_gloc(integer N, BoutReal t, BoutReal *u, BoutReal *udot, void *f_data) { - PvodeSolver *s; +void solver_gloc(integer N, BoutReal t, BoutReal* u, BoutReal* udot, void* f_data) { + PvodeSolver* s; - s = static_cast(f_data); + s = static_cast(f_data); s->gloc(N, t, u, udot); } // Preconditioner communication function void solver_cfn(integer UNUSED(N), BoutReal UNUSED(t), N_Vector UNUSED(u), - void *UNUSED(f_data)) { + void* UNUSED(f_data)) { // doesn't do anything at the moment } -#endif +#endif diff --git a/src/solver/impls/pvode/pvode.hxx b/src/solver/impls/pvode/pvode.hxx index 4997ed030c..dbe1b9aa50 100644 --- a/src/solver/impls/pvode/pvode.hxx +++ b/src/solver/impls/pvode/pvode.hxx @@ -34,11 +34,11 @@ class PvodeSolver; #define __PVODE_SOLVER_H__ #include -#include +#include +#include // main CVODE header file #include -#include // main CVODE header file -#include // band preconditioner function prototypes +#include // band preconditioner function prototypes namespace { RegisterSolver registersolverpvode("pvode"); diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.cxx b/src/solver/impls/rk3-ssp/rk3-ssp.cxx index 1501ceae7b..e0cd7f6bc1 100644 --- a/src/solver/impls/rk3-ssp/rk3-ssp.cxx +++ b/src/solver/impls/rk3-ssp/rk3-ssp.cxx @@ -1,14 +1,14 @@ #include "rk3-ssp.hxx" -#include -#include -#include -#include #include +#include +#include #include +#include +#include -#include +#include RK3SSP::RK3SSP(Options* opt) : Solver(opt), max_timestep((*options)["max_timestep"] @@ -20,9 +20,10 @@ RK3SSP::RK3SSP(Options* opt) .withDefault(500)) {} void RK3SSP::setMaxTimestep(BoutReal dt) { - if(dt > timestep) + if (dt > timestep) { return; // Already less than this - + } + timestep = dt; // Won't be used this time, but next } @@ -34,7 +35,7 @@ int RK3SSP::init() { // Calculate number of variables nlocal = getLocalN(); - + // Get total problem size int ntmp; if (bout::globals::mpi->MPI_Allreduce(&nlocal, &ntmp, 1, MPI_INT, MPI_SUM, @@ -42,10 +43,10 @@ int RK3SSP::init() { throw BoutException("MPI_Allreduce failed!"); } neq = ntmp; - - output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", - n3Dvars(), n2Dvars(), neq, nlocal); - + + output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(), + n2Dvars(), neq, nlocal); + // Allocate memory f.reallocate(nlocal); @@ -102,30 +103,33 @@ int RK3SSP::run() { return 0; } -void RK3SSP::take_step(BoutReal curtime, BoutReal dt, Array &start, - Array &result) { +void RK3SSP::take_step(BoutReal curtime, BoutReal dt, Array& start, + Array& result) { load_vars(std::begin(start)); run_rhs(curtime); save_derivs(std::begin(L)); BOUT_OMP(parallel for) - for(int i=0;i -#include +#include namespace { RegisterSolver registersolverrk3ssp("rk3ssp"); diff --git a/src/solver/impls/rk4/rk4.cxx b/src/solver/impls/rk4/rk4.cxx index ed013b9503..1c7c6f0105 100644 --- a/src/solver/impls/rk4/rk4.cxx +++ b/src/solver/impls/rk4/rk4.cxx @@ -1,15 +1,15 @@ #include "rk4.hxx" -#include -#include -#include -#include #include +#include +#include +#include +#include #include -#include +#include RK4Solver::RK4Solver(Options* opts) : Solver(opts), atol((*options)["atol"].doc("Absolute tolerance").withDefault(1.e-5)), @@ -28,11 +28,13 @@ RK4Solver::RK4Solver(Options* opts) } void RK4Solver::setMaxTimestep(BoutReal dt) { - if (dt > timestep) + if (dt > timestep) { return; // Already less than this - - if (adaptive) + } + + if (adaptive) { timestep = dt; // Won't be used this time, but next + } } int RK4Solver::init() { @@ -44,7 +46,7 @@ int RK4Solver::init() { // Calculate number of variables nlocal = getLocalN(); - + // Get total problem size int ntmp; if (bout::globals::mpi->MPI_Allreduce(&nlocal, &ntmp, 1, MPI_INT, MPI_SUM, @@ -52,10 +54,10 @@ int RK4Solver::init() { throw BoutException("MPI_Allreduce failed!"); } neq = ntmp; - - output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", - n3Dvars(), n2Dvars(), neq, nlocal); - + + output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(), + n2Dvars(), neq, nlocal); + // Allocate memory f0.reallocate(nlocal); f1.reallocate(nlocal); @@ -85,29 +87,29 @@ int RK4Solver::run() { int internal_steps = 0; do { // Take a single time step - + do { dt = timestep; running = true; - if((simtime + dt) >= target) { - dt = target - simtime; // Make sure the last timestep is on the output + if ((simtime + dt) >= target) { + dt = target - simtime; // Make sure the last timestep is on the output running = false; } - if(adaptive) { + if (adaptive) { // Take two half-steps - take_step(simtime, 0.5*dt, f0, f1); - take_step(simtime + 0.5*dt, 0.5*dt, f1, f2); - + take_step(simtime, 0.5 * dt, f0, f1); + take_step(simtime + 0.5 * dt, 0.5 * dt, f1, f2); + // Take a full step take_step(simtime, dt, f0, f1); - + // Check accuracy BoutReal local_err = 0.; BOUT_OMP(parallel for reduction(+: local_err) ) - for(int i=0;iMPI_Allreduce(&local_err, &err, 1, MPI_DOUBLE, MPI_SUM, @@ -118,40 +120,42 @@ int RK4Solver::run() { err /= static_cast(neq); internal_steps++; - if(internal_steps > mxstep) + if (internal_steps > mxstep) { throw BoutException("ERROR: MXSTEP exceeded. timestep = {:e}, err={:e}\n", timestep, err); + } - if((err > rtol) || (err < 0.1*rtol)) { + if ((err > rtol) || (err < 0.1 * rtol)) { // Need to change timestep. Error ~ dt^5 - timestep /= pow(err / (0.5*rtol), 0.2); - - if((max_timestep > 0) && (timestep > max_timestep)) + timestep /= pow(err / (0.5 * rtol), 0.2); + + if ((max_timestep > 0) && (timestep > max_timestep)) { timestep = max_timestep; + } } - if(err < rtol) { + if (err < rtol) { break; // Acceptable accuracy } - }else { + } else { // No adaptive timestepping take_step(simtime, dt, f0, f2); break; } - }while(true); - + } while (true); + // Taken a step, swap buffers swap(f2, f0); simtime += dt; - + call_timestep_monitors(simtime, dt); - }while(running); + } while (running); load_vars(std::begin(f0)); // Put result into variables // Call rhs function to get extra variables at this time run_rhs(simtime); - + iteration++; // Advance iteration number - + /// Call the monitor function if (call_monitors(simtime, s, getNumberOutputSteps())) { @@ -162,48 +166,53 @@ int RK4Solver::run() { return 0; } -void RK4Solver::resetInternalFields(){ +void RK4Solver::resetInternalFields() { //Zero out history - for(int i=0;i &start, - Array &result) { +void RK4Solver::take_step(BoutReal curtime, BoutReal dt, Array& start, + Array& result) { load_vars(std::begin(start)); run_rhs(curtime); save_derivs(std::begin(k1)); BOUT_OMP(parallel for) - for(int i=0;i -#include +#include namespace { RegisterSolver registersolverrk4("rk4"); diff --git a/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.cxx b/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.cxx index 3bd7c543ee..8e0638a605 100644 --- a/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.cxx +++ b/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.cxx @@ -1,6 +1,6 @@ #include "cashkarp.hxx" -CASHKARPScheme::CASHKARPScheme(Options *options):RKScheme(options){ +CASHKARPScheme::CASHKARPScheme(Options* options) : RKScheme(options) { //Set characteristics of scheme numStages = 6; numOrders = 2; @@ -13,12 +13,12 @@ CASHKARPScheme::CASHKARPScheme(Options *options):RKScheme(options){ timeCoeffs.reallocate(numStages); //Zero out arrays (shouldn't be needed, but do for testing) - for(int i=0;i -#include +#include class CASHKARPScheme : public RKScheme { public: diff --git a/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.cxx b/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.cxx index 68c2bb14a0..5f03eea7d5 100644 --- a/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.cxx +++ b/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.cxx @@ -1,6 +1,6 @@ #include "rk4simple.hxx" -RK4SIMPLEScheme::RK4SIMPLEScheme(Options *options):RKScheme(options){ +RK4SIMPLEScheme::RK4SIMPLEScheme(Options* options) : RKScheme(options) { //Set characteristics of scheme numStages = 11; numOrders = 2; @@ -13,12 +13,12 @@ RK4SIMPLEScheme::RK4SIMPLEScheme(Options *options):RKScheme(options){ timeCoeffs.reallocate(numStages); //Zero out arrays (shouldn't be needed, but do for testing) - for(int i=0;i &start, const BoutReal dt, - Array &resultFollow) { +BoutReal RK4SIMPLEScheme::setOutputStates(const Array& start, const BoutReal dt, + Array& resultFollow) { //return RKScheme::setOutputStates(start,dt,resultFollow); - if(followHighOrder){ - for(int i=0;i -#include +#include -class RK4SIMPLEScheme : public RKScheme{ +class RK4SIMPLEScheme : public RKScheme { public: - RK4SIMPLEScheme(Options *options); + RK4SIMPLEScheme(Options* options); - BoutReal setOutputStates(const Array &start,BoutReal dt, Array &resultFollow); + BoutReal setOutputStates(const Array& start, BoutReal dt, + Array& resultFollow); }; namespace { diff --git a/src/solver/impls/rkgeneric/impls/rkf34/rkf34.cxx b/src/solver/impls/rkgeneric/impls/rkf34/rkf34.cxx index d58c0c6407..a4271834df 100644 --- a/src/solver/impls/rkgeneric/impls/rkf34/rkf34.cxx +++ b/src/solver/impls/rkgeneric/impls/rkf34/rkf34.cxx @@ -7,9 +7,9 @@ RKF34Scheme::RKF34Scheme(Options* options) : RKScheme(options, false) { order = 3; label = "rkf34"; - if(followHighOrder){ + if (followHighOrder) { dtfac = 0.9; - }else{ + } else { dtfac = 0.9; //Could make this different if needed } @@ -19,12 +19,12 @@ RKF34Scheme::RKF34Scheme(Options* options) : RKScheme(options, false) { timeCoeffs.reallocate(numStages); //Zero out arrays (shouldn't be needed, but do for testing) - for(int i=0;i -#include +#include class RKF34Scheme : public RKScheme { public: diff --git a/src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx b/src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx index f32dd7d56a..f69371d7bd 100644 --- a/src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx +++ b/src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx @@ -1,6 +1,6 @@ #include "rkf45.hxx" -RKF45Scheme::RKF45Scheme(Options *options):RKScheme(options){ +RKF45Scheme::RKF45Scheme(Options* options) : RKScheme(options) { //Set characteristics of scheme numStages = 6; numOrders = 2; @@ -13,12 +13,12 @@ RKF45Scheme::RKF45Scheme(Options *options):RKScheme(options){ timeCoeffs.reallocate(numStages); //Zero out arrays (shouldn't be needed, but do for testing) - for(int i=0;i -#include +#include class RKF45Scheme : public RKScheme { public: diff --git a/src/solver/impls/rkgeneric/rkgeneric.cxx b/src/solver/impls/rkgeneric/rkgeneric.cxx index ead547861c..2325b309c5 100644 --- a/src/solver/impls/rkgeneric/rkgeneric.cxx +++ b/src/solver/impls/rkgeneric/rkgeneric.cxx @@ -2,14 +2,14 @@ #include "rkgeneric.hxx" #include -#include -#include -#include -#include +#include +#include +#include +#include #include -#include +#include RKGenericSolver::RKGenericSolver(Options* opts) : Solver(opts), atol((*options)["atol"].doc("Absolute tolerance").withDefault(1.e-5)), @@ -29,11 +29,13 @@ RKGenericSolver::RKGenericSolver(Options* opts) } void RKGenericSolver::setMaxTimestep(BoutReal dt) { - if(dt > timestep) + if (dt > timestep) { return; // Already less than this - - if(adaptive) + } + + if (adaptive) { timestep = dt; // Won't be used this time, but next + } } int RKGenericSolver::init() { @@ -41,11 +43,12 @@ int RKGenericSolver::init() { TRACE("Initialising RKGeneric solver"); Solver::init(); - output << "\n\tRunge-Kutta generic solver with scheme type "<getType()<<"\n"; + output << "\n\tRunge-Kutta generic solver with scheme type " << scheme->getType() + << "\n"; // Calculate number of variables nlocal = getLocalN(); - + // Get total problem size int ntmp; if (bout::globals::mpi->MPI_Allreduce(&nlocal, &ntmp, 1, MPI_INT, MPI_SUM, @@ -53,10 +56,10 @@ int RKGenericSolver::init() { throw BoutException("MPI_Allreduce failed!"); } neq = ntmp; - - output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", - n3Dvars(), n2Dvars(), neq, nlocal); - + + output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(), + n2Dvars(), neq, nlocal); + // Allocate memory f0.reallocate(nlocal); // Input f2.reallocate(nlocal); // Result--follow order @@ -70,13 +73,14 @@ int RKGenericSolver::init() { return 0; } -void RKGenericSolver::resetInternalFields(){ +void RKGenericSolver::resetInternalFields() { //Zero out history BOUT_OMP(parallel for) - for(int i=0;i= target) { - dt = target - simtime; // Make sure the last timestep is on the output + if ((simtime + dt) >= target) { + dt = target - simtime; // Make sure the last timestep is on the output running = false; } - BoutReal err; + BoutReal err; - //Take a step - err = take_step(simtime, dt, f0, f2); + //Take a step + err = take_step(simtime, dt, f0, f2); - //Calculate and check error if adaptive - if(adaptive) { - //Really the following should apply to both adaptive and non-adaptive - //approaches, but the non-adaptive can be determined without needing - //to do any solves so could perhaps be check during init instead. + //Calculate and check error if adaptive + if (adaptive) { + //Really the following should apply to both adaptive and non-adaptive + //approaches, but the non-adaptive can be determined without needing + //to do any solves so could perhaps be check during init instead. internal_steps++; - if(internal_steps > mxstep) + if (internal_steps > mxstep) { throw BoutException("ERROR: MXSTEP exceeded. timestep = {:e}, err={:e}\n", timestep, err); + } + + //Update the time step if required, note we ignore increases to the timestep + //when on the last internal step as here we may have an artificially small dt + if ((err > rtol) || ((err < 0.1 * rtol) && running)) { - //Update the time step if required, note we ignore increases to the timestep - //when on the last internal step as here we may have an artificially small dt - if((err > rtol) || ((err < 0.1*rtol) && running)) { - - //Get new timestep - timestep=scheme->updateTimestep(dt,err); + //Get new timestep + timestep = scheme->updateTimestep(dt, err); - //Limit timestep to specified maximum - if((max_timestep > 0) && (timestep > max_timestep)) + //Limit timestep to specified maximum + if ((max_timestep > 0) && (timestep > max_timestep)) { timestep = max_timestep; + } } - //If accuracy ok then break - if(err < rtol) break; + //If accuracy ok then break + if (err < rtol) { + break; + } - }else { + } else { // No adaptive timestepping so just accept step break; } - }while(true); - + } while (true); + // Taken a step, swap buffers to put result into f0 swap(f2, f0); simtime += dt; @@ -145,7 +153,7 @@ int RKGenericSolver::run() { //Call the per internal timestep monitors call_timestep_monitors(simtime, dt); - }while(running); + } while (running); load_vars(std::begin(f0)); // Put result into variables @@ -163,19 +171,19 @@ int RKGenericSolver::run() { //Returns the evolved state vector along with an error estimate BoutReal RKGenericSolver::take_step(const BoutReal timeIn, const BoutReal dt, - const Array &start, - Array &resultFollow) { + const Array& start, + Array& resultFollow) { //Calculate the intermediate stages - for(int curStage=0;curStagegetStageCount();curStage++){ + for (int curStage = 0; curStage < scheme->getStageCount(); curStage++) { //Use scheme to get this stage's time and state - BoutReal curTime=scheme->setCurTime(timeIn,dt,curStage); + BoutReal curTime = scheme->setCurTime(timeIn, dt, curStage); scheme->setCurState(start, tmpState, curStage, dt); //Get derivs for this stage load_vars(std::begin(tmpState)); run_rhs(curTime); - save_derivs(&(scheme->steps(curStage,0))); + save_derivs(&(scheme->steps(curStage, 0))); } return scheme->setOutputStates(start, dt, resultFollow); diff --git a/src/solver/impls/rkgeneric/rkgeneric.hxx b/src/solver/impls/rkgeneric/rkgeneric.hxx index 4d13eb9614..305f27679b 100644 --- a/src/solver/impls/rkgeneric/rkgeneric.hxx +++ b/src/solver/impls/rkgeneric/rkgeneric.hxx @@ -32,7 +32,7 @@ class RKGenericSolver; #include #include -#include +#include namespace { RegisterSolver registersolverrkgeneric("rkgeneric"); diff --git a/src/solver/impls/rkgeneric/rkscheme.cxx b/src/solver/impls/rkgeneric/rkscheme.cxx index 1218f4851e..812d0d7e4a 100644 --- a/src/solver/impls/rkgeneric/rkscheme.cxx +++ b/src/solver/impls/rkgeneric/rkscheme.cxx @@ -1,16 +1,16 @@ -#include "unused.hxx" +#include "bout/unused.hxx" #include #include -#include +#include #include -#include -#include +#include +#include // Implementations -#include "impls/rkf45/rkf45.hxx" #include "impls/cashkarp/cashkarp.hxx" #include "impls/rk4simple/rk4simple.hxx" #include "impls/rkf34/rkf34.hxx" +#include "impls/rkf45/rkf45.hxx" //////////////////// // PUBLIC @@ -37,8 +37,9 @@ void RKScheme::init(int nlocalIn, int neqIn, bool adaptiveIn, BoutReal atolIn, zeroSteps(); // Allocate array for storing alternative order result - if (adaptive) + if (adaptive) { resultAlt.reallocate(nlocal); // Result--alternative order + } // Will probably only want the following when debugging, but leave it on for now if (diagnose) { @@ -48,47 +49,53 @@ void RKScheme::init(int nlocalIn, int neqIn, bool adaptiveIn, BoutReal atolIn, } //Get the time at given stage -BoutReal RKScheme::setCurTime(const BoutReal timeIn, const BoutReal dt, const int curStage){ - return timeIn+dt*timeCoeffs[curStage]; +BoutReal RKScheme::setCurTime(const BoutReal timeIn, const BoutReal dt, + const int curStage) { + return timeIn + dt * timeCoeffs[curStage]; } //Get the state vector at given stage -void RKScheme::setCurState(const Array &start, Array &out, +void RKScheme::setCurState(const Array& start, Array& out, const int curStage, const BoutReal dt) { //Set the initial stage BOUT_OMP(parallel for) - for(int i=0;i &start, const BoutReal dt, - Array &resultFollow) { +BoutReal RKScheme::setOutputStates(const Array& start, const BoutReal dt, + Array& resultFollow) { //Only really need resultAlt in order to calculate the error, so if not adaptive could avoid it //*and* technically we can write resultFollow-resultAlt in terms of resultCoeffs and steps. int followInd, altInd; - if(followHighOrder){ - followInd=0; altInd=1; - }else{ - followInd=1; altInd=0; + if (followHighOrder) { + followInd = 0; + altInd = 1; + } else { + followInd = 1; + altInd = 0; } //NOTE: It's slightly slower to split construction of output @@ -105,10 +112,10 @@ BoutReal RKScheme::setOutputStates(const Array &start, const BoutReal */ //Get the result - constructOutput(start,dt,followInd,resultFollow); + constructOutput(start, dt, followInd, resultFollow); //If adaptive get the second state - if(adaptive){ + if (adaptive) { constructOutput(start, dt, altInd, resultAlt); } @@ -116,8 +123,8 @@ BoutReal RKScheme::setOutputStates(const Array &start, const BoutReal return getErr(resultFollow, resultAlt); } -BoutReal RKScheme::updateTimestep(const BoutReal dt, const BoutReal err){ - return dtfac*dt*pow(rtol/(2.0*err),1.0/(order+1.0)); +BoutReal RKScheme::updateTimestep(const BoutReal dt, const BoutReal err) { + return dtfac * dt * pow(rtol / (2.0 * err), 1.0 / (order + 1.0)); } //////////////////// @@ -125,11 +132,13 @@ BoutReal RKScheme::updateTimestep(const BoutReal dt, const BoutReal err){ //////////////////// //Estimate the error, given two solutions -BoutReal RKScheme::getErr(Array &solA, Array &solB) { - BoutReal err=0.; +BoutReal RKScheme::getErr(Array& solA, Array& solB) { + BoutReal err = 0.; //If not adaptive don't care about the error - if(!adaptive){return err;} + if (!adaptive) { + return err; + } //Get local part of relative error BoutReal local_err = 0.; @@ -139,7 +148,7 @@ BoutReal RKScheme::getErr(Array &solA, Array &solB) { // is called and hence the nrhs may no longer be exactly // repeatable with this parallelisation. BOUT_OMP(parallel for reduction(+:local_err)) - for(int i=0;i &solA, Array &solB) { return err; } -void RKScheme::constructOutput(const Array &start, const BoutReal dt, - const int index, Array &sol) { +void RKScheme::constructOutput(const Array& start, const BoutReal dt, + const int index, Array& sol) { //Initialise the return data BOUT_OMP(parallel for) - for(int i=0;i &start, const BoutReal dt, +void RKScheme::constructOutputs(const Array& start, const BoutReal dt, const int indexFollow, const int indexAlt, - Array &solFollow, Array &solAlt) { + Array& solFollow, Array& solAlt) { //Initialise the return data BOUT_OMP(parallel for) - for(int i=0;iatol) warn=true; + output << std::setw(10) << timeCoeffs[i] << " | " << std::setw(10) << tmp << endl; + if (std::abs(timeCoeffs[i] - tmp) > atol) { + warn = true; + } } //Optional warning - if(warn){ - output< -#include -#include -#include -#include +#include +#include +#include +#include +#include #include @@ -220,8 +220,7 @@ SlepcSolver::SlepcSolver(Options* options) { if (!selfSolve && !ddtMode) { // Use a sub-section called "advance" - advanceSolver = - SolverFactory::getInstance().create(options->getSection("advance")); + advanceSolver = SolverFactory::getInstance().create(options->getSection("advance")); } } @@ -385,7 +384,8 @@ void SlepcSolver::createShellMat() { &shellMat); // Define the mat_mult operation --> Define what routine returns M.x, where M // is the time advance operator and x are the initial field conditions - MatShellSetOperation(shellMat, MATOP_MULT, reinterpret_cast(&advanceStepWrapper)); + MatShellSetOperation(shellMat, MATOP_MULT, + reinterpret_cast(&advanceStepWrapper)); // The above function callback can cause issues as member functions have a hidden "this" // argument which means if Slepc calls this->advanceStep(Mat,Vec,Vec) this is actually diff --git a/src/solver/impls/slepc/slepc.hxx b/src/solver/impls/slepc/slepc.hxx index 50e92754c3..a837b1b026 100644 --- a/src/solver/impls/slepc/slepc.hxx +++ b/src/solver/impls/slepc/slepc.hxx @@ -33,8 +33,8 @@ #if not BOUT_HAS_SLEPC namespace { -RegisterUnavailableSolver registerunavailableslepc("slepc", - "BOUT++ was not configured with SLEPc"); +RegisterUnavailableSolver + registerunavailableslepc("slepc", "BOUT++ was not configured with SLEPc"); } #else @@ -54,11 +54,11 @@ class SlepcSolver; #undef MPI_Waitall #undef MPI_Waitany -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include #include @@ -76,10 +76,10 @@ RegisterSolver registersolverslepc("slepc"); class SlepcSolver : public Solver { public: - SlepcSolver(Options *options); + SlepcSolver(Options* options); ~SlepcSolver(); - int advanceStep(Mat &matOperator, Vec &inData, Vec &outData); + int advanceStep(Mat& matOperator, Vec& inData, Vec& outData); int compareEigs(PetscScalar ar, PetscScalar ai, PetscScalar br, PetscScalar bi); void monitor(PetscInt its, PetscInt nconv, PetscScalar eigr[], PetscScalar eigi[], PetscReal errest[], PetscInt nest); @@ -98,7 +98,7 @@ public: /// use of additional solver //////////////////////////////////////// - void setModel(PhysicsModel *model) override { // New API + void setModel(PhysicsModel* model) override { // New API Solver::setModel(model); if (!selfSolve) { advanceSolver->setModel(model); @@ -195,8 +195,8 @@ public: int compareState; - void slepcToBout(PetscScalar &reEigIn, PetscScalar &imEigIn, BoutReal &reEigOut, - BoutReal &imEigOut, bool force = false); + void slepcToBout(PetscScalar& reEigIn, PetscScalar& imEigIn, BoutReal& reEigOut, + BoutReal& imEigOut, bool force = false); Mat shellMat; //"Shell" matrix operator private: @@ -206,17 +206,18 @@ private: ST st; // Spectral transform object PetscBool stIsShell; // Is the ST a shell object? - std::unique_ptr advanceSolver{nullptr}; // Pointer to actual solver used to advance fields + std::unique_ptr advanceSolver{ + nullptr}; // Pointer to actual solver used to advance fields - void vecToFields(Vec &inVec); - void fieldsToVec(Vec &outVec); + void vecToFields(Vec& inVec); + void fieldsToVec(Vec& outVec); void createShellMat(); void createEPS(); void analyseResults(); - void boutToSlepc(BoutReal &reEigIn, BoutReal &imEigIn, PetscScalar &reEigOut, - PetscScalar &imEigOut, bool force = false); + void boutToSlepc(BoutReal& reEigIn, BoutReal& imEigIn, PetscScalar& reEigOut, + PetscScalar& imEigOut, bool force = false); SlepcLib slib; // Handles initialize / finalize bool ddtMode; // If true then slepc deals with the ddt operator diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx index 724d84e1c2..69280bd6c2 100644 --- a/src/solver/impls/snes/snes.cxx +++ b/src/solver/impls/snes/snes.cxx @@ -4,16 +4,16 @@ #include "snes.hxx" -#include -#include -#include -#include +#include +#include +#include +#include #include #include #include -#include +#include #include "petscsnes.h" /* diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx index 599b66fe14..f6de892fd6 100644 --- a/src/solver/impls/snes/snes.hxx +++ b/src/solver/impls/snes/snes.hxx @@ -39,7 +39,7 @@ class SNESSolver; #include #include -#include +#include #include #include @@ -85,8 +85,8 @@ public: PetscErrorCode precon(Vec x, Vec f); private: - BoutReal timestep; ///< Internal timestep - BoutReal dt; ///< Current timestep used in snes_function + BoutReal timestep; ///< Internal timestep + BoutReal dt; ///< Current timestep used in snes_function BoutReal dt_min_reset; ///< If dt falls below this, reset solve BoutReal max_timestep; ///< Maximum timestep @@ -98,7 +98,7 @@ private: int maxits; ///< Maximum nonlinear iterations int lower_its, upper_its; ///< Limits on iterations for timestep adjustment - bool diagnose; ///< Output additional diagnostics + bool diagnose; ///< Output additional diagnostics bool diagnose_failures; ///< Print diagnostics on SNES failures int nlocal; ///< Number of variables on local processor diff --git a/src/solver/impls/split-rk/split-rk.cxx b/src/solver/impls/split-rk/split-rk.cxx index aef9c4fc41..6fd21ae832 100644 --- a/src/solver/impls/split-rk/split-rk.cxx +++ b/src/solver/impls/split-rk/split-rk.cxx @@ -42,13 +42,13 @@ int SplitRK::init() { // Calculate number of variables nlocal = getLocalN(); - + // Get total problem size if (bout::globals::mpi->MPI_Allreduce(&nlocal, &neq, 1, MPI_INT, MPI_SUM, BoutComm::get())) { throw BoutException("MPI_Allreduce failed!"); } - + // Allocate memory state.reallocate(nlocal); @@ -57,7 +57,7 @@ int SplitRK::init() { u2.reallocate(nlocal); u3.reallocate(nlocal); dydt.reallocate(nlocal); - + // Put starting values into f save_vars(std::begin(state)); @@ -66,7 +66,7 @@ int SplitRK::init() { state1.reallocate(nlocal); state2.reallocate(nlocal); } - + ASSERT0(adapt_period > 0); int ninternal_steps = static_cast(std::ceil(getOutputTimestep() / timestep)); @@ -74,7 +74,7 @@ int SplitRK::init() { timestep = getOutputTimestep() / ninternal_steps; output.write(_("\tUsing a timestep {:e}\n"), timestep); - + return 0; } @@ -86,28 +86,28 @@ int SplitRK::run() { BoutReal target = simtime + getOutputTimestep(); - BoutReal dt; // The next timestep to take - bool running = true; // Changed to false to break out of inner loop - int internal_steps = 0; // Quit if this exceeds mxstep - + BoutReal dt; // The next timestep to take + bool running = true; // Changed to false to break out of inner loop + int internal_steps = 0; // Quit if this exceeds mxstep + do { // Take a single time step if (adaptive and (internal_steps % adapt_period == 0)) { do { // Keep adapting the timestep until the error is within tolerances - + dt = timestep; running = true; // Reset after maybe adapting timestep if ((simtime + dt) >= target) { - dt = target - simtime; // Make sure the last timestep is on the output - running = false; // Fall out of this inner loop after this step + dt = target - simtime; // Make sure the last timestep is on the output + running = false; // Fall out of this inner loop after this step } - + // Take two half-steps - take_step(simtime, 0.5*dt, state, state1); - take_step(simtime + 0.5*dt, 0.5*dt, state1, state2); - + take_step(simtime, 0.5 * dt, state, state1); + take_step(simtime + 0.5 * dt, 0.5 * dt, state1, state2); + // Take a full step take_step(simtime, dt, state, state1); @@ -115,9 +115,10 @@ int SplitRK::run() { BoutReal local_err = 0.; BOUT_OMP(parallel for reduction(+: local_err) ) for (int i = 0; i < nlocal; i++) { - local_err += fabs(state2[i] - state1[i]) / (fabs(state1[i]) + fabs(state2[i]) + atol); + local_err += + fabs(state2[i] - state1[i]) / (fabs(state1[i]) + fabs(state2[i]) + atol); } - + // Average over all processors BoutReal err; if (bout::globals::mpi->MPI_Allreduce(&local_err, &err, 1, MPI_DOUBLE, MPI_SUM, @@ -126,7 +127,7 @@ int SplitRK::run() { } err /= static_cast(neq); - + internal_steps++; if (internal_steps > mxstep) { throw BoutException("ERROR: MXSTEP exceeded. timestep = {:e}, err={:e}\n", @@ -140,7 +141,7 @@ int SplitRK::run() { if ((err > rtol) || (err < 0.1 * rtol)) { // Need to change timestep. Error ~ dt^2 - BoutReal factor = pow((0.5 * rtol) / err, 1./3); + BoutReal factor = pow((0.5 * rtol) / err, 1. / 3); if (factor > max_timestep_change) { factor = max_timestep_change; @@ -155,12 +156,13 @@ int SplitRK::run() { } if (diagnose) { - output.write("\tAdapting. timestep {:e} (factor {:e}). Max={:e}\n", timestep, factor, max_timestep); + output.write("\tAdapting. timestep {:e} (factor {:e}). Max={:e}\n", + timestep, factor, max_timestep); } } if (err < rtol) { swap(state, state2); // Put result in state - break; // Acceptable accuracy + break; // Acceptable accuracy } } while (true); } else { @@ -169,19 +171,19 @@ int SplitRK::run() { dt = timestep; running = true; // Reset after maybe adapting timestep if ((simtime + dt) >= target) { - dt = target - simtime; // Make sure the last timestep is on the output - running = false; // Fall out of this inner loop after this step + dt = target - simtime; // Make sure the last timestep is on the output + running = false; // Fall out of this inner loop after this step } - + take_step(simtime, timestep, state, state); internal_steps++; } - + simtime += dt; call_timestep_monitors(simtime, timestep); - + } while (running); - + load_vars(std::begin(state)); // Put result into variables // Call rhs function to get extra variables at this time run_rhs(simtime); @@ -199,58 +201,58 @@ int SplitRK::run() { void SplitRK::take_step(BoutReal curtime, BoutReal dt, Array& start, Array& result) { // Half step - take_diffusion_step(curtime, 0.5*dt, start, result); - + take_diffusion_step(curtime, 0.5 * dt, start, result); + // Full step take_advection_step(curtime, dt, result, result); // Half step - take_diffusion_step(curtime + 0.5*dt, 0.5*dt, result, result); + take_diffusion_step(curtime + 0.5 * dt, 0.5 * dt, result, result); } void SplitRK::take_diffusion_step(BoutReal curtime, BoutReal dt, Array& start, Array& result) { - const BoutReal weight = dt * 4./(SQ(nstages) + nstages - 2); - + const BoutReal weight = dt * 4. / (SQ(nstages) + nstages - 2); + load_vars(std::begin(start)); run_diffusive(curtime); - save_derivs(std::begin(dydt)); // dydt = f(y0) + save_derivs(std::begin(dydt)); // dydt = f(y0) // Stage j = 1 // y_m2 = y0 + weight/3.0 * f(y0) -> u2 BOUT_OMP(parallel for) for (int i = 0; i < dydt.size(); i++) { - u2[i] = start[i] + (weight/3.0) * dydt[i]; + u2[i] = start[i] + (weight / 3.0) * dydt[i]; } - + // Stage j = 2 // mu = 1.5, nu terms cancel load_vars(std::begin(u2)); - run_diffusive(curtime + (weight/3.0) * dt); + run_diffusive(curtime + (weight / 3.0) * dt); save_derivs(std::begin(u3)); // f(y_m2) -> u3 - + BOUT_OMP(parallel for) for (int i = 0; i < u3.size(); i++) { u1[i] = 1.5 * (u2[i] + weight * u3[i]) - 0.5 * start[i] - weight * dydt[i]; } - + BoutReal b_jm2 = 1. / 3; // b_{j - 2} BoutReal b_jm1 = 1. / 3; // b_{j - 1} - + for (int j = 3; j <= nstages; j++) { - - BoutReal b_j = (SQ(j) + j - 2.0) / (2.*j * (j + 1.)); - - BoutReal mu = (2.*j - 1.)/j * b_j / b_jm1; - BoutReal nu = -(j - 1.)/j * b_j / b_jm2; + + BoutReal b_j = (SQ(j) + j - 2.0) / (2. * j * (j + 1.)); + + BoutReal mu = (2. * j - 1.) / j * b_j / b_jm1; + BoutReal nu = -(j - 1.) / j * b_j / b_jm2; BoutReal a_jm1 = 1. - b_jm1; load_vars(std::begin(u1)); run_diffusive(curtime); save_derivs(std::begin(u3)); // f(y_m1) -> u3 - + BOUT_OMP(parallel for) for (int i = 0; i < u3.size(); i++) { // Next stage result in u3 @@ -265,7 +267,7 @@ void SplitRK::take_diffusion_step(BoutReal curtime, BoutReal dt, Array // Cycle u2 <- u1 <- u3 <- u2 // so that no new memory is allocated, and no arrays point to the same data swap(u1, u2); - swap(u1, u3); + swap(u1, u3); // Most recent now in u1, then u2, then u3 } @@ -275,28 +277,31 @@ void SplitRK::take_diffusion_step(BoutReal curtime, BoutReal dt, Array void SplitRK::take_advection_step(BoutReal curtime, BoutReal dt, Array& start, Array& result) { const int nlocal = getLocalN(); - + load_vars(std::begin(start)); run_convective(curtime); save_derivs(std::begin(dydt)); BOUT_OMP(parallel for) - for(int i=0;i #include +#include namespace { RegisterSolver registersolversplitrk("splitrk"); @@ -46,33 +46,35 @@ public: int init() override; int run() override; + private: - int nstages{2}; ///< Number of stages in the RKL - + int nstages{2}; ///< Number of stages in the RKL + BoutReal timestep{0.0}; ///< The internal timestep - bool adaptive{true}; ///< Adapt timestep using tolerances? - BoutReal atol{1e-10}; ///< Absolute tolerance - BoutReal rtol{1e-5}; ///< Relative tolerance + bool adaptive{true}; ///< Adapt timestep using tolerances? + BoutReal atol{1e-10}; ///< Absolute tolerance + BoutReal rtol{1e-5}; ///< Relative tolerance BoutReal max_timestep{1.0}; ///< Maximum timestep - BoutReal max_timestep_change{2.0}; ///< Maximum factor by which the timestep should be changed - int mxstep{1000}; ///< Maximum number of internal steps between outputs - int adapt_period{1}; ///< Number of steps between checks + BoutReal max_timestep_change{ + 2.0}; ///< Maximum factor by which the timestep should be changed + int mxstep{1000}; ///< Maximum number of internal steps between outputs + int adapt_period{1}; ///< Number of steps between checks + + bool diagnose{false}; ///< Turn on diagnostic output - bool diagnose{false}; ///< Turn on diagnostic output - int nlocal{0}, neq{0}; ///< Number of variables on local processor and in total - + /// System state Array state; - + /// Temporary time-stepping arrays - /// These are used by both diffusion and advection time-step routines + /// These are used by both diffusion and advection time-step routines Array u1, u2, u3, dydt; /// Arrays used for adaptive timestepping Array state1, state2; - + /// Take a combined step /// Uses 2nd order Strang splitting /// @@ -84,8 +86,8 @@ private: /// Uses the Runge-Kutta-Legendre 2nd order method /// /// Note: start and result can be the same - void take_diffusion_step(BoutReal curtime, BoutReal dt, - Array& start, Array& result); + void take_diffusion_step(BoutReal curtime, BoutReal dt, Array& start, + Array& result); /// Take a step of the advection terms /// Uses the Strong Stability Preserving Runge-Kutta 3rd order method diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx index ad684bd5b7..7d039498b0 100644 --- a/src/solver/solver.cxx +++ b/src/solver/solver.cxx @@ -22,17 +22,17 @@ #include "bout/build_config.hxx" -#include "bout/solver.hxx" -#include "boutcomm.hxx" -#include "boutexception.hxx" -#include "field_factory.hxx" -#include "initialprofiles.hxx" -#include "interpolation.hxx" -#include "msg_stack.hxx" -#include "output.hxx" +#include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" +#include "bout/field_factory.hxx" +#include "bout/initialprofiles.hxx" +#include "bout/interpolation.hxx" +#include "bout/msg_stack.hxx" +#include "bout/output.hxx" #include "bout/array.hxx" #include "bout/assert.hxx" #include "bout/region.hxx" +#include "bout/solver.hxx" #include "bout/sys/timer.hxx" #include "bout/sys/uuid.h" @@ -61,8 +61,8 @@ // Static member variables -int *Solver::pargc = nullptr; -char ***Solver::pargv = nullptr; +int* Solver::pargc = nullptr; +char*** Solver::pargv = nullptr; /************************************************************************** * Constructor @@ -105,16 +105,18 @@ Solver::Solver(Options* opts) * Add physics models **************************************************************************/ -void Solver::setModel(PhysicsModel *m) { - if(model) +void Solver::setModel(PhysicsModel* m) { + if (model) { throw BoutException("Solver can only evolve one model"); - - if(initialised) + } + + if (initialised) { throw BoutException("Solver already initialised"); - + } + // Initialise them model, which specifies which variables to evolve m->initialise(this); - + model = m; } @@ -126,19 +128,21 @@ void Solver::add(Field2D& v, const std::string& name, const std::string& descrip TRACE("Adding 2D field: Solver::add({:s})", name); #if CHECK > 0 - if (varAdded(name)) + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } #endif - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add to solver after initialisation\n"); + } // Set boundary conditions v.setBoundary(name); ddt(v).copyBoundary(v); // Set boundary to be the same as v VarStr d; - + d.var = &v; d.F_var = &ddt(v); d.location = v.getLocation(); @@ -156,19 +160,19 @@ void Solver::add(Field2D& v, const std::string& name, const std::string& descrip /// will be over-written anyway if (mms_initialise) { // Load solution at t = 0 - - FieldFactory *fact = FieldFactory::get(); - + + FieldFactory* fact = FieldFactory::get(); + v = fact->create2D("solution", Options::getRoot()->getSection(name), v.getMesh()); } else { initial_profile(name, v); } - + if (mms) { // Allocate storage for error variable d.MMS_err = bout::utils::make_unique(zeroFrom(v)); } - + // Check if the boundary regions should be evolved // First get option from section "all" // then use that as default for specific section @@ -185,25 +189,28 @@ void Solver::add(Field3D& v, const std::string& name, const std::string& descrip Mesh* mesh = v.getMesh(); -#if CHECK > 0 - if (varAdded(name)) +#if CHECK > 0 + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } #endif - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add to solver after initialisation\n"); + } // Set boundary conditions v.setBoundary(name); ddt(v).copyBoundary(v); // Set boundary to be the same as v if (mesh->StaggerGrids && (v.getLocation() != CELL_CENTRE)) { - output_info.write("\tVariable {:s} shifted to {:s}\n", name, toString(v.getLocation())); + output_info.write("\tVariable {:s} shifted to {:s}\n", name, + toString(v.getLocation())); ddt(v).setLocation(v.getLocation()); // Make sure both at the same location } VarStr d; - + d.var = &v; d.F_var = &ddt(v); d.location = v.getLocation(); @@ -216,38 +223,40 @@ void Solver::add(Field3D& v, const std::string& name, const std::string& descrip if (mms_initialise) { // Load solution at t = 0 - FieldFactory *fact = FieldFactory::get(); - + FieldFactory* fact = FieldFactory::get(); + v = fact->create3D("solution", &Options::root()[name], mesh, v.getLocation()); - + } else { initial_profile(name, v); } - + if (mms) { d.MMS_err = bout::utils::make_unique(zeroFrom(v)); } - + // Check if the boundary regions should be evolved // First get option from section "all" // then use that as default for specific section d.evolve_bndry = Options::root()["all"]["evolve_bndry"].withDefault(false); d.evolve_bndry = Options::root()[name]["evolve_bndry"].withDefault(d.evolve_bndry); - v.applyBoundary(true); // Make sure initial profile obeys boundary conditions + v.applyBoundary(true); // Make sure initial profile obeys boundary conditions v.setLocation(d.location); // Restore location if changed - + f3d.emplace_back(std::move(d)); } void Solver::add(Vector2D& v, const std::string& name, const std::string& description) { TRACE("Adding 2D vector: Solver::add({:s})", name); - if (varAdded(name)) + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add to solver after initialisation\n"); + } // Set boundary conditions v.setBoundary(name); @@ -283,11 +292,13 @@ void Solver::add(Vector2D& v, const std::string& name, const std::string& descri void Solver::add(Vector3D& v, const std::string& name, const std::string& description) { TRACE("Adding 3D vector: Solver::add({:s})", name); - if (varAdded(name)) + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add to solver after initialisation\n"); + } // Set boundary conditions v.setBoundary(name); @@ -327,19 +338,22 @@ void Solver::constraint(Field2D& v, Field2D& C_v, std::string name) { throw BoutException("ERROR: Constraint requested for variable with empty name\n"); } -#if CHECK > 0 - if (varAdded(name)) +#if CHECK > 0 + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } #endif - if (!has_constraints) + if (!has_constraints) { throw BoutException("ERROR: This solver doesn't support constraints\n"); + } - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add constraints to solver after initialisation\n"); + } VarStr d; - + d.constraint = true; d.var = &v; d.F_var = &C_v; @@ -356,18 +370,21 @@ void Solver::constraint(Field3D& v, Field3D& C_v, std::string name) { } #if CHECK > 0 - if (varAdded(name)) + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } #endif - if (!has_constraints) + if (!has_constraints) { throw BoutException("ERROR: This solver doesn't support constraints\n"); + } - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add constraints to solver after initialisation\n"); + } VarStr d; - + d.constraint = true; d.var = &v; d.F_var = &C_v; @@ -384,16 +401,19 @@ void Solver::constraint(Vector2D& v, Vector2D& C_v, std::string name) { throw BoutException("ERROR: Constraint requested for variable with empty name\n"); } -#if CHECK > 0 - if (varAdded(name)) +#if CHECK > 0 + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } #endif - if (!has_constraints) + if (!has_constraints) { throw BoutException("ERROR: This solver doesn't support constraints\n"); + } - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add constraints to solver after initialisation\n"); + } // Add suffix, depending on co- /contravariance if (v.covariant) { @@ -424,16 +444,19 @@ void Solver::constraint(Vector3D& v, Vector3D& C_v, std::string name) { throw BoutException("ERROR: Constraint requested for variable with empty name\n"); } -#if CHECK > 0 - if (varAdded(name)) +#if CHECK > 0 + if (varAdded(name)) { throw BoutException("Variable '{:s}' already added to Solver", name); + } #endif - if (!has_constraints) + if (!has_constraints) { throw BoutException("ERROR: This solver doesn't support constraints\n"); + } - if (initialised) + if (initialised) { throw BoutException("Error: Cannot add constraints to solver after initialisation\n"); + } // Add suffix, depending on co- /contravariance if (v.covariant) { @@ -478,10 +501,11 @@ int Solver::solve(int nout, BoutReal timestep) { output_progress.write( _("Solver running for {:d} outputs with output timestep of {:e}\n"), nout, timestep); - if (default_monitor_period > 1) + if (default_monitor_period > 1) { output_progress.write( _("Solver running for {:d} outputs with monitor timestep of {:e}\n"), nout / default_monitor_period, timestep * default_monitor_period); + } // Initialise if (init()) { @@ -633,8 +657,9 @@ int Solver::init() { TRACE("Solver::init()"); - if (initialised) + if (initialised) { throw BoutException(_("ERROR: Solver is already initialised\n")); + } output_progress.write(_("Initialising solver\n")); @@ -914,18 +939,18 @@ void Solver::addTimestepMonitor(TimestepMonitorFunc f) { timestep_monitors.push_front(f); } -void Solver::removeTimestepMonitor(TimestepMonitorFunc f) { - timestep_monitors.remove(f); -} +void Solver::removeTimestepMonitor(TimestepMonitorFunc f) { timestep_monitors.remove(f); } int Solver::call_timestep_monitors(BoutReal simtime, BoutReal lastdt) { - if (!monitor_timestep) + if (!monitor_timestep) { return 0; + } for (const auto& monitor : timestep_monitors) { const int ret = monitor(this, simtime, lastdt); - if (ret != 0) + if (ret != 0) { return ret; // Return first time an error is encountered + } } // Call physics model monitor @@ -979,133 +1004,144 @@ std::unique_ptr Solver::create(const SolverType& type, Options* opts) { **************************************************************************/ /// Perform an operation at a given Ind2D (jx,jy) location, moving data between BOUT++ and CVODE -void Solver::loop_vars_op(Ind2D i2d, BoutReal *udata, int &p, SOLVER_VAR_OP op, bool bndry) { +void Solver::loop_vars_op(Ind2D i2d, BoutReal* udata, int& p, SOLVER_VAR_OP op, + bool bndry) { // Use global mesh: FIX THIS! Mesh* mesh = bout::globals::mesh; int nz = mesh->LocalNz; - - switch(op) { - case SOLVER_VAR_OP::LOAD_VARS: { + + switch (op) { + case SOLVER_VAR_OP::LOAD_VARS: { /// Load variables from IDA into BOUT++ - + // Loop over 2D variables - for(const auto& f : f2d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f2d) { + if (bndry && !f.evolve_bndry) { continue; + } (*f.var)[i2d] = udata[p]; p++; } - - for (int jz=0; jz < nz; jz++) { - + + for (int jz = 0; jz < nz; jz++) { + // Loop over 3D variables - for(const auto& f : f3d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f3d) { + if (bndry && !f.evolve_bndry) { continue; + } (*f.var)[f.var->getMesh()->ind2Dto3D(i2d, jz)] = udata[p]; p++; - } + } } break; } case SOLVER_VAR_OP::LOAD_DERIVS: { /// Load derivatives from IDA into BOUT++ /// Used for preconditioner - + // Loop over 2D variables - for(const auto& f : f2d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f2d) { + if (bndry && !f.evolve_bndry) { continue; + } (*f.F_var)[i2d] = udata[p]; p++; } - - for (int jz=0; jz < nz; jz++) { - + + for (int jz = 0; jz < nz; jz++) { + // Loop over 3D variables - for(const auto& f : f3d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f3d) { + if (bndry && !f.evolve_bndry) { continue; + } (*f.F_var)[f.F_var->getMesh()->ind2Dto3D(i2d, jz)] = udata[p]; p++; - } + } } - + break; } case SOLVER_VAR_OP::SET_ID: { /// Set the type of equation (Differential or Algebraic) - + // Loop over 2D variables - for(const auto& f : f2d) { - if(bndry && !f.evolve_bndry) - continue; - if(f.constraint) { - udata[p] = 0; - }else { - udata[p] = 1; + for (const auto& f : f2d) { + if (bndry && !f.evolve_bndry) { + continue; + } + if (f.constraint) { + udata[p] = 0; + } else { + udata[p] = 1; } p++; } - - for (int jz=0; jz < nz; jz++) { - + + for (int jz = 0; jz < nz; jz++) { + // Loop over 3D variables - for(const auto& f : f3d) { - if(bndry && !f.evolve_bndry) - continue; - if(f.constraint) { - udata[p] = 0; - }else { - udata[p] = 1; - } - p++; + for (const auto& f : f3d) { + if (bndry && !f.evolve_bndry) { + continue; + } + if (f.constraint) { + udata[p] = 0; + } else { + udata[p] = 1; + } + p++; } } - + break; } case SOLVER_VAR_OP::SAVE_VARS: { /// Save variables from BOUT++ into IDA (only used at start of simulation) - + // Loop over 2D variables - for(const auto& f : f2d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f2d) { + if (bndry && !f.evolve_bndry) { continue; + } udata[p] = (*f.var)[i2d]; p++; } - - for (int jz=0; jz < nz; jz++) { - + + for (int jz = 0; jz < nz; jz++) { + // Loop over 3D variables - for(const auto& f : f3d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f3d) { + if (bndry && !f.evolve_bndry) { continue; + } udata[p] = (*f.var)[f.var->getMesh()->ind2Dto3D(i2d, jz)]; p++; - } + } } break; } /// Save time-derivatives from BOUT++ into CVODE (returning RHS result) case SOLVER_VAR_OP::SAVE_DERIVS: { - + // Loop over 2D variables - for(const auto& f : f2d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f2d) { + if (bndry && !f.evolve_bndry) { continue; + } udata[p] = (*f.F_var)[i2d]; p++; } - - for (int jz=0; jz < nz; jz++) { - + + for (int jz = 0; jz < nz; jz++) { + // Loop over 3D variables - for(const auto& f : f3d) { - if(bndry && !f.evolve_bndry) + for (const auto& f : f3d) { + if (bndry && !f.evolve_bndry) { continue; + } udata[p] = (*f.F_var)[f.F_var->getMesh()->ind2Dto3D(i2d, jz)]; p++; } @@ -1116,28 +1152,29 @@ void Solver::loop_vars_op(Ind2D i2d, BoutReal *udata, int &p, SOLVER_VAR_OP op, } /// Loop over variables and domain. Used for all data operations for consistency -void Solver::loop_vars(BoutReal *udata, SOLVER_VAR_OP op) { +void Solver::loop_vars(BoutReal* udata, SOLVER_VAR_OP op) { // Use global mesh: FIX THIS! Mesh* mesh = bout::globals::mesh; int p = 0; // Counter for location in udata array - + // All boundaries - for(const auto &i2d : mesh->getRegion2D("RGN_BNDRY")) { + for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) { loop_vars_op(i2d, udata, p, op, true); } - + // Bulk of points - for(const auto &i2d : mesh->getRegion2D("RGN_NOBNDRY")) { + for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) { loop_vars_op(i2d, udata, p, op, false); } } -void Solver::load_vars(BoutReal *udata) { +void Solver::load_vars(BoutReal* udata) { // Make sure data is allocated - for(const auto& f : f2d) + for (const auto& f : f2d) { f.var->allocate(); - for(const auto& f : f3d) { + } + for (const auto& f : f3d) { f.var->allocate(); f.var->setLocation(f.location); } @@ -1146,17 +1183,20 @@ void Solver::load_vars(BoutReal *udata) { // Mark each vector as either co- or contra-variant - for(const auto& v : v2d) + for (const auto& v : v2d) { v.var->covariant = v.covariant; - for(const auto& v : v3d) + } + for (const auto& v : v3d) { v.var->covariant = v.covariant; + } } -void Solver::load_derivs(BoutReal *udata) { +void Solver::load_derivs(BoutReal* udata) { // Make sure data is allocated - for(const auto& f : f2d) + for (const auto& f : f2d) { f.F_var->allocate(); - for(const auto& f : f3d) { + } + for (const auto& f : f3d) { f.F_var->allocate(); f.F_var->setLocation(f.location); } @@ -1165,52 +1205,62 @@ void Solver::load_derivs(BoutReal *udata) { // Mark each vector as either co- or contra-variant - for(const auto& v : v2d) + for (const auto& v : v2d) { v.F_var->covariant = v.covariant; - for(const auto& v : v3d) + } + for (const auto& v : v3d) { v.F_var->covariant = v.covariant; + } } // This function only called during initialisation -void Solver::save_vars(BoutReal *udata) { - for(const auto& f : f2d) - if(!f.var->isAllocated()) +void Solver::save_vars(BoutReal* udata) { + for (const auto& f : f2d) { + if (!f.var->isAllocated()) { throw BoutException(_("Variable '{:s}' not initialised"), f.name); + } + } - for(const auto& f : f3d) - if(!f.var->isAllocated()) + for (const auto& f : f3d) { + if (!f.var->isAllocated()) { throw BoutException(_("Variable '{:s}' not initialised"), f.name); + } + } // Make sure vectors in correct basis - for(const auto& v : v2d) { - if(v.covariant) { + for (const auto& v : v2d) { + if (v.covariant) { v.var->toCovariant(); - }else + } else { v.var->toContravariant(); + } } - for(const auto& v : v3d) { - if(v.covariant) { + for (const auto& v : v3d) { + if (v.covariant) { v.var->toCovariant(); - }else + } else { v.var->toContravariant(); + } } loop_vars(udata, SOLVER_VAR_OP::SAVE_VARS); } -void Solver::save_derivs(BoutReal *dudata) { +void Solver::save_derivs(BoutReal* dudata) { // Make sure vectors in correct basis - for(const auto& v : v2d) { - if(v.covariant) { + for (const auto& v : v2d) { + if (v.covariant) { v.F_var->toCovariant(); - }else + } else { v.F_var->toContravariant(); + } } - for(const auto& v : v3d) { - if(v.covariant) { + for (const auto& v : v3d) { + if (v.covariant) { v.F_var->toCovariant(); - }else + } else { v.F_var->toContravariant(); + } } // Make sure 3D fields are at the correct cell location @@ -1226,9 +1276,7 @@ void Solver::save_derivs(BoutReal *dudata) { loop_vars(dudata, SOLVER_VAR_OP::SAVE_DERIVS); } -void Solver::set_id(BoutReal *udata) { - loop_vars(udata, SOLVER_VAR_OP::SET_ID); -} +void Solver::set_id(BoutReal* udata) { loop_vars(udata, SOLVER_VAR_OP::SET_ID); } Field3D Solver::globalIndex(int localStart) { // Use global mesh: FIX THIS! @@ -1242,23 +1290,25 @@ Field3D Solver::globalIndex(int localStart) { int ind = localStart; int nz = mesh->LocalNz; - + // Find how many boundary cells are evolving int n2dbndry = 0; - for (const auto &f : f2d) { - if (f.evolve_bndry) + for (const auto& f : f2d) { + if (f.evolve_bndry) { ++n2dbndry; + } } int n3dbndry = 0; - for (const auto &f : f3d) { - if (f.evolve_bndry) + for (const auto& f : f3d) { + if (f.evolve_bndry) { ++n3dbndry; + } } - + if (n2dbndry + n3dbndry > 0) { // Some boundary points evolving - for (const auto &i2d : mesh->getRegion2D("RGN_BNDRY")) { + for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) { // Zero index contains 2D and 3D variables index[mesh->ind2Dto3D(i2d, 0)] = ind; ind += n2dbndry + n3dbndry; @@ -1271,7 +1321,7 @@ Field3D Solver::globalIndex(int localStart) { } // Bulk of points - for (const auto &i2d : mesh->getRegion2D("RGN_NOBNDRY")) { + for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) { // Zero index contains 2D and 3D variables index[mesh->ind2Dto3D(i2d, 0)] = ind; ind += n2d + n3d; @@ -1281,13 +1331,13 @@ Field3D Solver::globalIndex(int localStart) { ind += n3d; } } - + // Should have included all evolving variables ASSERT1(ind == localStart + getLocalN()); - + // Now swap guard cells mesh->communicate(index); - + return index; } @@ -1351,10 +1401,12 @@ int Solver::run_convective(BoutReal t, bool linear) { status = model->runRHS(t, linear); } else { // Zero if not split - for (const auto& f : f3d) + for (const auto& f : f3d) { *(f.F_var) = 0.0; - for (const auto& f : f2d) + } + for (const auto& f : f2d) { *(f.F_var) = 0.0; + } status = 0; } post_rhs(t); @@ -1381,10 +1433,12 @@ int Solver::run_diffusive(BoutReal t, bool linear) { status = model->runRHS(t, linear); } else { // Zero if not split - for (const auto& f : f3d) + for (const auto& f : f3d) { *(f.F_var) = 0.0; - for (const auto& f : f2d) + } + for (const auto& f : f2d) { *(f.F_var) = 0.0; + } status = 0; } rhs_ncalls_i++; @@ -1399,13 +1453,12 @@ void Solver::pre_rhs(BoutReal t) { f.var->applyBoundary(t); } } - + for (const auto& f : f3d) { if (!f.constraint) { f.var->applyBoundary(t); } } - } void Solver::post_rhs(BoutReal UNUSED(t)) { @@ -1439,11 +1492,12 @@ void Solver::post_rhs(BoutReal UNUSED(t)) { // Apply boundary conditions to the time-derivatives for (const auto& f : f2d) { - if (!f.constraint && f.evolve_bndry) { // If it's not a constraint and if the boundary is evolving + if (!f.constraint + && f.evolve_bndry) { // If it's not a constraint and if the boundary is evolving f.var->applyTDerivBoundary(); } } - + for (const auto& f : f3d) { if (!f.constraint && f.evolve_bndry) { f.var->applyTDerivBoundary(); @@ -1476,28 +1530,32 @@ int Solver::runJacobian(BoutReal time) { return model->runJacobian(time); } // Add source terms to time derivatives void Solver::add_mms_sources(BoutReal t) { - if(!mms) + if (!mms) { return; + } + + FieldFactory* fact = FieldFactory::get(); - FieldFactory *fact = FieldFactory::get(); - // Iterate over 2D variables - for(const auto& f : f2d) { - *f.F_var += fact->create2D("source", Options::getRoot()->getSection(f.name), f.var->getMesh(), (f.var)->getLocation(), t); + for (const auto& f : f2d) { + *f.F_var += fact->create2D("source", Options::getRoot()->getSection(f.name), + f.var->getMesh(), (f.var)->getLocation(), t); } - - for(const auto& f : f3d) { - *f.F_var += fact->create3D("source", Options::getRoot()->getSection(f.name), f.var->getMesh(), (f.var)->getLocation(), t); + + for (const auto& f : f3d) { + *f.F_var += fact->create3D("source", Options::getRoot()->getSection(f.name), + f.var->getMesh(), (f.var)->getLocation(), t); } } -// Calculate +// Calculate void Solver::calculate_mms_error(BoutReal t) { - FieldFactory *fact = FieldFactory::get(); - - for(const auto& f : f3d) { - Field3D solution = fact->create3D("solution", Options::getRoot()->getSection(f.name), f.var->getMesh(), (f.var)->getLocation(), t); - + FieldFactory* fact = FieldFactory::get(); + + for (const auto& f : f3d) { + Field3D solution = fact->create3D("solution", Options::getRoot()->getSection(f.name), + f.var->getMesh(), (f.var)->getLocation(), t); + *(f.MMS_err) = *(f.var) - solution; } } diff --git a/src/sys/bout_types.cxx b/src/sys/bout_types.cxx index 82b7e2911c..a7396fb9c6 100644 --- a/src/sys/bout_types.cxx +++ b/src/sys/bout_types.cxx @@ -1,7 +1,7 @@ -#include -#include +#include +#include #include -#include +#include namespace { template @@ -23,7 +23,7 @@ const T& safeAt(const std::map& mymap, const std::string& s) { } return found->second; } -} +} // namespace std::string toString(CELL_LOC location) { AUTO_TRACE(); @@ -37,8 +37,8 @@ std::string toString(CELL_LOC location) { CELL_LOC CELL_LOCFromString(const std::string& location_string) { AUTO_TRACE(); const static std::map stringtoCELL_LOC = { - STRENUM(CELL_DEFAULT), STRENUM(CELL_CENTRE), STRENUM(CELL_XLOW), - STRENUM(CELL_YLOW), STRENUM(CELL_ZLOW), STRENUM(CELL_VSHIFT)}; + STRENUM(CELL_DEFAULT), STRENUM(CELL_CENTRE), STRENUM(CELL_XLOW), + STRENUM(CELL_YLOW), STRENUM(CELL_ZLOW), STRENUM(CELL_VSHIFT)}; return safeAt(stringtoCELL_LOC, location_string); } @@ -140,8 +140,7 @@ std::string toString(DERIV deriv) { std::string toString(YDirectionType d) { AUTO_TRACE(); const static std::map YDirectionTypeToString = { - {YDirectionType::Standard, "Standard"}, - {YDirectionType::Aligned, "Aligned"}}; + {YDirectionType::Standard, "Standard"}, {YDirectionType::Aligned, "Aligned"}}; return safeAt(YDirectionTypeToString, d); } @@ -149,8 +148,7 @@ std::string toString(YDirectionType d) { YDirectionType YDirectionTypeFromString(const std::string& y_direction_string) { AUTO_TRACE(); const static std::map stringToYDirectionType = { - {"Standard", YDirectionType::Standard}, - {"Aligned", YDirectionType::Aligned}}; + {"Standard", YDirectionType::Standard}, {"Aligned", YDirectionType::Aligned}}; return safeAt(stringToYDirectionType, y_direction_string); } @@ -158,8 +156,7 @@ YDirectionType YDirectionTypeFromString(const std::string& y_direction_string) { std::string toString(ZDirectionType d) { AUTO_TRACE(); const static std::map ZDirectionTypeToString = { - {ZDirectionType::Standard, "Standard"}, - {ZDirectionType::Average, "Average"}}; + {ZDirectionType::Standard, "Standard"}, {ZDirectionType::Average, "Average"}}; return safeAt(ZDirectionTypeToString, d); } @@ -167,8 +164,7 @@ std::string toString(ZDirectionType d) { ZDirectionType ZDirectionTypeFromString(const std::string& z_direction_string) { AUTO_TRACE(); const static std::map stringToZDirectionType = { - {"Standard", ZDirectionType::Standard}, - {"Average", ZDirectionType::Average}}; + {"Standard", ZDirectionType::Standard}, {"Average", ZDirectionType::Average}}; return safeAt(stringToZDirectionType, z_direction_string); } diff --git a/src/sys/boutcomm.cxx b/src/sys/boutcomm.cxx index 9e24b35c3b..ecaeb866bb 100644 --- a/src/sys/boutcomm.cxx +++ b/src/sys/boutcomm.cxx @@ -1,15 +1,16 @@ -#include -#include +#include +#include BoutComm* BoutComm::instance = nullptr; BoutComm::BoutComm() : comm(MPI_COMM_NULL) {} BoutComm::~BoutComm() { - if(comm != MPI_COMM_NULL) + if (comm != MPI_COMM_NULL) { MPI_Comm_free(&comm); - - if(!isSet()) { + } + + if (!isSet()) { // If BoutComm was set, then assume that MPI_Finalize is called elsewhere // but might need to revisit if that isn't the case MPI_Finalize(); @@ -17,33 +18,30 @@ BoutComm::~BoutComm() { } void BoutComm::setComm(MPI_Comm c) { - if(comm != MPI_COMM_NULL) + if (comm != MPI_COMM_NULL) { MPI_Comm_free(&comm); + } MPI_Comm_dup(c, &comm); hasBeenSet = true; } MPI_Comm BoutComm::getComm() { - if(comm == MPI_COMM_NULL) { + if (comm == MPI_COMM_NULL) { // No communicator set. Initialise MPI - MPI_Init(pargc,pargv); - + MPI_Init(pargc, pargv); + // Duplicate MPI_COMM_WORLD MPI_Comm_dup(MPI_COMM_WORLD, &comm); } return comm; } -bool BoutComm::isSet() { - return hasBeenSet; -} +bool BoutComm::isSet() { return hasBeenSet; } // Static functions below. Must use getInstance() -MPI_Comm BoutComm::get() { - return getInstance()->getComm(); -} +MPI_Comm BoutComm::get() { return getInstance()->getComm(); } -void BoutComm::setArgs(int &c, char**&v) { +void BoutComm::setArgs(int& c, char**& v) { getInstance()->pargc = &c; getInstance()->pargv = &v; } @@ -61,7 +59,7 @@ int BoutComm::size() { } BoutComm* BoutComm::getInstance() { - if(instance == nullptr) { + if (instance == nullptr) { // Create the singleton object instance = new BoutComm(); } diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx index 4f0f2b9621..b92f322b1b 100644 --- a/src/sys/boutexception.cxx +++ b/src/sys/boutexception.cxx @@ -1,23 +1,23 @@ #include "bout/build_config.hxx" -#include -#include -#include +#include +#include #include -#include -#include -#include +#include +#include +#include +#include #if BOUT_USE_BACKTRACE -#include #include +#include #endif #include #include -void BoutParallelThrowRhsFail(int status, const char *message) { +void BoutParallelThrowRhsFail(int status, const char* message) { int allstatus; MPI_Allreduce(&status, &allstatus, 1, MPI_INT, MPI_LOR, BoutComm::get()); @@ -60,28 +60,30 @@ std::string BoutException::getBacktrace() const { // If we are compiled as PIE, need to get base pointer of .so and substract Dl_info info; - void * ptr=trace[i]; - if (dladdr(trace[i],&info)){ + void* ptr = trace[i]; + if (dladdr(trace[i], &info)) { // Additionally, check whether this is the default offset for an executable - if (info.dli_fbase != reinterpret_cast(0x400000)) + if (info.dli_fbase != reinterpret_cast(0x400000)) { ptr = reinterpret_cast(reinterpret_cast(trace[i]) - reinterpret_cast(info.dli_fbase)); + } } // Pipe stderr to /dev/null to avoid cluttering output // when addr2line fails or is not installed - const auto syscom = - fmt::format(FMT_STRING("addr2line {:p} -Cfpie {:.{}s} 2> /dev/null"), ptr, messages[i], p); + const auto syscom = fmt::format( + FMT_STRING("addr2line {:p} -Cfpie {:.{}s} 2> /dev/null"), ptr, messages[i], p); // last parameter is the file name of the symbol - FILE *fp = popen(syscom.c_str(), "r"); + FILE* fp = popen(syscom.c_str(), "r"); if (fp != nullptr) { char out[1024]; - char *retstr; + char* retstr; std::string buf; do { retstr = fgets(out, sizeof(out) - 1, fp); - if (retstr != nullptr) - buf+=retstr; + if (retstr != nullptr) { + buf += retstr; + } } while (retstr != nullptr); int status = pclose(fp); if (status == 0) { diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx index 351c5d4c30..7f629cfbb5 100644 --- a/src/sys/derivs.cxx +++ b/src/sys/derivs.cxx @@ -38,19 +38,19 @@ * **************************************************************************/ -#include -#include -#include -#include -#include -#include #include -#include +#include +#include +#include +#include +#include +#include +#include #include -#include -#include +#include +#include /******************************************************************************* * First central derivatives @@ -70,8 +70,8 @@ Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc, const std::strin ////////////// Y DERIVATIVE ///////////////// -Field3D DDY(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D DDY(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { return bout::derivatives::index::DDY(f, outloc, method, region) / f.getCoordinates(outloc)->dy; } @@ -83,8 +83,8 @@ Coordinates::FieldMetric DDY(const Field2D& f, CELL_LOC outloc, const std::strin ////////////// Z DERIVATIVE ///////////////// -Field3D DDZ(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D DDZ(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { return bout::derivatives::index::DDZ(f, outloc, method, region) / f.getCoordinates(outloc)->dz; } @@ -97,34 +97,39 @@ Coordinates::FieldMetric DDZ(const Field2D& f, CELL_LOC UNUSED(outloc), return tmp; } -Vector3D DDZ(const Vector3D &v, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Vector3D DDZ(const Vector3D& v, CELL_LOC outloc, const std::string& method, + const std::string& region) { Vector3D result(v.getMesh()); - Coordinates *metric = v.x.getCoordinates(outloc); + Coordinates* metric = v.x.getCoordinates(outloc); - if(v.covariant){ + if (v.covariant) { // From equation (2.6.32) in D'Haeseleer - result.x = DDZ(v.x, outloc, method, region) - v.x*metric->G1_13 - v.y*metric->G2_13 - v.z*metric->G3_13; - result.y = DDZ(v.y, outloc, method, region) - v.x*metric->G1_23 - v.y*metric->G2_23 - v.z*metric->G3_23; - result.z = DDZ(v.z, outloc, method, region) - v.x*metric->G1_33 - v.y*metric->G2_33 - v.z*metric->G3_33; + result.x = DDZ(v.x, outloc, method, region) - v.x * metric->G1_13 + - v.y * metric->G2_13 - v.z * metric->G3_13; + result.y = DDZ(v.y, outloc, method, region) - v.x * metric->G1_23 + - v.y * metric->G2_23 - v.z * metric->G3_23; + result.z = DDZ(v.z, outloc, method, region) - v.x * metric->G1_33 + - v.y * metric->G2_33 - v.z * metric->G3_33; result.covariant = true; - } - else{ + } else { // From equation (2.6.31) in D'Haeseleer - result.x = DDZ(v.x, outloc, method, region) + v.x*metric->G1_13 + v.y*metric->G1_23 + v.z*metric->G1_33; - result.y = DDZ(v.y, outloc, method, region) + v.x*metric->G2_13 + v.y*metric->G2_23 + v.z*metric->G2_33; - result.z = DDZ(v.z, outloc, method, region) + v.x*metric->G3_13 + v.y*metric->G3_23 + v.z*metric->G3_33; + result.x = DDZ(v.x, outloc, method, region) + v.x * metric->G1_13 + + v.y * metric->G1_23 + v.z * metric->G1_33; + result.y = DDZ(v.y, outloc, method, region) + v.x * metric->G2_13 + + v.y * metric->G2_23 + v.z * metric->G2_33; + result.z = DDZ(v.z, outloc, method, region) + v.x * metric->G3_13 + + v.y * metric->G3_23 + v.z * metric->G3_33; result.covariant = false; } - ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == v.getLocation())) || - (result.getLocation() == outloc)); + ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == v.getLocation())) + || (result.getLocation() == outloc)); return result; } -Vector2D DDZ(const Vector2D &v, CELL_LOC UNUSED(outloc), const std::string - &UNUSED(method), const std::string& UNUSED(region)) { +Vector2D DDZ(const Vector2D& v, CELL_LOC UNUSED(outloc), + const std::string& UNUSED(method), const std::string& UNUSED(region)) { Vector2D result(v.getMesh()); result.covariant = v.covariant; @@ -145,33 +150,33 @@ Vector2D DDZ(const Vector2D &v, CELL_LOC UNUSED(outloc), const std::string ////////////// X DERIVATIVE ///////////////// -Field3D D2DX2(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { - Coordinates *coords = f.getCoordinates(outloc); +Field3D D2DX2(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { + Coordinates* coords = f.getCoordinates(outloc); Field3D result = bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx); - if(coords->non_uniform) { + if (coords->non_uniform) { // Correction for non-uniform f.getMesh() result += coords->d1_dx * bout::derivatives::index::DDX(f, outloc, "DEFAULT", region) / coords->dx; } - ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == f.getLocation())) || - (result.getLocation() == outloc)); + ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == f.getLocation())) + || (result.getLocation() == outloc)); return result; } Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc, const std::string& method, const std::string& region) { - Coordinates *coords = f.getCoordinates(outloc); + Coordinates* coords = f.getCoordinates(outloc); auto result = bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx); - if(coords->non_uniform) { + if (coords->non_uniform) { // Correction for non-uniform f.getMesh() result += coords->d1_dx * bout::derivatives::index::DDX(f, outloc, "DEFAULT", region) / coords->dx; @@ -182,44 +187,44 @@ Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc, ////////////// Y DERIVATIVE ///////////////// -Field3D D2DY2(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { - Coordinates *coords = f.getCoordinates(outloc); +Field3D D2DY2(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { + Coordinates* coords = f.getCoordinates(outloc); Field3D result = bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy); - if(coords->non_uniform) { + if (coords->non_uniform) { // Correction for non-uniform f.getMesh() result += coords->d1_dy * bout::derivatives::index::DDY(f, outloc, "DEFAULT", region) / coords->dy; } - ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == f.getLocation())) || - (result.getLocation() == outloc)); + ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == f.getLocation())) + || (result.getLocation() == outloc)); return result; } Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc, const std::string& method, const std::string& region) { - Coordinates *coords = f.getCoordinates(outloc); + Coordinates* coords = f.getCoordinates(outloc); auto result = bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy); - if(coords->non_uniform) { + if (coords->non_uniform) { // Correction for non-uniform f.getMesh() result += coords->d1_dy * bout::derivatives::index::DDY(f, outloc, "DEFAULT", region) / coords->dy; } - + return result; } ////////////// Z DERIVATIVE ///////////////// -Field3D D2DZ2(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D D2DZ2(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { return bout::derivatives::index::D2DZ2(f, outloc, method, region) / SQ(f.getCoordinates(outloc)->dz); } @@ -234,8 +239,8 @@ Coordinates::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc, * Fourth derivatives *******************************************************************************/ -Field3D D4DX4(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D D4DX4(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { return bout::derivatives::index::D4DX4(f, outloc, method, region) / SQ(SQ(f.getCoordinates(outloc)->dx)); } @@ -246,8 +251,8 @@ Coordinates::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc, / SQ(SQ(f.getCoordinates(outloc)->dx)); } -Field3D D4DY4(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D D4DY4(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { return bout::derivatives::index::D4DY4(f, outloc, method, region) / SQ(SQ(f.getCoordinates(outloc)->dy)); } @@ -258,8 +263,8 @@ Coordinates::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc, / SQ(SQ(f.getCoordinates(outloc)->dy)); } -Field3D D4DZ4(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D D4DZ4(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { return bout::derivatives::index::D4DZ4(f, outloc, method, region) / SQ(SQ(f.getCoordinates(outloc)->dz)); } @@ -289,7 +294,7 @@ Coordinates::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc, // If staggering in x, take y-derivative at f's location. const auto y_location = - (outloc == CELL_XLOW or f.getLocation() == CELL_XLOW) ? CELL_DEFAULT : outloc; + (outloc == CELL_XLOW or f.getLocation() == CELL_XLOW) ? CELL_DEFAULT : outloc; auto dfdy = DDY(f, y_location, method, dy_region); @@ -314,7 +319,7 @@ Field3D D2DXDY(const Field3D& f, CELL_LOC outloc, const std::string& method, // If staggering in x, take y-derivative at f's location. const auto y_location = - (outloc == CELL_XLOW or f.getLocation() == CELL_XLOW) ? CELL_DEFAULT : outloc; + (outloc == CELL_XLOW or f.getLocation() == CELL_XLOW) ? CELL_DEFAULT : outloc; Field3D dfdy = DDY(f, y_location, method, dy_region); @@ -340,12 +345,12 @@ Coordinates::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc, } /// X-Z mixed derivative -Field3D D2DXDZ(const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc, const std::string& method, + const std::string& region) { // If staggering in z, take x-derivative at f's location. const auto x_location = - (outloc == CELL_ZLOW or f.getLocation() == CELL_ZLOW) ? CELL_DEFAULT : outloc; + (outloc == CELL_ZLOW or f.getLocation() == CELL_ZLOW) ? CELL_DEFAULT : outloc; return DDZ(DDX(f, x_location, method, region), outloc, method, region); } @@ -364,11 +369,11 @@ Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc, #endif } -Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc, MAYBE_UNUSED(const std::string& - method), const std::string& region) { +Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc, MAYBE_UNUSED(const std::string& method), + const std::string& region) { // If staggering in z, take y-derivative at f's location. const auto y_location = - (outloc == CELL_ZLOW or f.getLocation() == CELL_ZLOW) ? CELL_DEFAULT : outloc; + (outloc == CELL_ZLOW or f.getLocation() == CELL_ZLOW) ? CELL_DEFAULT : outloc; return DDZ(DDY(f, y_location, method, region), outloc, method, region); } @@ -389,8 +394,8 @@ Coordinates::FieldMetric VDDX(const Field2D& v, const Field2D& f, CELL_LOC outlo } /// General version for 2 or 3-D objects -Field3D VDDX(const Field3D &v, const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D VDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc, + const std::string& method, const std::string& region) { return bout::derivatives::index::VDDX(v, f, outloc, method, region) / f.getCoordinates(outloc)->dx; } @@ -405,8 +410,8 @@ Coordinates::FieldMetric VDDY(const Field2D& v, const Field2D& f, CELL_LOC outlo } // general case -Field3D VDDY(const Field3D &v, const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D VDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc, + const std::string& method, const std::string& region) { return bout::derivatives::index::VDDY(v, f, outloc, method, region) / f.getCoordinates(outloc)->dy; } @@ -437,8 +442,8 @@ Coordinates::FieldMetric VDDZ(MAYBE_UNUSED(const Field3D& v), const Field2D& f, } // general case -Field3D VDDZ(const Field3D &v, const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D VDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc, + const std::string& method, const std::string& region) { return bout::derivatives::index::VDDZ(v, f, outloc, method, region) / f.getCoordinates(outloc)->dz; } @@ -452,8 +457,8 @@ Coordinates::FieldMetric FDDX(const Field2D& v, const Field2D& f, CELL_LOC outlo / f.getCoordinates(outloc)->dx; } -Field3D FDDX(const Field3D &v, const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D FDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc, + const std::string& method, const std::string& region) { return bout::derivatives::index::FDDX(v, f, outloc, method, region) / f.getCoordinates(outloc)->dx; } @@ -466,8 +471,8 @@ Coordinates::FieldMetric FDDY(const Field2D& v, const Field2D& f, CELL_LOC outlo / f.getCoordinates(outloc)->dy; } -Field3D FDDY(const Field3D &v, const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D FDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc, + const std::string& method, const std::string& region) { return bout::derivatives::index::FDDY(v, f, outloc, method, region) / f.getCoordinates(outloc)->dy; } @@ -480,8 +485,8 @@ Coordinates::FieldMetric FDDZ(const Field2D& v, const Field2D& f, CELL_LOC outlo / f.getCoordinates(outloc)->dz; } -Field3D FDDZ(const Field3D &v, const Field3D &f, CELL_LOC outloc, const std::string &method, - const std::string& region) { +Field3D FDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc, + const std::string& method, const std::string& region) { return bout::derivatives::index::FDDZ(v, f, outloc, method, region) / f.getCoordinates(outloc)->dz; } diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx index 0355bdcc67..e9e913fdc5 100644 --- a/src/sys/expressionparser.cxx +++ b/src/sys/expressionparser.cxx @@ -26,8 +26,8 @@ #include +#include "bout/utils.hxx" #include "bout/sys/gettext.hxx" -#include "utils.hxx" using std::list; using std::string; @@ -43,7 +43,6 @@ double FieldGenerator::generate(const Context& ctx) { return generate(ctx.x(), ctx.y(), ctx.z(), ctx.t()); } - ///////////////////////////////////////////// namespace { // These classes only visible in this file @@ -54,9 +53,7 @@ class FieldX : public FieldGenerator { FieldGeneratorPtr clone(const list UNUSED(args)) override { return std::make_shared(); } - double generate(const Context& ctx) override { - return ctx.x(); - } + double generate(const Context& ctx) override { return ctx.x(); } std::string str() const override { return "x"s; } }; @@ -65,9 +62,7 @@ class FieldY : public FieldGenerator { FieldGeneratorPtr clone(const list UNUSED(args)) override { return std::make_shared(); } - double generate(const Context& ctx) override { - return ctx.y(); - } + double generate(const Context& ctx) override { return ctx.y(); } std::string str() const override { return "y"s; } }; @@ -76,9 +71,7 @@ class FieldZ : public FieldGenerator { FieldGeneratorPtr clone(const list UNUSED(args)) override { return std::make_shared(); } - double generate(const Context& ctx) override { - return ctx.z(); - } + double generate(const Context& ctx) override { return ctx.z(); } std::string str() const override { return "z"; } }; @@ -87,9 +80,7 @@ class FieldT : public FieldGenerator { FieldGeneratorPtr clone(const list UNUSED(args)) override { return std::make_shared(); } - double generate(const Context& ctx) override { - return ctx.t(); - } + double generate(const Context& ctx) override { return ctx.t(); } std::string str() const override { return "t"s; } }; @@ -100,6 +91,7 @@ class FieldParam : public FieldGenerator { return ctx.get(name); // Get a parameter } std::string str() const override { return "{"s + name + "}"s; } + private: std::string name; // The name of the parameter to look up }; @@ -135,56 +127,59 @@ class FieldContext : public FieldGenerator { result += "]("s + expr->str() + ")"s; return result; } + private: variable_list variables; ///< A list of context variables to modify FieldGeneratorPtr expr; ///< The expression to evaluate in the new context }; - /// Sum expressions in a loop, given symbol, count and expression - class FieldSum : public FieldGenerator { - public: - /// Loop a symbol counter SYM from 0 to count-1 - /// The count is calculated by evaluating COUNTEXPR, which must be a non-negative integer - /// Each iteration the expression EXPR is evaluated and the results summed. - FieldSum(const std::string& sym, FieldGeneratorPtr countexpr, FieldGeneratorPtr expr) - : sym(sym), countexpr(countexpr), expr(expr) {} - - double generate(const Context& ctx) override { - // Get the count by evaluating the count expression - BoutReal countval = countexpr->generate(ctx); - int count = ROUND(countval); - - // Check that the count is a non-negaitve integer - if (fabs(countval - static_cast(count)) > 1e-4) { - throw BoutException("Count {:e} is not an integer in sum expression", countval); - } - if (count < 0) { - throw BoutException("Negative count {:d} in sum expression", count); - } +/// Sum expressions in a loop, given symbol, count and expression +class FieldSum : public FieldGenerator { +public: + /// Loop a symbol counter SYM from 0 to count-1 + /// The count is calculated by evaluating COUNTEXPR, which must be a non-negative integer + /// Each iteration the expression EXPR is evaluated and the results summed. + FieldSum(const std::string& sym, FieldGeneratorPtr countexpr, FieldGeneratorPtr expr) + : sym(sym), countexpr(countexpr), expr(expr) {} - BoutReal result {0.0}; - Context new_context{ctx}; // Make a copy, so the counter value can be set - for (int i = 0; i < count; i++) { - // Evaluate the expression, setting the given symbol to the loop counter - new_context.set(sym, i); - result += expr->generate(new_context); - } - return result; + double generate(const Context& ctx) override { + // Get the count by evaluating the count expression + BoutReal countval = countexpr->generate(ctx); + int count = ROUND(countval); + + // Check that the count is a non-negaitve integer + if (fabs(countval - static_cast(count)) > 1e-4) { + throw BoutException("Count {:e} is not an integer in sum expression", countval); } - - std::string str() const override { - return "sum("s + sym + ","s + countexpr->str() + ","s + expr->str() + ")"s; + if (count < 0) { + throw BoutException("Negative count {:d} in sum expression", count); } - private: - std::string sym; - FieldGeneratorPtr countexpr, expr; - }; - + + BoutReal result{0.0}; + Context new_context{ctx}; // Make a copy, so the counter value can be set + for (int i = 0; i < count; i++) { + // Evaluate the expression, setting the given symbol to the loop counter + new_context.set(sym, i); + result += expr->generate(new_context); + } + return result; + } + + std::string str() const override { + return "sum("s + sym + ","s + countexpr->str() + ","s + expr->str() + ")"s; + } + +private: + std::string sym; + FieldGeneratorPtr countexpr, expr; +}; + } // namespace FieldGeneratorPtr FieldBinary::clone(const list args) { - if (args.size() != 2) + if (args.size() != 2) { throw ParseException("Binary operator expecting 2 arguments. Got {{}}", args.size()); + } return std::make_shared(args.front(), args.back(), op); } @@ -192,12 +187,17 @@ FieldGeneratorPtr FieldBinary::clone(const list args) { BoutReal FieldBinary::generate(const Context& ctx) { BoutReal lval = lhs->generate(ctx); BoutReal rval = rhs->generate(ctx); - switch(op) { - case '+': return lval + rval; - case '-': return lval - rval; - case '*': return lval * rval; - case '/': return lval / rval; - case '^': return pow(lval, rval); + switch (op) { + case '+': + return lval + rval; + case '-': + return lval - rval; + case '*': + return lval * rval; + case '/': + return lval / rval; + case '^': + return pow(lval, rval); } // Unknown operator. throw ParseException("Unknown binary operator '{:c}'", op); @@ -241,7 +241,7 @@ FieldGeneratorPtr ExpressionParser::parseString(const string& input) const { if (lex.curtok != 0) { throw ParseException("Tokens remaining unparsed in '{:s}'", input); } - + return expr; } @@ -249,7 +249,8 @@ FieldGeneratorPtr ExpressionParser::parseString(const string& input) const { // Private functions std::multiset -ExpressionParser::fuzzyFind(const std::string& name, std::string::size_type max_distance) const { +ExpressionParser::fuzzyFind(const std::string& name, + std::string::size_type max_distance) const { std::multiset matches; for (const auto& key : gen) { if ((key.first != name) and (lowercase(key.first) == lowercase(name))) { @@ -399,9 +400,10 @@ FieldGeneratorPtr ExpressionParser::parseParenExpr(LexInfo& lex) const { FieldGeneratorPtr g = parseExpression(lex); - if ((lex.curtok != ')') && (lex.curtok != ']')) + if ((lex.curtok != ')') && (lex.curtok != ']')) { throw ParseException("Expecting ')' or ']' but got curtok={:d} ({:c})", static_cast(lex.curtok), static_cast(lex.curtok)); + } lex.nextToken(); // eat ')' return g; @@ -412,25 +414,27 @@ FieldGeneratorPtr ExpressionParser::parseContextExpr(LexInfo& lex) const { lex.nextToken(); // eat '[' FieldContext::variable_list variables; - + while (lex.curtok != ']') { if (lex.curtok == 0) { throw ParseException("Expecting ']' in context expression"); } - + // Definition, ident = expression // First comes the identifier symbol if (lex.curtok != -2) { - throw ParseException("Expecting an identifier in context expression, but got curtok={:d} ({:c})", - static_cast(lex.curtok), lex.curtok); + throw ParseException( + "Expecting an identifier in context expression, but got curtok={:d} ({:c})", + static_cast(lex.curtok), lex.curtok); } string symbol = lex.curident; lex.nextToken(); - + // Now should be '=' if (lex.curtok != '=') { - throw ParseException("Expecting '=' after '{:s}' in context expression, but got curtok={:d} ({:c})", - symbol, static_cast(lex.curtok), lex.curtok); + throw ParseException( + "Expecting '=' after '{:s}' in context expression, but got curtok={:d} ({:c})", + symbol, static_cast(lex.curtok), lex.curtok); } lex.nextToken(); @@ -447,16 +451,17 @@ FieldGeneratorPtr ExpressionParser::parseContextExpr(LexInfo& lex) const { // Should now be '(' if (lex.curtok != '(') { - throw ParseException("Expecting '(' after ] context expression, but got curtok={:d} ({:c})", - static_cast(lex.curtok), static_cast(lex.curtok)); + throw ParseException( + "Expecting '(' after ] context expression, but got curtok={:d} ({:c})", + static_cast(lex.curtok), static_cast(lex.curtok)); } - + // Get the next expression to evaluate, put into FieldContext // Note: Ensure that only the first expression in parentheses is parsed // by calling parseParenExpr rather than parseExpression return std::make_shared(variables, parseParenExpr(lex)); } - + FieldGeneratorPtr ExpressionParser::parsePrimary(LexInfo& lex) const { switch (lex.curtok) { case -1: { // a number @@ -481,11 +486,12 @@ FieldGeneratorPtr ExpressionParser::parsePrimary(LexInfo& lex) const { return parseParenExpr(lex); } case '[': { - // Define a new context (scope). + // Define a new context (scope). return parseContextExpr(lex); } } - throw ParseException("Unexpected token {:d} ({:c})", static_cast(lex.curtok), static_cast(lex.curtok)); + throw ParseException("Unexpected token {:d} ({:c})", static_cast(lex.curtok), + static_cast(lex.curtok)); } FieldGeneratorPtr ExpressionParser::parseBinOpRHS(LexInfo& lex, int ExprPrec, @@ -493,26 +499,32 @@ FieldGeneratorPtr ExpressionParser::parseBinOpRHS(LexInfo& lex, int ExprPrec, while (true) { // Check for end of input - if ((lex.curtok == 0) || (lex.curtok == ')') || (lex.curtok == ',') || (lex.curtok == ']')) + if ((lex.curtok == 0) || (lex.curtok == ')') || (lex.curtok == ',') + || (lex.curtok == ']')) { return lhs; + } // Next token should be a binary operator auto it = bin_op.find(lex.curtok); - if (it == bin_op.end()) - throw ParseException("Unexpected binary operator '{:c}'", static_cast(lex.curtok)); + if (it == bin_op.end()) { + throw ParseException("Unexpected binary operator '{:c}'", + static_cast(lex.curtok)); + } FieldGeneratorPtr op = it->second.first; int TokPrec = it->second.second; - if (TokPrec < ExprPrec) + if (TokPrec < ExprPrec) { return lhs; + } lex.nextToken(); // Eat binop FieldGeneratorPtr rhs = parsePrimary(lex); - if ((lex.curtok == 0) || (lex.curtok == ')') || (lex.curtok == ',') || (lex.curtok == ']')) { + if ((lex.curtok == 0) || (lex.curtok == ')') || (lex.curtok == ',') + || (lex.curtok == ']')) { // Done list args; @@ -524,9 +536,11 @@ FieldGeneratorPtr ExpressionParser::parseBinOpRHS(LexInfo& lex, int ExprPrec, // Find next binop it = bin_op.find(lex.curtok); - if (it == bin_op.end()) - throw ParseException("Unexpected character '{:c}' ({:d})", static_cast(lex.curtok), static_cast(lex.curtok)); - + if (it == bin_op.end()) { + throw ParseException("Unexpected character '{:c}' ({:d})", + static_cast(lex.curtok), static_cast(lex.curtok)); + } + int NextPrec = it->second.second; if (TokPrec < NextPrec) { rhs = parseBinOpRHS(lex, TokPrec + 1, rhs); @@ -559,8 +573,9 @@ ExpressionParser::LexInfo::LexInfo(const std::string& input, std::string reserve } char ExpressionParser::LexInfo::nextToken() { - while (isspace(static_cast(LastChar))) + while (isspace(static_cast(LastChar))) { LastChar = static_cast(ss.get()); + } if (!ss.good()) { curtok = 0; @@ -568,7 +583,8 @@ char ExpressionParser::LexInfo::nextToken() { } // Handle numbers - if (isdigit(static_cast(LastChar)) || (LastChar == '.')) { // Number: [0-9.]+ + if (isdigit(static_cast(LastChar)) + || (LastChar == '.')) { // Number: [0-9.]+ bool gotdecimal = false, gotexponent = false; std::string NumStr; @@ -587,12 +603,14 @@ char ExpressionParser::LexInfo::nextToken() { // Next character should be a '+' or '-' or digit NumStr += 'e'; LastChar = static_cast(ss.get()); - if ((LastChar != '+') && (LastChar != '-') && !isdigit(static_cast(LastChar))) { + if ((LastChar != '+') && (LastChar != '-') + && !isdigit(static_cast(LastChar))) { throw ParseException( "ExpressionParser error: Expecting '+', '-' or number after 'e'"); } - } else if (!isdigit(static_cast(LastChar))) + } else if (!isdigit(static_cast(LastChar))) { break; + } NumStr += LastChar; LastChar = static_cast(ss.get()); @@ -669,9 +687,9 @@ char ExpressionParser::LexInfo::nextToken() { curtok = '*'; return curtok; } - + curident.clear(); - + LastChar = static_cast(ss.get()); // Skip the { do { curident += LastChar; @@ -687,7 +705,7 @@ char ExpressionParser::LexInfo::nextToken() { curtok = -3; return curtok; } - + // LastChar is unsigned, explicitly cast curtok = LastChar; LastChar = static_cast(ss.get()); diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx index 4bb05f1e4e..236de7f95b 100644 --- a/src/sys/generator_context.cxx +++ b/src/sys/generator_context.cxx @@ -1,46 +1,46 @@ #include "bout/sys/generator_context.hxx" -#include "boundary_region.hxx" +#include "bout/boundary_region.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" namespace bout { namespace generator { -Context::Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t) : localmesh(msh) { - - parameters["x"] = (loc == CELL_XLOW) ? - 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1)) : - msh->GlobalX(ix); - - parameters["y"] = (loc == CELL_YLOW) ? - PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1)) : - TWOPI * msh->GlobalY(iy); +Context::Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t) + : localmesh(msh) { - parameters["z"] = (loc == CELL_ZLOW) ? - TWOPI * (iz - 0.5) / static_cast(msh->LocalNz) : - TWOPI * iz / static_cast(msh->LocalNz); + parameters["x"] = (loc == CELL_XLOW) ? 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1)) + : msh->GlobalX(ix); + + parameters["y"] = (loc == CELL_YLOW) ? PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1)) + : TWOPI * msh->GlobalY(iy); + + parameters["z"] = (loc == CELL_ZLOW) + ? TWOPI * (iz - 0.5) / static_cast(msh->LocalNz) + : TWOPI * iz / static_cast(msh->LocalNz); parameters["t"] = t; } -Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, Mesh * msh) : localmesh(msh) { - +Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, Mesh* msh) + : localmesh(msh) { + // Add one to X index if boundary is in -x direction, so that XLOW is on the boundary int ix = (bndry->bx < 0) ? bndry->x + 1 : bndry->x; - - parameters["x"] = ((loc == CELL_XLOW) || (bndry->bx != 0)) ? - 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1)) : - msh->GlobalX(ix); + + parameters["x"] = ((loc == CELL_XLOW) || (bndry->bx != 0)) + ? 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1)) + : msh->GlobalX(ix); int iy = (bndry->by < 0) ? bndry->y + 1 : bndry->y; - parameters["y"] = ((loc == CELL_YLOW) || bndry->by) ? - PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1)) : - TWOPI * msh->GlobalY(iy); + parameters["y"] = ((loc == CELL_YLOW) || bndry->by) + ? PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1)) + : TWOPI * msh->GlobalY(iy); - parameters["z"] = (loc == CELL_ZLOW) ? - TWOPI * (iz - 0.5) / static_cast(msh->LocalNz) : - TWOPI * iz / static_cast(msh->LocalNz); + parameters["z"] = (loc == CELL_ZLOW) + ? TWOPI * (iz - 0.5) / static_cast(msh->LocalNz) + : TWOPI * iz / static_cast(msh->LocalNz); parameters["t"] = t; } diff --git a/src/sys/hyprelib.cxx b/src/sys/hyprelib.cxx index 951fea8392..e07e6fd27b 100644 --- a/src/sys/hyprelib.cxx +++ b/src/sys/hyprelib.cxx @@ -4,10 +4,10 @@ #include -#include "boutcomm.hxx" -#include "options.hxx" -#include "output.hxx" -#include "unused.hxx" +#include "bout/boutcomm.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" #include "bout/openmpwrap.hxx" #include diff --git a/src/sys/msg_stack.cxx b/src/sys/msg_stack.cxx index 3e1d26ed41..c2345f216b 100644 --- a/src/sys/msg_stack.cxx +++ b/src/sys/msg_stack.cxx @@ -25,9 +25,9 @@ **************************************************************************/ #include "bout/openmpwrap.hxx" -#include -#include #include +#include +#include #include #if BOUT_USE_OPENMP @@ -58,9 +58,7 @@ void MsgStack::pop() { if (position <= 0) { return; } - BOUT_OMP(single) { - --position; - } + BOUT_OMP(single) { --position; } } void MsgStack::pop(int id) { @@ -69,11 +67,12 @@ void MsgStack::pop(int id) { return; } #endif - if (id < 0) + if (id < 0) { id = 0; + } if (id <= static_cast(position)) { - position = id; + position = id; } } diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 5e5704930f..8b49b1f3f1 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -1,8 +1,8 @@ -#include -#include // Used for parsing expressions -#include -#include -#include +#include +#include // Used for parsing expressions +#include +#include +#include #include @@ -19,9 +19,9 @@ std::string Options::getDefaultSource() { return DEFAULT_SOURCE; } /// having been used constexpr auto conditionally_used_attribute = "conditionally used"; -Options *Options::root_instance{nullptr}; +Options* Options::root_instance{nullptr}; -Options &Options::root() { +Options& Options::root() { if (root_instance == nullptr) { // Create the singleton root_instance = new Options(); @@ -30,8 +30,9 @@ Options &Options::root() { } void Options::cleanup() { - if (root_instance == nullptr) + if (root_instance == nullptr) { return; + } delete root_instance; root_instance = nullptr; } @@ -39,7 +40,8 @@ void Options::cleanup() { Options::Options(const Options& other) : value(other.value), attributes(other.attributes), parent_instance(other.parent_instance), full_name(other.full_name), - is_section(other.is_section), children(other.children), value_used(other.value_used) { + is_section(other.is_section), children(other.children), + value_used(other.value_used) { // Ensure that this is the parent of all children, // otherwise will point to the original Options instance @@ -65,9 +67,11 @@ Options::Options(std::initializer_list> values) // use a lambda. And to make that lambda recursive, we need to have // a nested lambda. auto append_section_name = [](auto& children, const std::string& section_name) { - auto append_impl = [](auto& children, const std::string& section_name, auto& append_ref) mutable -> void { + auto append_impl = [](auto& children, const std::string& section_name, + auto& append_ref) mutable -> void { for (auto& child : children) { - child.second.full_name = fmt::format("{}:{}", section_name, child.second.full_name); + child.second.full_name = + fmt::format("{}:{}", section_name, child.second.full_name); if (child.second.is_section) { append_ref(child.second.children, section_name, append_ref); } @@ -91,10 +95,11 @@ Options& Options::operator[](const std::string& name) { TRACE("Options::operator[]"); if (isValue()) { - throw BoutException( - _("Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a section.\n" - "This is likely the result of clashing input options, and you may have to rename one of them.\n"), - full_name, name); + throw BoutException(_("Trying to index Option '{0}' with '{1}', but '{0}' is a " + "value, not a section.\n" + "This is likely the result of clashing input options, and you " + "may have to rename one of them.\n"), + full_name, name); } if (name.empty()) { @@ -129,10 +134,11 @@ const Options& Options::operator[](const std::string& name) const { TRACE("Options::operator[] const"); if (isValue()) { - throw BoutException( - _("Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a section.\n" - "This is likely the result of clashing input options, and you may have to rename one of them.\n"), - full_name, name); + throw BoutException(_("Trying to index Option '{0}' with '{1}', but '{0}' is a " + "value, not a section.\n" + "This is likely the result of clashing input options, and you " + "may have to rename one of them.\n"), + full_name, name); } if (name.empty()) { @@ -290,7 +296,8 @@ void Options::assign<>(Tensor val, std::string source) { _set_no_check(std::move(val), std::move(source)); } -template <> std::string Options::as(const std::string& UNUSED(similar_to)) const { +template <> +std::string Options::as(const std::string& UNUSED(similar_to)) const { if (is_section) { throw BoutException(_("Option {:s} has no value"), full_name); } @@ -299,7 +306,7 @@ template <> std::string Options::as(const std::string& UNUSED(simil value_used = true; std::string result = bout::utils::variantToString(value); - + output_info << _("\tOption ") << full_name << " = " << result; if (attributes.count("source")) { // Specify the source of the setting @@ -331,7 +338,8 @@ double parseExpression(const Options::ValueType& value, const Options* options, } } // namespace -template <> int Options::as(const int& UNUSED(similar_to)) const { +template <> +int Options::as(const int& UNUSED(similar_to)) const { if (is_section) { throw BoutException(_("Option {:s} has no value"), full_name); } @@ -340,14 +348,14 @@ template <> int Options::as(const int& UNUSED(similar_to)) const { if (bout::utils::holds_alternative(value)) { result = bout::utils::get(value); - + } else { // Cases which get a BoutReal then check if close to an integer BoutReal rval; - + if (bout::utils::holds_alternative(value)) { rval = bout::utils::get(value); - + } else if (bout::utils::holds_alternative(value)) { rval = parseExpression(value, this, "integer", full_name); @@ -355,10 +363,10 @@ template <> int Options::as(const int& UNUSED(similar_to)) const { // Another type which can't be converted throw BoutException(_("Value for option {:s} is not an integer"), full_name); } - + // Convert to int by rounding result = ROUND(rval); - + // Check that the value is close to an integer if (fabs(rval - static_cast(result)) > 1e-3) { throw BoutException(_("Value for option {:s} = {:e} is not an integer"), full_name, @@ -378,19 +386,20 @@ template <> int Options::as(const int& UNUSED(similar_to)) const { return result; } -template <> BoutReal Options::as(const BoutReal& UNUSED(similar_to)) const { +template <> +BoutReal Options::as(const BoutReal& UNUSED(similar_to)) const { if (is_section) { throw BoutException(_("Option {:s} has no value"), full_name); } BoutReal result; - + if (bout::utils::holds_alternative(value)) { result = static_cast(bout::utils::get(value)); - + } else if (bout::utils::holds_alternative(value)) { result = bout::utils::get(value); - + } else if (bout::utils::holds_alternative(value)) { result = parseExpression(value, this, "BoutReal", full_name); @@ -398,39 +407,40 @@ template <> BoutReal Options::as(const BoutReal& UNUSED(similar_to)) c throw BoutException(_("Value for option {:s} cannot be converted to a BoutReal"), full_name); } - + // Mark this option as used value_used = true; - + output_info << _("\tOption ") << full_name << " = " << result; if (attributes.count("source")) { // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } output_info << endl; - + return result; } -template <> bool Options::as(const bool& UNUSED(similar_to)) const { +template <> +bool Options::as(const bool& UNUSED(similar_to)) const { if (is_section) { throw BoutException(_("Option {:s} has no value"), full_name); } - + bool result; - + if (bout::utils::holds_alternative(value)) { result = bout::utils::get(value); - - } else if(bout::utils::holds_alternative(value)) { + + } else if (bout::utils::holds_alternative(value)) { // case-insensitve check, so convert string to lower case const auto strvalue = lowercase(bout::utils::get(value)); - + if ((strvalue == "y") or (strvalue == "yes") or (strvalue == "t") or (strvalue == "true") or (strvalue == "1")) { result = true; } else if ((strvalue == "n") or (strvalue == "no") or (strvalue == "f") - or (strvalue == "false") or (strvalue == "0")) { + or (strvalue == "false") or (strvalue == "0")) { result = false; } else { throw BoutException(_("\tOption '{:s}': Boolean expected. Got '{:s}'\n"), full_name, @@ -440,11 +450,11 @@ template <> bool Options::as(const bool& UNUSED(similar_to)) const { throw BoutException(_("Value for option {:s} cannot be converted to a bool"), full_name); } - + value_used = true; - + output_info << _("\tOption ") << full_name << " = " << toString(result); - + if (attributes.count("source")) { // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; @@ -454,7 +464,8 @@ template <> bool Options::as(const bool& UNUSED(similar_to)) const { return result; } -template <> Field3D Options::as(const Field3D& similar_to) const { +template <> +Field3D Options::as(const Field3D& similar_to) const { if (is_section) { throw BoutException("Option {:s} has no value", full_name); } @@ -464,10 +475,10 @@ template <> Field3D Options::as(const Field3D& similar_to) const { if (bout::utils::holds_alternative(value)) { Field3D stored_value = bout::utils::get(value); - + // Check that meta-data is consistent ASSERT1_FIELDS_COMPATIBLE(stored_value, similar_to); - + return stored_value; } @@ -482,8 +493,9 @@ template <> Field3D Options::as(const Field3D& similar_to) const { if (bout::utils::holds_alternative(value) or bout::utils::holds_alternative(value)) { - BoutReal scalar_value = bout::utils::variantStaticCastOrThrow(value); - + BoutReal scalar_value = + bout::utils::variantStaticCastOrThrow(value); + // Get metadata from similar_to, fill field with scalar_value return filledFrom(similar_to, scalar_value); } @@ -517,17 +529,18 @@ template <> Field3D Options::as(const Field3D& similar_to) const { full_name); } -template <> Field2D Options::as(const Field2D& similar_to) const { +template <> +Field2D Options::as(const Field2D& similar_to) const { if (is_section) { throw BoutException("Option {:s} has no value", full_name); } - + // Mark value as used value_used = true; if (bout::utils::holds_alternative(value)) { Field2D stored_value = bout::utils::get(value); - + // Check that meta-data is consistent ASSERT1_FIELDS_COMPATIBLE(stored_value, similar_to); @@ -536,7 +549,8 @@ template <> Field2D Options::as(const Field2D& similar_to) const { if (bout::utils::holds_alternative(value) or bout::utils::holds_alternative(value)) { - BoutReal scalar_value = bout::utils::variantStaticCastOrThrow(value); + BoutReal scalar_value = + bout::utils::variantStaticCastOrThrow(value); // Get metadata from similar_to, fill field with scalar_value return filledFrom(similar_to, scalar_value); @@ -866,9 +880,9 @@ void Options::setConditionallyUsed() { void Options::cleanCache() { FieldFactory::get()->cleanCache(); } -std::map Options::subsections() const { - std::map sections; - for (const auto &it : children) { +std::map Options::subsections() const { + std::map sections; + for (const auto& it : children) { if (it.second.is_section) { sections[it.first] = &it.second; } diff --git a/src/sys/options/optionparser.hxx b/src/sys/options/optionparser.hxx index 382d11d0f3..ff5bb61a6f 100644 --- a/src/sys/options/optionparser.hxx +++ b/src/sys/options/optionparser.hxx @@ -42,9 +42,9 @@ class OptionParser; #ifndef __OPTIONPARSER_H__ #define __OPTIONPARSER_H__ -#include "bout_types.hxx" -#include "options.hxx" -#include +#include "bout/bout_types.hxx" +#include "bout/options.hxx" +#include /// Base class for input file types class OptionParser { @@ -53,11 +53,12 @@ public: virtual ~OptionParser() = default; /// Read \p filename into \p options - virtual void read(Options *options, const std::string &filename) = 0; + virtual void read(Options* options, const std::string& filename) = 0; /// Write \p options to \p filename - virtual void write(Options *options, const std::string &filename) = 0; - private: + virtual void write(Options* options, const std::string& filename) = 0; + +private: }; #endif // __OPTIONPARSER_H__ diff --git a/src/sys/options/options_ini.cxx b/src/sys/options/options_ini.cxx index 17f9337b3e..a1e9bcaeb1 100644 --- a/src/sys/options/options_ini.cxx +++ b/src/sys/options/options_ini.cxx @@ -49,10 +49,10 @@ * **************************************************************************/ -#include -#include -#include #include "options_ini.hxx" +#include +#include +#include #include @@ -62,48 +62,48 @@ using namespace std; * Read input file **************************************************************************/ -void OptionINI::read(Options *options, const string &filename) { +void OptionINI::read(Options* options, const string& filename) { ifstream fin; fin.open(filename.c_str()); if (!fin.good()) { throw BoutException(_("\tOptions file '{:s}' not found\n"), filename); } - - Options *section = options; // Current section + + Options* section = options; // Current section do { string buffer = getNextLine(fin); - - if(!buffer.empty()) { + + if (!buffer.empty()) { if (buffer[0] == '[') { // A section header - - auto endpos = buffer.find_last_of(']'); + + auto endpos = buffer.find_last_of(']'); if (endpos == string::npos) { throw BoutException("\t'{:s}': Missing ']'\n\tLine: {:s}", filename, buffer); } buffer = trim(buffer, "[]"); - if(buffer.empty()) { + if (buffer.empty()) { throw BoutException("\t'{:s}': Missing section name\n\tLine: {:s}", filename, buffer); } - + section = options; size_t scorepos; - while((scorepos = buffer.find_first_of(':')) != string::npos) { + while ((scorepos = buffer.find_first_of(':')) != string::npos) { // sub-section - string sectionname = trim(buffer.substr(0,scorepos)); - buffer = trim(buffer.substr(scorepos+1)); - + string sectionname = trim(buffer.substr(0, scorepos)); + buffer = trim(buffer.substr(scorepos + 1)); + section = section->getSection(sectionname); } section = section->getSection(buffer); } else { // A key=value pair - + string key, value; // Get a key = value pair parse(buffer, key, value); @@ -112,17 +112,17 @@ void OptionINI::read(Options *options, const string &filename) { // Count net number of opening and closing brackets auto count_brackets = [](const string& input) { - int nbracket = 0; - for( auto ch : input) { - if ((ch == '(') || (ch == '[')) { - ++nbracket; - } - if ((ch == ')') || (ch == ']')) { - --nbracket; - } - } - return nbracket; - }; + int nbracket = 0; + for (auto ch : input) { + if ((ch == '(') || (ch == '[')) { + ++nbracket; + } + if ((ch == ')') || (ch == ']')) { + --nbracket; + } + } + return nbracket; + }; // Starting count int count = count_brackets(value); @@ -144,35 +144,34 @@ void OptionINI::read(Options *options, const string &filename) { // Add this to the current section section->set(key, value, filename); } // section test - } // buffer.empty - } while(!fin.eof()); + } // buffer.empty + } while (!fin.eof()); fin.close(); } -void OptionINI::write(Options *options, const std::string &filename) { +void OptionINI::write(Options* options, const std::string& filename) { TRACE("OptionsINI::write"); - + std::ofstream fout; fout.open(filename, ios::out | ios::trunc); if (!fout.good()) { throw BoutException(_("Could not open output file '{:s}'\n"), filename); } - + // Call recursive function to write to file fout << fmt::format("{:uds}", *options); fout.close(); } - /************************************************************************** * Private functions **************************************************************************/ // Returns the next useful line, stripped of comments and whitespace -string OptionINI::getNextLine(ifstream &fin) { +string OptionINI::getNextLine(ifstream& fin) { string line; getline(fin, line); @@ -181,8 +180,8 @@ string OptionINI::getNextLine(ifstream &fin) { return line; } -void OptionINI::parse(const string &buffer, string &key, string &value) { - // A key/value pair, separated by a '=' +void OptionINI::parse(const string& buffer, string& key, string& value) { + // A key/value pair, separated by a '=' size_t startpos = buffer.find_first_of('='); @@ -195,8 +194,8 @@ void OptionINI::parse(const string &buffer, string &key, string &value) { } key = trim(buffer.substr(0, startpos), " \t\r\n\""); - value = trim(buffer.substr(startpos+1), " \t\r\n\""); - + value = trim(buffer.substr(startpos + 1), " \t\r\n\""); + if (key.empty()) { throw BoutException(_("\tEmpty key\n\tLine: {:s}"), buffer); } diff --git a/src/sys/options/options_ini.hxx b/src/sys/options/options_ini.hxx index b87edd446a..d06a700f09 100644 --- a/src/sys/options/options_ini.hxx +++ b/src/sys/options/options_ini.hxx @@ -38,8 +38,8 @@ class OptionINI; #include "optionparser.hxx" -#include #include +#include /// Class for reading INI style configuration files /*! @@ -48,15 +48,15 @@ class OptionINI; class OptionINI : public OptionParser { public: /// Read options from file - void read(Options *options, const std::string &filename) override; + void read(Options* options, const std::string& filename) override; /// Write options to file - void write(Options *options, const std::string &filename) override; -private: + void write(Options* options, const std::string& filename) override; +private: // Helper functions for reading - void parse(const std::string &, std::string &, std::string &); - std::string getNextLine(std::ifstream &fin); + void parse(const std::string&, std::string&, std::string&); + std::string getNextLine(std::ifstream& fin); }; #endif // __OPTIONS_INI_H__ diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx index 6b7833a783..d7ceeaea60 100644 --- a/src/sys/options/options_netcdf.cxx +++ b/src/sys/options/options_netcdf.cxx @@ -2,10 +2,10 @@ #if BOUT_HAS_NETCDF && !BOUT_HAS_LEGACY_NETCDF -#include "options_netcdf.hxx" +#include "bout/options_netcdf.hxx" -#include "bout.hxx" -#include "globals.hxx" +#include "bout/bout.hxx" +#include "bout/globals.hxx" #include "bout/mesh.hxx" #include "bout/sys/timer.hxx" diff --git a/src/sys/optionsreader.cxx b/src/sys/optionsreader.cxx index 818155d156..8624f646df 100644 --- a/src/sys/optionsreader.cxx +++ b/src/sys/optionsreader.cxx @@ -1,8 +1,8 @@ -#include -#include -#include #include -#include +#include +#include +#include +#include // Interface for option file parsers #include "options/optionparser.hxx" @@ -10,18 +10,19 @@ // Individual parsers #include "options/options_ini.hxx" -#include +#include -OptionsReader *OptionsReader::instance = nullptr; +OptionsReader* OptionsReader::instance = nullptr; OptionsReader* OptionsReader::getInstance() { - if (instance == nullptr) + if (instance == nullptr) { instance = new OptionsReader(); // Create the singleton object + } return instance; } -void OptionsReader::read(Options *options, const std::string& filename) { +void OptionsReader::read(Options* options, const std::string& filename) { TRACE("OptionsReader::read"); if (filename.empty()) { throw BoutException("OptionsReader::read passed empty filename\n"); @@ -32,7 +33,7 @@ void OptionsReader::read(Options *options, const std::string& filename) { OptionINI{}.read(options, filename); } -void OptionsReader::write(Options *options, const std::string& filename) { +void OptionsReader::write(Options* options, const std::string& filename) { TRACE("OptionsReader::write"); if (filename.empty()) { throw BoutException("OptionsReader::write passed empty filename\n"); @@ -47,7 +48,8 @@ void OptionsReader::parseCommandLine(Options* options, int argc, char** argv) { return parseCommandLine(options, std::vector(argv, argv + argc)); } -void OptionsReader::parseCommandLine(Options *options, const std::vector& argv) { +void OptionsReader::parseCommandLine(Options* options, + const std::vector& argv) { // A key/value pair, separated by a '=' or a switch // and sections separated with an '_' but don't start with a '-' @@ -70,7 +72,8 @@ void OptionsReader::parseCommandLine(Options *options, const std::vectorgetSection(section); + while ((scorepos = key.find_first_of(':')) != std::string::npos) { + // sub-section + std::string section = key.substr(0, scorepos); + key = trim(key.substr(scorepos + 1)); + options = options->getSection(section); } if (key.empty() || value.empty()) { diff --git a/src/sys/output.cxx b/src/sys/output.cxx index e6d3b8efa3..0208733f16 100644 --- a/src/sys/output.cxx +++ b/src/sys/output.cxx @@ -26,8 +26,8 @@ #include #include #include -#include -#include +#include +#include void Output::enable() { add(std::cout); @@ -79,7 +79,7 @@ void Output::print(const std::string& message) { std::cout.flush(); } -Output *Output::getInstance() { +Output* Output::getInstance() { static Output instance; return &instance; } diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index 09c30fa75d..c772076131 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -2,33 +2,33 @@ #if BOUT_HAS_PETSC -#include "boutcomm.hxx" -#include "options.hxx" +#include "bout/boutcomm.hxx" +#include "bout/options.hxx" #include "bout/openmpwrap.hxx" #include -#include +#include // Define all the static member variables int PetscLib::count = 0; -char PetscLib::help[] = "BOUT++: Uses finite difference methods to solve plasma fluid problems in curvilinear coordinates"; -int *PetscLib::pargc = nullptr; -char ***PetscLib::pargv = nullptr; +char PetscLib::help[] = "BOUT++: Uses finite difference methods to solve plasma fluid " + "problems in curvilinear coordinates"; +int* PetscLib::pargc = nullptr; +char*** PetscLib::pargv = nullptr; PetscLogEvent PetscLib::USER_EVENT = 0; PetscLib::PetscLib(Options* opt) { - BOUT_OMP(critical(PetscLib)) - { - if(count == 0) { + BOUT_OMP(critical(PetscLib)) { + if (count == 0) { // Initialise PETSc output << "Initialising PETSc\n"; PETSC_COMM_WORLD = BoutComm::getInstance()->getComm(); - PetscInitialize(pargc,pargv,PETSC_NULL,help); + PetscInitialize(pargc, pargv, PETSC_NULL, help); PetscPopSignalHandler(); - PetscLogEventRegister("Total BOUT++",0,&USER_EVENT); - PetscLogEventBegin(USER_EVENT,0,0,0,0); + PetscLogEventRegister("Total BOUT++", 0, &USER_EVENT); + PetscLogEventBegin(USER_EVENT, 0, 0, 0, 0); // Load global PETSc options from the [petsc] section of the input setPetscOptions(Options::root()["petsc"], ""); @@ -52,13 +52,12 @@ PetscLib::PetscLib(Options* opt) { } PetscLib::~PetscLib() { - BOUT_OMP(critical(PetscLib)) - { + BOUT_OMP(critical(PetscLib)) { count--; - if(count == 0) { + if (count == 0) { // Finalise PETSc output << "Finalising PETSc\n"; - PetscLogEventEnd(USER_EVENT,0,0,0,0); + PetscLogEventEnd(USER_EVENT, 0, 0, 0, 0); PetscFinalize(); } } @@ -89,11 +88,10 @@ void PetscLib::setOptionsFromInputFile(SNES& snes) { } void PetscLib::cleanup() { - BOUT_OMP(critical(PetscLib)) - { - if(count > 0) { + BOUT_OMP(critical(PetscLib)) { + if (count > 0) { output << "Finalising PETSc. Warning: Instances of PetscLib still exist.\n"; - PetscLogEventEnd(USER_EVENT,0,0,0,0); + PetscLogEventEnd(USER_EVENT, 0, 0, 0, 0); PetscFinalize(); count = 0; // ensure that finalise is not called again later @@ -106,28 +104,29 @@ void PetscLib::setPetscOptions(Options& options, const std::string& prefix) { for (auto& i : options.getChildren()) { if (not i.second.isValue()) { throw BoutException("Found subsection {} in {} when reading PETSc options - only " - "values are allowed in the PETSc options, not subsections", i.first, options.str()); + "values are allowed in the PETSc options, not subsections", + i.first, options.str()); } // Note, option names in the input file don't start with "-", but need to be passed // to PETSc with "-" prepended - auto petsc_option_name = "-"+prefix+i.first; + auto petsc_option_name = "-" + prefix + i.first; auto str_value = i.second.as(); // "true" is the value given to an option with no value, when read from BOUT.inp. Also // when nullptr is passed to PetscOptionsSetValue for a boolean option, it defaults to // true so we should always be OK passing nullptr for null or "true". - const char* value = - str_value == "true" ? nullptr : str_value.c_str(); + const char* value = str_value == "true" ? nullptr : str_value.c_str(); #if PETSC_VERSION_GE(3, 7, 0) const auto ierr = PetscOptionsSetValue(nullptr, petsc_option_name.c_str(), value); #else -// no PetscOptions as first argument + // no PetscOptions as first argument const auto ierr = PetscOptionsSetValue(petsc_option_name.c_str(), value); #endif if (ierr) { - throw BoutException("PetscOptionsSetValue returned error code {} when setting {}", ierr, petsc_option_name); + throw BoutException("PetscOptionsSetValue returned error code {} when setting {}", + ierr, petsc_option_name); } } } diff --git a/src/sys/range.cxx b/src/sys/range.cxx index e0ea387199..f6f4849acd 100644 --- a/src/sys/range.cxx +++ b/src/sys/range.cxx @@ -1,10 +1,10 @@ #include -RangeIterator::RangeIterator(int start, int end, RangeIterator* join) - : is(start), ie(end), n(join) { - +RangeIterator::RangeIterator(int start, int end, RangeIterator* join) + : is(start), ie(end), n(join) { + cur = this; - if(start > end) { + if (start > end) { // Null range cur = n; } @@ -16,14 +16,14 @@ RangeIterator::RangeIterator(int start, int end, RangeIterator* join) } RangeIterator::RangeIterator(int start, int end, const RangeIterator& join) - : is(start), ie(end) { - + : is(start), ie(end) { + cur = this; n = new RangeIterator(join); delete_next = true; - - if(start > end) { + + if (start > end) { // Null range cur = n; } @@ -35,13 +35,14 @@ RangeIterator::RangeIterator(int start, int end, const RangeIterator& join) } RangeIterator::RangeIterator(const RangeIterator& r) { - ind = r.ind; - is = r.is; - ie = r.ie; - n = r.n; - cur = r.cur; - if(cur == &r) + ind = r.ind; + is = r.is; + ie = r.ie; + n = r.n; + cur = r.cur; + if (cur == &r) { cur = this; + } curend = r.curend; } @@ -55,8 +56,8 @@ void RangeIterator::first() { cur = this; ind = is; curend = ie; - - if(is > ie) { + + if (is > ie) { // Null range, skip to next cur = cur->n; if (cur != nullptr) { @@ -67,10 +68,11 @@ void RangeIterator::first() { } void RangeIterator::next() { - if(isDone()) + if (isDone()) { return; + } ind++; - if(ind > curend) { + if (ind > curend) { // End of this range cur = cur->n; if (cur != nullptr) { @@ -83,38 +85,43 @@ void RangeIterator::next() { bool RangeIterator::isDone() const { return cur == nullptr; } -bool RangeIterator::intersects(const RangeIterator &other, bool all) const { - if((other.is <= ie) && (other.ie >= is)) +bool RangeIterator::intersects(const RangeIterator& other, bool all) const { + if ((other.is <= ie) && (other.ie >= is)) { return true; - if (all && (n != nullptr)) + } + if (all && (n != nullptr)) { return n->intersects(other, all); + } return false; } bool RangeIterator::intersects(int ind, bool all) const { - if( (is <= ind) && (ie >= ind) ) + if ((is <= ind) && (ie >= ind)) { return true; - if (all && (n != nullptr)) + } + if (all && (n != nullptr)) { return n->intersects(ind, all); + } return false; } -RangeIterator& RangeIterator::operator=(const RangeIterator &r) { - ind = r.ind; - is = r.is; - ie = r.ie; - n = r.n; - cur = r.cur; - if(cur == &r) +RangeIterator& RangeIterator::operator=(const RangeIterator& r) { + ind = r.ind; + is = r.is; + ie = r.ie; + n = r.n; + cur = r.cur; + if (cur == &r) { cur = this; + } curend = r.curend; - + return *this; } -RangeIterator& RangeIterator::operator+=(const RangeIterator &r) { +RangeIterator& RangeIterator::operator+=(const RangeIterator& r) { // For now just put at the end - RangeIterator *it = this; + RangeIterator* it = this; while (it->n != nullptr) { it = it->n; } @@ -123,41 +130,42 @@ RangeIterator& RangeIterator::operator+=(const RangeIterator &r) { return *this; } -RangeIterator& RangeIterator::operator-=(const RangeIterator &r) { +RangeIterator& RangeIterator::operator-=(const RangeIterator& r) { // Find any ranges which overlap - RangeIterator *it = this; - do{ - const RangeIterator *itr = &r; + RangeIterator* it = this; + do { + const RangeIterator* itr = &r; do { // Check if it and itr overlap - if( it->intersects(*itr, false) ){ + if (it->intersects(*itr, false)) { // Overlap - - if( (itr->is <= it->is) && (itr->ie >= it->ie) ) { + + if ((itr->is <= it->is) && (itr->ie >= it->ie)) { // Total overlap - is = 1; ie = 0; // Make invalid - }else if( (itr->is > it->is) && (itr->ie >= it->ie) ) { + is = 1; + ie = 0; // Make invalid + } else if ((itr->is > it->is) && (itr->ie >= it->ie)) { // Removing upper end - it->ie = itr->is-1; - }else if( (itr->is <= it->is) && (itr->ie < it->ie) ) { + it->ie = itr->is - 1; + } else if ((itr->is <= it->is) && (itr->ie < it->ie)) { // Removing lower end - it->is = itr->ie+1; - }else { + it->is = itr->ie + 1; + } else { // Removing a chunk from the middle - it->n = new RangeIterator(itr->ie+1, it->ie, it->n); // Upper piece + it->n = new RangeIterator(itr->ie + 1, it->ie, it->n); // Upper piece it->delete_next = true; - it->ie = itr->is-1; // Truncate lower piece + it->ie = itr->is - 1; // Truncate lower piece } } itr = itr->n; } while (itr != nullptr); // Check if this range is still valid - if(is > ie) { + if (is > ie) { // Invalid range if (it->n != nullptr) { // Copy from next one - RangeIterator *tmp = it->n; + RangeIterator* tmp = it->n; *it = *it->n; // and delete the redundant object delete tmp; diff --git a/src/sys/slepclib.cxx b/src/sys/slepclib.cxx index 947e47f3b4..82614febb8 100644 --- a/src/sys/slepclib.cxx +++ b/src/sys/slepclib.cxx @@ -3,43 +3,45 @@ #if BOUT_HAS_SLEPC #include -#include +#include // Define all the static member variables int SlepcLib::count = 0; -char SlepcLib::help[] = "BOUT++: Uses finite difference methods to solve plasma fluid problems in curvilinear coordinates"; +char SlepcLib::help[] = "BOUT++: Uses finite difference methods to solve plasma fluid " + "problems in curvilinear coordinates"; int* SlepcLib::pargc = nullptr; char*** SlepcLib::pargv = nullptr; PetscLogEvent SlepcLib::USER_EVENT = 0; SlepcLib::SlepcLib() { - if(count == 0) { + if (count == 0) { // Initialise SLEPc output << "Initialising SLEPc\n"; - SlepcInitialize(pargc,pargv,PETSC_NULL,help); - PetscLogEventRegister("Total BOUT++",0,&USER_EVENT); - PetscLogEventBegin(USER_EVENT,0,0,0,0); + SlepcInitialize(pargc, pargv, PETSC_NULL, help); + PetscLogEventRegister("Total BOUT++", 0, &USER_EVENT); + PetscLogEventBegin(USER_EVENT, 0, 0, 0, 0); } count++; } SlepcLib::~SlepcLib() { count--; - if(count == 0) { + if (count == 0) { // Finalise Slepc output << "Finalising SLEPc\n"; - PetscLogEventEnd(USER_EVENT,0,0,0,0); + PetscLogEventEnd(USER_EVENT, 0, 0, 0, 0); SlepcFinalize(); } } void SlepcLib::cleanup() { - if(count == 0) + if (count == 0) { return; // Either never initialised, or already cleaned up + } output << "Finalising SLEPCc. Warning: Instances of SlepcLib still exist.\n"; - PetscLogEventEnd(USER_EVENT,0,0,0,0); + PetscLogEventEnd(USER_EVENT, 0, 0, 0, 0); SlepcFinalize(); count = 0; // ensure that finalise is not called again later diff --git a/src/sys/type_name.cxx b/src/sys/type_name.cxx index 61cf6bd331..c1082c499a 100644 --- a/src/sys/type_name.cxx +++ b/src/sys/type_name.cxx @@ -1,8 +1,8 @@ #include "bout/sys/type_name.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" namespace bout { namespace utils { @@ -11,7 +11,7 @@ template <> std::string typeName() { return "bool"; } - + template <> std::string typeName() { return "int"; @@ -41,5 +41,5 @@ template <> std::string typeName() { return "FieldPerp"; } -} -} +} // namespace utils +} // namespace bout diff --git a/src/sys/utils.cxx b/src/sys/utils.cxx index d562bade30..b31a8d6fb4 100644 --- a/src/sys/utils.cxx +++ b/src/sys/utils.cxx @@ -23,16 +23,16 @@ * **************************************************************************/ -#include -#include -#include -#include -#include #include -#include +#include #include +#include +#include #include #include +#include +#include +#include #include "fmt/chrono.h" @@ -43,8 +43,9 @@ // Allocate memory for a copy of given string char* copy_string(const char* s) { - if (s == nullptr) + if (s == nullptr) { return nullptr; + } const auto n = strlen(s); auto s2 = static_cast(malloc(n + 1)); @@ -53,7 +54,7 @@ char* copy_string(const char* s) { } // Convert a string to lower case -const std::string lowercase(const std::string &str) { +const std::string lowercase(const std::string& str) { std::string strlow(str); std::transform(strlow.begin(), strlow.end(), strlow.begin(), ::tolower); @@ -69,11 +70,11 @@ const std::string uppercase(const std::string& str) { } // Convert to lowercase, except for inside strings -const std::string lowercasequote(const std::string &str) { +const std::string lowercasequote(const std::string& str) { std::string strlow(str); bool quote = false, dquote = false; - for (char &i : strlow) { + for (char& i : strlow) { if (i == '\'') { quote ^= true; } else if (i == '"') { @@ -85,56 +86,57 @@ const std::string lowercasequote(const std::string &str) { return strlow; } -BoutReal stringToReal(const std::string &s) { +BoutReal stringToReal(const std::string& s) { std::stringstream ss(s); BoutReal val; - if(!(ss >> val)) { + if (!(ss >> val)) { throw BoutException("Could not convert string '{:s}' to BoutReal\n", s); } return val; } -int stringToInt(const std::string &s) { +int stringToInt(const std::string& s) { std::stringstream ss(s); int val; - if(!(ss >> val)) { + if (!(ss >> val)) { throw BoutException("Could not convert string '{:s}' to int\n", s); } return val; } -std::list &strsplit(const std::string &s, char delim, std::list &elems) { - std::stringstream ss(s); - std::string item; - while(std::getline(ss, item, delim)) { - elems.push_back(item); - } - return elems; +std::list& strsplit(const std::string& s, char delim, + std::list& elems) { + std::stringstream ss(s); + std::string item; + while (std::getline(ss, item, delim)) { + elems.push_back(item); + } + return elems; } -std::list strsplit(const std::string &s, char delim) { - std::list elems; - return strsplit(s, delim, elems); +std::list strsplit(const std::string& s, char delim) { + std::list elems; + return strsplit(s, delim, elems); } // Strips leading and trailing spaces from a string -std::string trim(const std::string &s, const std::string &c) { +std::string trim(const std::string& s, const std::string& c) { return trimLeft(trimRight(s, c), c); } -std::string trimRight(const std::string &s, const std::string &c) { +std::string trimRight(const std::string& s, const std::string& c) { std::string str(s); - return str.erase(s.find_last_not_of(c)+1); + return str.erase(s.find_last_not_of(c) + 1); } -std::string trimLeft(const std::string &s, const std::string &c) { +std::string trimLeft(const std::string& s, const std::string& c) { std::string str(s); return str.erase(0, s.find_first_not_of(c)); } // Strips the comments from a string // This is the compliment of trimLeft -std::string trimComments(const std::string &s, const std::string &c) { +std::string trimComments(const std::string& s, const std::string& c) { return s.substr(0, s.find_first_of(c)); } diff --git a/tests/MMS/GBS/gbs.cxx b/tests/MMS/GBS/gbs.cxx index 935bcd80f0..d0d1fcb039 100644 --- a/tests/MMS/GBS/gbs.cxx +++ b/tests/MMS/GBS/gbs.cxx @@ -14,27 +14,28 @@ #include "gbs.hxx" -#include -#include -#include +#include +#include +#include int GBS::init(bool restarting) { - Options *opt = Options::getRoot(); + Options* opt = Options::getRoot(); coords = mesh->getCoordinates(); // Switches in model section - Options *optgbs = opt->getSection("GBS"); + Options* optgbs = opt->getSection("GBS"); OPTION(optgbs, ionvis, false); - if(ionvis) + if (ionvis) { OPTION(optgbs, Ti, 10); // Ion temperature [eV] + } OPTION(optgbs, elecvis, false); // Include electron viscosity? OPTION(optgbs, resistivity, true); // Include resistivity? OPTION(optgbs, estatic, true); // Electrostatic? - - // option for ExB Poisson Bracket + + // option for ExB Poisson Bracket int bm_exb_flag; - OPTION(optgbs, bm_exb_flag, 2); // Arakawa default - switch(bm_exb_flag) { + OPTION(optgbs, bm_exb_flag, 2); // Arakawa default + switch (bm_exb_flag) { case 0: { bm_exb = BRACKET_STD; output << "\tBrackets for ExB: default differencing\n"; @@ -62,12 +63,15 @@ int GBS::init(bool restarting) { OPTION(opt->getSection("solver"), mms, false); - if(ionvis) + if (ionvis) { SAVE_REPEAT(Gi); - if(elecvis) + } + if (elecvis) { SAVE_REPEAT(Ge); - if(resistivity) + } + if (resistivity) { SAVE_REPEAT(nu); + } // Normalisation OPTION(optgbs, Tnorm, 100); // Reference temperature [eV] @@ -78,167 +82,194 @@ int GBS::init(bool restarting) { output.write("Normalisation Te={:e}, Ne={:e}, B={:e}\n", Tnorm, Nnorm, Bnorm); SAVE_ONCE4(Tnorm, Nnorm, Bnorm, AA); // Save - Cs0 = sqrt(SI::qe*Tnorm / (AA*SI::Mp)); // Reference sound speed [m/s] - Omega_ci = SI::qe*Bnorm / (AA*SI::Mp); // Ion cyclotron frequency [1/s] - rho_s0 = Cs0 / Omega_ci; - - mi_me = AA*SI::Mp/SI::Me; - beta_e = SI::qe*Tnorm*Nnorm / (SQ(Bnorm)/SI::mu0); - + Cs0 = sqrt(SI::qe * Tnorm / (AA * SI::Mp)); // Reference sound speed [m/s] + Omega_ci = SI::qe * Bnorm / (AA * SI::Mp); // Ion cyclotron frequency [1/s] + rho_s0 = Cs0 / Omega_ci; + + mi_me = AA * SI::Mp / SI::Me; + beta_e = SI::qe * Tnorm * Nnorm / (SQ(Bnorm) / SI::mu0); + output.write("\tmi_me={:e}, beta_e={:e}\n", mi_me, beta_e); SAVE_ONCE2(mi_me, beta_e); output.write("\t Cs={:e}, rho_s={:e}, Omega_ci={:e}\n", Cs0, rho_s0, Omega_ci); SAVE_ONCE3(Cs0, rho_s0, Omega_ci); - + // Collision times - BoutReal Coulomb = 6.6 - 0.5*log(Nnorm * 1e-20) + 1.5*log(Tnorm); - tau_e0 = 1. / (2.91e-6 * (Nnorm / 1e6) * Coulomb * pow(Tnorm, -3./2)); - tau_i0 = sqrt(AA) / (4.80e-8 * (Nnorm / 1e6) * Coulomb * pow(Tnorm, -3./2)); - + BoutReal Coulomb = 6.6 - 0.5 * log(Nnorm * 1e-20) + 1.5 * log(Tnorm); + tau_e0 = 1. / (2.91e-6 * (Nnorm / 1e6) * Coulomb * pow(Tnorm, -3. / 2)); + tau_i0 = sqrt(AA) / (4.80e-8 * (Nnorm / 1e6) * Coulomb * pow(Tnorm, -3. / 2)); + output.write("\ttau_e0={:e}, tau_i0={:e}\n", tau_e0, tau_i0); - + // Get switches from each variable section - Options *optne = opt->getSection("Ne"); + Options* optne = opt->getSection("Ne"); optne->get("evolve", evolve_Ne, true); optne->get("D", Dn, 1e-3); optne->get("H", Hn, -1.0); - if(mms) { + if (mms) { Sn = 0.0; - }else { + } else { std::string source; optne->get("source", source, "0.0"); Sn = FieldFactory::get()->create3D(source, NULL, mesh); Sn /= Omega_ci; SAVE_ONCE(Sn); } - - Options *optte = opt->getSection("Te"); + + Options* optte = opt->getSection("Te"); optte->get("evolve", evolve_Te, true); optte->get("D", Dte, 1e-3); optte->get("H", Hte, -1.0); - if(mms) { + if (mms) { Sp = 0.0; - }else { + } else { std::string source; optte->get("source", source, "0.0"); Sp = FieldFactory::get()->create3D(source, NULL, mesh); Sp /= Omega_ci; SAVE_ONCE(Sp); } - - Options *optvort = opt->getSection("Vort"); + + Options* optvort = opt->getSection("Vort"); optvort->get("evolve", evolve_Vort, true); optvort->get("D", Dvort, 1e-3); optvort->get("H", Hvort, -1.0); - Options *optve = opt->getSection("VePsi"); + Options* optve = opt->getSection("VePsi"); optve->get("evolve", evolve_Ve, true); optve->get("D", Dve, 1e-3); optve->get("H", Hve, -1.0); - Options *optvi = opt->getSection("Vi"); + Options* optvi = opt->getSection("Vi"); optvi->get("evolve", evolve_Vi, true); optvi->get("D", Dvi, 1e-3); optvi->get("H", Hvi, -1.0); - + OPTION(optgbs, parallel, true); - if(!parallel) { + if (!parallel) { // No parallel dynamics evolve_Ve = false; evolve_Vi = false; } - + // If evolving, add to solver. Otherwise, set to an initial (fixed) value. - if(evolve_Ne) { solver->add(Ne, "Ne"); evars.add(Ne); } - else { initial_profile("Ne", Ne); SAVE_ONCE(Ne); } - if(evolve_Vort) { solver->add(Vort, "Vort"); evars.add(Vort); } - else { initial_profile("Vort", Vort); SAVE_ONCE(Vort); } - if(evolve_Ve) { solver->add(VePsi, "VePsi"); evars.add(VePsi); } - else { initial_profile("VePsi", VePsi); SAVE_ONCE(VePsi); } - if(evolve_Vi) { solver->add(Vi, "Vi"); evars.add(Vi); } - else { initial_profile("Vi", Vi); SAVE_ONCE(Vi);} - if(evolve_Te) { solver->add(Te, "Te"); evars.add(Te); } - else { initial_profile("Te", Te); SAVE_ONCE(Te);} - - if(evolve_Ve && (!estatic)) { + if (evolve_Ne) { + solver->add(Ne, "Ne"); + evars.add(Ne); + } else { + initial_profile("Ne", Ne); + SAVE_ONCE(Ne); + } + if (evolve_Vort) { + solver->add(Vort, "Vort"); + evars.add(Vort); + } else { + initial_profile("Vort", Vort); + SAVE_ONCE(Vort); + } + if (evolve_Ve) { + solver->add(VePsi, "VePsi"); + evars.add(VePsi); + } else { + initial_profile("VePsi", VePsi); + SAVE_ONCE(VePsi); + } + if (evolve_Vi) { + solver->add(Vi, "Vi"); + evars.add(Vi); + } else { + initial_profile("Vi", Vi); + SAVE_ONCE(Vi); + } + if (evolve_Te) { + solver->add(Te, "Te"); + evars.add(Te); + } else { + initial_profile("Te", Te); + SAVE_ONCE(Te); + } + + if (evolve_Ve && (!estatic)) { SAVE_REPEAT2(psi, Ve); } - + // Load metric tensor from the mesh, passing length and B field normalisations LoadMetric(rho_s0, Bnorm); - - if(!restarting) { + + if (!restarting) { bool startprofiles; OPTION(optgbs, startprofiles, true); - if(startprofiles) { + if (startprofiles) { // Read profiles from the mesh - Field2D NeMesh; - if(mesh->get(NeMesh, "Ne0")) { + Field2D NeMesh; + if (mesh->get(NeMesh, "Ne0")) { output << "\nHERE\n"; // No Ne0. Try Ni0 - if(mesh->get(NeMesh, "Ni0")) { + if (mesh->get(NeMesh, "Ni0")) { output << "WARNING: Neither Ne0 nor Ni0 found in mesh input\n"; } } NeMesh *= 1e20; // Convert to m^-3 - + Field2D TeMesh; - if(mesh->get(TeMesh, "Te0")) { + if (mesh->get(TeMesh, "Te0")) { // No Te0 output << "WARNING: Te0 not found in mesh\n"; } - Field3D ViMesh; mesh->get(ViMesh, "Vi0"); - + Field3D ViMesh; + mesh->get(ViMesh, "Vi0"); + // Normalise NeMesh /= Nnorm; TeMesh /= Tnorm; ViMesh /= Cs0; - + // Add profiles in the mesh file Ne += NeMesh; Te += TeMesh; Vi += ViMesh; } - + // Check for negatives - if(min(Ne, true) < 0.0) { + if (min(Ne, true) < 0.0) { throw BoutException("Starting density is negative"); } - if(max(Ne, true) < 1e-5) { + if (max(Ne, true) < 1e-5) { throw BoutException("Starting density is too small"); } - if(min(Te, true) < 0.0) { + if (min(Te, true) < 0.0) { throw BoutException("Starting temperature is negative"); } - if(max(Te, true) < 1e-5) { + if (max(Te, true) < 1e-5) { throw BoutException("Starting temperature is too small"); } } - + SAVE_REPEAT(phi); - + phi.setBoundary("phi"); // For Y boundaries (if any) // Curvature OPTION(optgbs, curv_method, 1); // Get the method to use - - switch(curv_method) { - case 0: // bxcv vector, upwinding - case 1: { // bxcv vector, central differencing + + switch (curv_method) { + case 0: // bxcv vector, upwinding + case 1: { // bxcv vector, central differencing bxcv.covariant = false; // Read contravariant components GRID_LOAD(bxcv); // Specified components of b0 x kappa - + bool ShiftXderivs; Options::getRoot()->get("shiftXderivs", ShiftXderivs, false); // Read global flag - if(ShiftXderivs) { - Field2D sinty; GRID_LOAD(sinty); - bxcv.z += sinty*bxcv.x; + if (ShiftXderivs) { + Field2D sinty; + GRID_LOAD(sinty); + bxcv.z += sinty * bxcv.x; } // Normalise curvature bxcv.x /= Bnorm; - bxcv.y /= rho_s0*rho_s0; - bxcv.z *= rho_s0*rho_s0; + bxcv.y /= rho_s0 * rho_s0; + bxcv.z *= rho_s0 * rho_s0; break; } case 2: { // logB, read from input @@ -254,10 +285,9 @@ int GBS::init(bool restarting) { default: throw BoutException("Invalid value for curv_method"); }; - - + // Phi solver - phiSolver = Laplacian::create(opt->getSection("phiSolver")); + phiSolver = Laplacian::create(opt->getSection("phiSolver")); aparSolver = Laplacian::create(opt->getSection("aparSolver")); dx4 = SQ(SQ(coords->dx)); @@ -265,17 +295,20 @@ int GBS::init(bool restarting) { dz4 = SQ(SQ(coords->dz)); SAVE_REPEAT(Ve); - - output.write("dx = {:e}, dy = {:e}, dz = {:e}\n", coords->dx(2,2), coords->dy(2,2), coords->dz); - output.write("g11 = {:e}, g22 = {:e}, g33 = {:e}\n", coords->g11(2,2), coords->g22(2,2), coords->g33(2,2)); - output.write("g12 = {:e}, g23 = {:e}\n", coords->g12(2,2), coords->g23(2,2)); - output.write("g_11 = {:e}, g_22 = {:e}, g_33 = {:e}\n", coords->g_11(2,2), coords->g_22(2,2), coords->g_33(2,2)); - output.write("g_12 = {:e}, g_23 = {:e}\n", coords->g_12(2,2), coords->g_23(2,2)); - - std::shared_ptr gen = FieldFactory::get()->parse("source", Options::getRoot()->getSection("ne")); + output.write("dx = {:e}, dy = {:e}, dz = {:e}\n", coords->dx(2, 2), coords->dy(2, 2), + coords->dz); + output.write("g11 = {:e}, g22 = {:e}, g33 = {:e}\n", coords->g11(2, 2), + coords->g22(2, 2), coords->g33(2, 2)); + output.write("g12 = {:e}, g23 = {:e}\n", coords->g12(2, 2), coords->g23(2, 2)); + output.write("g_11 = {:e}, g_22 = {:e}, g_33 = {:e}\n", coords->g_11(2, 2), + coords->g_22(2, 2), coords->g_33(2, 2)); + output.write("g_12 = {:e}, g_23 = {:e}\n", coords->g_12(2, 2), coords->g_23(2, 2)); + + std::shared_ptr gen = + FieldFactory::get()->parse("source", Options::getRoot()->getSection("ne")); output << "Ne::source = " << gen->str() << endl; - + return 0; } @@ -283,88 +316,90 @@ void GBS::LoadMetric(BoutReal Lnorm, BoutReal Bnorm) { // Load metric coefficients from the mesh Field2D Rxy, Bpxy, Btxy, hthe, sinty; GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics - + // Checking for dpsi and qinty used in BOUT grids Field2D dx; - if(!mesh->get(dx, "dpsi")) { + if (!mesh->get(dx, "dpsi")) { output << "\tUsing dpsi as the x grid spacing\n"; coords->dx = dx; // Only use dpsi if found - }else { + } else { // dx will have been read already from the grid output << "\tUsing dx as the x grid spacing\n"; } - Rxy /= Lnorm; - hthe /= Lnorm; - sinty *= SQ(Lnorm)*Bnorm; - coords->dx /= SQ(Lnorm)*Bnorm; - + Rxy /= Lnorm; + hthe /= Lnorm; + sinty *= SQ(Lnorm) * Bnorm; + coords->dx /= SQ(Lnorm) * Bnorm; + Bpxy /= Bnorm; Btxy /= Bnorm; - coords->Bxy /= Bnorm; - + coords->Bxy /= Bnorm; + // Calculate metric components bool ShiftXderivs; Options::getRoot()->get("shiftXderivs", ShiftXderivs, false); // Read global flag - if(ShiftXderivs) { - sinty = 0.0; // I disappears from metric + if (ShiftXderivs) { + sinty = 0.0; // I disappears from metric } - + BoutReal sbp = 1.0; // Sign of Bp - if(min(Bpxy, true) < 0.0) + if (min(Bpxy, true) < 0.0) { sbp = -1.0; - - coords->g11 = SQ(Rxy*Bpxy); + } + + coords->g11 = SQ(Rxy * Bpxy); coords->g22 = 1.0 / SQ(hthe); - coords->g33 = SQ(sinty)*coords->g11 + SQ(coords->Bxy)/coords->g11; + coords->g33 = SQ(sinty) * coords->g11 + SQ(coords->Bxy) / coords->g11; coords->g12 = 0.0; - coords->g13 = -sinty*coords->g11; - coords->g23 = -sbp*Btxy/(hthe*Bpxy*Rxy); - + coords->g13 = -sinty * coords->g11; + coords->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy); + coords->J = hthe / Bpxy; - - coords->g_11 = 1.0/coords->g11 + SQ(sinty*Rxy); - coords->g_22 = SQ(coords->Bxy*hthe/Bpxy); - coords->g_33 = Rxy*Rxy; - coords->g_12 = sbp*Btxy*hthe*sinty*Rxy/Bpxy; - coords->g_13 = sinty*Rxy*Rxy; - coords->g_23 = sbp*Btxy*hthe*Rxy/Bpxy; - + + coords->g_11 = 1.0 / coords->g11 + SQ(sinty * Rxy); + coords->g_22 = SQ(coords->Bxy * hthe / Bpxy); + coords->g_33 = Rxy * Rxy; + coords->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy; + coords->g_13 = sinty * Rxy * Rxy; + coords->g_23 = sbp * Btxy * hthe * Rxy / Bpxy; + coords->geometry(); } // just define a macro for V_E dot Grad -#define vE_Grad(f, p) ( bracket(p, f, bm_exb) ) +#define vE_Grad(f, p) (bracket(p, f, bm_exb)) int GBS::rhs(BoutReal t) { - + output.print("TIME = {:e}\r", t); // Bypass logging, only to stdout - + // Communicate evolving variables mesh->communicate(evars); - + // Floor small values Te = floor(Te, 1e-3); Ne = floor(Ne, 1e-3); // Solve phi from Vorticity - if(mms) { + if (mms) { // Solve for potential, adding a source term - Field3D phiS = FieldFactory::get()->create3D("phi:source", Options::getRoot(), mesh, CELL_CENTRE, t); + Field3D phiS = FieldFactory::get()->create3D("phi:source", Options::getRoot(), mesh, + CELL_CENTRE, t); phi = phiSolver->solve(Vort + phiS); - }else { + } else { phi = phiSolver->solve(Vort); } - if(estatic) { + if (estatic) { // Electrostatic Ve = VePsi; mesh->communicate(Ve); - }else { - aparSolver->setCoefA(-Ne*0.5*mi_me*beta_e); - psi = aparSolver->solve(Ne*(Vi - VePsi)); + } else { + aparSolver->setCoefA(-Ne * 0.5 * mi_me * beta_e); + psi = aparSolver->solve(Ne * (Vi - VePsi)); - Ve = VePsi - 0.5*mi_me*beta_e*psi; + Ve = VePsi - 0.5 * mi_me * beta_e * psi; mesh->communicate(psi, Ve); } @@ -375,16 +410,16 @@ int GBS::rhs(BoutReal t) { phi.applyBoundary(); // Stress tensor - - Field3D tau_e = Omega_ci*tau_e0 * pow(Te, 1.5)/Ne; // Normalised collision time + + Field3D tau_e = Omega_ci * tau_e0 * pow(Te, 1.5) / Ne; // Normalised collision time Gi = 0.0; - if(ionvis) { - Field3D tau_i = Omega_ci*tau_i0 * pow(Ti, 1.5) / Ne; - Gi = -(0.96*Ti*Ne*tau_i) * ( 2.*Grad_par(Vi) + C(phi)/coords->Bxy ); + if (ionvis) { + Field3D tau_i = Omega_ci * tau_i0 * pow(Ti, 1.5) / Ne; + Gi = -(0.96 * Ti * Ne * tau_i) * (2. * Grad_par(Vi) + C(phi) / coords->Bxy); mesh->communicate(Gi); Gi.applyBoundary("neumann"); - }else{ + } else { mesh->communicate(Gi); } @@ -392,138 +427,123 @@ int GBS::rhs(BoutReal t) { mesh->communicate(logNe); Ge = 0.0; - if(elecvis) { - Ge = -(0.73*Te*Ne*tau_e) * (2.*Grad_par(Ve) + (5.*C(Te) + 5.*Te*C(logNe) + C(phi))/coords->Bxy); + if (elecvis) { + Ge = -(0.73 * Te * Ne * tau_e) + * (2. * Grad_par(Ve) + (5. * C(Te) + 5. * Te * C(logNe) + C(phi)) / coords->Bxy); mesh->communicate(Ge); Ge.applyBoundary("neumann"); - }else{ + } else { mesh->communicate(Ge); } - + // Collisional damping (normalised) nu = 1. / (1.96 * Ne * tau_e * mi_me); - + Field3D Pe = Ne * Te; - if(evolve_Ne) { + if (evolve_Ne) { // Density - ddt(Ne) = - - vE_Grad(Ne, phi) // ExB term - + (2./coords->Bxy) * (C(Pe) - Ne*C(phi)) // Perpendicular compression - + D(Ne, Dn) - + H(Ne, Hn) - ; - - if(parallel) { - ddt(Ne) -= Ne*Grad_par(Ve) + Vpar_Grad_par(Ve, Ne); // Parallel compression, advection + ddt(Ne) = -vE_Grad(Ne, phi) // ExB term + + (2. / coords->Bxy) * (C(Pe) - Ne * C(phi)) // Perpendicular compression + + D(Ne, Dn) + H(Ne, Hn); + + if (parallel) { + ddt(Ne) -= + Ne * Grad_par(Ve) + Vpar_Grad_par(Ve, Ne); // Parallel compression, advection } - - if(!mms) { + + if (!mms) { // Source term - ddt(Ne) += Sn*where(Sn, 1.0, Ne); + ddt(Ne) += Sn * where(Sn, 1.0, Ne); } } - - if(evolve_Te) { + + if (evolve_Te) { // Electron temperature - ddt(Te) = - - vE_Grad(Te, phi) - + (4./3.)*(Te/coords->Bxy)*( (7./2.)*C(Te) + (Te/Ne)*C(Ne) - C(phi) ) - + D(Te, Dte) - + H(Te, Hte) - ; - - if(parallel) { + ddt(Te) = -vE_Grad(Te, phi) + + (4. / 3.) * (Te / coords->Bxy) + * ((7. / 2.) * C(Te) + (Te / Ne) * C(Ne) - C(phi)) + + D(Te, Dte) + H(Te, Hte); + + if (parallel) { ddt(Te) -= Vpar_Grad_par(Ve, Te); - ddt(Te) += (2./3.)*Te*( 0.71*Grad_par(Vi) - 1.71*Grad_par(Ve) + 0.71*(Vi-Ve)*Grad_par(logNe)); + ddt(Te) += (2. / 3.) * Te + * (0.71 * Grad_par(Vi) - 1.71 * Grad_par(Ve) + + 0.71 * (Vi - Ve) * Grad_par(logNe)); } - - if(!mms) { + + if (!mms) { // Source term. Note: Power source, so divide by Ne - ddt(Te) += Sp*where(Sp, 1.0, Te*Ne) / Ne; - + ddt(Te) += Sp * where(Sp, 1.0, Te * Ne) / Ne; + // Source of particles shouldn't include energy, so Ne*Te=const // hence ddt(Te) = -(Te/Ne)*ddt(Ne) - ddt(Te) -= (Te/Ne)*Sn*where(Sn, 1.0, 0.0); + ddt(Te) -= (Te / Ne) * Sn * where(Sn, 1.0, 0.0); } } - - if(evolve_Vort) { + + if (evolve_Vort) { // Vorticity - ddt(Vort) = - - vE_Grad(Vort, phi) // ExB term - + 2.*coords->Bxy*C(Pe)/Ne + coords->Bxy*C(Gi)/(3.*Ne) - + D(Vort, Dvort) - + H(Vort, Hvort) - ; - - if(parallel) { - Field3D delV = Vi-Ve; + ddt(Vort) = -vE_Grad(Vort, phi) // ExB term + + 2. * coords->Bxy * C(Pe) / Ne + coords->Bxy * C(Gi) / (3. * Ne) + + D(Vort, Dvort) + H(Vort, Hvort); + + if (parallel) { + Field3D delV = Vi - Ve; mesh->communicate(delV); ddt(Vort) -= Vpar_Grad_par(Vi, Vort); // Parallel advection - ddt(Vort) += SQ(coords->Bxy)*( Grad_par(delV) + (Vi - Ve)*Grad_par(logNe) ); + ddt(Vort) += SQ(coords->Bxy) * (Grad_par(delV) + (Vi - Ve) * Grad_par(logNe)); } } - - if(evolve_Ve) { + + if (evolve_Ve) { // Electron velocity - - ddt(VePsi) = - - vE_Grad(Ve, phi) - - Vpar_Grad_par(Ve, Ve) - - mi_me*(2./3.)*Grad_par(Ge) - - mi_me*nu*(Ve - Vi) - + mi_me*Grad_par(phi) - - mi_me*( Te*Grad_par(logNe) + 1.71*Grad_par(Te) ) - + D(Ve, Dve) - + H(Ve, Hve) - ; + + ddt(VePsi) = + -vE_Grad(Ve, phi) - Vpar_Grad_par(Ve, Ve) - mi_me * (2. / 3.) * Grad_par(Ge) + - mi_me * nu * (Ve - Vi) + mi_me * Grad_par(phi) + - mi_me * (Te * Grad_par(logNe) + 1.71 * Grad_par(Te)) + D(Ve, Dve) + H(Ve, Hve); } - - if(evolve_Vi) { + + if (evolve_Vi) { // Ion velocity - - ddt(Vi) = - - vE_Grad(Vi, phi) - - Vpar_Grad_par(Vi, Vi) - - (2./3.)*Grad_par(Gi) - - (Grad_par(Te) + Te*Grad_par(logNe)) // Parallel pressure - + D(Vi, Dvi) - + H(Vi, Hvi) - ; + + ddt(Vi) = -vE_Grad(Vi, phi) - Vpar_Grad_par(Vi, Vi) - (2. / 3.) * Grad_par(Gi) + - (Grad_par(Te) + Te * Grad_par(logNe)) // Parallel pressure + + D(Vi, Dvi) + H(Vi, Hvi); } - + return 0; } -const Field3D GBS::C(const Field3D &f) { // Curvature operator - Field3D g; //Temporary in case we need to communicate - switch(curv_method) { +const Field3D GBS::C(const Field3D& f) { // Curvature operator + Field3D g; //Temporary in case we need to communicate + switch (curv_method) { case 0: - g = f ; + g = f; mesh->communicate(g); return V_dot_Grad(bxcv, g); case 1: - g = f ; + g = f; mesh->communicate(g); - return bxcv*Grad(g); + return bxcv * Grad(g); } - return coords->Bxy*bracket(logB, f, BRACKET_ARAKAWA); + return coords->Bxy * bracket(logB, f, BRACKET_ARAKAWA); } -const Field3D GBS::D(const Field3D &f, BoutReal d) { // Diffusion operator - if(d < 0.0) +const Field3D GBS::D(const Field3D& f, BoutReal d) { // Diffusion operator + if (d < 0.0) { return 0.0; + } return d * Delp2(f); } -const Field3D GBS::H(const Field3D &f, BoutReal h) { // Numerical hyper-diffusion operator - if(h < 0.0) +const Field3D GBS::H(const Field3D& f, BoutReal h) { // Numerical hyper-diffusion operator + if (h < 0.0) { return 0.0; - return -h*(dx4*D4DX4(f) + dz4*D4DZ4(f));// + dy4*D4DY4(f) + } + return -h * (dx4 * D4DX4(f) + dz4 * D4DZ4(f)); // + dy4*D4DY4(f) } - // Standard main() function BOUTMAIN(GBS); - diff --git a/tests/MMS/GBS/gbs.hxx b/tests/MMS/GBS/gbs.hxx index 97bcae32e5..e711e3ea83 100644 --- a/tests/MMS/GBS/gbs.hxx +++ b/tests/MMS/GBS/gbs.hxx @@ -6,22 +6,23 @@ class GBS; #include -#include #include +#include class GBS : public PhysicsModel { protected: int init(bool restarting); int rhs(BoutReal t); + private: // Evolving variables - Field3D Ne, Te; // Electron density and temperature - Field3D VePsi; // Parallel electron velocity - Field3D Vi; // Parallel ion velocity - Field3D Vort; // Vorticity + Field3D Ne, Te; // Electron density and temperature + Field3D VePsi; // Parallel electron velocity + Field3D Vi; // Parallel ion velocity + Field3D Vort; // Vorticity // Auxilliary variables - Field3D phi; // Electrostatic potential + Field3D phi; // Electrostatic potential Field3D psi, Ve; // Sources of density and energy @@ -29,23 +30,23 @@ private: // Stress tensor Field3D Gi, Ge; - + // Collisional damping - Field3D nu; + Field3D nu; // Curvature terms int curv_method; // Determines which method is used - Vector2D bxcv; // b x kappa = (B/2)Curl(b/B) - Field3D logB; // Used in bracket method + Vector2D bxcv; // b x kappa = (B/2)Curl(b/B) + Field3D logB; // Used in bracket method // Switches bool evolve_Ne, evolve_Vort, evolve_Ve, evolve_Vi, evolve_Te; bool ionvis, elecvis, resistivity; bool parallel; // Include parallel dynamics? - bool estatic; // Electrostatic - + bool estatic; // Electrostatic + // Bracket method for advection terms // Poisson brackets: b0 x Grad(f) dot Grad(g) / B = [f, g] - // Method to use: BRACKET_ARAKAWA, BRACKET_STD or BRACKET_SIMPLE + // Method to use: BRACKET_ARAKAWA, BRACKET_STD or BRACKET_SIMPLE /* * Bracket method * @@ -59,15 +60,15 @@ private: bool mms; - Coordinates *coords; - + Coordinates* coords; + // Stress tensor components BoutReal tau_e0, tau_i0; BoutReal Ti; // Ion temperature [eV] for stress tensor // Diffusion parameters BoutReal Dn, Dvort, Dve, Dvi, Dte; - + // Numerical hyper-diffusion parameters BoutReal Hn, Hvort, Hve, Hvi, Hte; @@ -78,18 +79,18 @@ private: // Group of fields for communication FieldGroup evars; // Evolving variables - + // Initialisation void LoadMetric(BoutReal Lnorm, BoutReal Bnorm); // Operators - const Field3D C(const Field3D &f); // Curvature operator - const Field3D D(const Field3D &f, BoutReal d); // Diffusion operator - const Field3D H(const Field3D &f, BoutReal h); // Hyper-diffusion + const Field3D C(const Field3D& f); // Curvature operator + const Field3D D(const Field3D& f, BoutReal d); // Diffusion operator + const Field3D H(const Field3D& f, BoutReal h); // Hyper-diffusion // Powers of the mesh spacing for H operator Field2D dx4, dy4; BoutReal dz4; - + // Laplacian solver std::unique_ptr phiSolver{nullptr}; std::unique_ptr aparSolver{nullptr}; diff --git a/tests/MMS/advection/advection.cxx b/tests/MMS/advection/advection.cxx index b32b0b438f..0c040a62f1 100644 --- a/tests/MMS/advection/advection.cxx +++ b/tests/MMS/advection/advection.cxx @@ -4,35 +4,36 @@ */ #include -#include -#include +#include +#include class AdvectMMS : public PhysicsModel { public: int init(bool) { solver->add(f, "f"); - + Options::getRoot()->get("method", method, 0); - g = FieldFactory::get()->create3D("g:solution", Options::getRoot(), mesh, CELL_CENTRE); + g = FieldFactory::get()->create3D("g:solution", Options::getRoot(), mesh, + CELL_CENTRE); - Coordinates *coords = mesh->getCoordinates(); + Coordinates* coords = mesh->getCoordinates(); dx_sq_sq = SQ(SQ(coords->dx)); dz_sq_sq = SQ(SQ(coords->dz)); - + return 0; } int rhs(BoutReal) { mesh->communicate(f); - ddt(f) = -bracket(g, f, (BRACKET_METHOD) method) - - (dx_sq_sq*D4DX4(f) + dz_sq_sq*D4DZ4(f)) - ; + ddt(f) = -bracket(g, f, (BRACKET_METHOD)method) + - (dx_sq_sq * D4DX4(f) + dz_sq_sq * D4DZ4(f)); return 0; } + private: int method; - Field3D f,g; + Field3D f, g; Field3D dx_sq_sq, dz_sq_sq; }; diff --git a/tests/MMS/diffusion/diffusion.cxx b/tests/MMS/diffusion/diffusion.cxx index 332290270d..5c4f7306ba 100644 --- a/tests/MMS/diffusion/diffusion.cxx +++ b/tests/MMS/diffusion/diffusion.cxx @@ -1,10 +1,10 @@ -#include +#include #include -#include -#include +#include #include -#include -#include +#include +#include +#include class Diffusion : public PhysicsModel { protected: @@ -12,7 +12,6 @@ class Diffusion : public PhysicsModel { int rhs(BoutReal t) override; }; - using bout::globals::mesh; Field3D N; @@ -20,25 +19,25 @@ Field3D N; BoutReal mu_N; // Parallel collisional diffusion coefficient BoutReal Lx, Ly, Lz; -Coordinates *coord; +Coordinates* coord; int Diffusion::init(bool UNUSED(restarting)) { // Get the options - Options *meshoptions = Options::getRoot()->getSection("mesh"); + Options* meshoptions = Options::getRoot()->getSection("mesh"); coord = mesh->getCoordinates(); - - meshoptions->get("Lx",Lx,1.0); - meshoptions->get("Ly",Ly,1.0); + + meshoptions->get("Lx", Lx, 1.0); + meshoptions->get("Ly", Ly, 1.0); /*this assumes equidistant grid*/ int nguard = mesh->xstart; - coord->dx = Lx/(mesh->GlobalNx - 2*nguard); - coord->dy = Ly/(mesh->GlobalNy - 2*nguard); + coord->dx = Lx / (mesh->GlobalNx - 2 * nguard); + coord->dy = Ly / (mesh->GlobalNy - 2 * nguard); - SAVE_ONCE2(Lx,Ly); + SAVE_ONCE2(Lx, Ly); - Options *cytooptions = Options::getRoot()->getSection("cyto"); + Options* cytooptions = Options::getRoot()->getSection("cyto"); cytooptions->get("dis", mu_N, 1); SAVE_ONCE(mu_N); @@ -70,7 +69,7 @@ int Diffusion::rhs(BoutReal t) { N.applyBoundary(t); - ddt(N) = mu_N* D2DX2(N); + ddt(N) = mu_N * D2DX2(N); return 0; } diff --git a/tests/MMS/diffusion2/diffusion.cxx b/tests/MMS/diffusion2/diffusion.cxx index e568c952c5..9df8686f0d 100644 --- a/tests/MMS/diffusion2/diffusion.cxx +++ b/tests/MMS/diffusion2/diffusion.cxx @@ -1,8 +1,8 @@ #include #include -#include -#include -#include +#include +#include +#include #include class Diffusion : public PhysicsModel { @@ -64,14 +64,17 @@ class Diffusion : public PhysicsModel { ddt(N) = 0.0; - if (Dx > 0.0) + if (Dx > 0.0) { ddt(N) += Dx * D2DX2(N); + } - if (Dy > 0.0) + if (Dy > 0.0) { ddt(N) += Dy * D2DY2(N); + } - if (Dz > 0.0) + if (Dz > 0.0) { ddt(N) += Dz * D2DZ2(N); + } return 0; } diff --git a/tests/MMS/elm-pb/elm_pb.cxx b/tests/MMS/elm-pb/elm_pb.cxx index 46351f6a8d..b138ebd01e 100644 --- a/tests/MMS/elm-pb/elm_pb.cxx +++ b/tests/MMS/elm-pb/elm_pb.cxx @@ -9,29 +9,29 @@ * *******************************************************************************/ -#include -#include -#include -#include -#include -#include -#include -#include #include -#include -#include - -#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include #include class ELMpb : public PhysicsModel { private: // 2D inital profiles - Field2D J0, P0; // Current and pressure - Vector2D b0xcv; // Curvature term - Field2D beta, gradparB; // Used for Vpar terms - Field2D phi0; // When diamagnetic terms used + Field2D J0, P0; // Current and pressure + Vector2D b0xcv; // Curvature term + Field2D beta, gradparB; // Used for Vpar terms + Field2D phi0; // When diamagnetic terms used // B field vectors Vector2D B0vec; // B0 field vector @@ -47,14 +47,14 @@ class ELMpb : public PhysicsModel { Field3D PsiExact; // Parameters - BoutReal density; // Number density [m^-3] + BoutReal density; // Number density [m^-3] BoutReal Bbar, Lbar, Tbar, Va; // Normalisation constants - BoutReal dnorm; // For diamagnetic terms: 1 / (2. * wci * Tbar) - BoutReal dia_fact; // Multiply diamagnetic term by this - BoutReal delta_i; // Normalized ion skin depth - BoutReal omega_i; // ion gyrofrequency + BoutReal dnorm; // For diamagnetic terms: 1 / (2. * wci * Tbar) + BoutReal dia_fact; // Multiply diamagnetic term by this + BoutReal delta_i; // Normalized ion skin depth + BoutReal omega_i; // ion gyrofrequency - BoutReal diffusion_par; // Parallel pressure diffusion + BoutReal diffusion_par; // Parallel pressure diffusion BoutReal viscos_perp; // Perpendicular viscosity @@ -105,14 +105,14 @@ class ELMpb : public PhysicsModel { bool zonal_field; bool zonal_bkgd; - BoutReal vac_lund, core_lund; // Lundquist number S = (Tau_R / Tau_A). -ve -> infty - BoutReal vac_resist, core_resist; // The resistivities (just 1 / S) - Field3D eta; // Resistivity profile (1 / S) - bool spitzer_resist; // Use Spitzer formula for resistivity - BoutReal Zeff; // Z effective for resistivity formula + BoutReal vac_lund, core_lund; // Lundquist number S = (Tau_R / Tau_A). -ve -> infty + BoutReal vac_resist, core_resist; // The resistivities (just 1 / S) + Field3D eta; // Resistivity profile (1 / S) + bool spitzer_resist; // Use Spitzer formula for resistivity + BoutReal Zeff; // Z effective for resistivity formula - BoutReal hyperresist; // Hyper-resistivity coefficient (in core only) - BoutReal ehyperviscos; // electron Hyper-viscosity coefficient + BoutReal hyperresist; // Hyper-resistivity coefficient (in core only) + BoutReal ehyperviscos; // electron Hyper-viscosity coefficient // Metric coefficients Field2D Rxy, Bpxy, Btxy, B0, hthe; @@ -120,20 +120,20 @@ class ELMpb : public PhysicsModel { bool mms; // True if testing with Method of Manufactured Solutions - const BoutReal MU0 = 4.0e-7*PI; - const BoutReal Mi = 2.0*1.6726e-27; // Ion mass + const BoutReal MU0 = 4.0e-7 * PI; + const BoutReal Mi = 2.0 * 1.6726e-27; // Ion mass // Communication objects FieldGroup comms; // Parallel gradient along perturbed field-line - const Field3D Grad_parP(const Field3D &f, CELL_LOC loc = CELL_DEFAULT) { + const Field3D Grad_parP(const Field3D& f, CELL_LOC loc = CELL_DEFAULT) { Field3D result; result = Grad_par(f, loc); - if(nonlinear) { - result -= bracket(Psi, f, bm_mag)*B0; + if (nonlinear) { + result -= bracket(Psi, f, bm_mag) * B0; } return result; @@ -153,24 +153,24 @@ class ELMpb : public PhysicsModel { mesh->get(P0, "pressure"); // Pascals // Load curvature term - b0xcv.covariant = false; // Read contravariant components + b0xcv.covariant = false; // Read contravariant components mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2 // Load metrics - if(mesh->get(Rxy, "Rxy")) { // m + if (mesh->get(Rxy, "Rxy")) { // m output_error.write("Error: Cannot read Rxy from grid\n"); return 1; } - if(mesh->get(Bpxy, "Bpxy")) { // T + if (mesh->get(Bpxy, "Bpxy")) { // T output_error.write("Error: Cannot read Bpxy from grid\n"); return 1; } mesh->get(Btxy, "Btxy"); // T - mesh->get(B0, "Bxy"); // T + mesh->get(B0, "Bxy"); // T mesh->get(hthe, "hthe"); // m - mesh->get(I, "sinty");// m^-2 T^-1 + mesh->get(I, "sinty"); // m^-2 T^-1 - Coordinates *coords = mesh->getCoordinates(); + Coordinates* coords = mesh->getCoordinates(); ////////////////////////////////////////////////////////////// // Read parameters from the options file @@ -184,21 +184,21 @@ class ELMpb : public PhysicsModel { // Prints out what values are assigned ///////////////////////////////////////////////////////////// - Options *globalOptions = Options::getRoot(); - Options *options = globalOptions->getSection("highbeta"); + Options* globalOptions = Options::getRoot(); + Options* options = globalOptions->getSection("highbeta"); - OPTION(options, density, 1.0e19); // Number density [m^-3] + OPTION(options, density, 1.0e19); // Number density [m^-3] // Effects to include/exclude OPTION(options, include_curvature, true); - OPTION(options, include_jpar0, true); + OPTION(options, include_jpar0, true); - OPTION(options, compress0, false); - OPTION(options, nonlinear, false); + OPTION(options, compress0, false); + OPTION(options, nonlinear, false); // option for ExB Poisson Bracket - OPTION(options, bm_exb_flag, 0); - switch(bm_exb_flag) { + OPTION(options, bm_exb_flag, 0); + switch (bm_exb_flag) { case 0: { bm_exb = BRACKET_STD; output << "\tBrackets for ExB: default differencing\n"; @@ -225,8 +225,8 @@ class ELMpb : public PhysicsModel { } // option for magnetic flutter Poisson Bracket - OPTION(options, bm_mag_flag, 0); - switch(bm_mag_flag) { + OPTION(options, bm_mag_flag, 0); + switch (bm_mag_flag) { case 0: { bm_mag = BRACKET_STD; output << "\tBrackets: default differencing\n"; @@ -252,51 +252,54 @@ class ELMpb : public PhysicsModel { return 1; } - OPTION(options, eHall, false); // electron Hall or electron parallel pressue gradient effects? - OPTION(options, AA, 1.0); // ion mass in units of proton mass + OPTION(options, eHall, + false); // electron Hall or electron parallel pressue gradient effects? + OPTION(options, AA, 1.0); // ion mass in units of proton mass - OPTION(options, diamag, false); // Diamagnetic effects? - OPTION(options, diamag_grad_t, diamag); // Grad_par(Te) term in Psi equation - OPTION(options, diamag_phi0, diamag); // Include equilibrium phi0 - OPTION(options, dia_fact, 1.0); // Scale diamagnetic effects by this factor + OPTION(options, diamag, false); // Diamagnetic effects? + OPTION(options, diamag_grad_t, diamag); // Grad_par(Te) term in Psi equation + OPTION(options, diamag_phi0, diamag); // Include equilibrium phi0 + OPTION(options, dia_fact, 1.0); // Scale diamagnetic effects by this factor // Toroidal filtering - OPTION(options, filter_z, false); // Filter a single n - OPTION(options, filter_z_mode, 1); - OPTION(options, low_pass_z, -1); // Low-pass filter - OPTION(options, zonal_flow, false); // zonal flow filter - OPTION(options, zonal_field, false); // zonal field filter - OPTION(options, zonal_bkgd, false); // zonal background P filter + OPTION(options, filter_z, false); // Filter a single n + OPTION(options, filter_z_mode, 1); + OPTION(options, low_pass_z, -1); // Low-pass filter + OPTION(options, zonal_flow, false); // zonal flow filter + OPTION(options, zonal_field, false); // zonal field filter + OPTION(options, zonal_bkgd, false); // zonal background P filter // Vacuum region control - OPTION(options, vacuum_pressure, 0.02); // Fraction of peak pressure - OPTION(options, vacuum_trans, 0.005); // Transition width in pressure + OPTION(options, vacuum_pressure, 0.02); // Fraction of peak pressure + OPTION(options, vacuum_trans, 0.005); // Transition width in pressure // Resistivity and hyper-resistivity options - OPTION(options, vac_lund, 0.0); // Lundquist number in vacuum region - OPTION(options, core_lund, 0.0); // Lundquist number in core region - OPTION(options, hyperresist, -1.0); - OPTION(options, ehyperviscos, -1.0); - OPTION(options, spitzer_resist, false); // Use Spitzer resistivity - OPTION(options, Zeff, 2.0); // Z effective + OPTION(options, vac_lund, 0.0); // Lundquist number in vacuum region + OPTION(options, core_lund, 0.0); // Lundquist number in core region + OPTION(options, hyperresist, -1.0); + OPTION(options, ehyperviscos, -1.0); + OPTION(options, spitzer_resist, false); // Use Spitzer resistivity + OPTION(options, Zeff, 2.0); // Z effective // Viscosity and hyper-viscosity - OPTION(options, viscos_perp, -1.0); // Perpendicular viscosity + OPTION(options, viscos_perp, -1.0); // Perpendicular viscosity // parallel pressure diffusion - OPTION(options, diffusion_par, -1.0); // Parallel pressure diffusion + OPTION(options, diffusion_par, -1.0); // Parallel pressure diffusion // Compressional terms - OPTION(options, phi_curv, true); - options->get("gamma", g, 5.0/3.0); + OPTION(options, phi_curv, true); + options->get("gamma", g, 5.0 / 3.0); OPTION(globalOptions->getSection("solver"), mms, false); - if(!include_curvature) + if (!include_curvature) { b0xcv = 0.0; + } - if(!include_jpar0) + if (!include_jpar0) { J0 = 0.0; + } ////////////////////////////////////////////////////////////// // INITIALIZE LAPLACIAN SOLVER @@ -308,82 +311,86 @@ class ELMpb : public PhysicsModel { bool ShiftXderivs; globalOptions->get("shiftXderivs", ShiftXderivs, false); // Read global flag - if(ShiftXderivs) { - if(mesh->IncIntShear) { + if (ShiftXderivs) { + if (mesh->IncIntShear) { // BOUT-06 style, using d/dx = d/dpsi + I * d/dz coords->IntShiftTorsion = I; - }else { + } else { // Dimits style, using local coordinate system - if(include_curvature) - b0xcv.z += I*b0xcv.x; - I = 0.0; // I disappears from metric + if (include_curvature) { + b0xcv.z += I * b0xcv.x; + } + I = 0.0; // I disappears from metric } } ////////////////////////////////////////////////////////////// // NORMALISE QUANTITIES - if(mesh->get(Bbar, "bmag")) // Typical magnetic field + if (mesh->get(Bbar, "bmag")) { // Typical magnetic field Bbar = 1.0; - if(mesh->get(Lbar, "rmag")) // Typical length scale + } + if (mesh->get(Lbar, "rmag")) { // Typical length scale Lbar = 1.0; + } - Va = sqrt(Bbar*Bbar / (MU0*density*Mi)); + Va = sqrt(Bbar * Bbar / (MU0 * density * Mi)); Tbar = Lbar / Va; - dnorm = dia_fact * Mi / (2.*1.602e-19*Bbar*Tbar); + dnorm = dia_fact * Mi / (2. * 1.602e-19 * Bbar * Tbar); - delta_i = AA*60.67*5.31e5/sqrt(density/1e6)/(Lbar*100.0); + delta_i = AA * 60.67 * 5.31e5 / sqrt(density / 1e6) / (Lbar * 100.0); output.write("Normalisations: Bbar = {:e} T Lbar = {:e} m\n", Bbar, Lbar); output.write(" Va = {:e} m/s Tbar = {:e} s\n", Va, Tbar); output.write(" dnorm = {:e}\n", dnorm); output.write(" Resistivity\n"); - if(eHall) + if (eHall) { output.write(" delta_i = {:e} AA = {:e} \n", delta_i, AA); + } - if(vac_lund > 0.0) { + if (vac_lund > 0.0) { output.write(" Vacuum Tau_R = {:e} s eta = {:e} Ohm m\n", vac_lund * Tbar, - MU0 * Lbar * Lbar / (vac_lund * Tbar)); + MU0 * Lbar * Lbar / (vac_lund * Tbar)); vac_resist = 1. / vac_lund; - }else { + } else { output.write(" Vacuum - Zero resistivity -\n"); vac_resist = 0.0; } - if(core_lund > 0.0) { - output.write(" Core Tau_R = {:e} s eta = {:e} Ohm m\n", core_lund * Tbar, - MU0 * Lbar * Lbar / (core_lund * Tbar)); + if (core_lund > 0.0) { + output.write(" Core Tau_R = {:e} s eta = {:e} Ohm m\n", + core_lund * Tbar, MU0 * Lbar * Lbar / (core_lund * Tbar)); core_resist = 1. / core_lund; - }else { + } else { output.write(" Core - Zero resistivity -\n"); core_resist = 0.0; } - if(ehyperviscos > 0.0) { + if (ehyperviscos > 0.0) { output.write(" electron Hyper-viscosity coefficient: {:e}\n", ehyperviscos); } Field2D Te; - Te = P0 / (2.0*density * 1.602e-19); // Temperature in eV + Te = P0 / (2.0 * density * 1.602e-19); // Temperature in eV - J0 = - MU0*Lbar * J0 / B0; - P0 = 2.0*MU0 * P0 / (Bbar*Bbar); + J0 = -MU0 * Lbar * J0 / B0; + P0 = 2.0 * MU0 * P0 / (Bbar * Bbar); b0xcv.x /= Bbar; - b0xcv.y *= Lbar*Lbar; - b0xcv.z *= Lbar*Lbar; + b0xcv.y *= Lbar * Lbar; + b0xcv.z *= Lbar * Lbar; - Rxy /= Lbar; + Rxy /= Lbar; Bpxy /= Bbar; Btxy /= Bbar; - B0 /= Bbar; + B0 /= Bbar; hthe /= Lbar; - coords->dx /= Lbar*Lbar*Bbar; - I *= Lbar*Lbar*Bbar; + coords->dx /= Lbar * Lbar * Bbar; + I *= Lbar * Lbar * Bbar; BoutReal pnorm = max(P0, true); // Maximum over all processors @@ -391,16 +398,17 @@ class ELMpb : public PhysicsModel { vacuum_trans *= pnorm; // Transitions from 0 in core to 1 in vacuum - vac_mask = (1.0 - tanh( (P0 - vacuum_pressure) / vacuum_trans )) / 2.0; + vac_mask = (1.0 - tanh((P0 - vacuum_pressure) / vacuum_trans)) / 2.0; - if(spitzer_resist) { + if (spitzer_resist) { // Use Spitzer resistivity output.write("\tTemperature: {:e} -> {:e} [eV]\n", min(Te), max(Te)); - eta = 0.51*1.03e-4*Zeff*20.*pow(Te, -1.5); // eta in Ohm-m. NOTE: ln(Lambda) = 20 + eta = 0.51 * 1.03e-4 * Zeff * 20. + * pow(Te, -1.5); // eta in Ohm-m. NOTE: ln(Lambda) = 20 output.write("\tSpitzer resistivity: {:e} -> {:e} [Ohm m]\n", min(eta), max(eta)); eta /= MU0 * Va * Lbar; - output.write("\t -> Lundquist {:e} -> {:e}\n", 1.0/max(eta), 1.0/min(eta)); - }else { + output.write("\t -> Lundquist {:e} -> {:e}\n", 1.0 / max(eta), 1.0 / min(eta)); + } else { // transition from 0 for large P0 to resistivity for small P0 eta = core_resist + (vac_resist - core_resist) * vac_mask; } @@ -409,22 +417,22 @@ class ELMpb : public PhysicsModel { /**************** CALCULATE METRICS ******************/ - coords->g11 = SQ(Rxy*Bpxy); + coords->g11 = SQ(Rxy * Bpxy); coords->g22 = 1.0 / SQ(hthe); - coords->g33 = SQ(I)*coords->g11 + SQ(B0)/coords->g11; + coords->g33 = SQ(I) * coords->g11 + SQ(B0) / coords->g11; coords->g12 = 0.0; - coords->g13 = -I*coords->g11; - coords->g23 = -Btxy/(hthe*Bpxy*Rxy); + coords->g13 = -I * coords->g11; + coords->g23 = -Btxy / (hthe * Bpxy * Rxy); coords->J = hthe / Bpxy; coords->Bxy = B0; - coords->g_11 = 1.0/coords->g11 + (SQ(I*Rxy)); - coords->g_22 = SQ(B0*hthe/Bpxy); - coords->g_33 = Rxy*Rxy; - coords->g_12 = Btxy*hthe*I*Rxy/Bpxy; - coords->g_13 = I*Rxy*Rxy; - coords->g_23 = Btxy*hthe*Rxy/Bpxy; + coords->g_11 = 1.0 / coords->g11 + (SQ(I * Rxy)); + coords->g_22 = SQ(B0 * hthe / Bpxy); + coords->g_33 = Rxy * Rxy; + coords->g_12 = Btxy * hthe * I * Rxy / Bpxy; + coords->g_13 = I * Rxy * Rxy; + coords->g_23 = Btxy * hthe * Rxy / Bpxy; coords->geometry(); // Calculate quantities from metric tensor @@ -450,24 +458,23 @@ class ELMpb : public PhysicsModel { SOLVE_FOR3(U, P, Psi); dump.add(Jpar, "jpar", 1); - if(compress0) { + if (compress0) { output.write("Including compression (Vpar) effects\n"); SOLVE_FOR(Vpar); - beta = B0*B0 / ( 0.5 + (B0*B0 / (g*P0))); + beta = B0 * B0 / (0.5 + (B0 * B0 / (g * P0))); gradparB = Grad_par(B0) / B0; - output.write("Beta in range {:e} -> {:e}\n", - min(beta), max(beta)); + output.write("Beta in range {:e} -> {:e}\n", min(beta), max(beta)); } // Phi solved in RHS (explicitly) dump.add(phi, "phi", 1); // Diamagnetic phi0 - if(diamag_phi0) { - phi0 = -0.5*dnorm*P0/B0; + if (diamag_phi0) { + phi0 = -0.5 * dnorm * P0 / B0; SAVE_ONCE(phi0); } @@ -480,7 +487,7 @@ class ELMpb : public PhysicsModel { /////////////// CHECK VACUUM /////////////////////// // In vacuum region, initial vorticity should equal zero - if(!restarting) { + if (!restarting) { // Only if not restarting: Check initial perturbation // Set U to zero where P0 < vacuum_pressure @@ -511,21 +518,22 @@ class ELMpb : public PhysicsModel { // Perform communications mesh->communicate(comms); - Coordinates *coords = mesh->getCoordinates(); + Coordinates* coords = mesh->getCoordinates(); //////////////////////////////////////////// // Transitions from 0 in core to 1 in vacuum - if(nonlinear) { - vac_mask = (1.0 - tanh( ((P0 + P) - vacuum_pressure) / vacuum_trans )) / 2.0; + if (nonlinear) { + vac_mask = (1.0 - tanh(((P0 + P) - vacuum_pressure) / vacuum_trans)) / 2.0; // Update resistivity - if(spitzer_resist) { + if (spitzer_resist) { // Use Spitzer formula Field3D Te; - Te = (P0+P)*Bbar*Bbar/(4.*MU0) / (density * 1.602e-19); // eV - eta = 0.51*1.03e-4*Zeff*20.*pow(Te, -1.5); // eta in Ohm-m. ln(Lambda) = 20 - eta /= MU0 * Va * Lbar; // Normalised eta - }else { + Te = (P0 + P) * Bbar * Bbar / (4. * MU0) / (density * 1.602e-19); // eV + eta = + 0.51 * 1.03e-4 * Zeff * 20. * pow(Te, -1.5); // eta in Ohm-m. ln(Lambda) = 20 + eta /= MU0 * Va * Lbar; // Normalised eta + } else { // Use specified core and vacuum Lundquist numbers eta = core_resist + (vac_resist - core_resist) * vac_mask; } @@ -533,16 +541,17 @@ class ELMpb : public PhysicsModel { //////////////////////////////////////////// // Inversion - if(mms) { + if (mms) { // Solve for potential, adding a source term - Field3D phiS = FieldFactory::get()->create3D("phi:source", Options::getRoot(), mesh, CELL_CENTRE, t); + Field3D phiS = FieldFactory::get()->create3D("phi:source", Options::getRoot(), mesh, + CELL_CENTRE, t); phi = phi_solver->solve(U + phiS, phi); - }else { + } else { phi = phi_solver->solve(U, phi); } - if(diamag) { - phi -= 0.5*dnorm * P / B0; + if (diamag) { + phi -= 0.5 * dnorm * P / B0; } // Apply a boundary condition on phi for target plates @@ -573,30 +582,32 @@ class ELMpb : public PhysicsModel { // Parallel electric field // Evolving vector potential - ddt(Psi) = -Grad_parP(phi, CELL_CENTRE) + eta*Jpar; + ddt(Psi) = -Grad_parP(phi, CELL_CENTRE) + eta * Jpar; - if(eHall) { - ddt(Psi) += 0.25*delta_i*(Grad_parP(B0*P, CELL_CENTRE) / B0 - +b0xGrad_dot_Grad(P0, Psi)); // electron parallel pressure + if (eHall) { + ddt(Psi) += 0.25 * delta_i + * (Grad_parP(B0 * P, CELL_CENTRE) / B0 + + b0xGrad_dot_Grad(P0, Psi)); // electron parallel pressure } - if(diamag_phi0) - ddt(Psi) -= b0xGrad_dot_Grad(phi0, Psi); // Equilibrium flow + if (diamag_phi0) { + ddt(Psi) -= b0xGrad_dot_Grad(phi0, Psi); // Equilibrium flow + } - if(diamag_grad_t) { + if (diamag_grad_t) { // grad_par(T_e) correction ddt(Psi) += 1.71 * dnorm * 0.5 * Grad_parP(P, CELL_YLOW) / B0; } // Hyper-resistivity - if(hyperresist > 0.0) { - ddt(Psi) -= eta*hyperresist * Delp2(Jpar); + if (hyperresist > 0.0) { + ddt(Psi) -= eta * hyperresist * Delp2(Jpar); } // electron Hyper-viscosity coefficient - if(ehyperviscos > 0.0) { - ddt(Psi) -= eta*ehyperviscos * Delp2(Jpar2); + if (ehyperviscos > 0.0) { + ddt(Psi) -= eta * ehyperviscos * Delp2(Jpar2); } //////////////////////////////////////////////////// @@ -604,65 +615,70 @@ class ELMpb : public PhysicsModel { ddt(U) = SQ(B0) * b0xGrad_dot_Grad(Psi, J0, CELL_CENTRE); // Grad j term - ddt(U) += b0xcv*Grad(P); // curvature term + ddt(U) += b0xcv * Grad(P); // curvature term // Parallel current term - ddt(U) -= SQ(B0)*Grad_parP(Jpar, CELL_CENTRE); // b dot grad j + ddt(U) -= SQ(B0) * Grad_parP(Jpar, CELL_CENTRE); // b dot grad j - if(diamag_phi0) - ddt(U) -= b0xGrad_dot_Grad(phi0, U); // Equilibrium flow + if (diamag_phi0) { + ddt(U) -= b0xGrad_dot_Grad(phi0, U); // Equilibrium flow + } - if(nonlinear) { - ddt(U) -= bracket(phi, U, bm_exb)*B0; // Advection + if (nonlinear) { + ddt(U) -= bracket(phi, U, bm_exb) * B0; // Advection } // Viscosity terms - if(viscos_perp > 0.0) - ddt(U) += viscos_perp * Delp2(U); // Perpendicular viscosity + if (viscos_perp > 0.0) { + ddt(U) += viscos_perp * Delp2(U); // Perpendicular viscosity + } - ddt(U) -= 10*(SQ(SQ(coords->dx))*D4DX4(U) + SQ(SQ(coords->dz))*D4DZ4(U)); + ddt(U) -= 10 * (SQ(SQ(coords->dx)) * D4DX4(U) + SQ(SQ(coords->dz)) * D4DZ4(U)); //////////////////////////////////////////////////// // Pressure equation ddt(P) = -b0xGrad_dot_Grad(phi, P0); + if (diamag_phi0) { + ddt(P) -= b0xGrad_dot_Grad(phi0, P); // Equilibrium flow + } - if(diamag_phi0) - ddt(P) -= b0xGrad_dot_Grad(phi0, P); // Equilibrium flow - - if(nonlinear) - ddt(P) -= bracket(phi, P, bm_exb)*B0; // Advection + if (nonlinear) { + ddt(P) -= bracket(phi, P, bm_exb) * B0; // Advection + } // Parallel diffusion terms - if(diffusion_par > 0.0) + if (diffusion_par > 0.0) { ddt(P) += diffusion_par * Grad2_par2(P); // Parallel diffusion + } - ddt(P) -= 10*(SQ(SQ(coords->dx))*D4DX4(P) + SQ(SQ(coords->dz))*D4DZ4(P)); + ddt(P) -= 10 * (SQ(SQ(coords->dx)) * D4DX4(P) + SQ(SQ(coords->dz)) * D4DZ4(P)); //////////////////////////////////////////////////// // Compressional effects - if(compress0) { + if (compress0) { //ddt(P) += beta*( - Grad_parP(Vpar, CELL_CENTRE) + Vpar*gradparB ); - ddt(P) -= beta*Div_par_CtoL(Vpar); + ddt(P) -= beta * Div_par_CtoL(Vpar); - if(phi_curv) { - ddt(P) -= 2.*beta*b0xcv*Grad(phi); + if (phi_curv) { + ddt(P) -= 2. * beta * b0xcv * Grad(phi); } // Vpar equation //ddt(Vpar) = -0.5*Grad_parP(P + P0, CELL_YLOW); - ddt(Vpar) = -0.5*Grad_par_LtoC(P + P0); + ddt(Vpar) = -0.5 * Grad_par_LtoC(P + P0); - if(nonlinear) - ddt(Vpar) -= bracket(phi, Vpar, bm_exb)*B0; // Advection + if (nonlinear) { + ddt(Vpar) -= bracket(phi, Vpar, bm_exb) * B0; // Advection + } } - if(filter_z) { + if (filter_z) { // Filter out all except filter_z_mode ddt(Psi) = filter(ddt(Psi), filter_z_mode); @@ -670,7 +686,7 @@ class ELMpb : public PhysicsModel { ddt(P) = filter(ddt(P), filter_z_mode); } - if(low_pass_z > 0) { + if (low_pass_z > 0) { // Low-pass filter, keeping n up to low_pass_z ddt(Psi) = lowPass(ddt(Psi), low_pass_z, zonal_field); diff --git a/tests/MMS/fieldalign/fieldalign.cxx b/tests/MMS/fieldalign/fieldalign.cxx index afa57132d7..34af497282 100644 --- a/tests/MMS/fieldalign/fieldalign.cxx +++ b/tests/MMS/fieldalign/fieldalign.cxx @@ -1,5 +1,5 @@ #include -#include +#include class FieldAlign : public PhysicsModel { protected: @@ -13,17 +13,21 @@ class FieldAlign : public PhysicsModel { } int rhs(BoutReal t) { - Coordinates *metric = mesh->getCoordinates(); + Coordinates* metric = mesh->getCoordinates(); mesh->communicate(f); f.applyBoundary(t); // df/dt = df/dtheta + df/dphi ddt(f) = - vx / G * (metric->g11*DDX(f) + metric->g12*DDY(f) + metric->g13*DDZ(f)) + - vy / G * (metric->g12*DDX(f) + metric->g22*DDY(f) + metric->g23*DDZ(f)) + // Upwinding with second-order central differencing - vz / G * (metric->g13*DDX(f) + metric->g23*DDY(f) + metric->g33*DDZ(f)); // (unstable without additional dissipation) - - SQ(SQ(metric->dx))*D4DX4(f) /*- SQ(SQ(metric->dy))*D4DY4(f)*/ - SQ(SQ(metric->dz))*D4DZ4(f); // Numerical dissipation terms + vx / G * (metric->g11 * DDX(f) + metric->g12 * DDY(f) + metric->g13 * DDZ(f)) + + vy / G * (metric->g12 * DDX(f) + metric->g22 * DDY(f) + metric->g23 * DDZ(f)) + + // Upwinding with second-order central differencing + vz / G + * (metric->g13 * DDX(f) + metric->g23 * DDY(f) + + metric->g33 * DDZ(f)); // (unstable without additional dissipation) + -SQ(SQ(metric->dx)) * D4DX4(f) /*- SQ(SQ(metric->dy))*D4DY4(f)*/ + - SQ(SQ(metric->dz)) * D4DZ4(f); // Numerical dissipation terms return 0; } diff --git a/tests/MMS/hw/hw.cxx b/tests/MMS/hw/hw.cxx index b0218baa54..4e9bf0ddfc 100644 --- a/tests/MMS/hw/hw.cxx +++ b/tests/MMS/hw/hw.cxx @@ -1,10 +1,10 @@ #include #include -#include -#include -#include -#include +#include +#include +#include +#include class Hw : public PhysicsModel { diff --git a/tests/MMS/laplace/laplace.cxx b/tests/MMS/laplace/laplace.cxx index ff994689b0..54dbaaba67 100644 --- a/tests/MMS/laplace/laplace.cxx +++ b/tests/MMS/laplace/laplace.cxx @@ -1,12 +1,12 @@ -#include +#include -#include -#include #include +#include +#include using bout::globals::mesh; -int main(int argc, char **argv) { +int main(int argc, char** argv) { int init_err = BoutInitialise(argc, argv); if (init_err < 0) { return 0; @@ -15,29 +15,29 @@ int main(int argc, char **argv) { } ////// Set mesh spacing - Options *meshoptions = Options::getRoot()->getSection("mesh"); + Options* meshoptions = Options::getRoot()->getSection("mesh"); BoutReal Lx; - meshoptions->get("Lx",Lx,1.0); + meshoptions->get("Lx", Lx, 1.0); /*this assumes equidistant grid*/ int nguard = mesh->xstart; - mesh->getCoordinates()->dx = Lx/(mesh->GlobalNx - 2*nguard); - mesh->getCoordinates()->dz = TWOPI*Lx/(mesh->LocalNz); + mesh->getCoordinates()->dx = Lx / (mesh->GlobalNx - 2 * nguard); + mesh->getCoordinates()->dz = TWOPI * Lx / (mesh->LocalNz); ///// // Create a Laplacian inversion solver auto lap = Laplacian::create(); - + FieldFactory fact(mesh); std::shared_ptr gen = fact.parse("input"); output << "GEN = " << gen->str() << endl; Field3D input = fact.create3D("input"); - + Field3D result = lap->solve(input); - + Field3D solution = fact.create3D("solution"); Field3D error = result - solution; diff --git a/tests/MMS/spatial/advection/advection.cxx b/tests/MMS/spatial/advection/advection.cxx index 7ed78938a9..29043de637 100644 --- a/tests/MMS/spatial/advection/advection.cxx +++ b/tests/MMS/spatial/advection/advection.cxx @@ -1,6 +1,6 @@ -#include "bout.hxx" -#include "derivs.hxx" -#include "field_factory.hxx" +#include "bout/bout.hxx" +#include "bout/derivs.hxx" +#include "bout/field_factory.hxx" using bout::globals::mesh; diff --git a/tests/MMS/spatial/d2dx2/test_d2dx2.cxx b/tests/MMS/spatial/d2dx2/test_d2dx2.cxx index ee3940f74d..6b35b719e1 100644 --- a/tests/MMS/spatial/d2dx2/test_d2dx2.cxx +++ b/tests/MMS/spatial/d2dx2/test_d2dx2.cxx @@ -2,9 +2,9 @@ * Test D2DX2 operator without time integration */ -#include -#include -#include +#include +#include +#include using bout::globals::mesh; diff --git a/tests/MMS/spatial/d2dz2/test_d2dz2.cxx b/tests/MMS/spatial/d2dz2/test_d2dz2.cxx index f39c2ab772..0b7aa2cde4 100644 --- a/tests/MMS/spatial/d2dz2/test_d2dz2.cxx +++ b/tests/MMS/spatial/d2dz2/test_d2dz2.cxx @@ -2,9 +2,9 @@ * Test D2DZ2 operator without time integration */ -#include -#include -#include +#include +#include +#include using bout::globals::mesh; diff --git a/tests/MMS/spatial/diffusion/diffusion.cxx b/tests/MMS/spatial/diffusion/diffusion.cxx index 4c821c9df6..ec397650ed 100644 --- a/tests/MMS/spatial/diffusion/diffusion.cxx +++ b/tests/MMS/spatial/diffusion/diffusion.cxx @@ -1,8 +1,8 @@ #include #include -#include -#include -#include +#include +#include +#include #include class Diffusion : public PhysicsModel { @@ -65,14 +65,17 @@ class Diffusion : public PhysicsModel { ddt(N) = 0.0; - if (Dx > 0.0) + if (Dx > 0.0) { ddt(N) += Dx * D2DX2(N); + } - if (Dy > 0.0) + if (Dy > 0.0) { ddt(N) += Dy * D2DY2(N); + } - if (Dz > 0.0) + if (Dz > 0.0) { ddt(N) += Dz * D2DZ2(N); + } return 0; } diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx index cfa88e7095..5a2599368e 100644 --- a/tests/MMS/spatial/fci/fci_mms.cxx +++ b/tests/MMS/spatial/fci/fci_mms.cxx @@ -1,6 +1,6 @@ -#include "bout.hxx" -#include "derivs.hxx" -#include "field_factory.hxx" +#include "bout/bout.hxx" +#include "bout/derivs.hxx" +#include "bout/field_factory.hxx" int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/tests/MMS/time/time.cxx b/tests/MMS/time/time.cxx index d97660cd7d..346662a8e3 100644 --- a/tests/MMS/time/time.cxx +++ b/tests/MMS/time/time.cxx @@ -5,36 +5,35 @@ * in the solver code itself. */ - +#include "bout/unused.hxx" #include -#include "unused.hxx" class TimeTest : public PhysicsModel { public: int init(MAYBE_UNUSED(bool restart)) { solver->add(f, "f"); // Solve a single 3D field - + setSplitOperator(); - + return 0; } - + int rhs(MAYBE_UNUSED(BoutReal time)) { ddt(f) = f; return 0; } - + int convective(MAYBE_UNUSED(BoutReal time)) { - ddt(f) = 0.5*f; + ddt(f) = 0.5 * f; return 0; } int diffusive(MAYBE_UNUSED(BoutReal time)) { - ddt(f) = 0.5*f; + ddt(f) = 0.5 * f; return 0; } + private: - Field3D f; + Field3D f; }; BOUTMAIN(TimeTest); - diff --git a/tests/MMS/tokamak/tokamak.cxx b/tests/MMS/tokamak/tokamak.cxx index c9dc580078..abaabef8f2 100644 --- a/tests/MMS/tokamak/tokamak.cxx +++ b/tests/MMS/tokamak/tokamak.cxx @@ -7,8 +7,8 @@ */ #include -#include -#include +#include +#include class TokamakMMS : public PhysicsModel { public: @@ -16,7 +16,7 @@ class TokamakMMS : public PhysicsModel { solver->add(laplacepar, "laplacepar"); solver->add(delp2, "delp2"); solver->add(advect, "advect"); - + // Load the metric tensor LoadMetric(1.0, 1.0); @@ -24,19 +24,22 @@ class TokamakMMS : public PhysicsModel { } int rhs(BoutReal time) { mesh->communicate(advect, delp2, laplacepar); - - drive = FieldFactory::get()->create3D("drive:solution", Options::getRoot(), mesh, CELL_CENTRE, time); - + + drive = FieldFactory::get()->create3D("drive:solution", Options::getRoot(), mesh, + CELL_CENTRE, time); + // Test bracket advection operator - ddt(advect) = -1e-3*bracket(drive, advect, BRACKET_ARAKAWA) - - 10.*(SQ(SQ(mesh->getCoordinates()->dx))*D4DX4(advect) + SQ(SQ(mesh->getCoordinates()->dz))*D4DZ4(advect)); - + ddt(advect) = -1e-3 * bracket(drive, advect, BRACKET_ARAKAWA) + - 10. + * (SQ(SQ(mesh->getCoordinates()->dx)) * D4DX4(advect) + + SQ(SQ(mesh->getCoordinates()->dz)) * D4DZ4(advect)); + // Test perpendicular diffusion operator - ddt(delp2) = 1e-5*Delp2(delp2); - + ddt(delp2) = 1e-5 * Delp2(delp2); + // Test parallel diffusion operator ddt(laplacepar) = Laplace_par(laplacepar); - + return 0; } void LoadMetric(BoutReal Lnorm, BoutReal Bnorm) { @@ -44,54 +47,55 @@ class TokamakMMS : public PhysicsModel { Field2D Rxy, Bpxy, Btxy, hthe, sinty; GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics - Coordinates *coords = mesh->getCoordinates(); - + Coordinates* coords = mesh->getCoordinates(); + // Checking for dpsi used in BOUT grids Field2D dx; - if(!mesh->get(dx, "dpsi")) { + if (!mesh->get(dx, "dpsi")) { output << "\tUsing dpsi as the x grid spacing\n"; coords->dx = dx; // Only use dpsi if found - }else { + } else { // dx will have been read already from the grid output << "\tUsing dx as the x grid spacing\n"; } - Rxy /= Lnorm; - hthe /= Lnorm; - sinty *= SQ(Lnorm)*Bnorm; - coords->dx /= SQ(Lnorm)*Bnorm; - + Rxy /= Lnorm; + hthe /= Lnorm; + sinty *= SQ(Lnorm) * Bnorm; + coords->dx /= SQ(Lnorm) * Bnorm; + Bpxy /= Bnorm; Btxy /= Bnorm; coords->Bxy /= Bnorm; - + // Calculate metric components bool ShiftXderivs; Options::getRoot()->get("shiftXderivs", ShiftXderivs, false); // Read global flag - if(ShiftXderivs) { - sinty = 0.0; // I disappears from metric + if (ShiftXderivs) { + sinty = 0.0; // I disappears from metric } - + BoutReal sbp = 1.0; // Sign of Bp - if(min(Bpxy, true) < 0.0) + if (min(Bpxy, true) < 0.0) { sbp = -1.0; + } - coords->g11 = SQ(Rxy*Bpxy); + coords->g11 = SQ(Rxy * Bpxy); coords->g22 = 1.0 / SQ(hthe); - coords->g33 = SQ(sinty)*coords->g11 + SQ(coords->Bxy)/coords->g11; + coords->g33 = SQ(sinty) * coords->g11 + SQ(coords->Bxy) / coords->g11; coords->g12 = 0.0; - coords->g13 = -sinty*coords->g11; - coords->g23 = -sbp*Btxy/(hthe*Bpxy*Rxy); - + coords->g13 = -sinty * coords->g11; + coords->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy); + coords->J = hthe / Bpxy; - - coords->g_11 = 1.0/coords->g11 + SQ(sinty*Rxy); - coords->g_22 = SQ(coords->Bxy*hthe/Bpxy); - coords->g_33 = Rxy*Rxy; - coords->g_12 = sbp*Btxy*hthe*sinty*Rxy/Bpxy; - coords->g_13 = sinty*Rxy*Rxy; - coords->g_23 = sbp*Btxy*hthe*Rxy/Bpxy; - + + coords->g_11 = 1.0 / coords->g11 + SQ(sinty * Rxy); + coords->g_22 = SQ(coords->Bxy * hthe / Bpxy); + coords->g_33 = Rxy * Rxy; + coords->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy; + coords->g_13 = sinty * Rxy * Rxy; + coords->g_23 = sbp * Btxy * hthe * Rxy / Bpxy; + coords->geometry(); } diff --git a/tests/MMS/wave-1d-y/wave.cxx b/tests/MMS/wave-1d-y/wave.cxx index 4a30fe877f..2b1940ea92 100644 --- a/tests/MMS/wave-1d-y/wave.cxx +++ b/tests/MMS/wave-1d-y/wave.cxx @@ -1,17 +1,17 @@ #include -#include -#include -#include +#include +#include +#include class Wave1D : public PhysicsModel { private: Field3D f, g; // Evolving variables - + protected: int init(bool UNUSED(restarting)) override { - g.setLocation(CELL_YLOW); // g staggered - + g.setLocation(CELL_YLOW); // g staggered + // Tell BOUT++ to solve f and g solver->add(f, "f"); solver->add(g, "g"); @@ -20,15 +20,14 @@ class Wave1D : public PhysicsModel { } int rhs(BoutReal UNUSED(t)) override { - mesh->communicate(f,g); // Communicate guard cells - + mesh->communicate(f, g); // Communicate guard cells + // Central differencing ddt(f) = DDY(g, CELL_CENTRE); ddt(g) = DDY(f, CELL_YLOW); - + return 0; } }; BOUTMAIN(Wave1D); // Create a main() function - diff --git a/tests/MMS/wave-1d/wave.cxx b/tests/MMS/wave-1d/wave.cxx index 3e118a8cd0..5aad3a2646 100644 --- a/tests/MMS/wave-1d/wave.cxx +++ b/tests/MMS/wave-1d/wave.cxx @@ -1,9 +1,9 @@ +#include #include -#include -#include #include -#include -#include +#include +#include +#include BoutReal Lx, Ly, Lz; // Size of the domain @@ -11,25 +11,26 @@ class Wave1D : public PhysicsModel { private: Field3D f, g; // Evolving variables - Coordinates *coord; + Coordinates* coord; + protected: int init(bool) override { // Coordinate system coord = mesh->getCoordinates(); - + // Get the options - Options &meshoptions = Options::root()["mesh"]; - + Options& meshoptions = Options::root()["mesh"]; + Lx = meshoptions["Lx"].withDefault(1.0); Ly = meshoptions["Ly"].withDefault(1.0); - + // this assumes equidistant grid int nguard = mesh->xstart; coord->dx = Lx / (mesh->GlobalNx - 2 * nguard); coord->dy = Ly / (mesh->GlobalNy - 2 * nguard); SAVE_ONCE(Lx, Ly); - + //set mesh coord->g11 = 1.0; coord->g22 = 1.0; @@ -37,7 +38,7 @@ class Wave1D : public PhysicsModel { coord->g12 = 0.0; coord->g13 = 0.0; coord->g23 = 0.0; - + coord->g_11 = 1.0; coord->g_22 = 1.0; coord->g_33 = 1.0; @@ -47,7 +48,7 @@ class Wave1D : public PhysicsModel { coord->geometry(); g.setLocation(CELL_XLOW); // g staggered to the left of f - + // Tell BOUT++ to solve f and g SOLVE_FOR(f, g); @@ -55,21 +56,20 @@ class Wave1D : public PhysicsModel { } int rhs(BoutReal t) override { - mesh->communicate(f,g); // Communicate guard cells - + mesh->communicate(f, g); // Communicate guard cells + //update time-dependent boundary conditions f.applyBoundary(t); g.applyBoundary(t); // Central differencing - ddt(f) = DDX(g, CELL_CENTRE);// + 20*SQ(coord->dx)*D2DX2(f); - ddt(g) = DDX(f, CELL_XLOW);// + 20*SQ(coord->dx)*D2DX2(g); - + ddt(f) = DDX(g, CELL_CENTRE); // + 20*SQ(coord->dx)*D2DX2(f); + ddt(g) = DDX(f, CELL_XLOW); // + 20*SQ(coord->dx)*D2DX2(g); + return 0; } }; - /////////////////////////////////////////////////////// BOUTMAIN(Wave1D); // Create a main() function diff --git a/tests/integrated/test-backtrace/boutexcept.cxx b/tests/integrated/test-backtrace/boutexcept.cxx index 23e6339117..bd965a9c2b 100644 --- a/tests/integrated/test-backtrace/boutexcept.cxx +++ b/tests/integrated/test-backtrace/boutexcept.cxx @@ -1,5 +1,5 @@ -#include "boutexception.hxx" -#include "msg_stack.hxx" +#include "bout/boutexception.hxx" +#include "bout/msg_stack.hxx" void troublemaker() { AUTO_TRACE(); diff --git a/tests/integrated/test-beuler/test_beuler.cxx b/tests/integrated/test-beuler/test_beuler.cxx index 4b53ad88f3..cfdae89eb2 100644 --- a/tests/integrated/test-beuler/test_beuler.cxx +++ b/tests/integrated/test-beuler/test_beuler.cxx @@ -1,6 +1,6 @@ +#include "bout/petsclib.hxx" #include "bout/physicsmodel.hxx" #include "bout/solver.hxx" -#include "bout/petsclib.hxx" #include #include diff --git a/tests/integrated/test-bout-override-default-option/test-bout-override-default-option.cxx b/tests/integrated/test-bout-override-default-option/test-bout-override-default-option.cxx index 06f519efc7..4c50579c47 100644 --- a/tests/integrated/test-bout-override-default-option/test-bout-override-default-option.cxx +++ b/tests/integrated/test-bout-override-default-option/test-bout-override-default-option.cxx @@ -1,4 +1,4 @@ -#include +#include // Use an integrated test for what is effectively a unit test of the // BOUT_OVERRIDE_DEFAULT_OPTION() macro because the functionality relies on the state of @@ -6,7 +6,7 @@ // called before the overridden defaults are tested. BOUT_OVERRIDE_DEFAULT_OPTION("OverrideDefaultValueOptionsMacro_str", - "macro_override_value"); + "macro_override_value"); BOUT_OVERRIDE_DEFAULT_OPTION("OverrideDefaultValueOptionsMacro_int", 42); BOUT_OVERRIDE_DEFAULT_OPTION("OverrideDefaultValueOptionsMacro_boutreal", 11.); @@ -14,15 +14,15 @@ int main() { Options& options = Options::root(); std::string value_str = - options["OverrideDefaultValueOptionsMacro_str"].withDefault("macro_default_value"); + options["OverrideDefaultValueOptionsMacro_str"].withDefault("macro_default_value"); int value_int = options["OverrideDefaultValueOptionsMacro_int"].withDefault(1); BoutReal value_boutreal = - options["OverrideDefaultValueOptionsMacro_boutreal"].withDefault(2.); + options["OverrideDefaultValueOptionsMacro_boutreal"].withDefault(2.); bool success = true; if (value_str != "macro_override_value") { output_error << "value_str=" << value_str << " but should be macro_override_value" - << endl; + << endl; success = false; } if (value_int != 42) { @@ -31,7 +31,7 @@ int main() { } if (value_boutreal != 11.) { output_error << "value_boutreal=" << value_boutreal << " but should be " << 11. - << endl; + << endl; success = false; } diff --git a/tests/integrated/test-collect/test-collect.cxx b/tests/integrated/test-collect/test-collect.cxx index 4a5da1d835..efb29ba904 100644 --- a/tests/integrated/test-collect/test-collect.cxx +++ b/tests/integrated/test-collect/test-collect.cxx @@ -1,4 +1,4 @@ -#include "bout.hxx" +#include "bout/bout.hxx" int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/tests/integrated/test-command-args/command-args.cxx b/tests/integrated/test-command-args/command-args.cxx index fc62bb7651..d986110736 100644 --- a/tests/integrated/test-command-args/command-args.cxx +++ b/tests/integrated/test-command-args/command-args.cxx @@ -1,7 +1,7 @@ -#include "bout.hxx" +#include "bout/bout.hxx" -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); BoutFinalise(); diff --git a/tests/integrated/test-communications/test-communications.cxx b/tests/integrated/test-communications/test-communications.cxx index 004b4656f6..d666b55aa3 100644 --- a/tests/integrated/test-communications/test-communications.cxx +++ b/tests/integrated/test-communications/test-communications.cxx @@ -1,4 +1,4 @@ -#include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); @@ -10,46 +10,46 @@ int main(int argc, char** argv) { // fill non-guard cells: // interior cells - BOUT_FOR(i, f.getRegion("RGN_NOBNDRY")) { - f[i] = mesh->GlobalNzNoBoundaries*( - mesh->GlobalNyNoBoundaries*mesh->getGlobalXIndexNoBoundaries(i.x()) - + mesh->getGlobalYIndexNoBoundaries(i.y())) + BOUT_FOR (i, f.getRegion("RGN_NOBNDRY")) { + f[i] = mesh->GlobalNzNoBoundaries + * (mesh->GlobalNyNoBoundaries * mesh->getGlobalXIndexNoBoundaries(i.x()) + + mesh->getGlobalYIndexNoBoundaries(i.y())) + i.z(); } // lower x-boundary cells - int startind = - mesh->GlobalNxNoBoundaries*mesh->GlobalNyNoBoundaries*mesh->GlobalNzNoBoundaries; + int startind = mesh->GlobalNxNoBoundaries * mesh->GlobalNyNoBoundaries + * mesh->GlobalNzNoBoundaries; if (mesh->firstX()) { for (int x = 0; x < mesh->xstart; x++) { for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(x, y, z) = - startind - + mesh->GlobalNzNoBoundaries*(mesh->GlobalNyNoBoundaries*x + - mesh->getGlobalYIndexNoBoundaries(y)) - + z; + f(x, y, z) = startind + + mesh->GlobalNzNoBoundaries + * (mesh->GlobalNyNoBoundaries * x + + mesh->getGlobalYIndexNoBoundaries(y)) + + z; } } } } - startind += mesh->xstart*mesh->GlobalNyNoBoundaries*mesh->GlobalNzNoBoundaries; + startind += mesh->xstart * mesh->GlobalNyNoBoundaries * mesh->GlobalNzNoBoundaries; // upper x-boundary cells if (mesh->lastX()) { for (int x = 0; x < mesh->xstart; x++) { for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - f(mesh->xend + 1 + x, y, z) = - startind - + mesh->GlobalNzNoBoundaries*(mesh->GlobalNyNoBoundaries*x + - mesh->getGlobalYIndexNoBoundaries(y)) - + z; + f(mesh->xend + 1 + x, y, z) = startind + + mesh->GlobalNzNoBoundaries + * (mesh->GlobalNyNoBoundaries * x + + mesh->getGlobalYIndexNoBoundaries(y)) + + z; } } } } - startind += mesh->xstart*mesh->GlobalNyNoBoundaries*mesh->GlobalNzNoBoundaries; + startind += mesh->xstart * mesh->GlobalNyNoBoundaries * mesh->GlobalNzNoBoundaries; // lower y-boundary cells for (auto it = mesh->iterateBndryLowerY(); !it.isDone(); it++) { @@ -57,13 +57,11 @@ int main(int argc, char** argv) { for (int y = 0; y < mesh->ystart; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { f(x, y, z) = - startind - + mesh->GlobalNzNoBoundaries*(mesh->getGlobalXIndex(x) + y) - + z; + startind + mesh->GlobalNzNoBoundaries * (mesh->getGlobalXIndex(x) + y) + z; } } } - startind += mesh->GlobalNx*mesh->ystart*mesh->GlobalNzNoBoundaries; + startind += mesh->GlobalNx * mesh->ystart * mesh->GlobalNzNoBoundaries; // upper y-boundary cells for (auto it = mesh->iterateBndryUpperY(); !it.isDone(); it++) { @@ -71,13 +69,11 @@ int main(int argc, char** argv) { for (int y = 0; y < mesh->ystart; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { f(x, mesh->yend + 1 + y, z) = - startind - + mesh->GlobalNzNoBoundaries*(mesh->getGlobalXIndex(x) + y) - + z; + startind + mesh->GlobalNzNoBoundaries * (mesh->getGlobalXIndex(x) + y) + z; } } } - startind += mesh->GlobalNx*mesh->ystart*mesh->GlobalNzNoBoundaries; + startind += mesh->GlobalNx * mesh->ystart * mesh->GlobalNzNoBoundaries; // communicate f to fill guard cells mesh->communicate(f); diff --git a/tests/integrated/test-coordinates-initialization/test-coordinates-initialization.cxx b/tests/integrated/test-coordinates-initialization/test-coordinates-initialization.cxx index 5a7f7cdc28..080b5d5397 100644 --- a/tests/integrated/test-coordinates-initialization/test-coordinates-initialization.cxx +++ b/tests/integrated/test-coordinates-initialization/test-coordinates-initialization.cxx @@ -2,14 +2,14 @@ * Test of initialization of Coordinates objects in Mesh::coords_map */ -#include "bout.hxx" -#include "optionsreader.hxx" +#include "bout/bout.hxx" +#include "bout/optionsreader.hxx" int main() { // Initialize options, needed to load mesh from BOUT.inp - Options *options = Options::getRoot(); - OptionsReader *reader = OptionsReader::getInstance(); + Options* options = Options::getRoot(); + OptionsReader* reader = OptionsReader::getInstance(); reader->read(options, "data/BOUT.inp"); bout::globals::mpi = new MpiWrapper(); diff --git a/tests/integrated/test-cyclic/test_cyclic.cxx b/tests/integrated/test-cyclic/test_cyclic.cxx index 484cccaac3..0f48a1b706 100644 --- a/tests/integrated/test-cyclic/test_cyclic.cxx +++ b/tests/integrated/test-cyclic/test_cyclic.cxx @@ -3,16 +3,16 @@ * */ -#include +#include -#include -#include -#include "utils.hxx" +#include "bout/utils.hxx" +#include +#include // Change this to dcomplex to test complex matrix inversion using T = BoutReal; -int main(int argc, char **argv) { +int main(int argc, char** argv) { // Initialise BOUT++, setting up mesh BoutInitialise(argc, argv); @@ -21,7 +21,7 @@ int main(int argc, char **argv) { int nsys; int n; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); OPTION(options, n, 5); OPTION(options, nsys, 1); BoutReal tol; @@ -43,35 +43,36 @@ int main(int argc, char **argv) { x.reallocate(nsys, n); // Set coefficients to some random numbers - for(int s=0;s -#include +#include int main() { - const std::string izfilename="sample.nc"; + const std::string izfilename = "sample.nc"; // Create a file format handler auto izfile = data_format(izfilename.c_str()); @@ -18,4 +18,3 @@ int main() { return 0; } - diff --git a/tests/integrated/test-delp2/test_delp2.cxx b/tests/integrated/test-delp2/test_delp2.cxx index 3e3d45c671..56211a0389 100644 --- a/tests/integrated/test-delp2/test_delp2.cxx +++ b/tests/integrated/test-delp2/test_delp2.cxx @@ -1,15 +1,15 @@ +#include "bout/unused.hxx" #include -#include "unused.hxx" class TestDelp2 : public PhysicsModel { protected: int init(bool UNUSED(restarting)) override { - Options *opt = Options::getRoot()->getSection("diffusion"); + Options* opt = Options::getRoot()->getSection("diffusion"); OPTION(opt, D, 0.1); OPTION(opt, useFFT, true); SOLVE_FOR(n); - + return 0; } diff --git a/tests/integrated/test-drift-instability/2fluid.cxx b/tests/integrated/test-drift-instability/2fluid.cxx index bbb6c77097..2870e5396a 100644 --- a/tests/integrated/test-drift-instability/2fluid.cxx +++ b/tests/integrated/test-drift-instability/2fluid.cxx @@ -4,12 +4,12 @@ *******************************************************************************/ #include -#include +#include -#include -#include -#include -#include +#include +#include +#include +#include #include #include @@ -129,8 +129,9 @@ class TwoFluid : public PhysicsModel { (globalOptions->getSection("Ti"))->get("evolve", evolve_ti, true); (globalOptions->getSection("Ajpar"))->get("evolve", evolve_ajpar, true); - if (ZeroElMass) + if (ZeroElMass) { evolve_ajpar = false; // Don't need ajpar - calculated from ohm's law + } /*************** INITIALIZE LAPLACIAN SOLVERS ********/ phi_solver = Laplacian::create(globalOptions->getSection("phisolver")); @@ -162,13 +163,15 @@ class TwoFluid : public PhysicsModel { if (nu_perp < 1.e-10) { mui_hat = (3. / 10.) * nuiix / wci; - } else + } else { mui_hat = nu_perp; + } if (estatic) { beta_p = 1.e-29; - } else + } else { beta_p = 4.03e-11 * Ni_x * Te_x / bmag / bmag; + } Vi_x = wci * rho_s; @@ -240,22 +243,25 @@ class TwoFluid : public PhysicsModel { solver->add(rho, "rho"); comms.add(rho); output.write("rho\n"); - } else + } else { initial_profile("rho", rho); + } if (evolve_ni) { solver->add(Ni, "Ni"); comms.add(Ni); output.write("ni\n"); - } else + } else { initial_profile("Ni", Ni); + } if (evolve_te) { solver->add(Te, "Te"); comms.add(Te); output.write("te\n"); - } else + } else { initial_profile("Te", Te); + } if (evolve_ajpar) { solver->add(Ajpar, "Ajpar"); @@ -272,15 +278,17 @@ class TwoFluid : public PhysicsModel { solver->add(Vi, "Vi"); comms.add(Vi); output.write("vi\n"); - } else + } else { initial_profile("Vi", Vi); + } if (evolve_ti) { solver->add(Ti, "Ti"); comms.add(Ti); output.write("ti\n"); - } else + } else { initial_profile("Ti", Ti); + } // Set boundary conditions jpar.setBoundary("jpar"); diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx index 438effbd9d..0a4611ad4a 100644 --- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx +++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx @@ -1,7 +1,7 @@ -#include "bout.hxx" -#include "derivs.hxx" -#include "field_factory.hxx" -#include "parallel_boundary_region.hxx" +#include "bout/bout.hxx" +#include "bout/derivs.hxx" +#include "bout/field_factory.hxx" +#include "bout/parallel_boundary_region.hxx" int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupcomm.cxx b/tests/integrated/test-fieldgroupComm/test_fieldgroupcomm.cxx index 10d19fdc6b..5289b05c80 100644 --- a/tests/integrated/test-fieldgroupComm/test_fieldgroupcomm.cxx +++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupcomm.cxx @@ -1,17 +1,16 @@ #include - -class TestFieldGroupComm : public PhysicsModel{ +class TestFieldGroupComm : public PhysicsModel { protected: int init(bool UNUSED(restarting)) { //Create identical fields - solver->add(fld1,"fld1"); - solver->add(fld2,"fld2"); - solver->add(fld3,"fld3"); + solver->add(fld1, "fld1"); + solver->add(fld2, "fld2"); + solver->add(fld3, "fld3"); //Create different communicators comm1.add(fld1); - comm2.add(fld2,fld2); + comm2.add(fld2, fld2); comm3.add(fld3); return 0; diff --git a/tests/integrated/test-globalfield/test_globalfield.cxx b/tests/integrated/test-globalfield/test_globalfield.cxx index 0a3185721c..de714758b0 100644 --- a/tests/integrated/test-globalfield/test_globalfield.cxx +++ b/tests/integrated/test-globalfield/test_globalfield.cxx @@ -4,9 +4,9 @@ * */ -#include -#include #include +#include +#include class Test_globalfield : public PhysicsModel { protected: @@ -14,9 +14,8 @@ class Test_globalfield : public PhysicsModel { int rhs(BoutReal UNUSED(t)) override; }; - int Test_globalfield::init(bool UNUSED(restarting)) { - + ///////////////////////////////////////////////////////////// // 2D fields @@ -25,102 +24,111 @@ int Test_globalfield::init(bool UNUSED(restarting)) { localX.allocate(); localY.allocate(); - - for(int x=0;xLocalNx;x++) { - for(int y=0;yLocalNy;y++) { - localX(x,y) = mesh->getGlobalXIndex(x); - localY(x,y) = mesh->getGlobalYIndex(y - mesh->ystart); + + for (int x = 0; x < mesh->LocalNx; x++) { + for (int y = 0; y < mesh->LocalNy; y++) { + localX(x, y) = mesh->getGlobalXIndex(x); + localY(x, y) = mesh->getGlobalYIndex(y - mesh->ystart); } } - + // Gather onto one processor (0 by default) GlobalField2D gX(mesh), gY(mesh); gX.gather(localX); gY.gather(localY); - - if(gX.dataIsLocal()) { + + if (gX.dataIsLocal()) { // Data is on this processor bool gather_pass = true; - for(int x=0;xxstart;x<=mesh->xend;x++) - for(int y=mesh->ystart;y<=mesh->yend;y++) { - if( (localX(x,y) != scatX(x,y)) || (localY(x,y) != scatY(x,y)) ) { - output.write("{:d}, {:d} : ({:e}, {:e}) ({:e}, {:e})", x, y, - localX(x,y), localY(x,y), scatX(x,y), scatY(x,y)); + for (int x = mesh->xstart; x <= mesh->xend; x++) { + for (int y = mesh->ystart; y <= mesh->yend; y++) { + if ((localX(x, y) != scatX(x, y)) || (localY(x, y) != scatY(x, y))) { + output.write("{:d}, {:d} : ({:e}, {:e}) ({:e}, {:e})", x, y, localX(x, y), + localY(x, y), scatX(x, y), scatY(x, y)); scatter_pass = false; } } + } output << "2D SCATTER TEST: " << scatter_pass << endl; - + ///////////////////////////////////////////////////////////// // 3D fields - // Create local variables, fill with data Field3D localX3D, localY3D; localX3D.allocate(); localY3D.allocate(); - - for(int x=0;xLocalNx;x++) - for(int y=0;yLocalNy;y++) - for(int z=0;zLocalNz;z++) { - localX3D(x,y,z) = mesh->getGlobalXIndex(x) + z; - localY3D(x,y,z) = mesh->getGlobalYIndex(y - mesh->ystart) + z; + + for (int x = 0; x < mesh->LocalNx; x++) { + for (int y = 0; y < mesh->LocalNy; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + localX3D(x, y, z) = mesh->getGlobalXIndex(x) + z; + localY3D(x, y, z) = mesh->getGlobalYIndex(y - mesh->ystart) + z; } - + } + } + // Gather onto one processor (0 by default) GlobalField3D gX3D(mesh), gY3D(mesh); gX3D.gather(localX3D); gY3D.gather(localY3D); - - if(gX3D.dataIsLocal()) { + + if (gX3D.dataIsLocal()) { // Data is on this processor bool gather_pass3D = true; - for(int x=0;xxstart;x<=mesh->xend;x++) - for(int y=mesh->ystart;y<=mesh->yend;y++) - for(int z=0;zLocalNz;z++) { - if( (localX3D(x,y,z) != scatX3D(x,y,z)) || (localY3D(x,y,z) != scatY3D(x,y,z)) ) { + for (int x = mesh->xstart; x <= mesh->xend; x++) { + for (int y = mesh->ystart; y <= mesh->yend; y++) { + for (int z = 0; z < mesh->LocalNz; z++) { + if ((localX3D(x, y, z) != scatX3D(x, y, z)) + || (localY3D(x, y, z) != scatY3D(x, y, z))) { output.write("{:d}, {:d}, {:d} : ({:e}, {:e}) ({:e}, {:e})", x, y, z, - localX3D(x,y,z), localY3D(x,y,z), scatX3D(x,y,z), scatY3D(x,y,z)); + localX3D(x, y, z), localY3D(x, y, z), scatX3D(x, y, z), + scatY3D(x, y, z)); scatter_pass3D = false; } } + } + } output << "2D SCATTER TEST: " << scatter_pass3D << endl; - return 1; // Signal an error, so quits } @@ -129,5 +137,4 @@ int Test_globalfield::rhs(BoutReal UNUSED(t)) { return 1; } - BOUTMAIN(Test_globalfield) diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata.cxx b/tests/integrated/test-griddata-yboundary-guards/test_griddata.cxx index 8353455aac..c3d906b761 100644 --- a/tests/integrated/test-griddata-yboundary-guards/test_griddata.cxx +++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata.cxx @@ -1,4 +1,4 @@ -#include +#include #include int main(int argc, char** argv) { @@ -12,7 +12,7 @@ int main(int argc, char** argv) { bout::writeDefaultOutputFile(dump); MPI_Barrier(BoutComm::get()); - + BoutFinalise(); return 0; } diff --git a/tests/integrated/test-griddata/test_griddata.cxx b/tests/integrated/test-griddata/test_griddata.cxx index b7d0d3949c..abe8c1f0d6 100644 --- a/tests/integrated/test-griddata/test_griddata.cxx +++ b/tests/integrated/test-griddata/test_griddata.cxx @@ -1,5 +1,5 @@ -#include #include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/tests/integrated/test-gyro/test_gyro.cxx b/tests/integrated/test-gyro/test_gyro.cxx index 3f31b27e3d..b3e5f0d82c 100644 --- a/tests/integrated/test-gyro/test_gyro.cxx +++ b/tests/integrated/test-gyro/test_gyro.cxx @@ -3,11 +3,11 @@ * */ -#include -#include -#include +#include +#include +#include -int main(int argc, char **argv) { +int main(int argc, char** argv) { // Initialise BOUT++, setting up mesh BoutInitialise(argc, argv); @@ -28,7 +28,7 @@ int main(int argc, char **argv) { output.write("\nFinished running test.\n\n"); MPI_Barrier(BoutComm::get()); // Wait for all processors to write data - + bout::checkForUnusedOptions(); BoutFinalise(); return 0; diff --git a/tests/integrated/test-initial/test_initial.cxx b/tests/integrated/test-initial/test_initial.cxx index fabeb705ef..333d50d72b 100644 --- a/tests/integrated/test-initial/test_initial.cxx +++ b/tests/integrated/test-initial/test_initial.cxx @@ -6,7 +6,7 @@ * */ -#include "initialprofiles.hxx" +#include "bout/initialprofiles.hxx" #include "bout/physicsmodel.hxx" int main(int argc, char** argv) { diff --git a/tests/integrated/test-integrate/test_integrate.cxx b/tests/integrated/test-integrate/test_integrate.cxx index 4bbb2dde9c..af28913b63 100644 --- a/tests/integrated/test-integrate/test_integrate.cxx +++ b/tests/integrated/test-integrate/test_integrate.cxx @@ -4,8 +4,7 @@ Illustrates how to use the Solver class as an ODE integrator */ -#include // Note: Need to use new API - +#include // Note: Need to use new API // This class represents a sub-problem to be solved class MyFunction : public PhysicsModel { @@ -14,57 +13,53 @@ class MyFunction : public PhysicsModel { solver->add(result, "result"); return 0; } - + int rhs(BoutReal UNUSED(time)) { ddt(result) = 1.0; return 0; } - + int outputMonitor(BoutReal simtime, int UNUSED(iter), int UNUSED(NOUT)) { output.write("MyFunction: time = {:e}\n", simtime); return 0; } - + Field3D result; + private: - }; - // This class represents the top-level model being solved class TestIntegrate : public PhysicsModel { public: - ~TestIntegrate() { - delete model; - } - + ~TestIntegrate() { delete model; } + int init(bool UNUSED(restarting)) { - + // Create a model model = new MyFunction(); - + // Create a solver, passing the options section "ode" ode = Solver::create(Options::getRoot()->getSection("ode")); - + // Specify the model to be solved ode->setModel(model); ode->solve(5, 0.1); // Number of outputs, step - + solver->add(f, "f"); return 0; } - + int rhs(BoutReal UNUSED(time)) { ddt(f) = model->result; return 0; } + private: - Field3D f; // Some variable being evolved - + std::unique_ptr ode{nullptr}; // Integration solver - MyFunction *model; + MyFunction* model; }; - BOUTMAIN(TestIntegrate); diff --git a/tests/integrated/test-interchange-instability/2fluid.cxx b/tests/integrated/test-interchange-instability/2fluid.cxx index 080c76db4d..5e57e166c4 100644 --- a/tests/integrated/test-interchange-instability/2fluid.cxx +++ b/tests/integrated/test-interchange-instability/2fluid.cxx @@ -3,12 +3,12 @@ * Same as Maxim's version of BOUT - simplified 2-fluid for benchmarking *******************************************************************************/ -#include +#include -#include -#include -#include -#include +#include +#include +#include +#include #include #include @@ -35,7 +35,8 @@ class Interchange : public PhysicsModel { // Laplacian inversion std::unique_ptr phi_solver; - Coordinates *coord; + Coordinates* coord; + protected: int init(bool UNUSED(restarting)) override { Field2D I; // Shear factor @@ -78,8 +79,8 @@ class Interchange : public PhysicsModel { /*************** READ OPTIONS *************************/ // Read some parameters - Options *globalOptions = Options::getRoot(); - Options *options = globalOptions->getSection("2fluid"); + Options* globalOptions = Options::getRoot(); + Options* options = globalOptions->getSection("2fluid"); OPTION(options, AA, 2.0); OPTION(options, ZZ, 1.0); @@ -100,14 +101,15 @@ class Interchange : public PhysicsModel { /************** CALCULATE PARAMETERS *****************/ rho_s = 1.02 * sqrt(AA * Te_x) / ZZ / bmag; - wci = 9.58e3*ZZ*bmag/AA; - + wci = 9.58e3 * ZZ * bmag / AA; + /************** PRINT Z INFORMATION ******************/ BoutReal hthe0; if (mesh->get(hthe0, "hthe0") == 0) { - output.write(" ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", - hthe0 / rho_s); + output.write( + " ****NOTE: input from BOUT, Z length needs to be divided by {:e}\n", + hthe0 / rho_s); } /************** NORMALISE QUANTITIES *****************/ @@ -176,9 +178,9 @@ class Interchange : public PhysicsModel { // Communicate variables mesh->communicate(rho, Ni, phi); Field3D pei = (Te0 + Ti0) * Ni; - + // DENSITY EQUATION - ddt(Ni) = - b0xGrad_dot_Grad(phi, Ni0) / coord->Bxy; + ddt(Ni) = -b0xGrad_dot_Grad(phi, Ni0) / coord->Bxy; // VORTICITY ddt(rho) = 2.0 * coord->Bxy * b0xcv * Grad(pei); diff --git a/tests/integrated/test-interpolate-z/test_interpolate.cxx b/tests/integrated/test-interpolate-z/test_interpolate.cxx index b72f4bceb5..d8d4cd6258 100644 --- a/tests/integrated/test-interpolate-z/test_interpolate.cxx +++ b/tests/integrated/test-interpolate-z/test_interpolate.cxx @@ -10,18 +10,18 @@ #include #include -#include "bout.hxx" +#include "bout/bout.hxx" +#include "bout/field_factory.hxx" +#include "bout/interpolation_z.hxx" #include "bout/constants.hxx" -#include "field_factory.hxx" #include "bout/sys/generator_context.hxx" -#include "interpolation_z.hxx" using bout::globals::mesh; /// Get a FieldGenerator from the options for a variable std::shared_ptr getGeneratorFromOptions(const std::string& varname, std::string& func) { - Options *options = Options::getRoot()->getSection(varname); + Options* options = Options::getRoot()->getSection(varname); options->get("solution", func, "0.0"); if (func.empty()) { @@ -30,7 +30,7 @@ std::shared_ptr getGeneratorFromOptions(const std::string& varna return FieldFactory::get()->parse(func); } -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); // Random number generator @@ -65,14 +65,14 @@ int main(int argc, char **argv) { // Bind the random number generator and distribution into a single function auto dice = std::bind(distribution, generator); - for (const auto &index : deltaz) { + for (const auto& index : deltaz) { // Get some random displacements BoutReal dz = index.z() + dice(); deltaz[index] = dz; // Get the global indices bout::generator::Context pos{index, CELL_CENTRE, deltaz.getMesh(), 0.0}; - pos.set("x", mesh->GlobalX(index.x()), - "z", TWOPI * static_cast(dz) / static_cast(mesh->LocalNz)); + pos.set("x", mesh->GlobalX(index.x()), "z", + TWOPI * static_cast(dz) / static_cast(mesh->LocalNz)); // Generate the analytic solution at the displacements a_solution[index] = a_gen->generate(pos); b_solution[index] = b_gen->generate(pos); diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx index 958409bbc1..6da8b220c0 100644 --- a/tests/integrated/test-interpolate/test_interpolate.cxx +++ b/tests/integrated/test-interpolate/test_interpolate.cxx @@ -10,16 +10,16 @@ #include #include -#include "bout.hxx" +#include "bout/bout.hxx" +#include "bout/field_factory.hxx" +#include "bout/interpolation_xz.hxx" #include "bout/constants.hxx" -#include "field_factory.hxx" #include "bout/sys/generator_context.hxx" -#include "interpolation_xz.hxx" /// Get a FieldGenerator from the options for a variable std::shared_ptr getGeneratorFromOptions(const std::string& varname, std::string& func) { - Options *options = Options::getRoot()->getSection(varname); + Options* options = Options::getRoot()->getSection(varname); options->get("solution", func, "0.0"); if (func.empty()) { @@ -28,7 +28,7 @@ std::shared_ptr getGeneratorFromOptions(const std::string& varna return FieldFactory::get()->parse(func); } -int main(int argc, char **argv) { +int main(int argc, char** argv) { BoutInitialise(argc, argv); // Random number generator @@ -66,7 +66,7 @@ int main(int argc, char **argv) { // Bind the random number generator and distribution into a single function auto dice = std::bind(distribution, generator); - for (const auto &index : deltax) { + for (const auto& index : deltax) { // Get some random displacements BoutReal dx = index.x() + dice(); BoutReal dz = index.z() + dice(); @@ -79,8 +79,8 @@ int main(int argc, char **argv) { deltaz[index] = dz; // Get the global indices bout::generator::Context pos{index, CELL_CENTRE, deltax.getMesh(), 0.0}; - pos.set("x", mesh->GlobalX(dx), - "z", TWOPI * static_cast(dz) / static_cast(mesh->LocalNz)); + pos.set("x", mesh->GlobalX(dx), "z", + TWOPI * static_cast(dz) / static_cast(mesh->LocalNz)); // Generate the analytic solution at the displacements a_solution[index] = a_gen->generate(pos); b_solution[index] = b_gen->generate(pos); diff --git a/tests/integrated/test-invertable-operator/invertable_operator.cxx b/tests/integrated/test-invertable-operator/invertable_operator.cxx index 72631e08c7..3c99c3dbbd 100644 --- a/tests/integrated/test-invertable-operator/invertable_operator.cxx +++ b/tests/integrated/test-invertable-operator/invertable_operator.cxx @@ -1,5 +1,5 @@ -#include -#include +#include +#include #include #include diff --git a/tests/integrated/test-invpar/test_invpar.cxx b/tests/integrated/test-invpar/test_invpar.cxx index 79d8dd121f..350437d66b 100644 --- a/tests/integrated/test-invpar/test_invpar.cxx +++ b/tests/integrated/test-invpar/test_invpar.cxx @@ -3,11 +3,11 @@ * */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include using bout::globals::mesh; @@ -35,8 +35,8 @@ int test(const std::string& acoef, const std::string& bcoef, const std::string& Field3D result = inv->solve(input); mesh->communicate(result); - Field3D deriv = A*result + B*Grad2_par2(result) + C*D2DYDZ(result) - + D*D2DZ2(result) + E*DDY(result); + Field3D deriv = A * result + B * Grad2_par2(result) + C * D2DYDZ(result) + + D * D2DZ2(result) + E * DDY(result); // Check the result bool success{true}; diff --git a/tests/integrated/test-laplace-hypre3d/test-laplace3d.cxx b/tests/integrated/test-laplace-hypre3d/test-laplace3d.cxx index 74d388c29e..69524d44da 100644 --- a/tests/integrated/test-laplace-hypre3d/test-laplace3d.cxx +++ b/tests/integrated/test-laplace-hypre3d/test-laplace3d.cxx @@ -23,9 +23,9 @@ * **************************************************************************/ -#include "bout.hxx" -#include "initialprofiles.hxx" -#include "invert_laplace.hxx" +#include "bout/bout.hxx" +#include "bout/initialprofiles.hxx" +#include "bout/invert_laplace.hxx" int main(int argc, char** argv) { diff --git a/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx b/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx index 739b4b81d1..a1231a6cdf 100644 --- a/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx +++ b/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx @@ -23,9 +23,9 @@ * **************************************************************************/ -#include "bout.hxx" -#include "initialprofiles.hxx" -#include "invert_laplace.hxx" +#include "bout/bout.hxx" +#include "bout/initialprofiles.hxx" +#include "bout/invert_laplace.hxx" int main(int argc, char** argv) { @@ -50,15 +50,15 @@ int main(int argc, char** argv) { int y = mesh->ystart - 1; if (x == mesh->xstart) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x-1, y, z) = 0.5*(f(x-1, y - 1, z) + f(x-1, y, z)); + guess(x - 1, y, z) = 0.5 * (f(x - 1, y - 1, z) + f(x - 1, y, z)); } } for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x, y, z) = 0.5*(f(x, y, z) + f(x, y + 1, z)); + guess(x, y, z) = 0.5 * (f(x, y, z) + f(x, y + 1, z)); } if (x == mesh->xend) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x+1, y, z) = 0.5*(f(x+1, y - 1, z) + f(x+1, y, z)); + guess(x + 1, y, z) = 0.5 * (f(x + 1, y - 1, z) + f(x + 1, y, z)); } } } @@ -67,15 +67,15 @@ int main(int argc, char** argv) { int y = mesh->yend + 1; if (x == mesh->xstart) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x-1, y, z) = 0.5*(f(x-1, y - 1, z) + f(x-1, y, z)); + guess(x - 1, y, z) = 0.5 * (f(x - 1, y - 1, z) + f(x - 1, y, z)); } } for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x, y, z) = 0.5*(f(x, y - 1, z) + f(x, y, z)); + guess(x, y, z) = 0.5 * (f(x, y - 1, z) + f(x, y, z)); } if (x == mesh->xend) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x+1, y, z) = 0.5*(f(x+1, y - 1, z) + f(x+1, y, z)); + guess(x + 1, y, z) = 0.5 * (f(x + 1, y - 1, z) + f(x + 1, y, z)); } } } @@ -83,7 +83,7 @@ int main(int argc, char** argv) { int x = mesh->xstart - 1; for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x, y, z) = 0.5*(f(x, y, z) + f(x + 1, y, z)); + guess(x, y, z) = 0.5 * (f(x, y, z) + f(x + 1, y, z)); } } } @@ -91,7 +91,7 @@ int main(int argc, char** argv) { int x = mesh->xend + 1; for (int y = mesh->ystart; y <= mesh->yend; y++) { for (int z = mesh->zstart; z <= mesh->zend; z++) { - guess(x, y, z) = 0.5*(f(x - 1, y, z) + f(x, y, z)); + guess(x, y, z) = 0.5 * (f(x - 1, y, z) + f(x, y, z)); } } } @@ -123,7 +123,7 @@ int main(int argc, char** argv) { /////////////////////////////////////////////////////////////////////////////////////// // Calculate error /////////////////////////////////////////////////////////////////////////////////////// - Field3D rhs_check = D*Laplace_perp(f) + Grad_perp(C2)*Grad_perp(f)/C1 + A*f; + Field3D rhs_check = D * Laplace_perp(f) + Grad_perp(C2) * Grad_perp(f) / C1 + A * f; Field3D error = rhs_check - rhs; BoutReal error_max = max(abs(error), true); diff --git a/tests/integrated/test-laplace/test_laplace.cxx b/tests/integrated/test-laplace/test_laplace.cxx index 7571833f74..94887c718e 100644 --- a/tests/integrated/test-laplace/test_laplace.cxx +++ b/tests/integrated/test-laplace/test_laplace.cxx @@ -3,9 +3,9 @@ * */ -#include -#include -#include +#include +#include +#include int main(int argc, char** argv) { diff --git a/tests/integrated/test-laplace2/test_laplace.cxx b/tests/integrated/test-laplace2/test_laplace.cxx index 01a37994ca..44e18c2974 100644 --- a/tests/integrated/test-laplace2/test_laplace.cxx +++ b/tests/integrated/test-laplace2/test_laplace.cxx @@ -3,10 +3,10 @@ * */ -#include #include -#include -#include +#include +#include +#include class Test_laplace : public PhysicsModel { protected: @@ -14,28 +14,27 @@ class Test_laplace : public PhysicsModel { int rhs(BoutReal UNUSED(t)) override; }; - int Test_laplace::init(bool UNUSED(restarting)) { FieldFactory f(mesh); - - Options *options = Options::getRoot(); + + Options* options = Options::getRoot(); // Read strings containing coefficients std::string in, acoef, ccoef; OPTION(options, in, "(1-gauss(x-0.5,0.2))*gauss(z-pi)"); OPTION(options, acoef, "gauss(x)"); - OPTION(options, ccoef, "sin(x) * gauss(x-0.5)"); + OPTION(options, ccoef, "sin(x) * gauss(x-0.5)"); // Create the coefficients Field3D input = f.create3D(in); Field2D a = f.create2D(acoef); Field3D c = f.create3D(ccoef); SAVE_ONCE3(input, a, c); - + // Create two solvers, using different options auto solver1 = Laplacian::create(options->getSection("solver1")); auto solver2 = Laplacian::create(options->getSection("solver2")); - + solver1->setCoefA(a); solver1->setCoefC(c); @@ -46,21 +45,21 @@ int Test_laplace::init(bool UNUSED(restarting)) { Field3D result2 = solver2->solve(input, result1); SAVE_ONCE2(result1, result2); - - Field3D check1 = a*result1 + Delp2(result1); + + Field3D check1 = a * result1 + Delp2(result1); check1.applyBoundary("dirichlet"); - Field3D check2 = a*result2 + Delp2(result2); + Field3D check2 = a * result2 + Delp2(result2); check2.applyBoundary("dirichlet"); SAVE_ONCE2(check1, check2); - + dump.write(); dump.close(); - + output << "\nFinished running test. Triggering error to quit\n\n"; - + MPI_Barrier(BoutComm::get()); // Wait for all processors to write data - + return 1; } @@ -69,5 +68,4 @@ int Test_laplace::rhs(BoutReal UNUSED(t)) { return 1; } - BOUTMAIN(Test_laplace) diff --git a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx index 9da09bc750..1b34fb922b 100644 --- a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx @@ -23,12 +23,12 @@ * **************************************************************************/ -#include #include #include -#include -#include -#include +#include +#include +#include +#include int main(int argc, char** argv) { @@ -41,7 +41,7 @@ int main(int argc, char** argv) { // A*Laplace_perp(f) + Grad_perp(A).Grad_perp(f) + B*f = rhs Field2D f, a, b, sol; Field2D error, absolute_error; //Absolute value of relative error: abs((f - sol)/f) - BoutReal max_error; //Output of test + BoutReal max_error; //Output of test initial_profile("f", f); initial_profile("a", a); @@ -55,16 +55,16 @@ int main(int argc, char** argv) { //////////////////////////////////////////////////////////////////////////////////////// Field2D rhs, rhs_check; - rhs = Laplace_perpXY(a, f) + b*f; + rhs = Laplace_perpXY(a, f) + b * f; laplacexy.setCoefs(a, b); sol = laplacexy.solve(rhs, 0.); - error = (f - sol)/f; + error = (f - sol) / f; absolute_error = f - sol; max_error = max(abs(absolute_error), true); - output<<"Magnitude of maximum absolute error is "<communicate(sol); rhs_check = Laplace_perpXY(a, sol); diff --git a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx index c0bd4479d7..128458eaaf 100644 --- a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx @@ -23,12 +23,12 @@ * **************************************************************************/ -#include #include #include -#include -#include -#include +#include +#include +#include +#include int main(int argc, char** argv) { @@ -38,7 +38,7 @@ int main(int argc, char** argv) { auto coords = mesh->getCoordinates(); auto& opt = Options::root(); - + LaplaceXY laplacexy; bool include_y_derivs = opt["laplacexy"]["include_y_derivs"]; @@ -48,7 +48,7 @@ int main(int argc, char** argv) { // A*Laplace_perp(f) + Grad_perp(A).Grad_perp(f) + B*f = rhs Field2D f, a, b, sol; Field2D error, absolute_error; //Absolute value of relative error: abs((f - sol)/f) - BoutReal max_error; //Output of test + BoutReal max_error; //Output of test initial_profile("f", f); initial_profile("a", a); @@ -70,13 +70,13 @@ int main(int argc, char** argv) { } laplacexy.setCoefs(a, b); - + sol = laplacexy.solve(rhs, 0.); - error = (f - sol)/f; + error = (f - sol) / f; absolute_error = f - sol; max_error = max(abs(absolute_error), true); - output<<"Magnitude of maximum absolute error is "<communicate(sol); if (include_y_derivs) { diff --git a/tests/integrated/test-laplacexy/loadmetric.cxx b/tests/integrated/test-laplacexy/loadmetric.cxx index 1765b63256..f4774b583f 100644 --- a/tests/integrated/test-laplacexy/loadmetric.cxx +++ b/tests/integrated/test-laplacexy/loadmetric.cxx @@ -1,8 +1,8 @@ +#include "bout/field2d.hxx" +#include "bout/globals.hxx" +#include "bout/output.hxx" +#include "bout/utils.hxx" #include "bout/mesh.hxx" -#include "field2d.hxx" -#include "globals.hxx" -#include "output.hxx" -#include "utils.hxx" #include "loadmetric.hxx" @@ -14,56 +14,56 @@ void LoadMetric(BoutReal Lnorm, BoutReal Bnorm) { auto coords = mesh->getCoordinates(); GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics - + // Checking for dpsi and qinty used in BOUT grids Field2D dx; - if(!mesh->get(dx, "dpsi")) { + if (!mesh->get(dx, "dpsi")) { output << "\tUsing dpsi as the x grid spacing\n"; coords->dx = dx; // Only use dpsi if found - }else { + } else { // dx will have been read already from the grid output << "\tUsing dx as the x grid spacing\n"; } Field2D qinty; - Rxy /= Lnorm; - hthe /= Lnorm; - sinty *= SQ(Lnorm)*Bnorm; - coords->dx /= SQ(Lnorm)*Bnorm; - + Rxy /= Lnorm; + hthe /= Lnorm; + sinty *= SQ(Lnorm) * Bnorm; + coords->dx /= SQ(Lnorm) * Bnorm; + Bpxy /= Bnorm; Btxy /= Bnorm; - coords->Bxy /= Bnorm; - + coords->Bxy /= Bnorm; + // Calculate metric components std::string ptstr; Options::getRoot()->get("mesh:paralleltransform", ptstr, "identity"); // Convert to lower case for comparison ptstr = lowercase(ptstr); - if(ptstr == "shifted") { - sinty = 0.0; // I disappears from metric + if (ptstr == "shifted") { + sinty = 0.0; // I disappears from metric } - + BoutReal sbp = 1.0; // Sign of Bp - if(min(Bpxy, true) < 0.0) + if (min(Bpxy, true) < 0.0) { sbp = -1.0; - - coords->g11 = pow(Rxy*Bpxy,2); - coords->g22 = 1.0 / pow(hthe,2); - coords->g33 = pow(sinty,2)*coords->g11 + pow(coords->Bxy,2)/coords->g11; + } + + coords->g11 = pow(Rxy * Bpxy, 2); + coords->g22 = 1.0 / pow(hthe, 2); + coords->g33 = pow(sinty, 2) * coords->g11 + pow(coords->Bxy, 2) / coords->g11; coords->g12 = 0.0; - coords->g13 = -sinty*coords->g11; - coords->g23 = -sbp*Btxy/(hthe*Bpxy*Rxy); - + coords->g13 = -sinty * coords->g11; + coords->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy); + coords->J = hthe / Bpxy; - - coords->g_11 = 1.0/coords->g11 + pow(sinty*Rxy,2); - coords->g_22 = pow(coords->Bxy*hthe/Bpxy,2); - coords->g_33 = Rxy*Rxy; - coords->g_12 = sbp*Btxy*hthe*sinty*Rxy/Bpxy; - coords->g_13 = sinty*Rxy*Rxy; - coords->g_23 = sbp*Btxy*hthe*Rxy/Bpxy; - + + coords->g_11 = 1.0 / coords->g11 + pow(sinty * Rxy, 2); + coords->g_22 = pow(coords->Bxy * hthe / Bpxy, 2); + coords->g_33 = Rxy * Rxy; + coords->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy; + coords->g_13 = sinty * Rxy * Rxy; + coords->g_23 = sbp * Btxy * hthe * Rxy / Bpxy; + coords->geometry(); } - diff --git a/tests/integrated/test-laplacexy/loadmetric.hxx b/tests/integrated/test-laplacexy/loadmetric.hxx index 16c9aafe17..141269d8b8 100644 --- a/tests/integrated/test-laplacexy/loadmetric.hxx +++ b/tests/integrated/test-laplacexy/loadmetric.hxx @@ -1,7 +1,7 @@ #ifndef __LOADMETRIC_H__ #define __LOADMETRIC_H__ -#include +#include void LoadMetric(BoutReal Lnorm, BoutReal Bnorm); diff --git a/tests/integrated/test-laplacexy/test-laplacexy.cxx b/tests/integrated/test-laplacexy/test-laplacexy.cxx index e3219e68f6..af14b5dfe1 100644 --- a/tests/integrated/test-laplacexy/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy/test-laplacexy.cxx @@ -23,12 +23,12 @@ * **************************************************************************/ -#include #include #include -#include -#include -#include +#include +#include +#include +#include using bout::globals::dump; using bout::globals::mesh; @@ -40,7 +40,7 @@ int main(int argc, char** argv) { auto coords = mesh->getCoordinates(); auto& opt = Options::root(); - + LaplaceXY laplacexy; bool include_y_derivs = opt["laplacexy"]["include_y_derivs"]; @@ -50,7 +50,7 @@ int main(int argc, char** argv) { // A*Laplace_perp(f) + Grad_perp(A).Grad_perp(f) + B*f = rhs Field2D f, a, b, sol; Field2D error, absolute_error; //Absolute value of relative error: abs((f - sol)/f) - BoutReal max_error; //Output of test + BoutReal max_error; //Output of test initial_profile("f", f); initial_profile("a", a); @@ -65,25 +65,26 @@ int main(int argc, char** argv) { Field2D rhs, rhs_check; if (include_y_derivs) { - rhs = a*Laplace_perp(f) + Grad_perp(a)*Grad_perp(f) + b*f; + rhs = a * Laplace_perp(f) + Grad_perp(a) * Grad_perp(f) + b * f; } else { - rhs = a*Delp2(f, CELL_DEFAULT, false) + coords->g11*DDX(a)*DDX(f) + b*f; + rhs = a * Delp2(f, CELL_DEFAULT, false) + coords->g11 * DDX(a) * DDX(f) + b * f; } laplacexy.setCoefs(a, b); - + sol = laplacexy.solve(rhs, 0.); - error = (f - sol)/f; + error = (f - sol) / f; absolute_error = f - sol; max_error = max(abs(absolute_error), true); - output<<"Magnitude of maximum absolute error is "<communicate(sol); if (include_y_derivs) { - rhs_check = a*Laplace_perp(sol) + Grad_perp(a)*Grad_perp(sol) + b*sol; + rhs_check = a * Laplace_perp(sol) + Grad_perp(a) * Grad_perp(sol) + b * sol; } else { - rhs_check = a*Delp2(sol, CELL_DEFAULT, false) + coords->g11*DDX(a)*DDX(sol) + b*sol; + rhs_check = + a * Delp2(sol, CELL_DEFAULT, false) + coords->g11 * DDX(a) * DDX(sol) + b * sol; } dump.add(a, "a"); diff --git a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx index 4ed2d973d4..93932e9792 100644 --- a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx @@ -25,10 +25,10 @@ #include #include -#include -#include -#include -#include +#include +#include +#include +#include int main(int argc, char** argv) { diff --git a/tests/integrated/test-laplacexz/test-laplacexz.cxx b/tests/integrated/test-laplacexz/test-laplacexz.cxx index dfa819b244..066867aa3b 100644 --- a/tests/integrated/test-laplacexz/test-laplacexz.cxx +++ b/tests/integrated/test-laplacexz/test-laplacexz.cxx @@ -8,11 +8,11 @@ * (pctype=lu, factor_package=superlu_dist) * -mat_superlu_dist_statprint */ -#include +#include #include -#include -#include +#include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); @@ -37,7 +37,7 @@ int main(int argc, char** argv) { // Now the normal test. output.write("Setting coefficients\n"); - inv->setCoefs(Field3D(1.0),Field3D(0.0)); + inv->setCoefs(Field3D(1.0), Field3D(0.0)); output.write("First solve\n"); @@ -47,7 +47,7 @@ int main(int argc, char** argv) { output.write("Second solve\n"); - inv->setCoefs(Field3D(2.0),Field3D(0.1)); + inv->setCoefs(Field3D(2.0), Field3D(0.1)); Field3D rhs2 = FieldFactory::get()->create3D("rhs", Options::getRoot(), bout::globals::mesh); diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx index 66819825d8..8223e50da9 100644 --- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx +++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx @@ -23,17 +23,17 @@ * **************************************************************************/ -#include #include -#include -#include -#include -#include +#include +#include #include -#include +#include +#include +#include +#include -BoutReal max_error_at_ystart(const Field3D &error); -Field3D this_Grad_perp_dot_Grad_perp(const Field3D &f, const Field3D &g); +BoutReal max_error_at_ystart(const Field3D& error); +Field3D this_Grad_perp_dot_Grad_perp(const Field3D& f, const Field3D& g); int main(int argc, char** argv) { @@ -43,7 +43,7 @@ int main(int argc, char** argv) { auto invert = Laplacian::create(); // Solving equations of the form d*Grad_perp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various boundary conditions - Field3D f1,a1,b1,c1,d1,sol1,bcheck1; + Field3D f1, a1, b1, c1, d1, sol1, bcheck1; Field3D absolute_error1; BoutReal max_error1; //Output of test @@ -56,7 +56,8 @@ int main(int argc, char** argv) { c1 = FieldFactory::get()->create3D("c1:function", Options::getRoot(), mesh); a1 = FieldFactory::get()->create3D("a1:function", Options::getRoot(), mesh); - b1 = d1*Delp2(f1, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c1,f1)/c1 + a1*f1; + b1 = d1 * Delp2(f1, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c1, f1) / c1 + + a1 * f1; sol1 = 0.; invert->setInnerBoundaryFlags(0); @@ -69,10 +70,11 @@ int main(int argc, char** argv) { sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); mesh->communicate(sol1); checkData(sol1); - bcheck1 = d1*Delp2(sol1, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c1,sol1)/c1 + a1*sol1; - absolute_error1 = f1-sol1; + bcheck1 = d1 * Delp2(sol1, CELL_DEFAULT, false) + + this_Grad_perp_dot_Grad_perp(c1, sol1) / c1 + a1 * sol1; + absolute_error1 = f1 - sol1; max_error1 = max_error_at_ystart(abs(absolute_error1, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b1): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error1 = -1; @@ -82,11 +84,11 @@ int main(int argc, char** argv) { } d1 = Delp2(f1, CELL_DEFAULT, false); - c1 = this_Grad_perp_dot_Grad_perp(c1,f1)/c1; - a1 = a1*f1; + c1 = this_Grad_perp_dot_Grad_perp(c1, f1) / c1; + a1 = a1 * f1; - output<create3D("c2:function", Options::getRoot(), mesh); a2 = FieldFactory::get()->create3D("a2:function", Options::getRoot(), mesh); - b2 = d2*Delp2(f2, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c2,f2)/c2 + a2*f2; + b2 = d2 * Delp2(f2, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c2, f2) / c2 + + a2 * f2; sol2 = 0.; invert->setInnerBoundaryFlags(INVERT_AC_GRAD); @@ -121,10 +124,11 @@ int main(int argc, char** argv) { try { sol2 = invert->solve(sliceXZ(b2, mesh->ystart)); mesh->communicate(sol2); - bcheck2 = d2*Delp2(sol2, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c2,sol2)/c2 + a2*sol2; - absolute_error2 = f2-sol2; + bcheck2 = d2 * Delp2(sol2, CELL_DEFAULT, false) + + this_Grad_perp_dot_Grad_perp(c2, sol2) / c2 + a2 * sol2; + absolute_error2 = f2 - sol2; max_error2 = max_error_at_ystart(abs(absolute_error2, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b2): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error2 = -1; @@ -133,8 +137,8 @@ int main(int argc, char** argv) { absolute_error2 = -1.; } - output<create3D("c3:function", Options::getRoot(), mesh); a3 = FieldFactory::get()->create3D("a3:function", Options::getRoot(), mesh); - b3 = d3*Delp2(f3, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c3,f3)/c3 + a3*f3; + b3 = d3 * Delp2(f3, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c3, f3) / c3 + + a3 * f3; sol3 = 0.; invert->setInnerBoundaryFlags(INVERT_SET); @@ -167,20 +172,28 @@ int main(int argc, char** argv) { // make field to pass in boundary conditions Field3D x0 = 0.; - if (mesh->firstX()) - for (int k=0;kLocalNz;k++) - x0(mesh->xstart-1,mesh->ystart,k) = 0.5*(f3(mesh->xstart-1,mesh->ystart,k)+f3(mesh->xstart,mesh->ystart,k)); - if (mesh->lastX()) - for (int k=0;kLocalNz;k++) - x0(mesh->xend+1,mesh->ystart,k) = 0.5*(f3(mesh->xend+1,mesh->ystart,k)+f3(mesh->xend,mesh->ystart,k)); + if (mesh->firstX()) { + for (int k = 0; k < mesh->LocalNz; k++) { + x0(mesh->xstart - 1, mesh->ystart, k) = + 0.5 + * (f3(mesh->xstart - 1, mesh->ystart, k) + f3(mesh->xstart, mesh->ystart, k)); + } + } + if (mesh->lastX()) { + for (int k = 0; k < mesh->LocalNz; k++) { + x0(mesh->xend + 1, mesh->ystart, k) = + 0.5 * (f3(mesh->xend + 1, mesh->ystart, k) + f3(mesh->xend, mesh->ystart, k)); + } + } try { sol3 = invert->solve(sliceXZ(b3, mesh->ystart), sliceXZ(x0, mesh->ystart)); mesh->communicate(sol3); - bcheck3 = d3*Delp2(sol3, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c3,f3)/c3 + a3*sol3; - absolute_error3 = f3-sol3; + bcheck3 = d3 * Delp2(sol3, CELL_DEFAULT, false) + + this_Grad_perp_dot_Grad_perp(c3, f3) / c3 + a3 * sol3; + absolute_error3 = f3 - sol3; max_error3 = max_error_at_ystart(abs(absolute_error3, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b3): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error3 = -1; @@ -189,8 +202,8 @@ int main(int argc, char** argv) { absolute_error3 = -1.; } - output<create3D("c4:function", Options::getRoot(), mesh); a4 = FieldFactory::get()->create3D("a4:function", Options::getRoot(), mesh); - b4 = d4*Delp2(f4, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c4,f4)/c4 + a4*f4; + b4 = d4 * Delp2(f4, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c4, f4) / c4 + + a4 * f4; sol4 = 0.; - invert->setInnerBoundaryFlags(INVERT_AC_GRAD+INVERT_SET); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD+INVERT_SET); + invert->setInnerBoundaryFlags(INVERT_AC_GRAD + INVERT_SET); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD + INVERT_SET); invert->setCoefA(a4); invert->setCoefC(c4); invert->setCoefD(d4); // make field to pass in boundary conditions x0 = 0.; - if (mesh->firstX()) - for (int k=0;kLocalNz;k++) + if (mesh->firstX()) { + for (int k = 0; k < mesh->LocalNz; k++) { x0(mesh->xstart - 1, mesh->ystart, k) = (f4(mesh->xstart, mesh->ystart, k) - f4(mesh->xstart - 1, mesh->ystart, k)) / mesh->getCoordinates()->dx(mesh->xstart, mesh->ystart, k) / sqrt(mesh->getCoordinates()->g_11(mesh->xstart, mesh->ystart, k)); - if (mesh->lastX()) - for (int k=0;kLocalNz;k++) + } + } + if (mesh->lastX()) { + for (int k = 0; k < mesh->LocalNz; k++) { x0(mesh->xend + 1, mesh->ystart, k) = (f4(mesh->xend + 1, mesh->ystart, k) - f4(mesh->xend, mesh->ystart, k)) / mesh->getCoordinates()->dx(mesh->xend, mesh->ystart, k) / sqrt(mesh->getCoordinates()->g_11(mesh->xend, mesh->ystart, k)); + } + } try { sol4 = invert->solve(sliceXZ(b4, mesh->ystart), sliceXZ(x0, mesh->ystart)); mesh->communicate(sol4); - bcheck4 = d4*Delp2(sol4, CELL_DEFAULT, false) + this_Grad_perp_dot_Grad_perp(c4,sol4)/c4 + a4*sol4; - absolute_error4 = f4-sol4; + bcheck4 = d4 * Delp2(sol4, CELL_DEFAULT, false) + + this_Grad_perp_dot_Grad_perp(c4, sol4) / c4 + a4 * sol4; + absolute_error4 = f4 - sol4; max_error4 = max_error_at_ystart(abs(absolute_error4, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b4): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error4 = -1; @@ -251,8 +270,8 @@ int main(int argc, char** argv) { absolute_error4 = -1.; } - output<getCoordinates()->g11 * ::DDX(f) * ::DDX(g) + mesh->getCoordinates()->g33 * ::DDZ(f) * ::DDZ(g) - + mesh->getCoordinates()->g13 * (DDX(f)*DDZ(g) + DDZ(f)*DDX(g)); - + Field3D result = mesh->getCoordinates()->g11 * ::DDX(f) * ::DDX(g) + + mesh->getCoordinates()->g33 * ::DDZ(f) * ::DDZ(g) + + mesh->getCoordinates()->g13 * (DDX(f) * DDZ(g) + DDZ(f) * DDX(g)); + return result; } -BoutReal max_error_at_ystart(const Field3D &error) { +BoutReal max_error_at_ystart(const Field3D& error) { auto* mesh = error.getMesh(); BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jz=0; jzLocalNz; jz++) - if (local_max_errorystart, jz)) local_max_error=error(jx, mesh->ystart, jz); - + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + if (local_max_error < error(jx, mesh->ystart, jz)) { + local_max_error = error(jx, mesh->ystart, jz); + } + } + } + BoutReal max_error; MPI_Allreduce(&local_max_error, &max_error, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get()); diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx index 05e0e32189..e428b9380c 100644 --- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx +++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx @@ -23,18 +23,18 @@ * **************************************************************************/ -#include +#include "../../../src/invert/laplace/impls/naulin/naulin_laplace.hxx" #include -#include -#include -#include -#include +#include +#include #include -#include -#include "../../../src/invert/laplace/impls/naulin/naulin_laplace.hxx" +#include +#include +#include +#include -BoutReal max_error_at_ystart(const Field3D &error); -Field3D this_Grad_perp_dot_Grad_perp(const Field3D &f, const Field3D &g); +BoutReal max_error_at_ystart(const Field3D& error); +Field3D this_Grad_perp_dot_Grad_perp(const Field3D& f, const Field3D& g); int main(int argc, char** argv) { @@ -45,7 +45,7 @@ int main(int argc, char** argv) { LaplaceNaulin invert(options); // Solving equations of the form d*Grad_perp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various boundary conditions - Field3D f1,a1,b1,c1,d1,sol1,bcheck1; + Field3D f1, a1, b1, c1, d1, sol1, bcheck1; Field3D absolute_error1; BoutReal max_error1; //Output of test @@ -60,7 +60,7 @@ int main(int argc, char** argv) { c1 = FieldFactory::get()->create3D("c1:function", Options::getRoot(), mesh); a1 = FieldFactory::get()->create3D("a1:function", Options::getRoot(), mesh); - b1 = d1*Delp2(f1) + this_Grad_perp_dot_Grad_perp(c1,f1)/c1 + a1*f1; + b1 = d1 * Delp2(f1) + this_Grad_perp_dot_Grad_perp(c1, f1) / c1 + a1 * f1; sol1 = 0.; invert.setInnerBoundaryFlags(0); @@ -73,10 +73,10 @@ int main(int argc, char** argv) { sol1 = invert.solve(b1); mesh->communicate(sol1); checkData(sol1); - bcheck1 = d1*Delp2(sol1) + this_Grad_perp_dot_Grad_perp(c1,sol1)/c1 + a1*sol1; - absolute_error1 = f1-sol1; + bcheck1 = d1 * Delp2(sol1) + this_Grad_perp_dot_Grad_perp(c1, sol1) / c1 + a1 * sol1; + absolute_error1 = f1 - sol1; max_error1 = max_error_at_ystart(abs(absolute_error1, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b1): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error1 = -1; @@ -85,9 +85,10 @@ int main(int argc, char** argv) { absolute_error1 = -1.; } - output<create3D("c2:function", Options::getRoot(), mesh); a2 = FieldFactory::get()->create3D("a2:function", Options::getRoot(), mesh); - b2 = d2*Delp2(f2) + this_Grad_perp_dot_Grad_perp(c2,f2)/c2 + a2*f2; + b2 = d2 * Delp2(f2) + this_Grad_perp_dot_Grad_perp(c2, f2) / c2 + a2 * f2; sol2 = 0.; invert.setInnerBoundaryFlags(INVERT_DC_GRAD + INVERT_AC_GRAD); @@ -123,10 +124,10 @@ int main(int argc, char** argv) { try { sol2 = invert.solve(b2); mesh->communicate(sol2); - bcheck2 = d2*Delp2(sol2) + this_Grad_perp_dot_Grad_perp(c2,sol2)/c2 + a2*sol2; - absolute_error2 = f2-sol2; + bcheck2 = d2 * Delp2(sol2) + this_Grad_perp_dot_Grad_perp(c2, sol2) / c2 + a2 * sol2; + absolute_error2 = f2 - sol2; max_error2 = max_error_at_ystart(abs(absolute_error2, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b2): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error2 = -1; @@ -135,9 +136,10 @@ int main(int argc, char** argv) { absolute_error2 = -1.; } - output<create3D("c3:function", Options::getRoot(), mesh); a3 = FieldFactory::get()->create3D("a3:function", Options::getRoot(), mesh); - b3 = d3*Delp2(f3) + this_Grad_perp_dot_Grad_perp(c3,f3)/c3 + a3*f3; + b3 = d3 * Delp2(f3) + this_Grad_perp_dot_Grad_perp(c3, f3) / c3 + a3 * f3; sol3 = 0.; invert.setInnerBoundaryFlags(INVERT_SET); @@ -172,20 +174,27 @@ int main(int argc, char** argv) { // make field to pass in boundary conditions Field3D x0 = 0.; - if (mesh->firstX()) - for (int k=0;kLocalNz;k++) - x0(mesh->xstart-1,mesh->ystart,k) = 0.5*(f3(mesh->xstart-1,mesh->ystart,k)+f3(mesh->xstart,mesh->ystart,k)); - if (mesh->lastX()) - for (int k=0;kLocalNz;k++) - x0(mesh->xend+1,mesh->ystart,k) = 0.5*(f3(mesh->xend+1,mesh->ystart,k)+f3(mesh->xend,mesh->ystart,k)); + if (mesh->firstX()) { + for (int k = 0; k < mesh->LocalNz; k++) { + x0(mesh->xstart - 1, mesh->ystart, k) = + 0.5 + * (f3(mesh->xstart - 1, mesh->ystart, k) + f3(mesh->xstart, mesh->ystart, k)); + } + } + if (mesh->lastX()) { + for (int k = 0; k < mesh->LocalNz; k++) { + x0(mesh->xend + 1, mesh->ystart, k) = + 0.5 * (f3(mesh->xend + 1, mesh->ystart, k) + f3(mesh->xend, mesh->ystart, k)); + } + } try { sol3 = invert.solve(b3, x0); mesh->communicate(sol3); - bcheck3 = d3*Delp2(sol3) + this_Grad_perp_dot_Grad_perp(c3,f3)/c3 + a3*sol3; - absolute_error3 = f3-sol3; + bcheck3 = d3 * Delp2(sol3) + this_Grad_perp_dot_Grad_perp(c3, f3) / c3 + a3 * sol3; + absolute_error3 = f3 - sol3; max_error3 = max_error_at_ystart(abs(absolute_error3, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b3): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error3 = -1; @@ -194,9 +203,10 @@ int main(int argc, char** argv) { absolute_error3 = -1.; } - output<create3D("c4:function", Options::getRoot(), mesh); a4 = FieldFactory::get()->create3D("a4:function", Options::getRoot(), mesh); - b4 = d4*Delp2(f4) + this_Grad_perp_dot_Grad_perp(c4,f4)/c4 + a4*f4; + b4 = d4 * Delp2(f4) + this_Grad_perp_dot_Grad_perp(c4, f4) / c4 + a4 * f4; sol4 = 0.; invert.setInnerBoundaryFlags(INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_SET); @@ -231,26 +241,30 @@ int main(int argc, char** argv) { // make field to pass in boundary conditions x0 = 0.; - if (mesh->firstX()) - for (int k=0;kLocalNz;k++) + if (mesh->firstX()) { + for (int k = 0; k < mesh->LocalNz; k++) { x0(mesh->xstart - 1, mesh->ystart, k) = (f4(mesh->xstart, mesh->ystart, k) - f4(mesh->xstart - 1, mesh->ystart, k)) / mesh->getCoordinates()->dx(mesh->xstart, mesh->ystart, k) / sqrt(mesh->getCoordinates()->g_11(mesh->xstart, mesh->ystart, k)); - if (mesh->lastX()) - for (int k=0;kLocalNz;k++) + } + } + if (mesh->lastX()) { + for (int k = 0; k < mesh->LocalNz; k++) { x0(mesh->xend + 1, mesh->ystart, k) = (f4(mesh->xend + 1, mesh->ystart, k) - f4(mesh->xend, mesh->ystart, k)) / mesh->getCoordinates()->dx(mesh->xend, mesh->ystart, k) / sqrt(mesh->getCoordinates()->g_11(mesh->xend, mesh->ystart, k)); + } + } try { sol4 = invert.solve(b4, x0); mesh->communicate(sol4); - bcheck4 = d4*Delp2(sol4) + this_Grad_perp_dot_Grad_perp(c4,sol4)/c4 + a4*sol4; - absolute_error4 = f4-sol4; + bcheck4 = d4 * Delp2(sol4) + this_Grad_perp_dot_Grad_perp(c4, sol4) / c4 + a4 * sol4; + absolute_error4 = f4 - sol4; max_error4 = max_error_at_ystart(abs(absolute_error4, "RGN_NOBNDRY")); - } catch (BoutException &err) { + } catch (BoutException& err) { output << "BoutException occured in invert->solve(b4): " << err.what() << endl << "Laplacian inversion failed to converge (probably)" << endl; max_error4 = -1; @@ -259,9 +273,10 @@ int main(int argc, char** argv) { absolute_error4 = -1.; } - output<g11 * ::DDX(f) * ::DDX(g) + coords->g33 * ::DDZ(f) * ::DDZ(g) + coords->g13 * (DDX(f) * DDZ(g) + DDZ(f) * DDX(g)); @@ -296,14 +310,18 @@ Field3D this_Grad_perp_dot_Grad_perp(const Field3D &f, const Field3D &g) { return result; } -BoutReal max_error_at_ystart(const Field3D &error) { +BoutReal max_error_at_ystart(const Field3D& error) { const auto* mesh = error.getMesh(); BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jz=0; jzLocalNz; jz++) - if (local_max_errorystart, jz)) local_max_error=error(jx, mesh->ystart, jz); - + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + if (local_max_error < error(jx, mesh->ystart, jz)) { + local_max_error = error(jx, mesh->ystart, jz); + } + } + } + BoutReal max_error; MPI_Allreduce(&local_max_error, &max_error, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get()); diff --git a/tests/integrated/test-nonuniform/test_delp2.cxx b/tests/integrated/test-nonuniform/test_delp2.cxx index 6c4da64f48..921e86d5e6 100644 --- a/tests/integrated/test-nonuniform/test_delp2.cxx +++ b/tests/integrated/test-nonuniform/test_delp2.cxx @@ -7,8 +7,8 @@ * */ -#include #include +#include class Test_delp2 : public PhysicsModel { protected: @@ -16,28 +16,26 @@ class Test_delp2 : public PhysicsModel { int rhs(BoutReal UNUSED(t)) override; }; - int Test_delp2::init(bool UNUSED(restarting)) { Field3D input, reference, result; - - GRID_LOAD(input); // Read input from file - GRID_LOAD(reference); // Reference solution - + + GRID_LOAD(input); // Read input from file + GRID_LOAD(reference); // Reference solution + result = Delp2(input); // Calculate perpendicular Laplacian result.applyBoundary("dirichlet"); // Apply Dirichlet boundary conditions - + SAVE_ONCE(input); - SAVE_ONCE(result); // Queue the output variable to be written - SAVE_ONCE(reference); // Write the reference solution too - + SAVE_ONCE(result); // Queue the output variable to be written + SAVE_ONCE(reference); // Write the reference solution too dump.write(); dump.close(); - + MPI_Barrier(BoutComm::get()); - + output << "\nFinished running test. Triggering error to quit\n\n"; - + return 1; } @@ -46,5 +44,4 @@ int Test_delp2::rhs(BoutReal UNUSED(t)) { return 1; } - BOUTMAIN(Test_delp2) diff --git a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx index 6d86bd0612..01c5749972 100644 --- a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx +++ b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx @@ -1,8 +1,8 @@ -#include "bout.hxx" +#include "bout/bout.hxx" -#include "options_netcdf.hxx" -#include "optionsreader.hxx" +#include "bout/options_netcdf.hxx" +#include "bout/optionsreader.hxx" using bout::OptionsNetCDF; @@ -17,14 +17,14 @@ int main(int argc, char** argv) { values.printUnused(); // Write to an INI text file - OptionsReader *reader = OptionsReader::getInstance(); + OptionsReader* reader = OptionsReader::getInstance(); reader->write(&values, "test-out.ini"); // Write to a NetCDF file OptionsNetCDF("test-out.nc").write(values); /////////////////////////// - + // Write the BOUT.inp settings to NetCDF file OptionsNetCDF("settings.nc").write(Options::root()); @@ -33,7 +33,7 @@ int main(int argc, char** argv) { // Write to INI file reader->write(&settings, "settings.ini"); - + /////////////////////////// // Write fields @@ -56,28 +56,28 @@ int main(int argc, char** argv) { fields2["f2d"] = f2d; fields2["f3d"] = f3d; fields2["fperp"] = fperp; - + // Write out again OptionsNetCDF("fields2.nc").write(fields2); - + /////////////////////////// // Time dependent values Options data; data["scalar"] = 1.0; data["scalar"].attributes["time_dimension"] = "t"; - + data["field"] = Field3D(2.0); data["field"].attributes["time_dimension"] = "t"; - + OptionsNetCDF("time.nc").write(data); - + // Update time-dependent values data["scalar"] = 2.0; data["field"] = Field3D(3.0); - + // Append data to file OptionsNetCDF("time.nc", OptionsNetCDF::FileMode::append).write(data); - + BoutFinalise(); }; diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx index 769222bb61..0b01241287 100644 --- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx @@ -23,667 +23,825 @@ * **************************************************************************/ -#include #include +#include // #include -#include -#include -#include +#include #include +#include +#include -BoutReal max_error_at_ystart(const Field3D &error); +BoutReal max_error_at_ystart(const Field3D& error); int main(int argc, char** argv) { BoutInitialise(argc, argv); { - Options *options = Options::getRoot()->getSection("petsc2nd"); - auto invert = Laplacian::create(options); - options = Options::getRoot()->getSection("petsc4th"); - auto invert_4th = Laplacian::create(options); - - // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d - Field3D f1,a1,b1,c1,d1,sol1; - BoutReal p,q; //Use to set parameters in constructing trial functions - Field3D error1,absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) - BoutReal max_error1; //Output of test - - using bout::globals::mesh; - - // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z. - // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point - BoutReal nx = mesh->GlobalNx-2*mesh->xstart - 1; - BoutReal nz = mesh->GlobalNz; - - //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - // Test 1: Gaussian x-profiles, 2nd order Krylov - p = 0.39503274; - q = 0.20974396; - f1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f1(jx, jy, jz) = 0. + exp(-(100.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-100.*pow(-p,2))*x + (-p*exp(-100.*pow(-p,2))-(1-p)*exp(-100.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))) //make the gradients zero at both x-boundaries - ; - ASSERT0(finite(f1(jx, jy, jz))); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f1(jx, jy, jz) = 0. + exp(-(60.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-60.*pow(-p,2))*x + (-p*exp(-60.*pow(-p,2))-(1-p)*exp(-60.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries + Options* options = Options::getRoot()->getSection("petsc2nd"); + auto invert = Laplacian::create(options); + options = Options::getRoot()->getSection("petsc4th"); + auto invert_4th = Laplacian::create(options); + + // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d + Field3D f1, a1, b1, c1, d1, sol1; + BoutReal p, q; //Use to set parameters in constructing trial functions + Field3D error1, + absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) + BoutReal max_error1; //Output of test + + using bout::globals::mesh; + + // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z. + // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point + BoutReal nx = mesh->GlobalNx - 2 * mesh->xstart - 1; + BoutReal nz = mesh->GlobalNz; + + //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + // Test 1: Gaussian x-profiles, 2nd order Krylov + p = 0.39503274; + q = 0.20974396; + f1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f1(jx, jy, jz) = + 0. + exp(-(100. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-100. * pow(-p, 2)) * x + + (-p * exp(-100. * pow(-p, 2)) + - (1 - p) * exp(-100. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos(2. * PI + * (z - q)))) //make the gradients zero at both x-boundaries + ; ASSERT0(finite(f1(jx, jy, jz))); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f1(jx, jy, jz) = 0. + exp(-(60.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-60.*pow(-p,2))*x + (-p*exp(-60.*pow(-p,2))-(1-p)*exp(-60.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - ASSERT0(finite(f1(jx, jy, jz))); - } - - f1.applyBoundary("neumann"); - - p = 0.512547; - q = 0.30908712; - d1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d1(jx, jy, jz) = 1. + 0.2*exp(-50.*pow(x-p,2)/4.)*sin(2.*PI*(z-q) * 3.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d1(jx, jy, jz) = 1. + 0.2*exp(-50.*pow(x-p,2)/4.)*sin(2.*PI*(z-q) * 3.); -// d1(jx, jy, jz) = d1(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d1(jx, jy, jz) = 1. + 0.2*exp(-50.*pow(x-p,2)/4.)*sin(2.*PI*(z-q) * 3.); -// d1(jx, jy, jz) = d1(jx-1, jy, jz); - } - - p = 0.18439023; - q = 0.401089473; - c1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c1(jx, jy, jz) = 1. + 0.15*exp(-50.*pow(x-p,2)*2.)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c1(jx, jy, jz) = 1. + 0.15*exp(-50.*pow(x-p,2)*2.)*sin(2.*PI*(z-q) * 2.); -// c1(jx, jy, jz) = c1(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c1(jx, jy, jz) = 1. + 0.15*exp(-50.*pow(x-p,2)*2.)*sin(2.*PI*(z-q) * 2.); -// c1(jx, jy, jz) = c1(jx-1, jy, jz); - } - - p = 0.612547; - q = 0.30908712; - a1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a1(jx, jy, jz) = -1. + 0.1*exp(-50.*pow(x-p,2)*2.5)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a1(jx, jy, jz) = -1. + 0.1*exp(-50.*pow(x-p,2)*2.5)*sin(2.*PI*(z-q) * 7.); -// a1(jx, jy, jz) = a1(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a1(jx, jy, jz) = -1. + 0.1*exp(-50.*pow(x-p,2)*2.5)*sin(2.*PI*(z-q) * 7.); -// a1(jx, jy, jz) = a1(jx-1, jy, jz); - } - - checkData(f1); - checkData(a1); - checkData(c1); - checkData(d1); - - mesh->communicate(f1,a1,c1,d1); - - b1 = d1*Delp2(f1) + Grad_perp(c1)*Grad_perp(f1)/c1 + a1*f1; - - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b1(jx, jy, jz) = b1(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b1(jx, jy, jz) = b1(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a1); - invert->setCoefC(c1); - invert->setCoefD(d1); - - checkData(b1); - - try { - sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); - error1 = (f1-sol1)/f1; - absolute_error1 = f1-sol1; -// max_error1 = max_error_at_ystart(abs(error1)); - max_error1 = max_error_at_ystart(abs(absolute_error1)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b1): " - << err.what() - << endl; - max_error1 = -1; - } - - output<setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setGlobalFlags(INVERT_4TH_ORDER); - invert_4th->setCoefA(a1); - invert_4th->setCoefC(c1); - invert_4th->setCoefD(d1); - - try { - sol2 = invert_4th->solve(sliceXZ(b1, mesh->ystart)); - error2 = (f1-sol2)/f1; - absolute_error2 = f1-sol2; -// max_error2 = max_error_at_ystart(abs(error2)); - max_error2 = max_error_at_ystart(abs(absolute_error2)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b1): " - << err.what() - << endl; - max_error2 = -1; - } - - output<firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b3(jx, jy, jz) = b3(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b3(jx, jy, jz) = b3(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a3); - invert->setCoefC(c3); - invert->setCoefD(d3); - - try { - sol3 = invert->solve(sliceXZ(b3, mesh->ystart)); - error3 = (f1-sol3)/f1; - absolute_error3 = f1-sol3; -// max_error3 = max_error_at_ystart(abs(error3)); - max_error3 = max_error_at_ystart(abs(absolute_error3)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b3): " - << err.what() - << endl; - max_error3 = -1; - } + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f1(jx, jy, jz) = + 0. + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-60. * pow(-p, 2)) * x + + (-p * exp(-60. * pow(-p, 2)) + - (1 - p) * exp(-60. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + ASSERT0(finite(f1(jx, jy, jz))); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f1(jx, jy, jz) = + 0. + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-60. * pow(-p, 2)) * x + + (-p * exp(-60. * pow(-p, 2)) + - (1 - p) * exp(-60. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + ASSERT0(finite(f1(jx, jy, jz))); + } + } + } + } + + f1.applyBoundary("neumann"); + + p = 0.512547; + q = 0.30908712; + d1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d1(jx, jy, jz) = + 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d1(jx, jy, jz) = + 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); + // d1(jx, jy, jz) = d1(jx+1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d1(jx, jy, jz) = + 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); + // d1(jx, jy, jz) = d1(jx-1, jy, jz); + } + } + } + } + + p = 0.18439023; + q = 0.401089473; + c1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c1(jx, jy, jz) = + 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c1(jx, jy, jz) = + 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); + // c1(jx, jy, jz) = c1(jx+1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c1(jx, jy, jz) = + 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); + // c1(jx, jy, jz) = c1(jx-1, jy, jz); + } + } + } + } + + p = 0.612547; + q = 0.30908712; + a1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a1(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a1(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); + // a1(jx, jy, jz) = a1(jx+1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a1(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); + // a1(jx, jy, jz) = a1(jx-1, jy, jz); + } + } + } + } - output<getSection("SPT"); - auto invert_SPT = Laplacian::create(SPT_options); - invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); - invert_SPT->setCoefA(a3); - invert_SPT->setCoefC(c3); - invert_SPT->setCoefD(d3); - - sol4 = invert_SPT->solve(sliceXZ(b3, mesh->ystart)); - error4 = (f1-sol4)/f1; - absolute_error4 = f1-sol4; -// max_error4 = max_error_at_ystart(abs(error4)); - max_error4 = max_error_at_ystart(abs(absolute_error4)); - - output<xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f5(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))) //make the gradients zero at both x-boundaries - ; - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f5(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f5(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - } - - p = 0.63298589; - q = 0.889237890; - d5.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d5(jx, jy, jz) = 1. + p*cos(2.*PI*x)*sin(2.*PI*(z-q) * 3.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d5(jx, jy, jz) = 1. + p*cos(2.*PI*x)*sin(2.*PI*(z-q) * 3.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d5(jx, jy, jz) = 1. + p*cos(2.*PI*x)*sin(2.*PI*(z-q) * 3.); - } - - p = 0.160983834; - q = 0.73050121087; - c5.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c5(jx, jy, jz) = 1. + p*cos(2.*PI*x*5)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c5(jx, jy, jz) = 1. + p*cos(2.*PI*x*5)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c5(jx, jy, jz) = 1. + p*cos(2.*PI*x*5)*sin(2.*PI*(z-q) * 2.); - } - - p = 0.5378950; - q = 0.2805870; - a5.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a5(jx, jy, jz) = -1. + p*cos(2.*PI*x*2.)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a5(jx, jy, jz) = -1. + p*cos(2.*PI*x*2.)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a5(jx, jy, jz) = -1. + p*cos(2.*PI*x*2.)*sin(2.*PI*(z-q) * 7.); - } - - f5.applyBoundary("neumann"); - mesh->communicate(f5,a5,c5,d5); - - b5 = d5*Delp2(f5) + Grad_perp(c5)*Grad_perp(f5)/c5 + a5*f5; - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b5(jx, jy, jz) = b5(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b5(jx, jy, jz) = b5(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a5); - invert->setCoefC(c5); - invert->setCoefD(d5); - - try { - sol5 = invert->solve(sliceXZ(b5, mesh->ystart)); - error5 = (f5-sol5)/f5; - absolute_error5 = f5-sol5; -// max_error5 = max_error_at_ystart(abs(error5)); - max_error5 = max_error_at_ystart(abs(absolute_error5)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b5): " - << err.what() - << endl; - max_error5 = -1; - } + checkData(f1); + checkData(a1); + checkData(c1); + checkData(d1); - output<setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setGlobalFlags(INVERT_4TH_ORDER); - invert_4th->setCoefA(a5); - invert_4th->setCoefC(c5); - invert_4th->setCoefD(d5); - - try { - sol6 = invert_4th->solve(sliceXZ(b5, mesh->ystart)); - error6 = (f5-sol6)/f5; - absolute_error6 = f5-sol6; -// max_error6 = max_error_at_ystart(abs(error6)); - max_error6 = max_error_at_ystart(abs(absolute_error6)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b6): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error6 = -1; - } + mesh->communicate(f1, a1, c1, d1); - output<firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b7(jx, jy, jz) = b7(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b7(jx, jy, jz) = b7(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a7); - invert->setCoefC(c7); - invert->setCoefD(d7); - - try { - sol7 = invert->solve(sliceXZ(b7, mesh->ystart)); - error7 = (f5-sol7)/f5; - absolute_error7 = f5-sol7; -// max_error7 = max_error_at_ystart(abs(error7)); - max_error7 = max_error_at_ystart(abs(absolute_error7)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b7): " - << err.what() - << endl; - max_error7 = -1; - } + b1 = d1 * Delp2(f1) + Grad_perp(c1) * Grad_perp(f1) / c1 + a1 * f1; - output<setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); - invert_SPT->setCoefA(a7); - invert_SPT->setCoefC(c7); - invert_SPT->setCoefD(d7); - - sol8 = invert_SPT->solve(sliceXZ(b7, mesh->ystart)); - error8 = (f5-sol8)/f5; - absolute_error8 = f5-sol8; -// max_error8 = max_error_at_ystart(abs(error8)); - max_error8 = max_error_at_ystart(abs(absolute_error8)); - - output<firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b1(jx, jy, jz) = b1(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b1(jx, jy, jz) = b1(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a1); + invert->setCoefC(c1); + invert->setCoefD(d1); + + checkData(b1); + + try { + sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); + error1 = (f1 - sol1) / f1; + absolute_error1 = f1 - sol1; + // max_error1 = max_error_at_ystart(abs(error1)); + max_error1 = max_error_at_ystart(abs(absolute_error1)); + } catch (BoutException& err) { + output << "BoutException occured in invert->solve(b1): " << err.what() << endl; + max_error1 = -1; + } + + output << endl << "Test 1: PETSc 2nd order" << endl; + // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setGlobalFlags(INVERT_4TH_ORDER); + invert_4th->setCoefA(a1); + invert_4th->setCoefC(c1); + invert_4th->setCoefD(d1); + + try { + sol2 = invert_4th->solve(sliceXZ(b1, mesh->ystart)); + error2 = (f1 - sol2) / f1; + absolute_error2 = f1 - sol2; + // max_error2 = max_error_at_ystart(abs(error2)); + max_error2 = max_error_at_ystart(abs(absolute_error2)); + } catch (BoutException& err) { + output << "BoutException occured in invert->solve(b1): " << err.what() << endl; + max_error2 = -1; + } + + output << endl << "Test 2: PETSc 4th order" << endl; + // output<<"Time to set up is "<firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b3(jx, jy, jz) = b3(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b3(jx, jy, jz) = b3(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a3); + invert->setCoefC(c3); + invert->setCoefD(d3); + + try { + sol3 = invert->solve(sliceXZ(b3, mesh->ystart)); + error3 = (f1 - sol3) / f1; + absolute_error3 = f1 - sol3; + // max_error3 = max_error_at_ystart(abs(error3)); + max_error3 = max_error_at_ystart(abs(absolute_error3)); + } catch (BoutException& err) { + output << "BoutException occured in invert->solve(b3): " << err.what() << endl; + max_error3 = -1; + } + + output << endl << "Test 3: with coefficients constant in z, PETSc 2nd order" << endl; + // output<<"Time to set up is "<getSection("SPT"); + auto invert_SPT = Laplacian::create(SPT_options); + invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); + invert_SPT->setCoefA(a3); + invert_SPT->setCoefC(c3); + invert_SPT->setCoefD(d3); + + sol4 = invert_SPT->solve(sliceXZ(b3, mesh->ystart)); + error4 = (f1 - sol4) / f1; + absolute_error4 = f1 - sol4; + // max_error4 = max_error_at_ystart(abs(error4)); + max_error4 = max_error_at_ystart(abs(absolute_error4)); + + output << endl << "Test 4: with coefficients constant in z, default solver" << endl; + // output<<"Time to set up is "<xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f5(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos(2. * PI + * (z - q)))) //make the gradients zero at both x-boundaries + ; + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f5(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f5(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + } + } + } + } + + p = 0.63298589; + q = 0.889237890; + d5.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d5(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d5(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d5(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); + } + } + } + } + + p = 0.160983834; + q = 0.73050121087; + c5.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c5(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c5(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c5(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); + } + } + } + } + + p = 0.5378950; + q = 0.2805870; + a5.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a5(jx, jy, jz) = -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a5(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a5(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); + } + } + } + } + + f5.applyBoundary("neumann"); + mesh->communicate(f5, a5, c5, d5); + + b5 = d5 * Delp2(f5) + Grad_perp(c5) * Grad_perp(f5) / c5 + a5 * f5; + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b5(jx, jy, jz) = b5(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b5(jx, jy, jz) = b5(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a5); + invert->setCoefC(c5); + invert->setCoefD(d5); + + try { + sol5 = invert->solve(sliceXZ(b5, mesh->ystart)); + error5 = (f5 - sol5) / f5; + absolute_error5 = f5 - sol5; + // max_error5 = max_error_at_ystart(abs(error5)); + max_error5 = max_error_at_ystart(abs(absolute_error5)); + } catch (BoutException& err) { + output << "BoutException occured in invert->solve(b5): " << err.what() << endl; + max_error5 = -1; + } + + output << endl << "Test 5: different profiles, PETSc 2nd order" << endl; + // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setGlobalFlags(INVERT_4TH_ORDER); + invert_4th->setCoefA(a5); + invert_4th->setCoefC(c5); + invert_4th->setCoefD(d5); + + try { + sol6 = invert_4th->solve(sliceXZ(b5, mesh->ystart)); + error6 = (f5 - sol6) / f5; + absolute_error6 = f5 - sol6; + // max_error6 = max_error_at_ystart(abs(error6)); + max_error6 = max_error_at_ystart(abs(absolute_error6)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b6): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error6 = -1; + } + + output << endl << "Test 6: different profiles, PETSc 4th order" << endl; + // output<<"Time to set up is "<firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b7(jx, jy, jz) = b7(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b7(jx, jy, jz) = b7(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a7); + invert->setCoefC(c7); + invert->setCoefD(d7); + + try { + sol7 = invert->solve(sliceXZ(b7, mesh->ystart)); + error7 = (f5 - sol7) / f5; + absolute_error7 = f5 - sol7; + // max_error7 = max_error_at_ystart(abs(error7)); + max_error7 = max_error_at_ystart(abs(absolute_error7)); + } catch (BoutException& err) { + output << "BoutException occured in invert->solve(b7): " << err.what() << endl; + max_error7 = -1; + } + + output + << endl + << "Test 7: different profiles, with coefficients constant in z, PETSc 2nd order" + << endl; + // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); + invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); + invert_SPT->setCoefA(a7); + invert_SPT->setCoefC(c7); + invert_SPT->setCoefD(d7); + + sol8 = invert_SPT->solve(sliceXZ(b7, mesh->ystart)); + error8 = (f5 - sol8) / f5; + absolute_error8 = f5 - sol8; + // max_error8 = max_error_at_ystart(abs(error8)); + max_error8 = max_error_at_ystart(abs(absolute_error8)); + + output + << endl + << "Test 8: different profiles, with coefficients constant in z, default solver" + << endl; + // output<<"Time to set up is "<xstart, mesh->ystart, 0); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jz=0; jzLocalNz; jz++) - if (local_max_errorystart, jz)) local_max_error=error(jx, mesh->ystart, jz); - + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + if (local_max_error < error(jx, mesh->ystart, jz)) { + local_max_error = error(jx, mesh->ystart, jz); + } + } + } + BoutReal max_error; MPI_Allreduce(&local_max_error, &max_error, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get()); diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx index 1be121dfa8..f6e94da943 100644 --- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx +++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx @@ -23,664 +23,853 @@ * **************************************************************************/ -#include #include +#include // #include -#include -#include -#include +#include #include +#include +#include -BoutReal max_error_at_ystart(const Field3D &error); +BoutReal max_error_at_ystart(const Field3D& error); int main(int argc, char** argv) { BoutInitialise(argc, argv); { - Options *options = Options::getRoot()->getSection("petsc2nd"); - auto invert = Laplacian::create(options); - options = Options::getRoot()->getSection("petsc4th"); - auto invert_4th = Laplacian::create(options); - - // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d - Field3D f1,a1,b1,c1,d1,sol1; - BoutReal p,q; //Use to set parameters in constructing trial functions - Field3D error1,absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) - BoutReal max_error1; //Output of test - - using bout::globals::mesh; - - // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z. - // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point - BoutReal nx = mesh->GlobalNx-2*mesh->xstart - 1; - BoutReal nz = mesh->GlobalNz; - - //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - // Test 1: Gaussian x-profiles, 2nd order Krylov - p = 0.39503274; - q = 0.20974396; - f1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f1(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))) //make the gradients zero at both x-boundaries - ; - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f1(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f1(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - } - - p = 0.512547; - q = 0.30908712; - d1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d1(jx, jy, jz) = 1.e-7*(1. + 0.2*exp(-50.*pow(x-p,2)/4.)*sin(2.*PI*(z-q) * 3.)); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d1(jx, jy, jz) = 1.e-7*(1. + 0.2*exp(-50.*pow(x-p,2)/4.)*sin(2.*PI*(z-q) * 3.)); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d1(jx, jy, jz) = 1.e-7*(1. + 0.2*exp(-50.*pow(x-p,2)/4.)*sin(2.*PI*(z-q) * 3.)); - } - - p = 0.18439023; - q = 0.401089473; - c1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c1(jx, jy, jz) = 1. + 1.e-6*0.15*exp(-50.*pow(x-p,2)*2.)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c1(jx, jy, jz) = 1. + 1.e-6*0.15*exp(-50.*pow(x-p,2)*2.)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c1(jx, jy, jz) = 1. + 1.e-6*0.15*exp(-50.*pow(x-p,2)*2.)*sin(2.*PI*(z-q) * 2.); - } - - p = 0.612547; - q = 0.30908712; - a1.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a1(jx, jy, jz) = -1. + 0.1*exp(-50.*pow(x-p,2)*2.5)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a1(jx, jy, jz) = -1. + 0.1*exp(-50.*pow(x-p,2)*2.5)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a1(jx, jy, jz) = -1. + 0.1*exp(-50.*pow(x-p,2)*2.5)*sin(2.*PI*(z-q) * 7.); - } - - mesh->communicate(f1,a1,c1,d1); - - f1.setBoundary("neumann"); - - b1 = d1*Delp2(f1) + Grad_perp(c1)*Grad_perp(f1)/c1 + a1*f1; - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b1(jx, jy, jz) = b1(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b1(jx, jy, jz) = b1(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a1); - invert->setCoefC(c1); - invert->setCoefD(d1); - - try { - sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); - error1 = (f1-sol1)/f1; - absolute_error1 = f1-sol1; -// max_error1 = max_error_at_ystart(abs(error1)); - max_error1 = max_error_at_ystart(abs(absolute_error1)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b1): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error1 = -1; - } - - output<setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setCoefA(a1); - invert_4th->setCoefC(c1); - invert_4th->setCoefD(d1); - - try { - sol2 = invert_4th->solve(sliceXZ(b1, mesh->ystart)); - error2 = (f1-sol2)/f1; - absolute_error2 = f1-sol2; -// max_error2 = max_error_at_ystart(abs(error2)); - max_error2 = max_error_at_ystart(abs(absolute_error2)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b1): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error2 = -1; - } - - output<firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b3(jx, jy, jz) = b3(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b3(jx, jy, jz) = b3(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a3); - invert->setCoefC(c3); - invert->setCoefD(d3); - - try { - sol3 = invert->solve(sliceXZ(b3, mesh->ystart)); - error3 = (f1-sol3)/f1; - absolute_error3 = f1-sol3; -// max_error3 = max_error_at_ystart(abs(error3)); - max_error3 = max_error_at_ystart(abs(absolute_error3)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b3): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error3 = -1; - } - - output<getSection("SPT"); - auto invert_SPT = Laplacian::create(SPT_options); - invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); - invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); - invert_SPT->setCoefA(a3); - invert_SPT->setCoefC(c3); - invert_SPT->setCoefD(d3); - - sol4 = invert_SPT->solve(sliceXZ(b3, mesh->ystart)); - error4 = (f1-sol4)/f1; - absolute_error4 = f1-sol4; -// max_error4 = max_error_at_ystart(abs(error4)); - max_error4 = max_error_at_ystart(abs(absolute_error4)); - - output<xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f5(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))) //make the gradients zero at both x-boundaries - ; - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f5(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - f5(jx, jy, jz) = 0. + exp(-(50.*pow(x-p,2)+1.-cos( 2.*PI*(z-q) ))) - - 50.*(2.*p*exp(-50.*pow(-p,2))*x + (-p*exp(-50.*pow(-p,2))-(1-p)*exp(-50.*pow(1-p,2)))*pow(x,2) )*exp(-(1.-cos( 2.*PI*(z-q) ))); //make the gradients zero at both x-boundaries - } - - p = 0.63298589; - q = 0.889237890; - d5.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d5(jx, jy, jz) = 1.e-7*(1. + p*cos(2.*PI*x)*sin(2.*PI*(z-q) * 3.)); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d5(jx, jy, jz) = 1.e-7*(1. + p*cos(2.*PI*x)*sin(2.*PI*(z-q) * 3.)); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - d5(jx, jy, jz) = 1.e-7*(1. + p*cos(2.*PI*x)*sin(2.*PI*(z-q) * 3.)); - } - - p = 0.160983834; - q = 0.73050121087; - c5.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c5(jx, jy, jz) = 1. + 1.e-6*p*cos(2.*PI*x*5)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c5(jx, jy, jz) = 1. + 1.e-6*p*cos(2.*PI*x*5)*sin(2.*PI*(z-q) * 2.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - c5(jx, jy, jz) = 1. + 1.e-6*p*cos(2.*PI*x*5)*sin(2.*PI*(z-q) * 2.); - } - - p = 0.5378950; - q = 0.2805870; - a5.allocate(); - for (int jx=mesh->xstart; jx<=mesh->xend; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a5(jx, jy, jz) = -1. + p*cos(2.*PI*x*2.)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a5(jx, jy, jz) = -1. + p*cos(2.*PI*x*2.)*sin(2.*PI*(z-q) * 7.); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx)-mesh->xstart)/nx; - BoutReal z = BoutReal(jz)/nz; - a5(jx, jy, jz) = -1. + p*cos(2.*PI*x*2.)*sin(2.*PI*(z-q) * 7.); - } - - mesh->communicate(f5,a5,c5,d5); - - b5 = d5*Delp2(f5) + Grad_perp(c5)*Grad_perp(f5)/c5 + a5*f5; - if (mesh->firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b5(jx, jy, jz) = b5(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b5(jx, jy, jz) = b5(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a5); - invert->setCoefC(c5); - invert->setCoefD(d5); - - try { - sol5 = invert->solve(sliceXZ(b5, mesh->ystart)); - error5 = (f5-sol5)/f5; - absolute_error5 = f5-sol5; -// max_error5 = max_error_at_ystart(abs(error5)); - max_error5 = max_error_at_ystart(abs(absolute_error5)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b5): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error5 = -1; - } + Options* options = Options::getRoot()->getSection("petsc2nd"); + auto invert = Laplacian::create(options); + options = Options::getRoot()->getSection("petsc4th"); + auto invert_4th = Laplacian::create(options); + + // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d + Field3D f1, a1, b1, c1, d1, sol1; + BoutReal p, q; //Use to set parameters in constructing trial functions + Field3D error1, + absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) + BoutReal max_error1; //Output of test + + using bout::globals::mesh; + + // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z. + // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point + BoutReal nx = mesh->GlobalNx - 2 * mesh->xstart - 1; + BoutReal nz = mesh->GlobalNz; + + //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + // Test 1: Gaussian x-profiles, 2nd order Krylov + p = 0.39503274; + q = 0.20974396; + f1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f1(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos(2. * PI + * (z - q)))) //make the gradients zero at both x-boundaries + ; + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f1(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f1(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + } + } + } + } + + p = 0.512547; + q = 0.30908712; + d1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d1(jx, jy, jz) = + 1.e-7 + * (1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.)); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d1(jx, jy, jz) = + 1.e-7 + * (1. + + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.)); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d1(jx, jy, jz) = + 1.e-7 + * (1. + + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.)); + } + } + } + } + + p = 0.18439023; + q = 0.401089473; + c1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c1(jx, jy, jz) = 1. + + 1.e-6 * 0.15 * exp(-50. * pow(x - p, 2) * 2.) + * sin(2. * PI * (z - q) * 2.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c1(jx, jy, jz) = 1. + + 1.e-6 * 0.15 * exp(-50. * pow(x - p, 2) * 2.) + * sin(2. * PI * (z - q) * 2.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c1(jx, jy, jz) = 1. + + 1.e-6 * 0.15 * exp(-50. * pow(x - p, 2) * 2.) + * sin(2. * PI * (z - q) * 2.); + } + } + } + } + + p = 0.612547; + q = 0.30908712; + a1.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a1(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a1(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a1(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); + } + } + } + } - output<setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setCoefA(a5); - invert_4th->setCoefC(c5); - invert_4th->setCoefD(d5); - - try { - sol6 = invert_4th->solve(sliceXZ(b5, mesh->ystart)); - error6 = (f5-sol6)/f5; - absolute_error6 = f5-sol6; -// max_error6 = max_error_at_ystart(abs(error6)); - max_error6 = max_error_at_ystart(abs(absolute_error6)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b6): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error6 = -1; - } + mesh->communicate(f1, a1, c1, d1); - output<firstX()) - for (int jx=mesh->xstart-1; jx>=0; jx--) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b7(jx, jy, jz) = b7(jx+1, jy, jz); - } - if (mesh->lastX()) - for (int jx=mesh->xend+1; jxLocalNx; jx++) - for (int jy=0; jyLocalNy; jy++) - for (int jz=0; jzLocalNz; jz++) { - b7(jx, jy, jz) = b7(jx-1, jy, jz); - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a7); - invert->setCoefC(c7); - invert->setCoefD(d7); - - try { - sol7 = invert->solve(sliceXZ(b7, mesh->ystart)); - error7 = (f5-sol7)/f5; - absolute_error7 = f5-sol7; -// max_error7 = max_error_at_ystart(abs(error7)); - max_error7 = max_error_at_ystart(abs(absolute_error7)); - } catch (BoutException &err) { - output << "BoutException occured in invert->solve(b7): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error7 = -1; - } + f1.setBoundary("neumann"); - output<setCoefA(a7); - invert_SPT->setCoefC(c7); - invert_SPT->setCoefD(d7); - - sol8 = invert_SPT->solve(sliceXZ(b7, mesh->ystart)); - error8 = (f5-sol8)/f5; - absolute_error8 = f5-sol8; -// max_error8 = max_error_at_ystart(abs(error8)); - max_error8 = max_error_at_ystart(abs(absolute_error8)); - - output<firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b1(jx, jy, jz) = b1(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b1(jx, jy, jz) = b1(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a1); + invert->setCoefC(c1); + invert->setCoefD(d1); + + try { + sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); + error1 = (f1 - sol1) / f1; + absolute_error1 = f1 - sol1; + // max_error1 = max_error_at_ystart(abs(error1)); + max_error1 = max_error_at_ystart(abs(absolute_error1)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b1): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error1 = -1; + } + + output << endl << "Test 1: PETSc 2nd order" << endl; + // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setCoefA(a1); + invert_4th->setCoefC(c1); + invert_4th->setCoefD(d1); + + try { + sol2 = invert_4th->solve(sliceXZ(b1, mesh->ystart)); + error2 = (f1 - sol2) / f1; + absolute_error2 = f1 - sol2; + // max_error2 = max_error_at_ystart(abs(error2)); + max_error2 = max_error_at_ystart(abs(absolute_error2)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b1): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error2 = -1; + } + + output << endl << "Test 2: PETSc 4th order" << endl; + // output<<"Time to set up is "<firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b3(jx, jy, jz) = b3(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b3(jx, jy, jz) = b3(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a3); + invert->setCoefC(c3); + invert->setCoefD(d3); + + try { + sol3 = invert->solve(sliceXZ(b3, mesh->ystart)); + error3 = (f1 - sol3) / f1; + absolute_error3 = f1 - sol3; + // max_error3 = max_error_at_ystart(abs(error3)); + max_error3 = max_error_at_ystart(abs(absolute_error3)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b3): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error3 = -1; + } + + output << endl << "Test 3: with coefficients constant in z, PETSc 2nd order" << endl; + // output<<"Time to set up is "<getSection("SPT"); + auto invert_SPT = Laplacian::create(SPT_options); + invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); + invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); + invert_SPT->setCoefA(a3); + invert_SPT->setCoefC(c3); + invert_SPT->setCoefD(d3); + + sol4 = invert_SPT->solve(sliceXZ(b3, mesh->ystart)); + error4 = (f1 - sol4) / f1; + absolute_error4 = f1 - sol4; + // max_error4 = max_error_at_ystart(abs(error4)); + max_error4 = max_error_at_ystart(abs(absolute_error4)); + + output << endl << "Test 4: with coefficients constant in z, default solver" << endl; + // output<<"Time to set up is "<xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f5(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos(2. * PI + * (z - q)))) //make the gradients zero at both x-boundaries + ; + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f5(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + f5(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-( + 1. + - cos( + 2. * PI + * (z - q)))); //make the gradients zero at both x-boundaries + } + } + } + } + + p = 0.63298589; + q = 0.889237890; + d5.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d5(jx, jy, jz) = + 1.e-7 * (1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.)); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d5(jx, jy, jz) = + 1.e-7 * (1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.)); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + d5(jx, jy, jz) = + 1.e-7 * (1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.)); + } + } + } + } + + p = 0.160983834; + q = 0.73050121087; + c5.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c5(jx, jy, jz) = + 1. + 1.e-6 * p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c5(jx, jy, jz) = + 1. + 1.e-6 * p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + c5(jx, jy, jz) = + 1. + 1.e-6 * p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); + } + } + } + } + + p = 0.5378950; + q = 0.2805870; + a5.allocate(); + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a5(jx, jy, jz) = -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); + } + } + } + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a5(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + BoutReal z = BoutReal(jz) / nz; + a5(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); + } + } + } + } + + mesh->communicate(f5, a5, c5, d5); + + b5 = d5 * Delp2(f5) + Grad_perp(c5) * Grad_perp(f5) / c5 + a5 * f5; + if (mesh->firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b5(jx, jy, jz) = b5(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b5(jx, jy, jz) = b5(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a5); + invert->setCoefC(c5); + invert->setCoefD(d5); + + try { + sol5 = invert->solve(sliceXZ(b5, mesh->ystart)); + error5 = (f5 - sol5) / f5; + absolute_error5 = f5 - sol5; + // max_error5 = max_error_at_ystart(abs(error5)); + max_error5 = max_error_at_ystart(abs(absolute_error5)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b5): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error5 = -1; + } + + output << endl << "Test 5: different profiles, PETSc 2nd order" << endl; + // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert_4th->setCoefA(a5); + invert_4th->setCoefC(c5); + invert_4th->setCoefD(d5); + + try { + sol6 = invert_4th->solve(sliceXZ(b5, mesh->ystart)); + error6 = (f5 - sol6) / f5; + absolute_error6 = f5 - sol6; + // max_error6 = max_error_at_ystart(abs(error6)); + max_error6 = max_error_at_ystart(abs(absolute_error6)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b6): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error6 = -1; + } + + output << endl << "Test 6: different profiles, PETSc 4th order" << endl; + // output<<"Time to set up is "<firstX()) { + for (int jx = mesh->xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b7(jx, jy, jz) = b7(jx + 1, jy, jz); + } + } + } + } + if (mesh->lastX()) { + for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { + for (int jy = 0; jy < mesh->LocalNy; jy++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + b7(jx, jy, jz) = b7(jx - 1, jy, jz); + } + } + } + } + + invert->setInnerBoundaryFlags(INVERT_AC_GRAD); + invert->setOuterBoundaryFlags(INVERT_AC_GRAD); + invert->setCoefA(a7); + invert->setCoefC(c7); + invert->setCoefD(d7); + + try { + sol7 = invert->solve(sliceXZ(b7, mesh->ystart)); + error7 = (f5 - sol7) / f5; + absolute_error7 = f5 - sol7; + // max_error7 = max_error_at_ystart(abs(error7)); + max_error7 = max_error_at_ystart(abs(absolute_error7)); + } catch (BoutException& err) { + output + << "BoutException occured in invert->solve(b7): Laplacian inversion failed to " + "converge (probably)" + << endl; + max_error7 = -1; + } + + output + << endl + << "Test 7: different profiles, with coefficients constant in z, PETSc 2nd order" + << endl; + // output<<"Time to set up is "<setCoefA(a7); + invert_SPT->setCoefC(c7); + invert_SPT->setCoefD(d7); + + sol8 = invert_SPT->solve(sliceXZ(b7, mesh->ystart)); + error8 = (f5 - sol8) / f5; + absolute_error8 = f5 - sol8; + // max_error8 = max_error_at_ystart(abs(error8)); + max_error8 = max_error_at_ystart(abs(absolute_error8)); + + output + << endl + << "Test 8: different profiles, with coefficients constant in z, default solver" + << endl; + // output<<"Time to set up is "<xstart, mesh->ystart, 0); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) - for (int jz = 0; jz < mesh->LocalNz; jz++) + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { if (local_max_error < error(jx, mesh->ystart, jz)) { local_max_error = error(jx, mesh->ystart, jz); } + } + } BoutReal max_error; diff --git a/tests/integrated/test-region-iterator/test_region_iterator.cxx b/tests/integrated/test-region-iterator/test_region_iterator.cxx index b4030ca90c..c89bf9ed2c 100644 --- a/tests/integrated/test-region-iterator/test_region_iterator.cxx +++ b/tests/integrated/test-region-iterator/test_region_iterator.cxx @@ -1,11 +1,12 @@ -#include #include +#include -#include #include +#include class Test_region_iterator : public PhysicsModel { Field3D n; + protected: int init(bool UNUSED(restarting)) override; int rhs(BoutReal UNUSED(t)) override; @@ -13,49 +14,66 @@ class Test_region_iterator : public PhysicsModel { int Test_region_iterator::init(bool UNUSED(restarting)) { - Field3D a=1.0, b=1.0, c=2.0; + Field3D a = 1.0, b = 1.0, c = 2.0; using bout::globals::mesh; Region reg(0, mesh->LocalNx - 1, 0, mesh->LocalNy - 1, 0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz); - BOUT_FOR(i, reg) { + BOUT_FOR (i, reg) { a[i] = 3.0; b[i] = c[i]; } //Check expected results - int nerr=0; - for (const auto &i : a.getRegion(RGN_ALL)) { - if (a[i] != 3.0) nerr++; + int nerr = 0; + for (const auto& i : a.getRegion(RGN_ALL)) { + if (a[i] != 3.0) { + nerr++; + } } - if(nerr != 0 ) throw BoutException("Unexpected values found in 'a', count {:d}",nerr); - nerr=0; - for (const auto &i : b.getRegion(RGN_ALL)) { - if (b[i] != c[i]) nerr++; + if (nerr != 0) { + throw BoutException("Unexpected values found in 'a', count {:d}", nerr); + } + nerr = 0; + for (const auto& i : b.getRegion(RGN_ALL)) { + if (b[i] != c[i]) { + nerr++; + } + } + if (nerr != 0) { + throw BoutException("Unexpected values found in 'b', count {:d}", nerr); } - if(nerr != 0 ) throw BoutException("Unexpected values found in 'b', count {:d}",nerr); - - Field3D d=1.0, e=1.0, f=2.0; - BOUT_FOR(i, d.getRegion("RGN_NOBNDRY")) { + Field3D d = 1.0, e = 1.0, f = 2.0; + BOUT_FOR (i, d.getRegion("RGN_NOBNDRY")) { d[i] = 3.0; e[i] = f[i]; } //Check expected results - nerr=0; + nerr = 0; //Expect to find differences just in the boundaries, so work out how many boundary points there area - const int nerrExpected = (2*mesh->xstart*mesh->LocalNy + 2*mesh->ystart*(mesh->LocalNx-mesh->xstart*2))*mesh->LocalNz; - for (const auto &i : d.getRegion(RGN_ALL)) { - if (d[i] != 3.0) nerr++; + const int nerrExpected = (2 * mesh->xstart * mesh->LocalNy + + 2 * mesh->ystart * (mesh->LocalNx - mesh->xstart * 2)) + * mesh->LocalNz; + for (const auto& i : d.getRegion(RGN_ALL)) { + if (d[i] != 3.0) { + nerr++; + } + } + if (nerr != nerrExpected) { + throw BoutException("Unexpected values found in 'd', count {:d}", nerr); } - if(nerr != nerrExpected ) throw BoutException("Unexpected values found in 'd', count {:d}",nerr); - nerr=0; - for (const auto &i : e.getRegion(RGN_ALL)) { - if (e[i] != f[i]) nerr++; + nerr = 0; + for (const auto& i : e.getRegion(RGN_ALL)) { + if (e[i] != f[i]) { + nerr++; + } + } + if (nerr != nerrExpected) { + throw BoutException("Unexpected values found in 'e', count {:d}", nerr); } - if(nerr != nerrExpected ) throw BoutException("Unexpected values found in 'e', count {:d}",nerr); SOLVE_FOR(n); return 0; @@ -66,5 +84,4 @@ int Test_region_iterator::rhs(BoutReal UNUSED(t)) { return 0; } - BOUTMAIN(Test_region_iterator) diff --git a/tests/integrated/test-restarting/test_restarting.cxx b/tests/integrated/test-restarting/test_restarting.cxx index 1dc459bd47..ea315a170d 100644 --- a/tests/integrated/test-restarting/test_restarting.cxx +++ b/tests/integrated/test-restarting/test_restarting.cxx @@ -1,10 +1,11 @@ +#include "bout/unused.hxx" #include -#include "unused.hxx" class RestartTest : public PhysicsModel { private: Field3D f3d; Field2D f2d; + protected: int init(bool UNUSED(restarting)) override { // Evolve a 3D and a 2D field @@ -12,9 +13,9 @@ class RestartTest : public PhysicsModel { return 0; } int rhs(BoutReal UNUSED(time)) override { - // Simple time evolution - ddt(f3d) = 0.1*f3d; - ddt(f2d) = -0.1*f2d; + // Simple time evolution + ddt(f3d) = 0.1 * f3d; + ddt(f2d) = -0.1 * f2d; return 0; } }; diff --git a/tests/integrated/test-slepc-solver/test-slepc-solver.cxx b/tests/integrated/test-slepc-solver/test-slepc-solver.cxx index 7f61b18ea4..259fd49a53 100644 --- a/tests/integrated/test-slepc-solver/test-slepc-solver.cxx +++ b/tests/integrated/test-slepc-solver/test-slepc-solver.cxx @@ -13,6 +13,7 @@ class TestEigenSolver : public PhysicsModel { ddt(field) = field * exp(time); return 0; } + private: Field3D field; }; diff --git a/tests/integrated/test-smooth/test_smooth.cxx b/tests/integrated/test-smooth/test_smooth.cxx index 2bebbf3999..96a1b84b16 100644 --- a/tests/integrated/test-smooth/test_smooth.cxx +++ b/tests/integrated/test-smooth/test_smooth.cxx @@ -3,9 +3,9 @@ * */ -#include -#include -#include +#include +#include +#include int main(int argc, char** argv) { diff --git a/tests/integrated/test-snb/test_snb.cxx b/tests/integrated/test-snb/test_snb.cxx index 16bb1d5af4..8e1b55bca0 100644 --- a/tests/integrated/test-snb/test_snb.cxx +++ b/tests/integrated/test-snb/test_snb.cxx @@ -1,9 +1,9 @@ #include #include -#include -#include -#include -#include +#include +#include +#include +#include // Convert __LINE__ to string S__LINE__ #define S(x) #x diff --git a/tests/integrated/test-solver/test_solver.cxx b/tests/integrated/test-solver/test_solver.cxx index 58ef36f9c0..ee64c6097f 100644 --- a/tests/integrated/test-solver/test_solver.cxx +++ b/tests/integrated/test-solver/test_solver.cxx @@ -1,6 +1,6 @@ #include "bout/constants.hxx" -#include "bout/physicsmodel.hxx" #include "bout/petsclib.hxx" +#include "bout/physicsmodel.hxx" #include "bout/slepclib.hxx" #include diff --git a/tests/integrated/test-squash/squash.cxx b/tests/integrated/test-squash/squash.cxx index 95a6edceb6..f8a449eacf 100644 --- a/tests/integrated/test-squash/squash.cxx +++ b/tests/integrated/test-squash/squash.cxx @@ -11,7 +11,7 @@ class SquashRun : public PhysicsModel { solver->add(f3, "f3"); return 0; } - + // Calculate time-derivatives int rhs(BoutReal UNUSED(t)) { ddt(f2) = 1; @@ -19,8 +19,8 @@ class SquashRun : public PhysicsModel { f2.applyBoundary(); f3.applyBoundary(); return 0; - } - + } + private: Field2D f2; Field3D f3; diff --git a/tests/integrated/test-stopCheck-file/test_stopCheck.cxx b/tests/integrated/test-stopCheck-file/test_stopCheck.cxx index 90d5328d9d..46fceb446e 100644 --- a/tests/integrated/test-stopCheck-file/test_stopCheck.cxx +++ b/tests/integrated/test-stopCheck-file/test_stopCheck.cxx @@ -3,19 +3,20 @@ * */ -#include +#include "bout/unused.hxx" #include -#include "unused.hxx" +#include class Test_stopcheck : public PhysicsModel { Field3D N; + protected: int init(bool UNUSED(restarting)) override; int rhs(BoutReal UNUSED(t)) override; }; int Test_stopcheck::init(bool UNUSED(restarting)) { - solver->add(N,"N"); + solver->add(N, "N"); return 0; } @@ -25,5 +26,4 @@ int Test_stopcheck::rhs(BoutReal UNUSED(t)) { return 0; } - BOUTMAIN(Test_stopcheck) diff --git a/tests/integrated/test-stopCheck/test_stopCheck.cxx b/tests/integrated/test-stopCheck/test_stopCheck.cxx index 07f0af63c4..328805f155 100644 --- a/tests/integrated/test-stopCheck/test_stopCheck.cxx +++ b/tests/integrated/test-stopCheck/test_stopCheck.cxx @@ -3,9 +3,9 @@ * */ -#include +#include "bout/unused.hxx" #include -#include "unused.hxx" +#include class Test_stopcheck : public PhysicsModel { protected: @@ -13,11 +13,10 @@ class Test_stopcheck : public PhysicsModel { int rhs(BoutReal UNUSED(t)) override; }; - Field3D N; int Test_stopcheck::init(bool UNUSED(restarting)) { - solver->add(N,"N"); + solver->add(N, "N"); return 0; } @@ -27,5 +26,4 @@ int Test_stopcheck::rhs(BoutReal UNUSED(t)) { return 0; } - BOUTMAIN(Test_stopcheck) diff --git a/tests/integrated/test-subdir/bar/bar.cxx b/tests/integrated/test-subdir/bar/bar.cxx index f9fd6b48b0..ca578d8297 100644 --- a/tests/integrated/test-subdir/bar/bar.cxx +++ b/tests/integrated/test-subdir/bar/bar.cxx @@ -1,4 +1,2 @@ -#include -void bar(){ - output.print("Bar!\n"); -} +#include +void bar() { output.print("Bar!\n"); } diff --git a/tests/integrated/test-subdir/fuu/fuu.cxx b/tests/integrated/test-subdir/fuu/fuu.cxx index f4d3fb2d2b..6a94432cc6 100644 --- a/tests/integrated/test-subdir/fuu/fuu.cxx +++ b/tests/integrated/test-subdir/fuu/fuu.cxx @@ -1,5 +1,3 @@ #include "fuu.hxx" -void fuu(){ - output.write("\tFuu!\n"); -} +void fuu() { output.write("\tFuu!\n"); } diff --git a/tests/integrated/test-subdir/fuu/fuu.hxx b/tests/integrated/test-subdir/fuu/fuu.hxx index fcf6baaaa5..d45dd31df9 100644 --- a/tests/integrated/test-subdir/fuu/fuu.hxx +++ b/tests/integrated/test-subdir/fuu/fuu.hxx @@ -1,7 +1,7 @@ #ifndef EXAMPLE_MAKE_SUBDIR_FUU_FUU_HXX_ #define EXAMPLE_MAKE_SUBDIR_FUU_FUU_HXX_ -#include +#include void fuu(); diff --git a/tests/integrated/test-subdir/subdirs.cxx b/tests/integrated/test-subdir/subdirs.cxx index 09c5661616..b8779c7e42 100644 --- a/tests/integrated/test-subdir/subdirs.cxx +++ b/tests/integrated/test-subdir/subdirs.cxx @@ -7,22 +7,21 @@ void bar(); class SubDirs : public PhysicsModel { private: Field3D n; - + protected: int init(bool UNUSED(restart)) override { - n=1; + n = 1; SOLVE_FOR(n); // test functions fuu(); bar(); return 0; } - + int rhs(BoutReal UNUSED(time)) override { - ddt(n)=0; + ddt(n) = 0; return 0; } }; BOUTMAIN(SubDirs); - diff --git a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx index b05cd7c2fe..87b9e0a094 100644 --- a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx +++ b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx @@ -1,5 +1,5 @@ -#include "bout.hxx" -#include "field_factory.hxx" +#include "bout/bout.hxx" +#include "bout/field_factory.hxx" int main(int argc, char** argv) { BoutInitialise(argc, argv); @@ -11,12 +11,12 @@ int main(int argc, char** argv) { using bout::globals::mesh; // zero guard cells to check that communication is doing something - for (int x=0; xLocalNx; x++) { - for (int z=0; zLocalNz; z++) { - for (int y=0; yystart; y++) { + for (int x = 0; x < mesh->LocalNx; x++) { + for (int z = 0; z < mesh->LocalNz; z++) { + for (int y = 0; y < mesh->ystart; y++) { test_aligned(x, y, z) = 0.; } - for (int y=mesh->yend+1; yLocalNy; y++) { + for (int y = mesh->yend + 1; y < mesh->LocalNy; y++) { test_aligned(x, y, z) = 0.; } } diff --git a/tests/integrated/test-twistshift/test-twistshift.cxx b/tests/integrated/test-twistshift/test-twistshift.cxx index 6b8ea95c96..ccde8b82b6 100644 --- a/tests/integrated/test-twistshift/test-twistshift.cxx +++ b/tests/integrated/test-twistshift/test-twistshift.cxx @@ -1,5 +1,5 @@ -#include "bout.hxx" -#include "field_factory.hxx" +#include "bout/bout.hxx" +#include "bout/field_factory.hxx" int main(int argc, char** argv) { BoutInitialise(argc, argv); @@ -11,12 +11,12 @@ int main(int argc, char** argv) { using bout::globals::mesh; // zero guard cells to check that communication is doing something - for (int x=0; xLocalNx; x++) { - for (int z=0; zLocalNz; z++) { - for (int y=0; yystart; y++) { + for (int x = 0; x < mesh->LocalNx; x++) { + for (int z = 0; z < mesh->LocalNz; z++) { + for (int y = 0; y < mesh->ystart; y++) { test_aligned(x, y, z) = 0.; } - for (int y=mesh->yend+1; yLocalNy; y++) { + for (int y = mesh->yend + 1; y < mesh->LocalNy; y++) { test_aligned(x, y, z) = 0.; } } diff --git a/tests/integrated/test-vec/testVec.cxx b/tests/integrated/test-vec/testVec.cxx index 3f89b8529d..bd0e5f2b80 100644 --- a/tests/integrated/test-vec/testVec.cxx +++ b/tests/integrated/test-vec/testVec.cxx @@ -1,6 +1,6 @@ #include -#include // Gives the vec diff options +#include // Gives the vec diff options class VecTest : public PhysicsModel { protected: @@ -13,7 +13,6 @@ class VecTest : public PhysicsModel { std::string ownOpType; }; - int VecTest::init(bool UNUSED(restarting)) { TRACE("Halt in VecTest::init"); SOLVE_FOR(n); diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx b/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx index 691bd89ecc..22d1fb9e07 100644 --- a/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx +++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx @@ -1,39 +1,44 @@ -#include -#include #include "../../../src/mesh/parallel/shiftedmetricinterp.hxx" +#include +#include // Y derivative using yup() and ydown() fields -Field3D DDY_yud(const Field3D &f) { +Field3D DDY_yud(const Field3D& f) { Field3D result{0.0}; const auto* mesh = f.getMesh(); - for(int i=0;iLocalNx;i++) - for(int j=mesh->ystart;j<=mesh->yend;j++) - for(int k=0;kLocalNz;k++) - result(i,j,k) = 0.5*(f.yup()(i,j+1,k) - f.ydown()(i,j-1,k)); + for (int i = 0; i < mesh->LocalNx; i++) { + for (int j = mesh->ystart; j <= mesh->yend; j++) { + for (int k = 0; k < mesh->LocalNz; k++) { + result(i, j, k) = 0.5 * (f.yup()(i, j + 1, k) - f.ydown()(i, j - 1, k)); + } + } + } return result; } // Y derivative constructed from interpolation weights -Field3D DDY_weights(const Field3D &f) { +Field3D DDY_weights(const Field3D& f) { ParallelTransform& pt = f.getCoordinates()->getParallelTransform(); Field3D result{0.0}; const auto* mesh = f.getMesh(); - for(int i=mesh->xstart;i<=mesh->xend;i++){ - for(int j=mesh->ystart;j<=mesh->yend;j++){ - for(int k=0;kLocalNz;k++){ - std::vector pw_up = pt.getWeightsForYUpApproximation(i,j,k); - std::vector pw_down = pt.getWeightsForYDownApproximation(i,j,k); - - for (const auto &p : pw_up){ - result(i,j,k) += 0.5*p.weight*f(p.i,p.j,p.k); - } - for (const auto &p : pw_down){ - result(i,j,k) -= 0.5*p.weight*f(p.i,p.j,p.k); - } + for (int i = mesh->xstart; i <= mesh->xend; i++) { + for (int j = mesh->ystart; j <= mesh->yend; j++) { + for (int k = 0; k < mesh->LocalNz; k++) { + std::vector pw_up = + pt.getWeightsForYUpApproximation(i, j, k); + std::vector pw_down = + pt.getWeightsForYDownApproximation(i, j, k); + + for (const auto& p : pw_up) { + result(i, j, k) += 0.5 * p.weight * f(p.i, p.j, p.k); + } + for (const auto& p : pw_down) { + result(i, j, k) -= 0.5 * p.weight * f(p.i, p.j, p.k); + } } } } @@ -49,7 +54,7 @@ int main(int argc, char** argv) { // Read variable from mesh Field3D var; mesh->get(var, "var"); - + // Var starts in orthogonal X-Z coordinates // Calculate yup and ydown diff --git a/tests/integrated/test-yupdown/test_yupdown.cxx b/tests/integrated/test-yupdown/test_yupdown.cxx index cd60ca4a6c..e5889411ad 100644 --- a/tests/integrated/test-yupdown/test_yupdown.cxx +++ b/tests/integrated/test-yupdown/test_yupdown.cxx @@ -1,14 +1,17 @@ -#include -#include +#include +#include // Y derivative assuming field is aligned in Y const Field3D DDY_aligned(const Field3D& f) { Field3D result = emptyFrom(f); const auto* mesh = f.getMesh(); - for (int i = 0; i < mesh->LocalNx; i++) - for (int j = mesh->ystart; j <= mesh->yend; j++) - for (int k = 0; k < mesh->LocalNz; k++) + for (int i = 0; i < mesh->LocalNx; i++) { + for (int j = mesh->ystart; j <= mesh->yend; j++) { + for (int k = 0; k < mesh->LocalNz; k++) { result(i, j, k) = 0.5 * (f(i, j + 1, k) - f(i, j - 1, k)); + } + } + } return result; } diff --git a/tests/unit/bout_test_main.cxx b/tests/unit/bout_test_main.cxx index 3fcc28dac3..5aaaa0e8a7 100644 --- a/tests/unit/bout_test_main.cxx +++ b/tests/unit/bout_test_main.cxx @@ -1,7 +1,7 @@ #include -#include "fft.hxx" -#include "output.hxx" +#include "bout/fft.hxx" +#include "bout/output.hxx" #include "bout/array.hxx" #include "bout/globalindexer.hxx" #include "gtest/gtest.h" diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx index fc1a0670fb..f2ea0a7112 100644 --- a/tests/unit/fake_parallel_mesh.hxx +++ b/tests/unit/fake_parallel_mesh.hxx @@ -8,12 +8,12 @@ #include #include "../../src/mesh/impls/bout/boutmesh.hxx" -#include "boundary_region.hxx" -#include "boutcomm.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" -#include "unused.hxx" +#include "bout/boundary_region.hxx" +#include "bout/boutcomm.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" +#include "bout/unused.hxx" #include "bout/coordinates.hxx" #include "bout/fieldgroup.hxx" #include "bout/mesh.hxx" @@ -48,7 +48,7 @@ public: : BoutMesh((nxpe * (nx - 2)) + 2, nype * ny, nz, 1, 1, nxpe, nype, pe_xind, pe_yind), yUpMesh(nullptr), yDownMesh(nullptr), xInMesh(nullptr), xOutMesh(nullptr), - mpiSmart(new FakeMpiWrapper(this)) { + mpiSmart(new FakeMpiWrapper(this)) { StaggerGrids = false; periodicX = false; IncIntShear = false; @@ -92,14 +92,14 @@ public: if (xInMesh != nullptr && xInMesh != this) { FieldGroup xInGroup = makeGroup(xInMesh, ids); if (!disable_corners) { - xInMesh->wait(xInMesh->sendY(xInGroup, nullptr)); + xInMesh->wait(xInMesh->sendY(xInGroup, nullptr)); } xInMesh->parentSendX(xInGroup, nullptr, disable_corners); } if (xOutMesh != nullptr && xOutMesh != this) { FieldGroup xOutGroup = makeGroup(xOutMesh, ids); if (!disable_corners) { - xOutMesh->wait(xOutMesh->sendY(xOutGroup, nullptr)); + xOutMesh->wait(xOutMesh->sendY(xOutGroup, nullptr)); } xOutMesh->parentSendX(xOutGroup, nullptr, disable_corners); } @@ -241,8 +241,8 @@ public: } else { *indx = MPI_UNDEFINED; wait_any_count = -1; - mesh->communicatingX = false; - mesh->communicatingY = false; + mesh->communicatingX = false; + mesh->communicatingY = false; } return 0; } diff --git a/tests/unit/field/test_field.cxx b/tests/unit/field/test_field.cxx index b5d586e512..16b2a0f9c9 100644 --- a/tests/unit/field/test_field.cxx +++ b/tests/unit/field/test_field.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" -#include "field.hxx" -#include "output.hxx" +#include "bout/boutexception.hxx" +#include "bout/field.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx index 303a849c7c..a13b1dd754 100644 --- a/tests/unit/field/test_field2d.cxx +++ b/tests/unit/field/test_field2d.cxx @@ -4,23 +4,23 @@ #include "gtest/gtest.h" +#include "bout/boutexception.hxx" +#include "bout/field2d.hxx" +#include "bout/output.hxx" +#include "test_extras.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" -#include "boutexception.hxx" -#include "field2d.hxx" -#include "output.hxx" -#include "test_extras.hxx" -#include "unused.hxx" -#include "utils.hxx" #include #include #include /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -229,7 +229,7 @@ TEST_F(Field2DTest, IterateOverWholeField) { // Basic test first: do we visit the correct number of elements? int count = 0; - for (auto &UNUSED(i) : field) { + for (auto& UNUSED(i) : field) { ++count; } @@ -258,7 +258,7 @@ TEST_F(Field2DTest, IterateOverWholeField) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field) { + for (auto& i : field) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -282,7 +282,7 @@ TEST_F(Field2DTest, IterateOverRegionInd2D_RGN_ALL) { const int num_sentinels = test_indices.size(); // Assign sentinel value to watch out for to our chosen points - for (const auto &index : test_indices) { + for (const auto& index : test_indices) { field(index[0], index[1]) = sentinel; } @@ -290,7 +290,7 @@ TEST_F(Field2DTest, IterateOverRegionInd2D_RGN_ALL) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion("RGN_ALL")) { + for (auto& i : field.getRegion("RGN_ALL")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -315,7 +315,7 @@ TEST_F(Field2DTest, IterateOverRegionInd3D_RGN_ALL) { const int num_sentinels = test_indices.size() * nz; // Assign sentinel value to watch out for to our chosen points - for (const auto &index : test_indices) { + for (const auto& index : test_indices) { field(index[0], index[1]) = sentinel; } @@ -323,7 +323,7 @@ TEST_F(Field2DTest, IterateOverRegionInd3D_RGN_ALL) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getMesh()->getRegion3D("RGN_ALL")) { + for (auto& i : field.getMesh()->getRegion3D("RGN_ALL")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -363,7 +363,7 @@ TEST_F(Field2DTest, IterateOverRGN_NOBNDRY) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion(RGN_NOBNDRY)) { + for (auto& i : field.getRegion(RGN_NOBNDRY)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -404,7 +404,7 @@ TEST_F(Field2DTest, IterateOverRGN_NOX) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion(RGN_NOX)) { + for (auto& i : field.getRegion(RGN_NOX)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -445,7 +445,7 @@ TEST_F(Field2DTest, IterateOverRGN_NOY) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion(RGN_NOY)) { + for (auto& i : field.getRegion(RGN_NOY)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -488,7 +488,7 @@ TEST_F(Field2DTest, IterateOverRGN_NOZ) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion(RGN_NOZ)) { + for (auto& i : field.getRegion(RGN_NOZ)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -531,7 +531,7 @@ TEST_F(Field2DTest, IterateOverRGN_XGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_XGUARDS")) { + for (const auto& i : field.getRegion("RGN_XGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -574,7 +574,7 @@ TEST_F(Field2DTest, IterateOverRGN_YGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_YGUARDS")) { + for (const auto& i : field.getRegion("RGN_YGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -616,7 +616,7 @@ TEST_F(Field2DTest, IterateOverRGN_ZGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_ZGUARDS")) { + for (const auto& i : field.getRegion("RGN_ZGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -661,7 +661,7 @@ TEST_F(Field2DTest, IterateOverRGN_NOCORNERS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_NOCORNERS")) { + for (const auto& i : field.getRegion("RGN_NOCORNERS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y()}); @@ -674,7 +674,6 @@ TEST_F(Field2DTest, IterateOverRGN_NOCORNERS) { EXPECT_TRUE(region_indices == result_indices); } - TEST_F(Field2DTest, Indexing) { Field2D field; @@ -702,14 +701,14 @@ TEST_F(Field2DTest, IndexingAs3D) { } } - EXPECT_DOUBLE_EQ(field(2, 2), 4 + nz -1); + EXPECT_DOUBLE_EQ(field(2, 2), 4 + nz - 1); } TEST_F(Field2DTest, ConstIndexingAs3D) { const Field2D field = 3.0; Field2D field2; field2.allocate(); - + for (int i = 0; i < nx; ++i) { for (int j = 0; j < ny; ++j) { for (int k = 0; k < nz; ++k) { @@ -734,7 +733,7 @@ TEST_F(Field2DTest, IndexingInd3D) { } } - Ind3D ind{(2*ny + 2)*nz + 2}; + Ind3D ind{(2 * ny + 2) * nz + 2}; EXPECT_DOUBLE_EQ(field[ind], 10); } @@ -754,7 +753,7 @@ TEST_F(Field2DTest, ConstIndexingInd3D) { const Field2D field2{field1}; - Ind3D ind{(2*ny + 2)*nz + 2}; + Ind3D ind{(2 * ny + 2) * nz + 2}; EXPECT_DOUBLE_EQ(field2[ind], 10); } @@ -803,7 +802,7 @@ TEST_F(Field2DTest, CheckData) { field(1, 1) = std::nan(""); EXPECT_THROW(checkData(field), BoutException); - + field = 1.0; field(0, 0) = std::nan(""); @@ -834,7 +833,7 @@ TEST_F(Field2DTest, InvalidateGuards) { const int nmesh = nx * ny; int sum = 0; - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 0.0; // Reset field value sum++; } @@ -842,7 +841,7 @@ TEST_F(Field2DTest, InvalidateGuards) { // Count the number of non-boundary points sum = 0; - for (const auto &i : field.getRegion(RGN_NOBNDRY)) { + for (const auto& i : field.getRegion(RGN_NOBNDRY)) { field[i] = 0.0; // Reset field value sum++; } @@ -858,9 +857,10 @@ TEST_F(Field2DTest, InvalidateGuards) { EXPECT_NO_THROW(checkData(field(localmesh->xstart, localmesh->ystart))); sum = 0; - for (const auto &i : field) { - if (!finite(field[i])) + for (const auto& i : field) { + if (!finite(field[i])) { sum++; + } } EXPECT_EQ(sum, nbndry); } @@ -1429,7 +1429,8 @@ TEST_F(Field2DTest, OperatorEqualsField2D) { // to 'field'. // Note that Aligned y-direction type is not really allowed for Field2D, but // we don't check anywhere at the moment. - Field2D field2{mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; + Field2D field2{ + mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; field = field2; @@ -1445,7 +1446,8 @@ TEST_F(Field2DTest, EmptyFrom) { // to 'field2'. // Note that Aligned y-direction type is not really allowed for Field2D, but // we don't check anywhere at the moment. - Field2D field{mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; + Field2D field{ + mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; field = 5.; Field2D field2{emptyFrom(field)}; @@ -1461,7 +1463,8 @@ TEST_F(Field2DTest, ZeroFrom) { // to 'field2'. // Note that Aligned y-direction type is not really allowed for Field2D, but // we don't check anywhere at the moment. - Field2D field{mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; + Field2D field{ + mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; field = 5.; Field2D field2{zeroFrom(field)}; diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx index 49b2368459..813adc212e 100644 --- a/tests/unit/field/test_field3d.cxx +++ b/tests/unit/field/test_field3d.cxx @@ -6,23 +6,23 @@ #include "gtest/gtest.h" +#include "bout/boutexception.hxx" +#include "bout/field3d.hxx" +#include "bout/output.hxx" +#include "test_extras.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" -#include "boutexception.hxx" -#include "field3d.hxx" -#include "output.hxx" -#include "test_extras.hxx" -#include "unused.hxx" -#include "utils.hxx" #include #include #include /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -258,14 +258,14 @@ TEST_F(Field3DTest, MultipleParallelSlices) { EXPECT_TRUE(field.hasParallelSlices()); - auto &yup = field.yup(); + auto& yup = field.yup(); EXPECT_NE(&field, &yup); - auto &ydown = field.ydown(); + auto& ydown = field.ydown(); EXPECT_NE(&field, &ydown); - auto &yup1 = field.yup(1); + auto& yup1 = field.yup(1); EXPECT_NE(&field, &yup1); EXPECT_NE(&yup, &yup1); - auto &ydown1 = field.ydown(1); + auto& ydown1 = field.ydown(1); EXPECT_NE(&field, &ydown1); EXPECT_NE(&ydown, &ydown1); @@ -385,7 +385,7 @@ TEST_F(Field3DTest, IterateOverWholeField) { // Basic test first: do we visit the correct number of elements? int count = 0; - for (const auto &UNUSED(i) : field) { + for (const auto& UNUSED(i) : field) { ++count; } @@ -418,7 +418,7 @@ TEST_F(Field3DTest, IterateOverWholeField) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field) { + for (const auto& i : field) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -443,7 +443,7 @@ TEST_F(Field3DTest, IterateOverRegionInd3D_RGN_ALL) { const int num_sentinels = test_indices.size(); // Assign sentinel value to watch out for to our chosen points - for (const auto &index : test_indices) { + for (const auto& index : test_indices) { field(index[0], index[1], index[2]) = sentinel; } @@ -451,7 +451,7 @@ TEST_F(Field3DTest, IterateOverRegionInd3D_RGN_ALL) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getMesh()->getRegion("RGN_ALL")) { + for (const auto& i : field.getMesh()->getRegion("RGN_ALL")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -488,7 +488,7 @@ TEST_F(Field3DTest, IterateOverRGN_NOBNDRY) { const int num_sentinels = region_indices.size(); // Assign sentinel value to watch out for to our chosen points - for (const auto &index : test_indices) { + for (const auto& index : test_indices) { field(index[0], index[1], index[2]) = sentinel; } @@ -496,7 +496,7 @@ TEST_F(Field3DTest, IterateOverRGN_NOBNDRY) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion(RGN_NOBNDRY)) { + for (const auto& i : field.getRegion(RGN_NOBNDRY)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -544,7 +544,7 @@ TEST_F(Field3DTest, IterateOverRGN_NOX) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion(RGN_NOX)) { + for (const auto& i : field.getRegion(RGN_NOX)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -593,7 +593,7 @@ TEST_F(Field3DTest, IterateOverRGN_NOY) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion(RGN_NOY)) { + for (const auto& i : field.getRegion(RGN_NOY)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -696,7 +696,7 @@ TEST_F(Field3DTest, IterateOverRGN_XGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_XGUARDS")) { + for (const auto& i : field.getRegion("RGN_XGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -744,7 +744,7 @@ TEST_F(Field3DTest, IterateOverRGN_YGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_YGUARDS")) { + for (const auto& i : field.getRegion("RGN_YGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -790,7 +790,7 @@ TEST_F(Field3DTest, IterateOverRGN_ZGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_ZGUARDS")) { + for (const auto& i : field.getRegion("RGN_ZGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -842,7 +842,7 @@ TEST_F(Field3DTest, IterateOverRGN_NOCORNERS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_NOCORNERS")) { + for (const auto& i : field.getRegion("RGN_NOCORNERS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.y(), i.z()}); @@ -859,12 +859,12 @@ TEST_F(Field3DTest, IterateOver2DRGN_ALL) { Field3D field; field.allocate(); - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 1.0 + i.z(); } BoutReal sum = 0.0; - for (const auto &i : field.getMesh()->getRegion2D("RGN_ALL")) { + for (const auto& i : field.getMesh()->getRegion2D("RGN_ALL")) { sum += field(i, 0); EXPECT_EQ(field(i, 0), 1.0); EXPECT_EQ(i.z(), 0); @@ -877,12 +877,12 @@ TEST_F(Field3DTest, IterateOver2DRGN_NOBNDRY) { Field3D field; field.allocate(); - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 1.0 + i.z(); } BoutReal sum = 0.0; - for (const auto &i : field.getMesh()->getRegion2D("RGN_NOBNDRY")) { + for (const auto& i : field.getMesh()->getRegion2D("RGN_NOBNDRY")) { sum += field(i, 0); EXPECT_EQ(field(i, 0), 1.0); EXPECT_EQ(i.z(), 0); @@ -895,12 +895,12 @@ TEST_F(Field3DTest, IterateOver2DRGN_NOX) { Field3D field; field.allocate(); - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 1.0 + i.z(); } BoutReal sum = 0.0; - for (const auto &i : field.getMesh()->getRegion2D("RGN_NOX")) { + for (const auto& i : field.getMesh()->getRegion2D("RGN_NOX")) { sum += field(i, 0); EXPECT_EQ(field(i, 0), 1.0); EXPECT_EQ(i.z(), 0); @@ -913,12 +913,12 @@ TEST_F(Field3DTest, IterateOver2DRGN_NOY) { Field3D field; field.allocate(); - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 1.0 + i.z(); } BoutReal sum = 0.0; - for (const auto &i : field.getMesh()->getRegion2D("RGN_NOY")) { + for (const auto& i : field.getMesh()->getRegion2D("RGN_NOY")) { sum += field(i, 0); EXPECT_EQ(field(i, 0), 1.0); EXPECT_EQ(i.z(), 0); @@ -956,7 +956,7 @@ TEST_F(Field3DTest, IndexingInd3D) { } } - Ind3D ind{(2*ny + 2)*nz + 2}; + Ind3D ind{(2 * ny + 2) * nz + 2}; EXPECT_DOUBLE_EQ(field[ind], 6); } @@ -976,7 +976,7 @@ TEST_F(Field3DTest, ConstIndexingInd3D) { const Field3D field2{field1}; - Ind3D ind{(2*ny + 2)*nz + 2}; + Ind3D ind{(2 * ny + 2) * nz + 2}; EXPECT_DOUBLE_EQ(field2[ind], 6); } @@ -1040,7 +1040,7 @@ TEST_F(Field3DTest, IndexingToZPointer) { } } - for (const auto &i : field) { + for (const auto& i : field) { EXPECT_EQ(field[i], -1.0); } @@ -1069,7 +1069,7 @@ TEST_F(Field3DTest, ConstIndexingToZPointer) { } } - for (const auto &i : field2) { + for (const auto& i : field2) { EXPECT_EQ(field2[i], 1.0); } @@ -1191,7 +1191,7 @@ TEST_F(Field3DTest, InvalidateGuards) { const int nmesh = nx * ny * nz; int sum = 0; - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 0.0; // Reset field value sum++; } @@ -1199,7 +1199,7 @@ TEST_F(Field3DTest, InvalidateGuards) { // Count the number of non-boundary points sum = 0; - for (const auto &i : field.getRegion(RGN_NOBNDRY)) { + for (const auto& i : field.getRegion(RGN_NOBNDRY)) { field[i] = 0.0; // Reset field value sum++; } @@ -1215,9 +1215,10 @@ TEST_F(Field3DTest, InvalidateGuards) { EXPECT_NO_THROW(checkData(field(localmesh->xstart, localmesh->ystart, 0))); sum = 0; - for (const auto &i : field) { - if (!finite(field[i])) + for (const auto& i : field) { + if (!finite(field[i])) { sum++; + } } EXPECT_EQ(sum, nbndry); } @@ -1285,7 +1286,7 @@ TEST_F(Field3DTest, AssignFromFieldPerp) { field2 = 2.0; field = field2; - for (const auto &i : field) { + for (const auto& i : field) { if (i.y() == yindex) { EXPECT_EQ(field[i], 2.0); } else { @@ -2103,9 +2104,9 @@ TEST_F(Field3DTest, Mean) { field(2, 4, 3) = 109.0; // mean doesn't include guard cells by default - const int npoints_all = nx*ny*nz; + const int npoints_all = nx * ny * nz; const BoutReal mean_value_nobndry = 50.0; - const BoutReal mean_value_all = 50.0 + 10.0/npoints_all; + const BoutReal mean_value_all = 50.0 + 10.0 / npoints_all; EXPECT_EQ(mean(field, false), mean_value_nobndry); EXPECT_EQ(mean(field, false, "RGN_ALL"), mean_value_all); @@ -2408,7 +2409,8 @@ TEST_F(Field3DTest, OperatorEqualsField3D) { // to 'field'. // Note that Average z-direction type is not really allowed for Field3D, but // we don't check anywhere at the moment. - Field3D field2{mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; + Field3D field2{ + mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; field = field2; @@ -2424,7 +2426,8 @@ TEST_F(Field3DTest, EmptyFrom) { // to 'field2'. // Note that Average z-direction type is not really allowed for Field3D, but // we don't check anywhere at the moment. - Field3D field{mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; + Field3D field{ + mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; field = 5.; Field3D field2{emptyFrom(field)}; @@ -2440,7 +2443,8 @@ TEST_F(Field3DTest, ZeroFrom) { // to 'field2'. // Note that Average z-direction type is not really allowed for Field3D, but // we don't check anywhere at the moment. - Field3D field{mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; + Field3D field{ + mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}}; field = 5.; Field3D field2{zeroFrom(field)}; diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx index 0f5d18ba8a..a65127fee4 100644 --- a/tests/unit/field/test_field_factory.cxx +++ b/tests/unit/field/test_field_factory.cxx @@ -1,15 +1,15 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "field_factory.hxx" -#include "output.hxx" +#include "bout/boutexception.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/field_factory.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" -#include "bout/traits.hxx" #include "bout/paralleltransform.hxx" +#include "bout/traits.hxx" /// Global mesh namespace bout { @@ -226,7 +226,6 @@ TYPED_TEST(FieldFactoryCreationTest, CreateZStaggered) { auto expected = makeField( [](typename TypeParam::ind_type& index) -> BoutReal { - auto offset = BoutReal{0.0}; if (bout::utils::is_Field3D::value) { offset = 0.5; @@ -482,7 +481,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreateMaxX) { TYPED_TEST(FieldFactoryCreationTest, CreateClampX) { // Check that the first argument is within low and high limits // Also check that each input can be an expression - + auto output = this->create("clamp(1 + 1, 1, 3)"); EXPECT_TRUE(IsFieldEqual(output, 2.)); @@ -490,7 +489,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreateClampX) { output = this->create("clamp(-1, 2 - 1, 3)"); EXPECT_TRUE(IsFieldEqual(output, 1.)); - + output = this->create("clamp(5, 1, 6 / 2)"); EXPECT_TRUE(IsFieldEqual(output, 3.)); @@ -599,9 +598,10 @@ TYPED_TEST(FieldFactoryCreationTest, CreateOnMesh) { // testing class FieldFactoryExposer : public FieldFactory { public: - explicit FieldFactoryExposer(Mesh* mesh, Options* opt = nullptr) : FieldFactory(mesh, opt) {} - using FieldFactory::resolve; + explicit FieldFactoryExposer(Mesh* mesh, Options* opt = nullptr) + : FieldFactory(mesh, opt) {} using FieldFactory::fuzzyFind; + using FieldFactory::resolve; }; // The following tests still use the FieldFactory, but don't need to @@ -793,16 +793,17 @@ TEST_F(FieldFactoryTest, Recursion) { // Create a factory with a max_recursion_depth != 0 FieldFactory factory_rec(nullptr, &opt); - + // Fibonacci sequence: 1 1 2 3 5 8 opt["fib"] = "where({n} - 2.5, [n={n}-1](fib) + [n={n}-2](fib), 1)"; - + auto gen = factory_rec.parse("fib", &opt); EXPECT_DOUBLE_EQ(gen->generate(Context().set("n", 3)), 2); EXPECT_DOUBLE_EQ(gen->generate(Context().set("n", 4)), 3); EXPECT_DOUBLE_EQ(gen->generate(Context().set("n", 5)), 5); EXPECT_DOUBLE_EQ(gen->generate(Context().set("n", 6)), 8); - EXPECT_THROW(gen->generate(Context().set("n", 7)), BoutException); // Max recursion exceeded + EXPECT_THROW(gen->generate(Context().set("n", 7)), + BoutException); // Max recursion exceeded } TEST_F(FieldFactoryTest, ResolveGlobalOptions) { @@ -906,7 +907,7 @@ class FieldFactoryCreateAndTransformTest : public FakeMeshFixture { TEST_F(FieldFactoryCreateAndTransformTest, Create2D) { mesh->getCoordinates()->setParallelTransform( - bout::utils::make_unique(*mesh, true)); + bout::utils::make_unique(*mesh, true)); FieldFactory factory; @@ -921,7 +922,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create2D) { TEST_F(FieldFactoryCreateAndTransformTest, Create3D) { mesh->getCoordinates()->setParallelTransform( - bout::utils::make_unique(*mesh, true)); + bout::utils::make_unique(*mesh, true)); FieldFactory factory; @@ -935,7 +936,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create3D) { TEST_F(FieldFactoryCreateAndTransformTest, Create2DNoTransform) { mesh->getCoordinates()->setParallelTransform( - bout::utils::make_unique(*mesh, true)); + bout::utils::make_unique(*mesh, true)); Options options; options["input"]["transform_from_field_aligned"] = false; @@ -952,7 +953,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create2DNoTransform) { TEST_F(FieldFactoryCreateAndTransformTest, Create3DNoTransform) { mesh->getCoordinates()->setParallelTransform( - bout::utils::make_unique(*mesh, true)); + bout::utils::make_unique(*mesh, true)); Options options; options["input"]["transform_from_field_aligned"] = false; @@ -968,7 +969,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create3DNoTransform) { TEST_F(FieldFactoryCreateAndTransformTest, Create2DCantTransform) { mesh->getCoordinates()->setParallelTransform( - bout::utils::make_unique(*mesh, false)); + bout::utils::make_unique(*mesh, false)); FieldFactory factory{mesh}; @@ -983,7 +984,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create2DCantTransform) { TEST_F(FieldFactoryCreateAndTransformTest, Create3DCantTransform) { mesh->getCoordinates()->setParallelTransform( - bout::utils::make_unique(*mesh, false)); + bout::utils::make_unique(*mesh, false)); FieldFactory factory{mesh}; diff --git a/tests/unit/field/test_fieldgroup.cxx b/tests/unit/field/test_fieldgroup.cxx index 167b1c3387..b87d54f214 100644 --- a/tests/unit/field/test_fieldgroup.cxx +++ b/tests/unit/field/test_fieldgroup.cxx @@ -1,11 +1,11 @@ -#include "gtest/gtest.h" #include "test_extras.hxx" +#include "gtest/gtest.h" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" #include "bout/fieldgroup.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "vector2d.hxx" -#include "vector3d.hxx" #include diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx index a1143e1ed1..6c28d856cc 100644 --- a/tests/unit/field/test_fieldperp.cxx +++ b/tests/unit/field/test_fieldperp.cxx @@ -3,15 +3,15 @@ #pragma GCC diagnostic ignored "-Wdeprecated-declarations" #include "gtest/gtest.h" +#include "bout/boutexception.hxx" +#include "bout/fieldperp.hxx" +#include "bout/output.hxx" +#include "test_extras.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/array.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" -#include "boutexception.hxx" -#include "fieldperp.hxx" -#include "test_extras.hxx" -#include "output.hxx" -#include "unused.hxx" -#include "utils.hxx" #include #include @@ -21,9 +21,9 @@ #include /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -43,7 +43,7 @@ TEST_F(FieldPerpTest, Allocate) { EXPECT_TRUE(field.isAllocated()); int counter = 0; - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 1.; // Hits Array bounds checking counter++; } @@ -78,7 +78,7 @@ TEST_F(FieldPerpTest, SliceXZ) { EXPECT_EQ(result.getIndex(), yindex); EXPECT_TRUE(areFieldsCompatible(masterField, result)); - for (const auto &i : result) { + for (const auto& i : result) { EXPECT_EQ(result[i], 1.0); } } @@ -279,7 +279,7 @@ TEST_F(FieldPerpTest, IterateOverWholeField) { // Basic test first: do we visit the correct number of elements? int count = 0; - for (auto &UNUSED(i) : field) { + for (auto& UNUSED(i) : field) { ++count; } @@ -308,7 +308,7 @@ TEST_F(FieldPerpTest, IterateOverWholeField) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field) { + for (auto& i : field) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -345,7 +345,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_ALL) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field) { + for (auto& i : field) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -389,7 +389,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_NOZ) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion(RGN_NOZ)) { + for (auto& i : field.getRegion(RGN_NOZ)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -431,7 +431,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_NOX) { BoutReal sum = 0.0; std::set> result_indices; - for (auto &i : field.getRegion(RGN_NOX)) { + for (auto& i : field.getRegion(RGN_NOX)) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -475,7 +475,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_XGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_XGUARDS")) { + for (const auto& i : field.getRegion("RGN_XGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -517,7 +517,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_YGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_YGUARDS")) { + for (const auto& i : field.getRegion("RGN_YGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -559,7 +559,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_ZGUARDS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_ZGUARDS")) { + for (const auto& i : field.getRegion("RGN_ZGUARDS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -605,7 +605,7 @@ TEST_F(FieldPerpTest, IterateOverRGN_NOCORNERS) { BoutReal sum = 0.0; std::set> result_indices; - for (const auto &i : field.getRegion("RGN_NOCORNERS")) { + for (const auto& i : field.getRegion("RGN_NOCORNERS")) { sum += field[i]; if (field[i] == sentinel) { result_indices.insert({i.x(), i.z()}); @@ -618,7 +618,6 @@ TEST_F(FieldPerpTest, IterateOverRGN_NOCORNERS) { EXPECT_TRUE(region_indices == result_indices); } - TEST_F(FieldPerpTest, Indexing) { FieldPerp field; @@ -830,7 +829,7 @@ TEST_F(FieldPerpTest, InvalidateGuards) { const int nmesh = nx * nz; int sum = 0; - for (const auto &i : field) { + for (const auto& i : field) { field[i] = 0.0; // Reset field value sum++; } @@ -838,7 +837,7 @@ TEST_F(FieldPerpTest, InvalidateGuards) { // Count the number of non-boundary points sum = 0; - for (const auto &i : field.getRegion(RGN_NOX)) { + for (const auto& i : field.getRegion(RGN_NOX)) { field[i] = 0.0; // Reset field value sum++; } @@ -854,9 +853,10 @@ TEST_F(FieldPerpTest, InvalidateGuards) { EXPECT_NO_THROW(checkData(field(localmesh->xstart, 0))); sum = 0; - for (const auto &i : field) { - if (!finite(field[i])) + for (const auto& i : field) { + if (!finite(field[i])) { sum++; + } } EXPECT_EQ(sum, nbndry); } @@ -1742,7 +1742,8 @@ TEST_F(FieldPerpTest, OperatorEqualsFieldPerp) { // to 'field'. // Note that Average z-direction type is not really allowed for FieldPerp, but // we don't check anywhere at the moment. - FieldPerp field2{mesh_staggered, CELL_XLOW, 2, {YDirectionType::Aligned, ZDirectionType::Average}}; + FieldPerp field2{ + mesh_staggered, CELL_XLOW, 2, {YDirectionType::Aligned, ZDirectionType::Average}}; field = field2; @@ -1758,7 +1759,8 @@ TEST_F(FieldPerpTest, EmptyFrom) { // to 'field2'. // Note that Average z-direction type is not really allowed for FieldPerp, but // we don't check anywhere at the moment. - FieldPerp field{mesh_staggered, CELL_XLOW, 3, {YDirectionType::Aligned, ZDirectionType::Average}}; + FieldPerp field{ + mesh_staggered, CELL_XLOW, 3, {YDirectionType::Aligned, ZDirectionType::Average}}; field = 5.; FieldPerp field2{emptyFrom(field)}; @@ -1775,7 +1777,8 @@ TEST_F(FieldPerpTest, ZeroFrom) { // to 'field2'. // Note that Average z-direction type is not really allowed for FieldPerp, but // we don't check anywhere at the moment. - FieldPerp field{mesh_staggered, CELL_XLOW, 3, {YDirectionType::Aligned, ZDirectionType::Average}}; + FieldPerp field{ + mesh_staggered, CELL_XLOW, 3, {YDirectionType::Aligned, ZDirectionType::Average}}; field = 5.; FieldPerp field2{zeroFrom(field)}; @@ -1830,5 +1833,4 @@ TEST_F(FieldPerpTest, Inequality) { EXPECT_FALSE(field1 == field5); } - #pragma GCC diagnostic pop diff --git a/tests/unit/field/test_initialprofiles.cxx b/tests/unit/field/test_initialprofiles.cxx index db4d7e2ec4..bbf0697f6e 100644 --- a/tests/unit/field/test_initialprofiles.cxx +++ b/tests/unit/field/test_initialprofiles.cxx @@ -1,9 +1,9 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" -#include "field.hxx" -#include "initialprofiles.hxx" -#include "output.hxx" +#include "bout/boutexception.hxx" +#include "bout/field.hxx" +#include "bout/initialprofiles.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx index 122f56a3ab..4d3bf1cd3d 100644 --- a/tests/unit/field/test_vector2d.cxx +++ b/tests/unit/field/test_vector2d.cxx @@ -1,20 +1,20 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" +#include "bout/boutexception.hxx" #if not(BOUT_USE_METRIC_3D) -#include "output.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" -#include "unused.hxx" -#include "vector2d.hxx" -#include "vector3d.hxx" +#include "bout/unused.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -24,12 +24,13 @@ using namespace bout::globals; /// Test fixture to make sure the global mesh is our fake one class Vector2DTest : public ::testing::Test { WithQuietOutput quiet{output_info}; + protected: Vector2DTest() { // Delete any existing mesh if (mesh != nullptr) { // Delete boundary regions - for (auto &r : mesh->getBoundaries()) { + for (auto& r : mesh->getBoundaries()) { delete r; } @@ -64,7 +65,7 @@ class Vector2DTest : public ::testing::Test { virtual ~Vector2DTest() { if (mesh != nullptr) { // Delete boundary regions - for (auto &r : mesh->getBoundaries()) { + for (auto& r : mesh->getBoundaries()) { delete r; } delete mesh; @@ -94,15 +95,15 @@ TEST_F(Vector2DTest, ApplyBoundaryString) { v.applyBoundary("dirichlet(1.0)"); // boundary cell in x - EXPECT_DOUBLE_EQ(v.x(0,2), 2.0); - EXPECT_DOUBLE_EQ(v.y(4,2), 2.0); - + EXPECT_DOUBLE_EQ(v.x(0, 2), 2.0); + EXPECT_DOUBLE_EQ(v.y(4, 2), 2.0); + // boundary cell in y - EXPECT_DOUBLE_EQ(v.x(2,0), 2.0); - EXPECT_DOUBLE_EQ(v.z(2,4), 2.0); + EXPECT_DOUBLE_EQ(v.x(2, 0), 2.0); + EXPECT_DOUBLE_EQ(v.z(2, 4), 2.0); // Middle cell not changed - EXPECT_DOUBLE_EQ(v.x(2,2), 0.0); + EXPECT_DOUBLE_EQ(v.x(2, 2), 0.0); } TEST_F(Vector2DTest, Is3D) { @@ -165,7 +166,7 @@ TEST_F(Vector2DTest, SetLocationXLOW) { } TEST_F(Vector2DTest, SetLocationYLOW) { - FakeMesh local_mesh{Vector2DTest::nx,Vector2DTest::ny,Vector2DTest::nz}; + FakeMesh local_mesh{Vector2DTest::nx, Vector2DTest::ny, Vector2DTest::nz}; local_mesh.setCoordinates(nullptr); local_mesh.StaggerGrids = true; local_mesh.setCoordinates(nullptr, CELL_YLOW); @@ -180,7 +181,7 @@ TEST_F(Vector2DTest, SetLocationYLOW) { } TEST_F(Vector2DTest, SetLocationZLOW) { - FakeMesh local_mesh{Vector2DTest::nx,Vector2DTest::ny,Vector2DTest::nz}; + FakeMesh local_mesh{Vector2DTest::nx, Vector2DTest::ny, Vector2DTest::nz}; local_mesh.setCoordinates(nullptr); local_mesh.StaggerGrids = true; local_mesh.setCoordinates(nullptr, CELL_ZLOW); @@ -195,7 +196,7 @@ TEST_F(Vector2DTest, SetLocationZLOW) { } TEST_F(Vector2DTest, SetLocationVSHIFT) { - FakeMesh local_mesh{Vector2DTest::nx,Vector2DTest::ny,Vector2DTest::nz}; + FakeMesh local_mesh{Vector2DTest::nx, Vector2DTest::ny, Vector2DTest::nz}; local_mesh.setCoordinates(nullptr); local_mesh.StaggerGrids = true; local_mesh.setCoordinates(nullptr, CELL_XLOW); @@ -393,7 +394,7 @@ TEST_F(Vector2DTest, MultiplyEqualsBoutReal) { vector.y = 5.0; vector.z = 6.0; - BoutReal real {4.0}; + BoutReal real{4.0}; vector *= real; @@ -423,7 +424,7 @@ TEST_F(Vector2DTest, MultiplyVector2DBoutReal) { vector.y = 2.0; vector.z = 3.0; - BoutReal real {2.0}; + BoutReal real{2.0}; Vector2D result = vector * real; @@ -468,7 +469,7 @@ TEST_F(Vector2DTest, MultiplyBoutRealVector2D) { vector.y = 2.0; vector.z = 3.0; - BoutReal real {2.0}; + BoutReal real{2.0}; Vector2D result = real * vector; @@ -543,7 +544,7 @@ TEST_F(Vector2DTest, DivideVector2DBoutReal) { vector.y = 2.0; vector.z = 3.0; - BoutReal real {2.0}; + BoutReal real{2.0}; Vector2D result = vector / real; diff --git a/tests/unit/field/test_vector3d.cxx b/tests/unit/field/test_vector3d.cxx index 693e596714..6b8a972b78 100644 --- a/tests/unit/field/test_vector3d.cxx +++ b/tests/unit/field/test_vector3d.cxx @@ -1,18 +1,18 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" -#include "output.hxx" +#include "bout/boutexception.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" -#include "unused.hxx" -#include "vector3d.hxx" +#include "bout/unused.hxx" +#include "bout/vector3d.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -62,7 +62,7 @@ class Vector3DTest : public ::testing::Test { ~Vector3DTest() override { if (mesh != nullptr) { // Delete boundary regions - for (auto &r : mesh->getBoundaries()) { + for (auto& r : mesh->getBoundaries()) { delete r; } } @@ -94,15 +94,15 @@ TEST_F(Vector3DTest, ApplyBoundaryString) { v.applyBoundary("dirichlet(1.0)"); // boundary cell in x - EXPECT_DOUBLE_EQ(v.x(0,2,0), 2.0); - EXPECT_DOUBLE_EQ(v.y(4,2,1), 2.0); - + EXPECT_DOUBLE_EQ(v.x(0, 2, 0), 2.0); + EXPECT_DOUBLE_EQ(v.y(4, 2, 1), 2.0); + // boundary cell in y - EXPECT_DOUBLE_EQ(v.x(2,0,2), 2.0); - EXPECT_DOUBLE_EQ(v.z(2,4,0), 2.0); + EXPECT_DOUBLE_EQ(v.x(2, 0, 2), 2.0); + EXPECT_DOUBLE_EQ(v.z(2, 4, 0), 2.0); // Middle cell not changed - EXPECT_DOUBLE_EQ(v.x(2,2,1), 0.0); + EXPECT_DOUBLE_EQ(v.x(2, 2, 1), 0.0); } TEST_F(Vector3DTest, Is3D) { @@ -165,7 +165,7 @@ TEST_F(Vector3DTest, SetLocationXLOW) { } TEST_F(Vector3DTest, SetLocationYLOW) { - FakeMesh local_mesh{Vector3DTest::nx,Vector3DTest::ny,Vector3DTest::nz}; + FakeMesh local_mesh{Vector3DTest::nx, Vector3DTest::ny, Vector3DTest::nz}; local_mesh.setCoordinates(nullptr); local_mesh.StaggerGrids = true; local_mesh.setCoordinates(nullptr, CELL_YLOW); @@ -180,7 +180,7 @@ TEST_F(Vector3DTest, SetLocationYLOW) { } TEST_F(Vector3DTest, SetLocationZLOW) { - FakeMesh local_mesh{Vector3DTest::nx,Vector3DTest::ny,Vector3DTest::nz}; + FakeMesh local_mesh{Vector3DTest::nx, Vector3DTest::ny, Vector3DTest::nz}; local_mesh.setCoordinates(nullptr); local_mesh.StaggerGrids = true; local_mesh.setCoordinates(nullptr, CELL_ZLOW); @@ -195,7 +195,7 @@ TEST_F(Vector3DTest, SetLocationZLOW) { } TEST_F(Vector3DTest, SetLocationVSHIFT) { - FakeMesh local_mesh{Vector3DTest::nx,Vector3DTest::ny,Vector3DTest::nz}; + FakeMesh local_mesh{Vector3DTest::nx, Vector3DTest::ny, Vector3DTest::nz}; local_mesh.setCoordinates(nullptr); local_mesh.StaggerGrids = true; local_mesh.setCoordinates(nullptr, CELL_XLOW); @@ -410,7 +410,7 @@ TEST_F(Vector3DTest, MultiplyEqualsBoutReal) { vector.y = 5.0; vector.z = 6.0; - BoutReal real {4.0}; + BoutReal real{4.0}; vector *= real; @@ -440,7 +440,7 @@ TEST_F(Vector3DTest, MultiplyVector3DBoutReal) { vector.y = 2.0; vector.z = 3.0; - BoutReal real {2.0}; + BoutReal real{2.0}; Vector3D result = vector * real; @@ -485,7 +485,7 @@ TEST_F(Vector3DTest, MultiplyBoutRealVector3D) { vector.y = 2.0; vector.z = 3.0; - BoutReal real {2.0}; + BoutReal real{2.0}; Vector3D result = real * vector; @@ -560,7 +560,7 @@ TEST_F(Vector3DTest, DivideVector3DBoutReal) { vector.y = 2.0; vector.z = 3.0; - BoutReal real {2.0}; + BoutReal real{2.0}; Vector3D result = vector / real; diff --git a/tests/unit/field/test_where.cxx b/tests/unit/field/test_where.cxx index 493a925eb9..7f61521503 100644 --- a/tests/unit/field/test_where.cxx +++ b/tests/unit/field/test_where.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" -#include "field.hxx" +#include "bout/field.hxx" #include "test_extras.hxx" -#include "where.hxx" +#include "bout/where.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/include/bout/test_array.cxx b/tests/unit/include/bout/test_array.cxx index 94a501d714..6b74b058fb 100644 --- a/tests/unit/include/bout/test_array.cxx +++ b/tests/unit/include/bout/test_array.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" +#include "bout/boutexception.hxx" #include "bout/array.hxx" -#include "boutexception.hxx" #include #include diff --git a/tests/unit/include/bout/test_assert.cxx b/tests/unit/include/bout/test_assert.cxx index 869e334a37..1dbba1dcdc 100644 --- a/tests/unit/include/bout/test_assert.cxx +++ b/tests/unit/include/bout/test_assert.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" #include -#include +#include TEST(AssertTest, Assert0) { EXPECT_NO_THROW(ASSERT0(true)); diff --git a/tests/unit/include/bout/test_bout_enum_class.cxx b/tests/unit/include/bout/test_bout_enum_class.cxx index 20ddf06f90..53660182ac 100644 --- a/tests/unit/include/bout/test_bout_enum_class.cxx +++ b/tests/unit/include/bout/test_bout_enum_class.cxx @@ -1,5 +1,5 @@ -#include #include "test_extras.hxx" +#include #include "bout/bout_enum_class.hxx" diff --git a/tests/unit/include/bout/test_deriv_store.cxx b/tests/unit/include/bout/test_deriv_store.cxx index 649450097a..f98765dd00 100644 --- a/tests/unit/include/bout/test_deriv_store.cxx +++ b/tests/unit/include/bout/test_deriv_store.cxx @@ -1,10 +1,10 @@ #include "gtest/gtest.h" #include -#include -#include -#include -#include +#include +#include +#include +#include #include diff --git a/tests/unit/include/bout/test_generic_factory.cxx b/tests/unit/include/bout/test_generic_factory.cxx index 383ab6b9cc..9368356151 100644 --- a/tests/unit/include/bout/test_generic_factory.cxx +++ b/tests/unit/include/bout/test_generic_factory.cxx @@ -1,6 +1,6 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" +#include "bout/boutexception.hxx" #include "bout/generic_factory.hxx" #include @@ -45,7 +45,8 @@ constexpr decltype(BaseFactory::default_type) BaseFactory::default_type; BaseFactory::RegisterInFactory registerme("base"); BaseFactory::RegisterInFactory registerme1("derived1"); BaseFactory::RegisterInFactory registerme2("derived2"); -BaseFactory::RegisterUnavailableInFactory dontregisterme("not here", "this is only a test"); +BaseFactory::RegisterUnavailableInFactory dontregisterme("not here", + "this is only a test"); } // namespace class BaseComplicated { diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx index 70efcf4c47..6afe69741e 100644 --- a/tests/unit/include/bout/test_hypre_interface.cxx +++ b/tests/unit/include/bout/test_hypre_interface.cxx @@ -3,7 +3,7 @@ #include "gtest/gtest.h" #include -#include "field3d.hxx" +#include "bout/field3d.hxx" #include "bout/hypre_interface.hxx" #if BOUT_HAS_HYPRE @@ -37,7 +37,7 @@ using FieldTypes = ::testing::Types; TYPED_TEST_SUITE(HypreVectorTest, FieldTypes); TYPED_TEST(HypreVectorTest, FieldConstructor) { - BOUT_FOR(i, this->field.getRegion("RGN_ALL")) { + BOUT_FOR (i, this->field.getRegion("RGN_ALL")) { this->field[i] = static_cast(i.ind); } @@ -120,12 +120,12 @@ TYPED_TEST(HypreVectorTest, Assemble) { } TYPED_TEST(HypreVectorTest, GetElements) { - BOUT_FOR(i, this->field.getRegion("RGN_ALL")) { + BOUT_FOR (i, this->field.getRegion("RGN_ALL")) { this->field[i] = static_cast(i.ind); } HypreVector vector(this->field, this->indexer); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { EXPECT_EQ(vector(i), this->field[i]); } } @@ -133,7 +133,7 @@ TYPED_TEST(HypreVectorTest, GetElements) { TYPED_TEST(HypreVectorTest, SetElements) { HypreVector vector{this->field, this->indexer}; - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { vector(i) = static_cast(i.ind); this->field[i] = static_cast(i.ind); } @@ -295,7 +295,7 @@ TYPED_TEST(HypreMatrixTest, SetAddGetValue) { TYPED_TEST(HypreMatrixTest, SetElements) { HypreMatrix matrix(this->indexer); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { matrix.setVal(i, i, static_cast(this->indexer->getGlobal(i))); } @@ -303,7 +303,7 @@ TYPED_TEST(HypreMatrixTest, SetElements) { auto raw_matrix = matrix.get(); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { BOUT_FOR_SERIAL(j, this->field.getRegion("RGN_NOBNDRY")) { auto i_index = static_cast(this->indexer->getGlobal(i)); auto j_index = static_cast(this->indexer->getGlobal(j)); @@ -338,7 +338,7 @@ TYPED_TEST(HypreMatrixTest, GetElements) { } matrix.assemble(); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { BOUT_FOR_SERIAL(j, this->field.getRegion("RGN_NOBNDRY")) { if (i == j) { EXPECT_EQ(matrix.getVal(i, j), diff --git a/tests/unit/include/bout/test_macro_for_each.cxx b/tests/unit/include/bout/test_macro_for_each.cxx index f012ffb43d..4def977dae 100644 --- a/tests/unit/include/bout/test_macro_for_each.cxx +++ b/tests/unit/include/bout/test_macro_for_each.cxx @@ -4,7 +4,8 @@ #include -#define INC(x) {++(x);} +#define INC(x) \ + { ++(x); } // Test that the macro is expanded // the correct number of times @@ -41,15 +42,14 @@ TEST(MacroForEachTest, NoBraces) { int a = 0; // Only the first expansion is disabled - if(false) + if (false) { MACRO_FOR_EACH(INC, a, a, a); + } EXPECT_EQ(a, 2); } -void inc(int &val) { - val++; -} +void inc(int& val) { val++; } TEST(MacroForEachFnTest, IncludeSemiColon) { int a = 0; @@ -83,4 +83,3 @@ TEST(MacroForEachFnTest, Order) { MACRO_FOR_EACH_FN(PUSH_NAME, a, b, c); EXPECT_EQ(ss.str(), "abc"); } - diff --git a/tests/unit/include/bout/test_monitor.cxx b/tests/unit/include/bout/test_monitor.cxx index 55028681e7..7bbde4abc2 100644 --- a/tests/unit/include/bout/test_monitor.cxx +++ b/tests/unit/include/bout/test_monitor.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" +#include "bout/boutexception.hxx" #include "bout/monitor.hxx" -#include "boutexception.hxx" TEST(MonitorTest, IsMultiple) { EXPECT_TRUE(isMultiple(1., 4.)); diff --git a/tests/unit/include/bout/test_petsc_indexer.cxx b/tests/unit/include/bout/test_petsc_indexer.cxx index 8a05b9e7bc..bd0ed6fd97 100644 --- a/tests/unit/include/bout/test_petsc_indexer.cxx +++ b/tests/unit/include/bout/test_petsc_indexer.cxx @@ -79,38 +79,45 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { indicesGlobalDefault; // Check each of the interior global indices is unique - BOUT_FOR(i, f.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, f.getRegion("RGN_NOBNDRY")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalSquare.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalSquare.insert(global).second); global = this->globalStarIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalStar.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalStar.insert(global).second); global = this->globalDefaultIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalDefault.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalDefault.insert(global).second); } // Check indices of X guard cells are unique - BOUT_FOR(i, f.getRegion("RGN_XGUARDS")) { + BOUT_FOR (i, f.getRegion("RGN_XGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalSquare.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalSquare.insert(global).second); global = this->globalStarIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalStar.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalStar.insert(global).second); EXPECT_LT(this->globalDefaultIndexer.getGlobal(i), 0); } // Check indices of Y guard cells are unique if (!std::is_same::value) { - BOUT_FOR(i, f.getRegion("RGN_YGUARDS")) { + BOUT_FOR (i, f.getRegion("RGN_YGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalSquare.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalSquare.insert(global).second); global = this->globalStarIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) EXPECT_TRUE(indicesGlobalStar.insert(global).second); + BOUT_OMP(critical) + EXPECT_TRUE(indicesGlobalStar.insert(global).second); EXPECT_LT(this->globalDefaultIndexer.getGlobal(i), 0); } } @@ -128,16 +135,16 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { } TYPED_TEST(IndexerTest, TestIsLocal) { - BOUT_FOR(i, this->globalSquareIndexer.getRegionAll()) { + BOUT_FOR (i, this->globalSquareIndexer.getRegionAll()) { EXPECT_TRUE(this->globalSquareIndexer.isLocal(i)); } - BOUT_FOR(i, this->globalStarIndexer.getRegionAll()) { + BOUT_FOR (i, this->globalStarIndexer.getRegionAll()) { EXPECT_TRUE(this->globalStarIndexer.isLocal(i)); } - BOUT_FOR(i, this->globalDefaultIndexer.getRegionAll()) { + BOUT_FOR (i, this->globalDefaultIndexer.getRegionAll()) { EXPECT_TRUE(this->globalDefaultIndexer.isLocal(i)); } - BOUT_FOR(i, this->localIndexer.getRegionAll()) { + BOUT_FOR (i, this->localIndexer.getRegionAll()) { EXPECT_TRUE(this->localIndexer.isLocal(i)); } } @@ -168,7 +175,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { Region rgn; rgn = this->globalSquareIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->ny * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), this->globalSquareIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalSquareIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -178,7 +185,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { } rgn = this->globalStarIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->ny * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), this->globalStarIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalStarIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -188,7 +195,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { } rgn = this->globalDefaultIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->ny * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), this->globalDefaultIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalDefaultIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -198,7 +205,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { } rgn = this->localIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), 0); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), this->localIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->localIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -231,10 +238,14 @@ TYPED_TEST(IndexerTest, TestGetRegionLowerY) { } else { rgn = this->globalSquareIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), (this->nx + 2 * this->guardx) * this->nz); - BOUT_FOR(i, rgn) { EXPECT_LT(i.y(), this->globalSquareIndexer.getMesh()->ystart); } + BOUT_FOR (i, rgn) { + EXPECT_LT(i.y(), this->globalSquareIndexer.getMesh()->ystart); + } rgn = this->globalStarIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->nz); - BOUT_FOR(i, rgn) { EXPECT_LT(i.y(), this->globalStarIndexer.getMesh()->ystart); } + BOUT_FOR (i, rgn) { + EXPECT_LT(i.y(), this->globalStarIndexer.getMesh()->ystart); + } } rgn = this->globalDefaultIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), 0); @@ -252,10 +263,14 @@ TYPED_TEST(IndexerTest, TestGetRegionUpperY) { } else { rgn = this->globalSquareIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), (this->nx + 2 * this->guardx) * this->nz); - BOUT_FOR(i, rgn) { EXPECT_GT(i.y(), this->globalSquareIndexer.getMesh()->yend); } + BOUT_FOR (i, rgn) { + EXPECT_GT(i.y(), this->globalSquareIndexer.getMesh()->yend); + } rgn = this->globalStarIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->nz); - BOUT_FOR(i, rgn) { EXPECT_GT(i.y(), this->globalStarIndexer.getMesh()->yend); } + BOUT_FOR (i, rgn) { + EXPECT_GT(i.y(), this->globalStarIndexer.getMesh()->yend); + } } rgn = this->globalDefaultIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), 0); @@ -267,10 +282,14 @@ TYPED_TEST(IndexerTest, TestGetRegionInnerX) { Region rgn; rgn = this->globalSquareIndexer.getRegionInnerX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR(i, rgn) { EXPECT_LT(i.x(), this->globalSquareIndexer.getMesh()->xstart); } + BOUT_FOR (i, rgn) { + EXPECT_LT(i.x(), this->globalSquareIndexer.getMesh()->xstart); + } rgn = this->globalStarIndexer.getRegionInnerX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR(i, rgn) { EXPECT_LT(i.x(), this->globalStarIndexer.getMesh()->xstart); } + BOUT_FOR (i, rgn) { + EXPECT_LT(i.x(), this->globalStarIndexer.getMesh()->xstart); + } rgn = this->globalDefaultIndexer.getRegionInnerX(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->localIndexer.getRegionInnerX(); @@ -281,10 +300,14 @@ TYPED_TEST(IndexerTest, TestGetRegionOuterX) { Region rgn; rgn = this->globalSquareIndexer.getRegionOuterX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR(i, rgn) { EXPECT_GT(i.x(), this->globalSquareIndexer.getMesh()->xend); } + BOUT_FOR (i, rgn) { + EXPECT_GT(i.x(), this->globalSquareIndexer.getMesh()->xend); + } rgn = this->globalStarIndexer.getRegionOuterX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR(i, rgn) { EXPECT_GT(i.x(), this->globalStarIndexer.getMesh()->xend); } + BOUT_FOR (i, rgn) { + EXPECT_GT(i.x(), this->globalStarIndexer.getMesh()->xend); + } rgn = this->globalDefaultIndexer.getRegionOuterX(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->localIndexer.getRegionOuterX(); @@ -441,7 +464,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex3D) { IndexerPtr index = this->getIndexer(indexers, this->pe_xind, this->pe_yind); // Test x boundaries - BOUT_FOR(i, this->localmesh->getRegion3D("RGN_XGUARDS")) { + BOUT_FOR (i, this->localmesh->getRegion3D("RGN_XGUARDS")) { if (i.x() < this->xstart && i.y() >= this->ystart && i.y() <= this->yend) { int global = index->getGlobal(i); if (this->pe_xind > 0) { @@ -467,22 +490,22 @@ TEST_P(ParallelIndexerTest, TestConvertIndex3D) { } // Test y boundaries - BOUT_FOR(i, this->localmesh->getRegion3D("RGN_YGUARDS")) { + BOUT_FOR (i, this->localmesh->getRegion3D("RGN_YGUARDS")) { if (i.y() < this->ystart) { - + if (i.x() == this->xstart) { - const int global = index->getGlobal(i.xm()), - otherXind = (this->pe_xind == 0) ? this->pe_xind : this->pe_xind - 1, - otherYind = this->pe_yind - 1; - const Ind3D otherInd = i.offset((this->pe_xind == 0) ? -1 : - this->xend - this->xstart, - this->yend - this->ystart + 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xm()), + otherXind = (this->pe_xind == 0) ? this->pe_xind : this->pe_xind - 1, + otherYind = this->pe_yind - 1; + const Ind3D otherInd = + i.offset((this->pe_xind == 0) ? -1 : this->xend - this->xstart, + this->yend - this->ystart + 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } - + int global = index->getGlobal(i); int otherGlobal = this->getIndexer(indexers, this->pe_xind, this->pe_yind - 1) @@ -490,31 +513,32 @@ TEST_P(ParallelIndexerTest, TestConvertIndex3D) { EXPECT_EQ(global, otherGlobal); if (i.x() == this->xend) { - const int global = index->getGlobal(i.xp()), - otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind : this->pe_xind + 1, - otherYind = this->pe_yind - 1; - const Ind3D otherInd = i.offset((this->pe_xind == this->nxpe - 1) ? 1 : - this->xstart - this->xend, - this->yend - this->ystart + 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xp()), + otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind + : this->pe_xind + 1, + otherYind = this->pe_yind - 1; + const Ind3D otherInd = + i.offset((this->pe_xind == this->nxpe - 1) ? 1 : this->xstart - this->xend, + this->yend - this->ystart + 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } - + } else if (i.y() >= this->yend && i.x() >= this->xstart && i.x() <= this->xend) { if (i.x() == this->xstart) { - const int global = index->getGlobal(i.xm()), - otherXind = (this->pe_xind == 0) ? this->pe_xind : this->pe_xind - 1, - otherYind = this->pe_yind + 1; - const Ind3D otherInd = i.offset((this->pe_xind == 0) ? -1 : - this->xend - this->xstart, - this->ystart - this->yend - 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xm()), + otherXind = (this->pe_xind == 0) ? this->pe_xind : this->pe_xind - 1, + otherYind = this->pe_yind + 1; + const Ind3D otherInd = + i.offset((this->pe_xind == 0) ? -1 : this->xend - this->xstart, + this->ystart - this->yend - 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } int global = index->getGlobal(i); @@ -524,18 +548,18 @@ TEST_P(ParallelIndexerTest, TestConvertIndex3D) { EXPECT_EQ(global, otherGlobal); if (i.x() == this->xend) { - const int global = index->getGlobal(i.xp()), - otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind : this->pe_xind + 1, - otherYind = this->pe_yind + 1; - const Ind3D otherInd = i.offset((this->pe_xind == this->nxpe - 1) ? 1 : - this->xstart - this->xend, - this->ystart - this->yend - 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xp()), + otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind + : this->pe_xind + 1, + otherYind = this->pe_yind + 1; + const Ind3D otherInd = + i.offset((this->pe_xind == this->nxpe - 1) ? 1 : this->xstart - this->xend, + this->ystart - this->yend - 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } - } } } @@ -545,7 +569,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex2D) { IndexerPtr index = this->getIndexer(indexers, this->pe_xind, this->pe_yind); // Test x boundaries - BOUT_FOR(i, this->localmesh->getRegion2D("RGN_XGUARDS")) { + BOUT_FOR (i, this->localmesh->getRegion2D("RGN_XGUARDS")) { if (i.x() < this->xstart) { int global = index->getGlobal(i); if (this->pe_xind > 0) { @@ -571,7 +595,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex2D) { } // Test y boundaries - BOUT_FOR(i, this->localmesh->getRegion2D("RGN_YGUARDS")) { + BOUT_FOR (i, this->localmesh->getRegion2D("RGN_YGUARDS")) { if (i.y() < this->ystart && i.x() >= this->xstart && i.x() <= this->xend) { int global = index->getGlobal(i); int otherGlobal = @@ -580,52 +604,53 @@ TEST_P(ParallelIndexerTest, TestConvertIndex2D) { EXPECT_EQ(global, otherGlobal); if (i.x() == this->xend) { - const int global = index->getGlobal(i.xp()), - otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind : this->pe_xind + 1, - otherYind = this->pe_yind - 1; - const Ind2D otherInd = i.offset((this->pe_xind == this->nxpe - 1) ? 1 : - this->xstart - this->xend, - this->yend - this->ystart + 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xp()), + otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind + : this->pe_xind + 1, + otherYind = this->pe_yind - 1; + const Ind2D otherInd = + i.offset((this->pe_xind == this->nxpe - 1) ? 1 : this->xstart - this->xend, + this->yend - this->ystart + 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } - + } else if (i.y() >= this->yend) { if (i.x() == this->xstart) { - const int global = index->getGlobal(i.xm()), - otherXind = (this->pe_xind == 0) ? this->pe_xind : this->pe_xind - 1, - otherYind = this->pe_yind + 1; - const Ind2D otherInd = i.offset((this->pe_xind == 0) ? -1 : - this->xend - this->xstart, - this->ystart - this->yend - 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xm()), + otherXind = (this->pe_xind == 0) ? this->pe_xind : this->pe_xind - 1, + otherYind = this->pe_yind + 1; + const Ind2D otherInd = + i.offset((this->pe_xind == 0) ? -1 : this->xend - this->xstart, + this->ystart - this->yend - 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } - int global = index->getGlobal(i); + int global = index->getGlobal(i); int otherGlobal = this->getIndexer(indexers, this->pe_xind, this->pe_yind + 1) ->getGlobal(i.ym(this->yend - this->ystart + 1)); EXPECT_EQ(global, otherGlobal); if (i.x() == this->xend) { - const int global = index->getGlobal(i.xp()), - otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind : this->pe_xind + 1, - otherYind = this->pe_yind + 1; - const Ind2D otherInd = i.offset((this->pe_xind == this->nxpe - 1) ? 1 : - this->xstart - this->xend, - this->ystart - this->yend - 1, 0); - const int otherGlobal = - this->getIndexer(indexers, otherXind, otherYind)->getGlobal(otherInd); - EXPECT_NE(global, -1); - EXPECT_EQ(global, otherGlobal); + const int global = index->getGlobal(i.xp()), + otherXind = (this->pe_xind == this->nxpe - 1) ? this->pe_xind + : this->pe_xind + 1, + otherYind = this->pe_yind + 1; + const Ind2D otherInd = + i.offset((this->pe_xind == this->nxpe - 1) ? 1 : this->xstart - this->xend, + this->ystart - this->yend - 1, 0); + const int otherGlobal = this->getIndexer(indexers, otherXind, otherYind) + ->getGlobal(otherInd); + EXPECT_NE(global, -1); + EXPECT_EQ(global, otherGlobal); } - } } } @@ -635,7 +660,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndexPerp) { IndexerPtr index = this->getIndexer(indexers, this->pe_xind, this->pe_yind); // Test x boundaries - BOUT_FOR(i, this->localmesh->getRegionPerp("RGN_XGUARDS")) { + BOUT_FOR (i, this->localmesh->getRegionPerp("RGN_XGUARDS")) { if (i.x() < this->xstart) { int global = index->getGlobal(i); if (this->pe_xind > 0) { @@ -672,7 +697,7 @@ TEST_P(ParallelIndexerTest, TestRegions3D) { rgn = index->getRegionNobndry(); EXPECT_EQ(rgn.size(), (this->nx - 2) * this->ny * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), index->getMesh()->xstart); EXPECT_LE(i.x(), index->getMesh()->xend); EXPECT_GE(i.y(), index->getMesh()->ystart); @@ -692,7 +717,7 @@ TEST_P(ParallelIndexerTest, TestRegions3D) { rgn = index->getRegionInnerX(); if (this->pe_xind == 0) { EXPECT_EQ(rgn.size(), this->ny * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -703,7 +728,7 @@ TEST_P(ParallelIndexerTest, TestRegions3D) { rgn = index->getRegionOuterX(); if (this->pe_xind == this->nxpe - 1) { EXPECT_EQ(rgn.size(), this->ny * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xend + 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -724,7 +749,7 @@ TEST_P(ParallelIndexerTest, TestRegions2D) { rgn = index->getRegionNobndry(); EXPECT_EQ(rgn.size(), (this->nx - 2) * this->ny); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), index->getMesh()->xstart); EXPECT_LE(i.x(), index->getMesh()->xend); EXPECT_GE(i.y(), index->getMesh()->ystart); @@ -744,7 +769,7 @@ TEST_P(ParallelIndexerTest, TestRegions2D) { rgn = index->getRegionInnerX(); if (this->pe_xind == 0) { EXPECT_EQ(rgn.size(), this->ny); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -755,7 +780,7 @@ TEST_P(ParallelIndexerTest, TestRegions2D) { rgn = index->getRegionOuterX(); if (this->pe_xind == this->nxpe - 1) { EXPECT_EQ(rgn.size(), this->ny); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xend + 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -776,7 +801,7 @@ TEST_P(ParallelIndexerTest, TestRegionsPerp) { rgn = index->getRegionNobndry(); EXPECT_EQ(rgn.size(), (this->nx - 2) * this->nz); - BOUT_FOR(i, rgn) { + BOUT_FOR (i, rgn) { EXPECT_GE(i.x(), index->getMesh()->xstart); EXPECT_LE(i.x(), index->getMesh()->xend); } @@ -794,14 +819,18 @@ TEST_P(ParallelIndexerTest, TestRegionsPerp) { rgn = index->getRegionInnerX(); if (this->pe_xind == 0) { EXPECT_EQ(rgn.size(), this->nz); - BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); } + BOUT_FOR (i, rgn) { + EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); + } } else { EXPECT_EQ(rgn.size(), 0); } rgn = index->getRegionOuterX(); if (this->pe_xind == this->nxpe - 1) { EXPECT_EQ(rgn.size(), this->nz); - BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xend + 1); } + BOUT_FOR (i, rgn) { + EXPECT_EQ(i.x(), index->getMesh()->xend + 1); + } } else { EXPECT_EQ(rgn.size(), 0); } diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index 5661ed7e3f..d2720ecccd 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -7,9 +7,9 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" #include "bout/operatorstencil.hxx" #include "bout/petsc_interface.hxx" #include "bout/region.hxx" @@ -87,9 +87,7 @@ class PetscMatrixTest : public FakeMeshFixture { PetscErrorPrintf = PetscErrorPrintfNone; } - virtual ~PetscMatrixTest() { - PetscErrorPrintf = PetscErrorPrintfDefault; - } + virtual ~PetscMatrixTest() { PetscErrorPrintf = PetscErrorPrintfDefault; } }; using FieldTypes = ::testing::Types; @@ -172,12 +170,13 @@ TYPED_TEST(PetscMatrixTest, TestGetElements) { Mat* rawmat = matrix.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); - BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { BOUT_FOR_SERIAL(j, this->field.getRegion("RGN_NOY")) { int i_ind = this->indexer->getGlobal(i); int j_ind = this->indexer->getGlobal(j); PetscScalar matContents; - BOUT_OMP(critical) MatGetValues(*rawmat, 1, &i_ind, 1, &j_ind, &matContents); + BOUT_OMP(critical) + MatGetValues(*rawmat, 1, &i_ind, 1, &j_ind, &matContents); if (i == j) { EXPECT_EQ(matContents, static_cast(i.ind)); } else { @@ -264,8 +263,7 @@ TYPED_TEST(PetscMatrixTest, TestDestroy) { // Test getting yup TYPED_TEST(PetscMatrixTest, TestYUp) { - PetscMatrix matrix(this->indexer, false), - expected(this->indexer, false); + PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); MockTransform* transform = this->pt; SCOPED_TRACE("YUp"); if (std::is_same::value) { @@ -294,8 +292,7 @@ TYPED_TEST(PetscMatrixTest, TestYUp) { // Test getting ydown TYPED_TEST(PetscMatrixTest, TestYDown) { - PetscMatrix matrix(this->indexer, false), - expected(this->indexer, false); + PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YDown"); @@ -324,8 +321,7 @@ TYPED_TEST(PetscMatrixTest, TestYDown) { // Test getting ynext(0) TYPED_TEST(PetscMatrixTest, TestYNext0) { - PetscMatrix matrix(this->indexer), - expected(this->indexer); + PetscMatrix matrix(this->indexer), expected(this->indexer); BoutReal val = 3.141592; SCOPED_TRACE("YNext0"); matrix.ynext(0)(this->indexA, this->indexB) = val; @@ -340,8 +336,7 @@ TYPED_TEST(PetscMatrixTest, TestYNext0) { // Test getting ynext(1) TYPED_TEST(PetscMatrixTest, TestYNextPos) { - PetscMatrix matrix(this->indexer, false), - expected(this->indexer, false); + PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextPos"); @@ -367,8 +362,7 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { // Test getting ynext(-1) TYPED_TEST(PetscMatrixTest, TestYNextNeg) { - PetscMatrix matrix(this->indexer, false), - expected(this->indexer, false); + PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextNeg"); @@ -410,7 +404,7 @@ TYPED_TEST(PetscMatrixTest, TestSwap) { TYPED_TEST(PetscMatrixTest, TestMatrixVectorMultiplyIdentity) { PetscMatrix matrix(this->indexer); this->field.allocate(); - BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { this->field[i] = static_cast(i.ind); matrix(i, i) = 1.0; } @@ -419,7 +413,7 @@ TYPED_TEST(PetscMatrixTest, TestMatrixVectorMultiplyIdentity) { matrix.assemble(); PetscVector product = matrix * vector; TypeParam prodField = product.toField(); - BOUT_FOR(i, prodField.getRegion("RGN_NOY")) { + BOUT_FOR (i, prodField.getRegion("RGN_NOY")) { EXPECT_NEAR(prodField[i], this->field[i], 1.e-10); } } @@ -440,7 +434,7 @@ TYPED_TEST(PetscMatrixTest, TestMatrixVectorMultiplyOnes) { matrix.assemble(); PetscVector product = matrix * vector; TypeParam prodField = product.toField(); - BOUT_FOR(i, prodField.getRegion("RGN_NOY")) { + BOUT_FOR (i, prodField.getRegion("RGN_NOY")) { EXPECT_NEAR(prodField[i], total, 1.e-10); } } diff --git a/tests/unit/include/bout/test_petsc_vector.cxx b/tests/unit/include/bout/test_petsc_vector.cxx index 9815eecbab..095e212abe 100644 --- a/tests/unit/include/bout/test_petsc_vector.cxx +++ b/tests/unit/include/bout/test_petsc_vector.cxx @@ -5,9 +5,9 @@ #include "test_extras.hxx" #include "gtest/gtest.h" -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" #include "bout/operatorstencil.hxx" #include "bout/petsc_interface.hxx" #include "bout/region.hxx" @@ -44,9 +44,7 @@ class PetscVectorTest : public FakeMeshFixture { PetscErrorPrintf = PetscErrorPrintfNone; } - virtual ~PetscVectorTest() { - PetscErrorPrintf = PetscErrorPrintfDefault; - } + virtual ~PetscVectorTest() { PetscErrorPrintf = PetscErrorPrintfDefault; } }; using FieldTypes = ::testing::Types; @@ -71,7 +69,7 @@ void testVectorsEqual(Vec* v1, Vec* v2) { // Test constructor from field TYPED_TEST(PetscVectorTest, FieldConstructor) { - BOUT_FOR(i, this->field.getRegion("RGN_ALL")) { + BOUT_FOR (i, this->field.getRegion("RGN_ALL")) { this->field[i] = static_cast(i.ind); } PetscVector vector(this->field, this->indexer); @@ -82,7 +80,9 @@ TYPED_TEST(PetscVectorTest, FieldConstructor) { VecGetLocalSize(*vectorPtr, &n); ASSERT_EQ(n, this->field.getNx() * this->field.getNy() * this->field.getNz()); TypeParam result = vector.toField(); - BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { EXPECT_EQ(result[i], this->field[i]); } + BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { + EXPECT_EQ(result[i], this->field[i]); + } } // Test copy constructor @@ -118,7 +118,9 @@ TYPED_TEST(PetscVectorTest, FieldAssignment) { VecGetLocalSize(*vectorPtr, &n); ASSERT_EQ(n, this->field.getNx() * this->field.getNy() * this->field.getNz()); TypeParam result = vector.toField(); - BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { EXPECT_EQ(result[i], val[i]); } + BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { + EXPECT_EQ(result[i], val[i]); + } } // Test copy assignment @@ -144,7 +146,7 @@ TYPED_TEST(PetscVectorTest, MoveAssignment) { // Test getting elements TYPED_TEST(PetscVectorTest, TestGetElements) { PetscVector vector(this->field, this->indexer); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { vector(i) = (2.5 * this->field[i] - 1.0); } Vec* rawvec = vector.get(); @@ -153,7 +155,7 @@ TYPED_TEST(PetscVectorTest, TestGetElements) { VecAssemblyEnd(*rawvec); VecGetArray(*rawvec, &vecContents); TypeParam result = vector.toField(); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { EXPECT_EQ(result[i], 2.5 * this->field[i] - 1.0); } } @@ -161,7 +163,7 @@ TYPED_TEST(PetscVectorTest, TestGetElements) { // Test getting constant elements TYPED_TEST(PetscVectorTest, TestGetElementsConst) { const PetscVector vector(this->field, this->indexer); - BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { const BoutReal element = vector(i); EXPECT_EQ(element, this->field[i]); } diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index 6021144956..e6780ac059 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -1,12 +1,12 @@ #include "gtest/gtest.h" +#include "bout/boutexception.hxx" +#include "bout/output.hxx" +#include "test_extras.hxx" +#include "bout/unused.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" #include "bout/region.hxx" -#include "boutexception.hxx" -#include "output.hxx" -#include "test_extras.hxx" -#include "unused.hxx" #include #include @@ -16,9 +16,9 @@ #include /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -49,12 +49,18 @@ TEST_F(RegionTest, regionFromRange) { EXPECT_EQ(region2.getIndices().size(), 1); // Invalid range results in empty region - { Region region3(0, -1, 0, 0, 0, 0, 1, 1); - EXPECT_EQ(region3.size(), 0);} - { Region region3(0, 0, 1, 0, 0, 0, 1, 1); - EXPECT_EQ(region3.size(), 0);} - { Region region3(0, 0, 0, 0, 20, 10, 1, 1); - EXPECT_EQ(region3.size(), 0);} + { + Region region3(0, -1, 0, 0, 0, 0, 1, 1); + EXPECT_EQ(region3.size(), 0); + } + { + Region region3(0, 0, 1, 0, 0, 0, 1, 1); + EXPECT_EQ(region3.size(), 0); + } + { + Region region3(0, 0, 0, 0, 20, 10, 1, 1); + EXPECT_EQ(region3.size(), 0); + } // Invalid size throws if CHECK >= 1 #if CHECK >= 1 @@ -71,7 +77,7 @@ TEST_F(RegionTest, regionFromIndices) { {0, 3}, {5, 7}, {9, 10}, {12, 12}, {14, 20}}; std::vector indicesIn; int maxContiguousSizeUsed = 0; - for (auto &block : blocksIn) { + for (auto& block : blocksIn) { int currBlockSize = 1 + block.second - block.first; maxContiguousSizeUsed = currBlockSize > maxContiguousSizeUsed ? currBlockSize : maxContiguousSizeUsed; @@ -186,11 +192,11 @@ TEST_F(RegionTest, defaultRegions) { } TEST_F(RegionTest, regionLoopAll) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); // Need to use a Field3D as a jig as OpenMP complicates things here Field3D a{0.}; - BOUT_FOR(i, region) { + BOUT_FOR (i, region) { a[i] = 1.0; } @@ -204,10 +210,10 @@ TEST_F(RegionTest, regionLoopAll) { } TEST_F(RegionTest, regionLoopNoBndry) { - const auto ®ion = mesh->getRegion3D("RGN_NOBNDRY"); + const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); Field3D a{0.}; - BOUT_FOR(i, region) { + BOUT_FOR (i, region) { a[i] = 1.0; } @@ -234,12 +240,10 @@ TEST_F(RegionTest, regionLoopNoBndry) { } TEST_F(RegionTest, regionLoopAllSerial) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); int count = 0; - BOUT_FOR_SERIAL(i, region) { - ++count; - } + BOUT_FOR_SERIAL(i, region) { ++count; } const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz; @@ -247,12 +251,10 @@ TEST_F(RegionTest, regionLoopAllSerial) { } TEST_F(RegionTest, regionLoopNoBndrySerial) { - const auto ®ion = mesh->getRegion3D("RGN_NOBNDRY"); + const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); int count = 0; - BOUT_FOR_SERIAL(i, region) { - ++count; - } + BOUT_FOR_SERIAL(i, region) { ++count; } const int ninner = (mesh->LocalNz * (1 + mesh->xend - mesh->xstart) * (1 + mesh->yend - mesh->ystart)); @@ -261,7 +263,7 @@ TEST_F(RegionTest, regionLoopNoBndrySerial) { } TEST_F(RegionTest, regionLoopAllSection) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); int count = 0; BOUT_OMP(parallel) { @@ -276,7 +278,7 @@ TEST_F(RegionTest, regionLoopAllSection) { } TEST_F(RegionTest, regionLoopNoBndrySection) { - const auto ®ion = mesh->getRegion3D("RGN_NOBNDRY"); + const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); int count = 0; BOUT_OMP(parallel) { @@ -292,13 +294,11 @@ TEST_F(RegionTest, regionLoopNoBndrySection) { } TEST_F(RegionTest, regionLoopAllInner) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); Field3D a{0.}; BOUT_OMP(parallel) { - BOUT_FOR_INNER(i, region) { - a[i] = 1.0; - } + BOUT_FOR_INNER(i, region) { a[i] = 1.0; } } for (int i = 0; i < mesh->LocalNx; ++i) { @@ -311,13 +311,11 @@ TEST_F(RegionTest, regionLoopAllInner) { } TEST_F(RegionTest, regionLoopNoBndryInner) { - const auto ®ion = mesh->getRegion3D("RGN_NOBNDRY"); + const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); Field3D a{0.}; BOUT_OMP(parallel) { - BOUT_FOR_INNER(i, region) { - a[i] = 1.0; - } + BOUT_FOR_INNER(i, region) { a[i] = 1.0; } } const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz; @@ -348,7 +346,7 @@ TEST_F(RegionTest, regionAsSorted) { {0, 3}, {5, 7}, {9, 10}, {12, 12}, {14, 20}}; Region::RegionIndices indicesIn; - for (auto &block : blocksIn) { + for (auto& block : blocksIn) { for (int i = block.first; i <= block.second; i++) { indicesIn.push_back(Ind3D{i}); } @@ -1027,14 +1025,16 @@ TEST_F(RegionTest, regionGetStatsHomogenous) { std::ostringstream strRepresentation; strRepresentation << stats; std::ostringstream expectedStrRepresentation; - expectedStrRepresentation << "Total blocks : "<< numBlocks; - expectedStrRepresentation << ", " << "min(count)/max(count) :"; + expectedStrRepresentation << "Total blocks : " << numBlocks; + expectedStrRepresentation << ", " + << "min(count)/max(count) :"; expectedStrRepresentation << " " << minBlockSize << " (" << numMaxBlocks << ")/"; expectedStrRepresentation << " " << maxBlockSize << " (" << numMaxBlocks << ")"; - expectedStrRepresentation << ", " << "Max imbalance : " << maxImbalance; - expectedStrRepresentation << ", " << "Small block count : " << numSmallBlocks; + expectedStrRepresentation << ", " + << "Max imbalance : " << maxImbalance; + expectedStrRepresentation << ", " + << "Small block count : " << numSmallBlocks; EXPECT_EQ(strRepresentation.str(), expectedStrRepresentation.str()); - } TEST_F(RegionTest, regionGetStatsHeterogenous) { @@ -1476,7 +1476,7 @@ TYPED_TEST(RegionIndexTest, RangeBasedForLoop) { typename Region::RegionIndices region2; int count = 0; - for (const auto &iter : range) { + for (const auto& iter : range) { ++count; region2.push_back(iter); } @@ -1685,7 +1685,7 @@ const int IndexOffsetTest::ny = 5; const int IndexOffsetTest::nz = 7; TEST_F(IndexOffsetTest, X) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1700,7 +1700,7 @@ TEST_F(IndexOffsetTest, X) { } TEST_F(IndexOffsetTest, Y) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1715,7 +1715,7 @@ TEST_F(IndexOffsetTest, Y) { } TEST_F(IndexOffsetTest, Z) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1730,7 +1730,7 @@ TEST_F(IndexOffsetTest, Z) { } TEST_F(IndexOffsetTest, XPlusOne) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1755,7 +1755,7 @@ TEST_F(IndexOffsetTest, XPlusOne) { } TEST_F(IndexOffsetTest, YPlusOne) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1782,7 +1782,7 @@ TEST_F(IndexOffsetTest, YPlusOne) { } TEST_F(IndexOffsetTest, ZPlusOne) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1803,7 +1803,7 @@ TEST_F(IndexOffsetTest, ZPlusOne) { } TEST_F(IndexOffsetTest, XPlusOneGeneric) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1828,7 +1828,7 @@ TEST_F(IndexOffsetTest, XPlusOneGeneric) { } TEST_F(IndexOffsetTest, YPlusOneGeneric) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1855,7 +1855,7 @@ TEST_F(IndexOffsetTest, YPlusOneGeneric) { } TEST_F(IndexOffsetTest, ZPlusOneGeneric) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1876,7 +1876,7 @@ TEST_F(IndexOffsetTest, ZPlusOneGeneric) { } TEST_F(IndexOffsetTest, XMinusOne) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1901,7 +1901,7 @@ TEST_F(IndexOffsetTest, XMinusOne) { } TEST_F(IndexOffsetTest, YMinusOne) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1928,7 +1928,7 @@ TEST_F(IndexOffsetTest, YMinusOne) { } TEST_F(IndexOffsetTest, ZMinusOne) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1949,7 +1949,7 @@ TEST_F(IndexOffsetTest, ZMinusOne) { } TEST_F(IndexOffsetTest, XMinusOneGeneric) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -1974,7 +1974,7 @@ TEST_F(IndexOffsetTest, XMinusOneGeneric) { } TEST_F(IndexOffsetTest, YMinusOneGeneric) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2001,7 +2001,7 @@ TEST_F(IndexOffsetTest, YMinusOneGeneric) { } TEST_F(IndexOffsetTest, ZMinusOneGeneric) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2022,7 +2022,7 @@ TEST_F(IndexOffsetTest, ZMinusOneGeneric) { } TEST_F(IndexOffsetTest, XPlusTwo) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2047,7 +2047,7 @@ TEST_F(IndexOffsetTest, XPlusTwo) { } TEST_F(IndexOffsetTest, YPlusTwo) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2074,7 +2074,7 @@ TEST_F(IndexOffsetTest, YPlusTwo) { } TEST_F(IndexOffsetTest, ZPlusTwo) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2095,7 +2095,7 @@ TEST_F(IndexOffsetTest, ZPlusTwo) { } TEST_F(IndexOffsetTest, XMinusTwo) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2122,7 +2122,7 @@ TEST_F(IndexOffsetTest, XMinusTwo) { } TEST_F(IndexOffsetTest, YMinusTwo) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2147,7 +2147,7 @@ TEST_F(IndexOffsetTest, YMinusTwo) { } TEST_F(IndexOffsetTest, ZMinusTwo) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2168,7 +2168,7 @@ TEST_F(IndexOffsetTest, ZMinusTwo) { } TEST_F(IndexOffsetTest, Offset111) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2193,7 +2193,7 @@ TEST_F(IndexOffsetTest, Offset111) { } TEST_F(IndexOffsetTest, Offsetm1m1m1) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2219,7 +2219,7 @@ TEST_F(IndexOffsetTest, Offsetm1m1m1) { #if CHECK > 2 TEST_F(IndexOffsetTest, ZNegativeOffsetInd3D) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2229,7 +2229,7 @@ TEST_F(IndexOffsetTest, ZNegativeOffsetInd3D) { #endif TEST_F(IndexOffsetTest, ZOffsetZeroInd3D) { - const auto ®ion = mesh->getRegion3D("RGN_ALL"); + const auto& region = mesh->getRegion3D("RGN_ALL"); auto index = region.cbegin(); @@ -2239,7 +2239,7 @@ TEST_F(IndexOffsetTest, ZOffsetZeroInd3D) { } TEST_F(IndexOffsetTest, XInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2252,7 +2252,7 @@ TEST_F(IndexOffsetTest, XInd2D) { } TEST_F(IndexOffsetTest, YInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2265,7 +2265,7 @@ TEST_F(IndexOffsetTest, YInd2D) { } TEST_F(IndexOffsetTest, ZInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2278,7 +2278,7 @@ TEST_F(IndexOffsetTest, ZInd2D) { } TEST_F(IndexOffsetTest, XPlusOneInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2301,7 +2301,7 @@ TEST_F(IndexOffsetTest, XPlusOneInd2D) { } TEST_F(IndexOffsetTest, YPlusOneInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2326,7 +2326,7 @@ TEST_F(IndexOffsetTest, YPlusOneInd2D) { } TEST_F(IndexOffsetTest, ZPlusOneInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2345,7 +2345,7 @@ TEST_F(IndexOffsetTest, ZPlusOneInd2D) { } TEST_F(IndexOffsetTest, XPlusOneInd2DGeneric) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2368,7 +2368,7 @@ TEST_F(IndexOffsetTest, XPlusOneInd2DGeneric) { } TEST_F(IndexOffsetTest, YPlusOneInd2DGeneric) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2393,7 +2393,7 @@ TEST_F(IndexOffsetTest, YPlusOneInd2DGeneric) { } TEST_F(IndexOffsetTest, ZPlusOneInd2DGeneric) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2412,7 +2412,7 @@ TEST_F(IndexOffsetTest, ZPlusOneInd2DGeneric) { } TEST_F(IndexOffsetTest, XMinusOneInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2435,7 +2435,7 @@ TEST_F(IndexOffsetTest, XMinusOneInd2D) { } TEST_F(IndexOffsetTest, YMinusOneInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2460,7 +2460,7 @@ TEST_F(IndexOffsetTest, YMinusOneInd2D) { } TEST_F(IndexOffsetTest, ZMinusOneInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2479,7 +2479,7 @@ TEST_F(IndexOffsetTest, ZMinusOneInd2D) { } TEST_F(IndexOffsetTest, XMinusOneInd2DGeneric) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2502,7 +2502,7 @@ TEST_F(IndexOffsetTest, XMinusOneInd2DGeneric) { } TEST_F(IndexOffsetTest, YMinusOneInd2DGeneric) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2527,7 +2527,7 @@ TEST_F(IndexOffsetTest, YMinusOneInd2DGeneric) { } TEST_F(IndexOffsetTest, ZMinusOneInd2DGeneric) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2546,7 +2546,7 @@ TEST_F(IndexOffsetTest, ZMinusOneInd2DGeneric) { } TEST_F(IndexOffsetTest, XPlusTwoInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2569,7 +2569,7 @@ TEST_F(IndexOffsetTest, XPlusTwoInd2D) { } TEST_F(IndexOffsetTest, YPlusTwoInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2594,7 +2594,7 @@ TEST_F(IndexOffsetTest, YPlusTwoInd2D) { } TEST_F(IndexOffsetTest, ZPlusTwoInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2603,7 +2603,7 @@ TEST_F(IndexOffsetTest, ZPlusTwoInd2D) { #if CHECK > 2 TEST_F(IndexOffsetTest, ZNegativeOffsetInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2613,7 +2613,7 @@ TEST_F(IndexOffsetTest, ZNegativeOffsetInd2D) { #endif TEST_F(IndexOffsetTest, ZOffsetZeroInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2623,7 +2623,7 @@ TEST_F(IndexOffsetTest, ZOffsetZeroInd2D) { } TEST_F(IndexOffsetTest, XMinusTwoInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2646,7 +2646,7 @@ TEST_F(IndexOffsetTest, XMinusTwoInd2D) { } TEST_F(IndexOffsetTest, YMinusTwoInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2671,14 +2671,14 @@ TEST_F(IndexOffsetTest, YMinusTwoInd2D) { } TEST_F(IndexOffsetTest, ZMinusTwoInd2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); EXPECT_EQ(index->zmm(), *index); } TEST_F(IndexOffsetTest, Offset111Ind2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); @@ -2701,7 +2701,7 @@ TEST_F(IndexOffsetTest, Offset111Ind2D) { } TEST_F(IndexOffsetTest, Offsetm1m1m1Ind2D) { - const auto ®ion = mesh->getRegion2D("RGN_ALL"); + const auto& region = mesh->getRegion2D("RGN_ALL"); auto index = region.cbegin(); diff --git a/tests/unit/include/bout/test_single_index_ops.cxx b/tests/unit/include/bout/test_single_index_ops.cxx index 6d1dda8784..037e695214 100644 --- a/tests/unit/include/bout/test_single_index_ops.cxx +++ b/tests/unit/include/bout/test_single_index_ops.cxx @@ -2,8 +2,8 @@ #include "test_extras.hxx" -#include "derivs.hxx" -#include "difops.hxx" +#include "bout/derivs.hxx" +#include "bout/difops.hxx" #include "bout/single_index_ops.hxx" #include @@ -34,7 +34,9 @@ FieldType random_field(std::default_random_engine& re) { FieldType result; result.allocate(); // Fill with random numbers - BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = unif(re); } + BOUT_FOR (i, result.getRegion("RGN_ALL")) { + result[i] = unif(re); + } return result; } @@ -54,7 +56,9 @@ TEST_F(SingleIndexOpsTest, DDX) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = DDX(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = DDX(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -79,7 +83,9 @@ TEST_F(SingleIndexOpsTest, DDY) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = DDY(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = DDY(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -101,7 +107,9 @@ TEST_F(SingleIndexOpsTest, DDZ) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = DDZ(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = DDZ(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -129,7 +137,7 @@ TEST_F(SingleIndexOpsTest, bracket2d3d) { indexops.allocate(); auto input_acc = Field2DAccessor<>(input); auto input2_acc = FieldAccessor<>(input2); - BOUT_FOR(i, indexops.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, indexops.getRegion("RGN_NOBNDRY")) { indexops[i] = bracket(input_acc, input2_acc, i); } @@ -156,7 +164,7 @@ TEST_F(SingleIndexOpsTest, bracket3d3d) { indexops.allocate(); auto input_acc = FieldAccessor<>(input); auto input2_acc = FieldAccessor<>(input2); - BOUT_FOR(i, indexops.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, indexops.getRegion("RGN_NOBNDRY")) { indexops[i] = bracket(input_acc, input2_acc, i); } @@ -183,7 +191,9 @@ TEST_F(SingleIndexOpsTest, Delp2_3D) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = Delp2(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = Delp2(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -218,7 +228,7 @@ TEST_F(SingleIndexOpsTest, b0xGrad_dot_Grad_3D_2D) { indexops.allocate(); auto input1_acc = FieldAccessor<>(input1); auto input2_acc = Field2DAccessor<>(input2); - BOUT_FOR(i, input1.getRegion("RGN_NOBNDRY")) { + BOUT_FOR (i, input1.getRegion("RGN_NOBNDRY")) { indexops[i] = b0xGrad_dot_Grad(input1_acc, input2_acc, i); } @@ -243,7 +253,9 @@ TEST_F(SingleIndexOpsTest, D2DY2) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = D2DY2(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = D2DY2(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -266,7 +278,9 @@ TEST_F(SingleIndexOpsTest, Grad_par) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = Grad_par(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = Grad_par(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -289,7 +303,9 @@ TEST_F(SingleIndexOpsTest, Div_par) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = Div_par(input_acc, i); } + BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { + indexops[i] = Div_par(input_acc, i); + } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); diff --git a/tests/unit/include/bout/test_template_combinations.cxx b/tests/unit/include/bout/test_template_combinations.cxx index 00b07ca362..d30e69e818 100644 --- a/tests/unit/include/bout/test_template_combinations.cxx +++ b/tests/unit/include/bout/test_template_combinations.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" #include -#include -#include +#include +#include #include diff --git a/tests/unit/include/bout/test_traits.cxx b/tests/unit/include/bout/test_traits.cxx index 68b1c2b005..98f0c542ad 100644 --- a/tests/unit/include/bout/test_traits.cxx +++ b/tests/unit/include/bout/test_traits.cxx @@ -1,9 +1,9 @@ #include "gtest/gtest.h" -#include "field.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "fieldperp.hxx" +#include "bout/field.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/fieldperp.hxx" #include "bout/traits.hxx" #include diff --git a/tests/unit/include/test_cyclic_reduction.cxx b/tests/unit/include/test_cyclic_reduction.cxx index 930fb4ae52..29ecf9e4d0 100644 --- a/tests/unit/include/test_cyclic_reduction.cxx +++ b/tests/unit/include/test_cyclic_reduction.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" -#include "boutcomm.hxx" -#include "cyclic_reduction.hxx" +#include "bout/boutcomm.hxx" +#include "bout/cyclic_reduction.hxx" #include "test_extras.hxx" #include "bout/array.hxx" diff --git a/tests/unit/include/test_derivs.cxx b/tests/unit/include/test_derivs.cxx index 0cf35c3366..185b4877a0 100644 --- a/tests/unit/include/test_derivs.cxx +++ b/tests/unit/include/test_derivs.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" -#include "bout_types.hxx" -#include "fft.hxx" -#include "field3d.hxx" +#include "bout/bout_types.hxx" +#include "bout/fft.hxx" +#include "bout/field3d.hxx" #include "test_extras.hxx" #include "bout/constants.hxx" #include "bout/deriv_store.hxx" @@ -39,7 +39,7 @@ namespace { // well! This has to be sufficiently loose for the least accurate // method to pass, or we need to also match up tolerances to methods constexpr BoutReal derivatives_tolerance{5.e-3}; -} +} // namespace class DerivativesTest : public ::testing::TestWithParam> { @@ -106,7 +106,8 @@ class DerivativesTest // Make the input and expected output fields // Weird `(i.*dir)()` syntax here in order to call the direction method // C++17 makes this nicer with std::invoke - input = makeField([&](Index& i) { return std::sin((i.*dir)() * box_length); }, mesh); + input = makeField( + [&](Index& i) { return std::sin((i.*dir)() * box_length); }, mesh); // Make the velocity field velocity = makeField([&](Index& UNUSED(i)) { return 2.0; }, mesh); @@ -116,17 +117,21 @@ class DerivativesTest switch (std::get<1>(GetParam())) { case DERIV::Standard: expected = makeField( - [&](Index& i) { return std::cos((i.*dir)() * box_length) * box_length; }, mesh); + [&](Index& i) { return std::cos((i.*dir)() * box_length) * box_length; }, mesh); break; case DERIV::StandardSecond: expected = makeField( - [&](Index& i) { return -std::sin((i.*dir)() * box_length) * pow(box_length, 2); }, - mesh); + [&](Index& i) { + return -std::sin((i.*dir)() * box_length) * pow(box_length, 2); + }, + mesh); break; case DERIV::StandardFourth: expected = makeField( - [&](Index& i) { return std::sin((i.*dir)() * box_length) * pow(box_length, 4); }, - mesh); + [&](Index& i) { + return std::sin((i.*dir)() * box_length) * pow(box_length, 4); + }, + mesh); break; // For now advection derivatives (upwind, flux) can have the same expected // result as the velocity field is constant @@ -191,83 +196,83 @@ auto methodDirectionTupleToString( // Instantiate the test for X, Y, Z for first derivatives INSTANTIATE_TEST_SUITE_P(FirstX, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FirstY, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FirstZ, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, + DIRECTION::Z)), + methodDirectionTupleToString); // Instantiate the test for X, Y, Z for second derivatives INSTANTIATE_TEST_SUITE_P(SecondX, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(SecondY, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(SecondZ, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, + DIRECTION::Z)), + methodDirectionTupleToString); // Instantiate the test for X, Y, Z for fourth derivatives INSTANTIATE_TEST_SUITE_P(FourthX, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FourthY, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FourthZ, DerivativesTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, + DIRECTION::Z)), + methodDirectionTupleToString); // Instantiate the test for X, Y, Z for upwind derivatives INSTANTIATE_TEST_SUITE_P(UpwindX, DerivativesTestAdvection, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(UpwindY, DerivativesTestAdvection, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(UpwindZ, DerivativesTestAdvection, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, + DIRECTION::Z)), + methodDirectionTupleToString); // Instantiate the test for X, Y, Z for flux derivatives INSTANTIATE_TEST_SUITE_P(FluxX, DerivativesTestAdvection, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FluxY, DerivativesTestAdvection, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FluxZ, DerivativesTestAdvection, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, + DIRECTION::Z)), + methodDirectionTupleToString); // All standard derivatives have the same signature, so we can use a // single test, just instantiate it for each direction/order combination @@ -294,8 +299,7 @@ TEST_P(DerivativesTestAdvection, Sanity) { result.allocate(); derivative(velocity, input, result, region); - EXPECT_TRUE( - IsFieldEqual(result, expected, "RGN_NOBNDRY", derivatives_tolerance)); + EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_NOBNDRY", derivatives_tolerance)); } ///////////////////////////////////////////////////////////////////// @@ -307,32 +311,32 @@ TEST_P(DerivativesTestAdvection, Sanity) { using FirstDerivativesInterfaceTest = DerivativesTest; INSTANTIATE_TEST_SUITE_P(X, FirstDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FirstY, FirstDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(FirstZ, FirstDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Standard, + DIRECTION::Z)), + methodDirectionTupleToString); TEST_P(FirstDerivativesInterfaceTest, Sanity) { Field3D result; switch (std::get<0>(GetParam())) { - case DIRECTION::X: - result = bout::derivatives::index::DDX(input); - break; - case DIRECTION::Y: - result = bout::derivatives::index::DDY(input); - break; - case DIRECTION::Z: - result = bout::derivatives::index::DDZ(input); - break; + case DIRECTION::X: + result = bout::derivatives::index::DDX(input); + break; + case DIRECTION::Y: + result = bout::derivatives::index::DDY(input); + break; + case DIRECTION::Z: + result = bout::derivatives::index::DDZ(input); + break; default: break; } @@ -343,32 +347,32 @@ TEST_P(FirstDerivativesInterfaceTest, Sanity) { using SecondDerivativesInterfaceTest = DerivativesTest; INSTANTIATE_TEST_SUITE_P(X, SecondDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Y, SecondDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Z, SecondDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardSecond, + DIRECTION::Z)), + methodDirectionTupleToString); TEST_P(SecondDerivativesInterfaceTest, Sanity) { Field3D result; switch (std::get<0>(GetParam())) { - case DIRECTION::X: - result = bout::derivatives::index::D2DX2(input); - break; - case DIRECTION::Y: - result = bout::derivatives::index::D2DY2(input); - break; - case DIRECTION::Z: - result = bout::derivatives::index::D2DZ2(input); - break; + case DIRECTION::X: + result = bout::derivatives::index::D2DX2(input); + break; + case DIRECTION::Y: + result = bout::derivatives::index::D2DY2(input); + break; + case DIRECTION::Z: + result = bout::derivatives::index::D2DZ2(input); + break; default: break; } @@ -379,32 +383,32 @@ TEST_P(SecondDerivativesInterfaceTest, Sanity) { using FourthDerivativesInterfaceTest = DerivativesTest; INSTANTIATE_TEST_SUITE_P(X, FourthDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Y, FourthDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Z, FourthDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::StandardFourth, + DIRECTION::Z)), + methodDirectionTupleToString); TEST_P(FourthDerivativesInterfaceTest, Sanity) { Field3D result; switch (std::get<0>(GetParam())) { - case DIRECTION::X: - result = bout::derivatives::index::D4DX4(input); - break; - case DIRECTION::Y: - result = bout::derivatives::index::D4DY4(input); - break; - case DIRECTION::Z: - result = bout::derivatives::index::D4DZ4(input); - break; + case DIRECTION::X: + result = bout::derivatives::index::D4DX4(input); + break; + case DIRECTION::Y: + result = bout::derivatives::index::D4DY4(input); + break; + case DIRECTION::Z: + result = bout::derivatives::index::D4DZ4(input); + break; default: break; } @@ -412,24 +416,23 @@ TEST_P(FourthDerivativesInterfaceTest, Sanity) { EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_NOBNDRY", derivatives_tolerance)); } - using UpwindDerivativesInterfaceTest = DerivativesTest; // Instantiate the test for X, Y, Z for upwind derivatives INSTANTIATE_TEST_SUITE_P(X, UpwindDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Y, UpwindDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Z, UpwindDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Upwind, + DIRECTION::Z)), + methodDirectionTupleToString); TEST_P(UpwindDerivativesInterfaceTest, Sanity) { Field3D result; @@ -455,19 +458,19 @@ using FluxDerivativesInterfaceTest = DerivativesTest; // Instantiate the test for X, Y, Z for flux derivatives INSTANTIATE_TEST_SUITE_P(X, FluxDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, - DIRECTION::X)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, + DIRECTION::X)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Y, FluxDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, - DIRECTION::Y)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, + DIRECTION::Y)), + methodDirectionTupleToString); INSTANTIATE_TEST_SUITE_P(Z, FluxDerivativesInterfaceTest, - ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, - DIRECTION::Z)), - methodDirectionTupleToString); + ::testing::ValuesIn(getMethodsForDirection(DERIV::Flux, + DIRECTION::Z)), + methodDirectionTupleToString); TEST_P(FluxDerivativesInterfaceTest, Sanity) { Field3D result; diff --git a/tests/unit/include/test_mask.cxx b/tests/unit/include/test_mask.cxx index d8f3c69529..6ba85d06cf 100644 --- a/tests/unit/include/test_mask.cxx +++ b/tests/unit/include/test_mask.cxx @@ -1,13 +1,13 @@ #include "gtest/gtest.h" -#include "mask.hxx" -#include "boutexception.hxx" +#include "bout/boutexception.hxx" +#include "bout/mask.hxx" #include "test_extras.hxx" /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -114,7 +114,7 @@ TEST_F(MaskTest, CreateOnMesh) { constexpr int nx{2}; constexpr int ny{3}; constexpr int nz{4}; - + FakeMesh mesh{nx, ny, nz}; BoutMask mask{mesh}; @@ -132,7 +132,7 @@ TEST_F(MaskTest, CreateOnMeshWithValueTrue) { constexpr int nx{2}; constexpr int ny{3}; constexpr int nz{4}; - + FakeMesh mesh{nx, ny, nz}; BoutMask mask{mesh, true}; @@ -150,7 +150,7 @@ TEST_F(MaskTest, CreateOnMeshWithValueFalse) { constexpr int nx{2}; constexpr int ny{3}; constexpr int nz{4}; - + FakeMesh mesh{nx, ny, nz}; BoutMask mask{mesh, false}; diff --git a/tests/unit/invert/laplace/test_laplace_cyclic.cxx b/tests/unit/invert/laplace/test_laplace_cyclic.cxx index d4b3cea8ad..a2f7a3a30a 100644 --- a/tests/unit/invert/laplace/test_laplace_cyclic.cxx +++ b/tests/unit/invert/laplace/test_laplace_cyclic.cxx @@ -6,16 +6,16 @@ #include #include "../../../../src/invert/laplace/impls/cyclic/cyclic_laplace.hxx" -#include "invert_laplace.hxx" +#include "bout/invert_laplace.hxx" #include "test_extras.hxx" #include "gtest/gtest.h" -#include "derivs.hxx" -#include "difops.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "options.hxx" -#include "vecops.hxx" +#include "bout/derivs.hxx" +#include "bout/difops.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" +#include "bout/vecops.hxx" #include "bout/griddata.hxx" #include "bout/mesh.hxx" @@ -51,7 +51,7 @@ class CyclicForwardOperator { bool inner_x_neumann, outer_x_neumann; // If false then use Dirichlet conditions void applyBoundaries(Field3D& newF, const Field3D& f) { - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_INNER_X")) { if (inner_x_neumann) { newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -59,7 +59,7 @@ class CyclicForwardOperator { } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { if (outer_x_neumann) { newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -90,12 +90,12 @@ class CyclicTest : public FakeMeshFixture, coef2.allocate(); coef3.allocate(); - BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion2D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; coef2[i] = x + y; } - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; BoutReal z = i.z() / (BoutReal)nz - 0.5; diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx index 261e7fff7f..1509fac2bb 100644 --- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx +++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx @@ -4,16 +4,16 @@ #include #include "../../../../src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx" -#include "invert_laplace.hxx" +#include "bout/invert_laplace.hxx" #include "test_extras.hxx" #include "gtest/gtest.h" -#include "derivs.hxx" -#include "difops.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "options.hxx" -#include "vecops.hxx" +#include "bout/derivs.hxx" +#include "bout/difops.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" +#include "bout/vecops.hxx" #include "bout/griddata.hxx" #include "bout/hypre_interface.hxx" #include "bout/mesh.hxx" @@ -59,7 +59,7 @@ class ForwardOperator { lower_y_neumann, upper_y_neumann; void applyBoundaries(Field3D& newF, Field3D& f) { - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_INNER_X")) { if (inner_x_neumann) { newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -67,7 +67,7 @@ class ForwardOperator { } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { if (outer_x_neumann) { newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -75,7 +75,7 @@ class ForwardOperator { } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { if (lower_y_neumann) { newF[i] = (f[i.yp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -83,7 +83,7 @@ class ForwardOperator { } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { if (upper_y_neumann) { newF[i] = (f[i] - f[i.ym()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -108,12 +108,12 @@ class LaplaceHypre3dTest coef2.allocate(); coef3.allocate(); - BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion2D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; coef2[i] = x + y; } - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; BoutReal z = i.z() / (BoutReal)nz - 0.5; @@ -167,7 +167,9 @@ TEST_P(LaplaceHypre3dTest, TestMatrixConstruction3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefA_2D) { @@ -179,7 +181,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefA_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefA_3D) { @@ -191,7 +195,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefA_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefC_2D) { @@ -204,7 +210,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefC_3D) { @@ -217,7 +225,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefC1_2D) { @@ -229,7 +239,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC1_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefC1_3D) { @@ -241,7 +253,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC1_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefC2_2D) { @@ -253,7 +267,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC2_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefC2_3D) { @@ -265,7 +281,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC2_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefD_2D) { @@ -277,7 +295,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefD_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefD_3D) { @@ -289,7 +309,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefD_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefEx_2D) { @@ -301,7 +323,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEx_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefEx_3D) { @@ -313,7 +337,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEx_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefEz_2D) { @@ -325,7 +351,9 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEz_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSetCoefEz_3D) { @@ -337,19 +365,25 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEz_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSolve3D) { Field3D expected = f3; const Field3D actual = solver.solve(forward(f3)); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSolve3DGuess) { Field3D expected = f3, guess = f3 * 1.01; const Field3D actual = solver.solve(forward(f3), guess); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + EXPECT_NEAR(expected[i], actual[i], tol); + } } TEST_P(LaplaceHypre3dTest, TestSolvePerp) { diff --git a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx index 7f80ba742c..63fe78897a 100644 --- a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx +++ b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx @@ -3,27 +3,27 @@ #include #include -#include "gtest/gtest.h" -#include "test_extras.hxx" -#include "invert_laplace.hxx" #include "../../../../src/invert/laplace/impls/petsc3damg/petsc3damg.hxx" +#include "bout/invert_laplace.hxx" +#include "test_extras.hxx" +#include "gtest/gtest.h" -#include "bout/mesh.hxx" +#include "bout/derivs.hxx" +#include "bout/difops.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/options.hxx" +#include "bout/vecops.hxx" #include "bout/griddata.hxx" -#include "options.hxx" -#include "field2d.hxx" -#include "field3d.hxx" -#include "derivs.hxx" -#include "difops.hxx" -#include "vecops.hxx" +#include "bout/mesh.hxx" #include "bout/petsc_interface.hxx" #if BOUT_HAS_PETSC /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -34,8 +34,8 @@ class ForwardOperator { public: ForwardOperator() {} ForwardOperator(bool xin_neumann, bool xout_neumann, bool ydown_neumann, - bool yup_neumann) : a(0.0), c1(1.0), c2(1.0), d(1.0), - ex(0.0), ez(0.0) { + bool yup_neumann) + : a(0.0), c1(1.0), c2(1.0), d(1.0), ex(0.0), ez(0.0) { coords = mesh->getCoordinates(CELL_CENTER); inner_x_neumann = xin_neumann; outer_x_neumann = xout_neumann; @@ -43,10 +43,10 @@ class ForwardOperator { upper_y_neumann = yup_neumann; } - const Field3D operator()(Field3D &f) { + const Field3D operator()(Field3D& f) { auto result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY") - + (Grad(f)*Grad(c2)-DDY(c2)*DDY(f)/coords->g_22)/c1 - + a*f + ex*DDX(f) + ez*DDZ(f); + + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f + + ex * DDX(f) + ez * DDZ(f); applyBoundaries(result, f); return result; } @@ -55,77 +55,75 @@ class ForwardOperator { Coordinates* coords; private: - bool inner_x_neumann, outer_x_neumann, // If false then use Dirichlet conditions - lower_y_neumann, upper_y_neumann; + bool inner_x_neumann, outer_x_neumann, // If false then use Dirichlet conditions + lower_y_neumann, upper_y_neumann; - void applyBoundaries(Field3D& newF, Field3D &f) { - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) { + void applyBoundaries(Field3D& newF, Field3D& f) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_INNER_X")) { if (inner_x_neumann) { - newF[i] = (f[i.xp()] - f[i])/ coords->dx[i] / sqrt(coords->g_11[i]); + newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { - newF[i] = 0.5 * (f[i] + f[i.xp()]); + newF[i] = 0.5 * (f[i] + f[i.xp()]); } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { if (outer_x_neumann) { - newF[i] = (f[i] - f[i.xm()])/ coords->dx[i] / sqrt(coords->g_11[i]); + newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { - newF[i] = 0.5 * (f[i.xm()] + f[i]); + newF[i] = 0.5 * (f[i.xm()] + f[i]); } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { if (lower_y_neumann) { - newF[i] = (f[i.yp()] - f[i])/ coords->dx[i] / sqrt(coords->g_11[i]); + newF[i] = (f[i.yp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { - newF[i] = 0.5 * (f[i] + f[i.yp()]); + newF[i] = 0.5 * (f[i] + f[i.yp()]); } } - BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { + BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { if (upper_y_neumann) { - newF[i] = (f[i] - f[i.ym()])/ coords->dx[i] / sqrt(coords->g_11[i]); + newF[i] = (f[i] - f[i.ym()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { - newF[i] = 0.5 * (f[i.ym()] + f[i]); + newF[i] = 0.5 * (f[i.ym()] + f[i]); } } } }; - -class Petsc3dAmgTest : public FakeMeshFixture, - public testing::WithParamInterface > { +class Petsc3dAmgTest + : public FakeMeshFixture, + public testing::WithParamInterface> { public: - WithQuietOutput info{output_info}, warn{output_warn}, progress{output_progress}, all{output}; - Petsc3dAmgTest() : FakeMeshFixture(), solver(getOptions(GetParam())) - { + WithQuietOutput info{output_info}, warn{output_warn}, progress{output_progress}, + all{output}; + Petsc3dAmgTest() : FakeMeshFixture(), solver(getOptions(GetParam())) { PetscErrorPrintf = PetscErrorPrintfNone; - int nx = mesh->GlobalNx, - ny = mesh->GlobalNy, - nz = mesh->GlobalNz; - static_cast(bout::globals::mesh)->setGridDataSource(new GridFromOptions(Options::getRoot())); + int nx = mesh->GlobalNx, ny = mesh->GlobalNy, nz = mesh->GlobalNz; + static_cast(bout::globals::mesh) + ->setGridDataSource(new GridFromOptions(Options::getRoot())); bout::globals::mesh->getCoordinates()->geometry(); f3.allocate(); coef2.allocate(); coef3.allocate(); - BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) { - BoutReal x = i.x()/(BoutReal)nx - 0.5; - BoutReal y = i.y()/(BoutReal)ny - 0.5; + BOUT_FOR (i, mesh->getRegion2D("RGN_ALL")) { + BoutReal x = i.x() / (BoutReal)nx - 0.5; + BoutReal y = i.y() / (BoutReal)ny - 0.5; coef2[i] = x + y; } - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { - BoutReal x = i.x()/(BoutReal)nx - 0.5; - BoutReal y = i.y()/(BoutReal)ny - 0.5; - BoutReal z = i.z()/(BoutReal)nz - 0.5; - f3[i] = 1e3*exp(-0.5*sqrt(x*x + y*y + z*z)/sigmasq); - coef3[i] = x + y + sin(2*3.14159265358979323846*z); + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + BoutReal x = i.x() / (BoutReal)nx - 0.5; + BoutReal y = i.y() / (BoutReal)ny - 0.5; + BoutReal z = i.z() / (BoutReal)nz - 0.5; + f3[i] = 1e3 * exp(-0.5 * sqrt(x * x + y * y + z * z) / sigmasq); + coef3[i] = x + y + sin(2 * 3.14159265358979323846 * z); } auto param = GetParam(); - forward = ForwardOperator(std::get<0>(param), std::get<1>(param), - std::get<2>(param), std::get<3>(param)); + forward = ForwardOperator(std::get<0>(param), std::get<1>(param), std::get<2>(param), + std::get<3>(param)); } ~Petsc3dAmgTest() { @@ -141,228 +139,228 @@ class Petsc3dAmgTest : public FakeMeshFixture, ForwardOperator forward; private: - static Options* getOptions(std::tuple param) { - Options *options = Options::getRoot()->getSection("laplace"); + Options* options = Options::getRoot()->getSection("laplace"); (*options)["type"] = "petsc3damg"; - (*options)["inner_boundary_flags"] = (std::get<0>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; - (*options)["outer_boundary_flags"] = (std::get<1>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; - (*options)["lower_boundary_flags"] = (std::get<2>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; - (*options)["upper_boundary_flags"] = (std::get<3>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; + (*options)["inner_boundary_flags"] = + (std::get<0>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; + (*options)["outer_boundary_flags"] = + (std::get<1>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; + (*options)["lower_boundary_flags"] = + (std::get<2>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; + (*options)["upper_boundary_flags"] = + (std::get<3>(param) ? INVERT_AC_GRAD : 0) + INVERT_RHS; (*options)["fourth_order"] = false; - (*options)["atol"] = tol/30; // Need to specify smaller than desired tolerance to - (*options)["rtol"] = tol/30; // ensure it is satisfied for every element. + (*options)["atol"] = tol / 30; // Need to specify smaller than desired tolerance to + (*options)["rtol"] = tol / 30; // ensure it is satisfied for every element. return options; } - }; INSTANTIATE_TEST_SUITE_P(LaplacePetsc3dAmgTest, Petsc3dAmgTest, - testing::Values(std::make_tuple(false, false, false, false), - std::make_tuple(false, false, false, true), - std::make_tuple(false, false, true, false), - std::make_tuple(false, true, false, false), - std::make_tuple(true, false, false, false))); - -TEST_P(Petsc3dAmgTest, TestMatrixConstruction3D){ - PetscMatrix &matrix = solver.getMatrix3D(); + testing::Values(std::make_tuple(false, false, false, false), + std::make_tuple(false, false, false, true), + std::make_tuple(false, false, true, false), + std::make_tuple(false, true, false, false), + std::make_tuple(true, false, false, false))); + +TEST_P(Petsc3dAmgTest, TestMatrixConstruction3D) { + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefA_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefA_2D) { solver.setCoefA(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.a = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefA_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefA_3D) { solver.setCoefA(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.a = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefC_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefC_2D) { solver.setCoefC(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.c1 = coef2; forward.c2 = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefC_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefC_3D) { solver.setCoefC(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.c1 = coef3; forward.c2 = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } - } -TEST_P(Petsc3dAmgTest, TestSetCoefC1_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefC1_2D) { solver.setCoefC1(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.c1 = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefC1_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefC1_3D) { solver.setCoefC1(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.c1 = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } - } -TEST_P(Petsc3dAmgTest, TestSetCoefC2_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefC2_2D) { solver.setCoefC2(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.c2 = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefC2_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefC2_3D) { solver.setCoefC2(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.c2 = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefD_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefD_2D) { solver.setCoefD(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.d = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefD_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefD_3D) { solver.setCoefD(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.d = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefEx_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefEx_2D) { solver.setCoefEx(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.ex = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefEx_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefEx_3D) { solver.setCoefEx(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.ex = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefEz_2D){ +TEST_P(Petsc3dAmgTest, TestSetCoefEz_2D) { solver.setCoefEz(coef2); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.ez = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSetCoefEz_3D){ +TEST_P(Petsc3dAmgTest, TestSetCoefEz_3D) { solver.setCoefEz(coef3); - PetscMatrix &matrix = solver.getMatrix3D(); + PetscMatrix& matrix = solver.getMatrix3D(); PetscVector vector(f3, solver.getIndexer()); forward.ez = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSolve3D){ +TEST_P(Petsc3dAmgTest, TestSolve3D) { Field3D expected = f3; const Field3D actual = solver.solve(forward(f3)); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSolve3DGuess){ - Field3D expected = f3, guess = f3*1.01; +TEST_P(Petsc3dAmgTest, TestSolve3DGuess) { + Field3D expected = f3, guess = f3 * 1.01; const Field3D actual = solver.solve(forward(f3), guess); - BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } -TEST_P(Petsc3dAmgTest, TestSolvePerp){ +TEST_P(Petsc3dAmgTest, TestSolvePerp) { FieldPerp f(1.0); EXPECT_THROW(solver.solve(f), BoutException); } diff --git a/tests/unit/invert/test_fft.cxx b/tests/unit/invert/test_fft.cxx index 046e81fc84..f8be568095 100644 --- a/tests/unit/invert/test_fft.cxx +++ b/tests/unit/invert/test_fft.cxx @@ -2,8 +2,8 @@ #include "gtest/gtest.h" -#include "dcomplex.hxx" -#include "fft.hxx" +#include "bout/dcomplex.hxx" +#include "bout/fft.hxx" #include "test_extras.hxx" #include "bout/array.hxx" #include "bout/constants.hxx" diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx index 53cd35eeae..49d7365e09 100644 --- a/tests/unit/mesh/data/test_gridfromoptions.cxx +++ b/tests/unit/mesh/data/test_gridfromoptions.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" -#include "options.hxx" -#include "output.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" #include "bout/constants.hxx" #include "bout/griddata.hxx" @@ -228,7 +228,8 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealXOffset) { std::vector result{}; std::vector expected{4., 5., 6., 7., 8., 9., 10., 11., 12.}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nx, 1, GridDataSource::Direction::X)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nx, 1, + GridDataSource::Direction::X)); EXPECT_EQ(result, expected); } @@ -240,7 +241,8 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealXMeshOffset) { mesh_from_options.OffsetY = 100; mesh_from_options.OffsetZ = 100; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nx, 0, GridDataSource::Direction::X)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nx, 0, + GridDataSource::Direction::X)); EXPECT_EQ(result, expected); } @@ -253,38 +255,50 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealXNone) { TEST_F(GridFromOptionsTest, GetVectorBoutRealY) { std::vector result{}; - std::vector expected{3., 3. + TWOPI, 3. + (2. * TWOPI), 3. + (3. * TWOPI), - 3. + (4. * TWOPI), 3. + (5. * TWOPI), 3. + (6. * TWOPI), - 3. + (7. * TWOPI), 3. + (8. * TWOPI), 3. + (9. * TWOPI), + std::vector expected{3., + 3. + TWOPI, + 3. + (2. * TWOPI), + 3. + (3. * TWOPI), + 3. + (4. * TWOPI), + 3. + (5. * TWOPI), + 3. + (6. * TWOPI), + 3. + (7. * TWOPI), + 3. + (8. * TWOPI), + 3. + (9. * TWOPI), 3. + (10. * TWOPI)}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", ny, 0, GridDataSource::Direction::Y)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", ny, 0, + GridDataSource::Direction::Y)); EXPECT_EQ(result, expected); } TEST_F(GridFromOptionsTest, GetVectorBoutRealYOffset) { std::vector result{}; - std::vector expected{3. + TWOPI, 3. + (2. * TWOPI), 3. + (3. * TWOPI), - 3. + (4. * TWOPI), 3. + (5. * TWOPI), 3. + (6. * TWOPI), - 3. + (7. * TWOPI), 3. + (8. * TWOPI), 3. + (9. * TWOPI), + std::vector expected{3. + TWOPI, 3. + (2. * TWOPI), 3. + (3. * TWOPI), + 3. + (4. * TWOPI), 3. + (5. * TWOPI), 3. + (6. * TWOPI), + 3. + (7. * TWOPI), 3. + (8. * TWOPI), 3. + (9. * TWOPI), 3. + (10. * TWOPI), 3. + (11. * TWOPI)}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", ny, 1, GridDataSource::Direction::Y)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", ny, 1, + GridDataSource::Direction::Y)); EXPECT_EQ(result, expected); } TEST_F(GridFromOptionsTest, GetVectorBoutRealYMeshOffset) { std::vector result{}; - std::vector expected{3. - TWOPI, 3., 3. + TWOPI, 3. + (2. * TWOPI), - 3. + (3. * TWOPI), 3. + (4. * TWOPI), 3. + (5. * TWOPI), - 3. + (6. * TWOPI), 3. + (7. * TWOPI), 3. + (8. * TWOPI), + std::vector expected{3. - TWOPI, 3., + 3. + TWOPI, 3. + (2. * TWOPI), + 3. + (3. * TWOPI), 3. + (4. * TWOPI), + 3. + (5. * TWOPI), 3. + (6. * TWOPI), + 3. + (7. * TWOPI), 3. + (8. * TWOPI), 3. + (9. * TWOPI)}; mesh_from_options.OffsetX = 100; mesh_from_options.OffsetY = 1; mesh_from_options.OffsetZ = 100; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", ny, 0, GridDataSource::Direction::Y)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", ny, 0, + GridDataSource::Direction::Y)); EXPECT_EQ(result, expected); } @@ -297,13 +311,11 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealYNone) { TEST_F(GridFromOptionsTest, GetVectorBoutRealZ) { std::vector result{}; - std::vector expected{3., - 3. + (1. * TWOPI / nz), - 3. + (2. * TWOPI / nz), - 3. + (3. * TWOPI / nz), - 3. + (4. * TWOPI / nz)}; + std::vector expected{3., 3. + (1. * TWOPI / nz), 3. + (2. * TWOPI / nz), + 3. + (3. * TWOPI / nz), 3. + (4. * TWOPI / nz)}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 0, GridDataSource::Direction::Z)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 0, + GridDataSource::Direction::Z)); EXPECT_EQ(result, expected); } @@ -313,21 +325,22 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealZOffset) { 3. + (3. * TWOPI / nz), 3. + (4. * TWOPI / nz), 3. + (5. * TWOPI / nz)}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 1, GridDataSource::Direction::Z)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 1, + GridDataSource::Direction::Z)); EXPECT_EQ(result, expected); } TEST_F(GridFromOptionsTest, GetVectorBoutRealZMeshOffset) { std::vector result{}; - std::vector expected{3. + (-1. * TWOPI / nz), 3., - 3. + (1. * TWOPI / nz), 3. + (2. * TWOPI / nz), - 3. + (3. * TWOPI / nz)}; + std::vector expected{3. + (-1. * TWOPI / nz), 3., 3. + (1. * TWOPI / nz), + 3. + (2. * TWOPI / nz), 3. + (3. * TWOPI / nz)}; mesh_from_options.OffsetX = 100; mesh_from_options.OffsetY = 100; mesh_from_options.OffsetZ = 1; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 0, GridDataSource::Direction::Z)); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 0, + GridDataSource::Direction::Z)); EXPECT_EQ(result, expected); } @@ -385,11 +398,16 @@ TEST_F(GridFromOptionsTest, CoordinatesXlowInterp) { mesh_from_options.communicate(expected_xlow); - EXPECT_TRUE(IsFieldEqual(coords->g11, expected_xlow + 5., "RGN_NOBNDRY", this_tolerance)); - EXPECT_TRUE(IsFieldEqual(coords->g22, expected_xlow + 4., "RGN_NOBNDRY", this_tolerance)); - EXPECT_TRUE(IsFieldEqual(coords->g33, expected_xlow + 3., "RGN_NOBNDRY", this_tolerance)); - EXPECT_TRUE(IsFieldEqual(coords->g12, expected_xlow + 2., "RGN_NOBNDRY", this_tolerance)); - EXPECT_TRUE(IsFieldEqual(coords->g13, expected_xlow + 1., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g11, expected_xlow + 5., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g22, expected_xlow + 4., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g33, expected_xlow + 3., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g12, expected_xlow + 2., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g13, expected_xlow + 1., "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(IsFieldEqual(coords->g23, expected_xlow, "RGN_NOBNDRY", this_tolerance)); } @@ -415,7 +433,8 @@ TEST_F(GridFromOptionsTest, CoordinatesXlowRead) { Field2D expected_xlow = makeField( [](Field2D::ind_type& index) { - return (nx - index.x() + 0.5) + (TWOPI * index.y()) + (TWOPI * index.z() / nz) + 3; + return (nx - index.x() + 0.5) + (TWOPI * index.y()) + (TWOPI * index.z() / nz) + + 3; }, &mesh_from_options); @@ -443,7 +462,7 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowInterp) { // make the mesh have boundaries to avoid NaNs in guard cells after interpolating mesh_from_options.createBoundaries(); - auto *coords = mesh_from_options.getCoordinates(CELL_YLOW); + auto* coords = mesh_from_options.getCoordinates(CELL_YLOW); Field2D expected_ylow = makeField( [](Field2D::ind_type& index) { @@ -453,15 +472,20 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowInterp) { mesh_from_options.communicate(expected_ylow); - EXPECT_TRUE(IsFieldEqual(coords->g11, expected_ylow + 5., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g11, expected_ylow + 5., "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(coords->g11.getLocation() == CELL_YLOW); - EXPECT_TRUE(IsFieldEqual(coords->g22, expected_ylow + 4., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g22, expected_ylow + 4., "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(coords->g22.getLocation() == CELL_YLOW); - EXPECT_TRUE(IsFieldEqual(coords->g33, expected_ylow + 3., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g33, expected_ylow + 3., "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(coords->g33.getLocation() == CELL_YLOW); - EXPECT_TRUE(IsFieldEqual(coords->g12, expected_ylow + 2., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g12, expected_ylow + 2., "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(coords->g12.getLocation() == CELL_YLOW); - EXPECT_TRUE(IsFieldEqual(coords->g13, expected_ylow + 1., "RGN_NOBNDRY", this_tolerance)); + EXPECT_TRUE( + IsFieldEqual(coords->g13, expected_ylow + 1., "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(coords->g13.getLocation() == CELL_YLOW); EXPECT_TRUE(IsFieldEqual(coords->g23, expected_ylow, "RGN_NOBNDRY", this_tolerance)); EXPECT_TRUE(coords->g23.getLocation() == CELL_YLOW); @@ -492,7 +516,8 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowRead) { Field2D expected_ylow = makeField( [](Field2D::ind_type& index) { - return index.x() + (TWOPI * (ny - index.y() + 0.5)) + (TWOPI * index.z() / nz) + 3; + return index.x() + (TWOPI * (ny - index.y() + 0.5)) + (TWOPI * index.z() / nz) + + 3; }, &mesh_from_options); diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx index b177d75267..d60e1cc0c7 100644 --- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx +++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx @@ -2,7 +2,7 @@ #include "gtest/gtest.h" -#include "fft.hxx" +#include "bout/fft.hxx" #include "test_extras.hxx" #if BOUT_HAS_FFTW @@ -124,8 +124,7 @@ TEST_F(ShiftedMetricTest, ToFieldAligned) { Field3D result = toFieldAligned(input); - EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", - FFTTolerance)); + EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", FFTTolerance)); EXPECT_TRUE(IsFieldEqual(fromFieldAligned(result), input)); EXPECT_TRUE(areFieldsCompatible(result, expected)); EXPECT_FALSE(areFieldsCompatible(result, input)); @@ -166,10 +165,8 @@ TEST_F(ShiftedMetricTest, FromFieldAligned) { Field3D result = fromFieldAligned(input); // Loosen tolerance a bit due to FFTs - EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", - FFTTolerance)); - EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), input, - "RGN_ALL", FFTTolerance)); + EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", FFTTolerance)); + EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), input, "RGN_ALL", FFTTolerance)); EXPECT_TRUE(areFieldsCompatible(result, expected)); EXPECT_FALSE(areFieldsCompatible(result, input)); } @@ -264,8 +261,8 @@ TEST_F(ShiftedMetricTest, FromFieldAlignedFieldPerp) { // FieldPerp does not have a getRegion2D() method. Values are never set in // the x-guard or x-boundary cells EXPECT_TRUE(IsFieldEqual(result, sliceXZ(expected, 4), "RGN_NOBNDRY", FFTTolerance)); - EXPECT_TRUE(IsFieldEqual(toFieldAligned(result, "RGN_NOX"), sliceXZ(input, 4), "RGN_NOBNDRY", - FFTTolerance)); + EXPECT_TRUE(IsFieldEqual(toFieldAligned(result, "RGN_NOX"), sliceXZ(input, 4), + "RGN_NOBNDRY", FFTTolerance)); EXPECT_TRUE(areFieldsCompatible(result, sliceXZ(expected, 4))); EXPECT_FALSE(areFieldsCompatible(result, sliceXZ(input, 4))); } diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx index 589ef971b1..b552f7629e 100644 --- a/tests/unit/mesh/test_boundary_factory.cxx +++ b/tests/unit/mesh/test_boundary_factory.cxx @@ -1,15 +1,15 @@ #include "gtest/gtest.h" -#include "boundary_factory.hxx" -#include "boundary_op.hxx" -#include "boundary_region.hxx" +#include "bout/boundary_factory.hxx" +#include "bout/boundary_op.hxx" +#include "bout/boundary_region.hxx" #include "test_extras.hxx" /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -18,9 +18,9 @@ using namespace bout::globals; class TestBoundary : public BoundaryOp { public: - BoundaryOp *clone(BoundaryRegion *UNUSED(region), const std::list &args, - const std::map &keywords) override { - auto *testboundary = new TestBoundary(); + BoundaryOp* clone(BoundaryRegion* UNUSED(region), const std::list& args, + const std::map& keywords) override { + auto* testboundary = new TestBoundary(); testboundary->args = args; testboundary->keywords = keywords; return testboundary; @@ -28,8 +28,8 @@ class TestBoundary : public BoundaryOp { std::list args; std::map keywords; - void apply(Field2D &UNUSED(f)) override {} - void apply(Field3D &UNUSED(f)) override {} + void apply(Field2D& UNUSED(f)) override {} + void apply(Field3D& UNUSED(f)) override {} }; class BoundaryFactoryTest : public ::testing::Test { diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx index 0d57eeb42d..3b3cd70538 100644 --- a/tests/unit/mesh/test_boutmesh.cxx +++ b/tests/unit/mesh/test_boutmesh.cxx @@ -2,8 +2,8 @@ #include "gtest/gtest.h" #include "../src/mesh/impls/bout/boutmesh.hxx" -#include "options.hxx" -#include "output.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" #include "bout/griddata.hxx" #include "test_extras.hxx" @@ -2149,7 +2149,8 @@ TEST(BoutMeshTest, GetPossibleBoundariesDND) { WithQuietOutput warn{output_warn}; BoutMeshExposer mesh_DND_1x6(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 1})); - BoutMeshExposer mesh_DND_32x64(createDisconnectedDoubleNull({12, 3, 1, 1, 32, 64, 0, 4})); + BoutMeshExposer mesh_DND_32x64( + createDisconnectedDoubleNull({12, 3, 1, 1, 32, 64, 0, 4})); std::set boundaries{"core", "pf", "sol", "upper_target", "lower_target"}; diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx index 9d766f65b6..83c285de5c 100644 --- a/tests/unit/mesh/test_coordinates.cxx +++ b/tests/unit/mesh/test_coordinates.cxx @@ -1,10 +1,10 @@ #include "gtest/gtest.h" +#include "bout/output.hxx" #include "bout/build_config.hxx" -#include "bout/coordinates.hxx" #include "bout/constants.hxx" +#include "bout/coordinates.hxx" #include "bout/mesh.hxx" -#include "output.hxx" #include "test_extras.hxx" @@ -27,24 +27,24 @@ constexpr BoutReal default_dz{TWOPI / CoordinatesTest::nz}; TEST_F(CoordinatesTest, ZLength) { Coordinates coords{mesh, - FieldMetric{1.0}, // dx - FieldMetric{1.0}, // dy - FieldMetric{1.0}, // dz - FieldMetric{1.0}, // J - FieldMetric{1.0}, // Bxy - FieldMetric{1.0}, // g11 - FieldMetric{1.0}, // g22 - FieldMetric{1.0}, // g33 - FieldMetric{0.0}, // g12 - FieldMetric{0.0}, // g13 - FieldMetric{0.0}, // g23 - FieldMetric{1.0}, // g_11 - FieldMetric{1.0}, // g_22 - FieldMetric{1.0}, // g_23 - FieldMetric{0.0}, // g_12 - FieldMetric{0.0}, // g_13 - FieldMetric{0.0}, // g_23 - FieldMetric{0.0}, // ShiftTorsion + FieldMetric{1.0}, // dx + FieldMetric{1.0}, // dy + FieldMetric{1.0}, // dz + FieldMetric{1.0}, // J + FieldMetric{1.0}, // Bxy + FieldMetric{1.0}, // g11 + FieldMetric{1.0}, // g22 + FieldMetric{1.0}, // g33 + FieldMetric{0.0}, // g12 + FieldMetric{0.0}, // g13 + FieldMetric{0.0}, // g23 + FieldMetric{1.0}, // g_11 + FieldMetric{1.0}, // g_22 + FieldMetric{1.0}, // g_23 + FieldMetric{0.0}, // g_12 + FieldMetric{0.0}, // g_13 + FieldMetric{0.0}, // g_23 + FieldMetric{0.0}, // ShiftTorsion FieldMetric{0.0}}; // IntShiftTorsion // No call to Coordinates::geometry() needed here @@ -60,24 +60,24 @@ TEST_F(CoordinatesTest, ZLength3D) { makeField([](const Ind2D& i) -> BoutReal { return i.x() + i.y(); }); Coordinates coords{mesh, - FieldMetric{1.0}, // dx - FieldMetric{1.0}, // dy - dz, // dz - FieldMetric{1.0}, // J - FieldMetric{1.0}, // Bxy - FieldMetric{1.0}, // g11 - FieldMetric{1.0}, // g22 - FieldMetric{1.0}, // g33 - FieldMetric{0.0}, // g12 - FieldMetric{0.0}, // g13 - FieldMetric{0.0}, // g23 - FieldMetric{1.0}, // g_11 - FieldMetric{1.0}, // g_22 - FieldMetric{1.0}, // g_23 - FieldMetric{0.0}, // g_12 - FieldMetric{0.0}, // g_13 - FieldMetric{0.0}, // g_23 - FieldMetric{0.0}, // ShiftTorsion + FieldMetric{1.0}, // dx + FieldMetric{1.0}, // dy + dz, // dz + FieldMetric{1.0}, // J + FieldMetric{1.0}, // Bxy + FieldMetric{1.0}, // g11 + FieldMetric{1.0}, // g22 + FieldMetric{1.0}, // g33 + FieldMetric{0.0}, // g12 + FieldMetric{0.0}, // g13 + FieldMetric{0.0}, // g23 + FieldMetric{1.0}, // g_11 + FieldMetric{1.0}, // g_22 + FieldMetric{1.0}, // g_23 + FieldMetric{0.0}, // g_12 + FieldMetric{0.0}, // g_13 + FieldMetric{0.0}, // g_23 + FieldMetric{0.0}, // ShiftTorsion FieldMetric{0.0}}; // IntShiftTorsion // No call to Coordinates::geometry() needed here @@ -87,24 +87,24 @@ TEST_F(CoordinatesTest, ZLength3D) { TEST_F(CoordinatesTest, Jacobian) { Coordinates coords{mesh, - FieldMetric{1.0}, // dx - FieldMetric{1.0}, // dy - FieldMetric{1.0}, // dz - FieldMetric{1.0}, // J - FieldMetric{1.0}, // Bxy - FieldMetric{1.0}, // g11 - FieldMetric{1.0}, // g22 - FieldMetric{1.0}, // g33 - FieldMetric{0.0}, // g12 - FieldMetric{0.0}, // g13 - FieldMetric{0.0}, // g23 - FieldMetric{1.0}, // g_11 - FieldMetric{1.0}, // g_22 - FieldMetric{1.0}, // g_23 - FieldMetric{0.0}, // g_12 - FieldMetric{0.0}, // g_13 - FieldMetric{0.0}, // g_23 - FieldMetric{0.0}, // ShiftTorsion + FieldMetric{1.0}, // dx + FieldMetric{1.0}, // dy + FieldMetric{1.0}, // dz + FieldMetric{1.0}, // J + FieldMetric{1.0}, // Bxy + FieldMetric{1.0}, // g11 + FieldMetric{1.0}, // g22 + FieldMetric{1.0}, // g33 + FieldMetric{0.0}, // g12 + FieldMetric{0.0}, // g13 + FieldMetric{0.0}, // g23 + FieldMetric{1.0}, // g_11 + FieldMetric{1.0}, // g_22 + FieldMetric{1.0}, // g_23 + FieldMetric{0.0}, // g_12 + FieldMetric{0.0}, // g_13 + FieldMetric{0.0}, // g_23 + FieldMetric{0.0}, // ShiftTorsion FieldMetric{0.0}}; // IntShiftTorsion // No call to Coordinates::geometry() needed here @@ -118,24 +118,24 @@ TEST_F(CoordinatesTest, Jacobian) { // #if not(BOUT_USE_METRIC_3D) TEST_F(CoordinatesTest, CalcContravariant) { Coordinates coords{mesh, - FieldMetric{1.0}, // dx - FieldMetric{1.0}, // dy - FieldMetric{1.0}, // dz - FieldMetric{0.0}, // J - FieldMetric{0.0}, // Bxy - FieldMetric{1.0}, // g11 - FieldMetric{1.0}, // g22 - FieldMetric{1.0}, // g33 - FieldMetric{0.0}, // g12 - FieldMetric{0.0}, // g13 - FieldMetric{0.0}, // g23 - FieldMetric{0.0}, // g_11 - FieldMetric{0.0}, // g_22 - FieldMetric{0.0}, // g_23 - FieldMetric{0.0}, // g_12 - FieldMetric{0.0}, // g_13 - FieldMetric{0.0}, // g_23 - FieldMetric{0.0}, // ShiftTorsion + FieldMetric{1.0}, // dx + FieldMetric{1.0}, // dy + FieldMetric{1.0}, // dz + FieldMetric{0.0}, // J + FieldMetric{0.0}, // Bxy + FieldMetric{1.0}, // g11 + FieldMetric{1.0}, // g22 + FieldMetric{1.0}, // g33 + FieldMetric{0.0}, // g12 + FieldMetric{0.0}, // g13 + FieldMetric{0.0}, // g23 + FieldMetric{0.0}, // g_11 + FieldMetric{0.0}, // g_22 + FieldMetric{0.0}, // g_23 + FieldMetric{0.0}, // g_12 + FieldMetric{0.0}, // g_13 + FieldMetric{0.0}, // g_23 + FieldMetric{0.0}, // ShiftTorsion FieldMetric{0.0}}; // IntShiftTorsion // No call to Coordinates::geometry() needed here @@ -153,24 +153,24 @@ TEST_F(CoordinatesTest, CalcContravariant) { TEST_F(CoordinatesTest, CalcCovariant) { Coordinates coords{mesh, - FieldMetric{1.0}, // dx - FieldMetric{1.0}, // dy - FieldMetric{1.0}, // dz - FieldMetric{0.0}, // J - FieldMetric{0.0}, // Bxy - FieldMetric{0.0}, // g11 - FieldMetric{0.0}, // g22 - FieldMetric{0.0}, // g33 - FieldMetric{0.0}, // g12 - FieldMetric{0.0}, // g13 - FieldMetric{0.0}, // g23 - FieldMetric{1.0}, // g_11 - FieldMetric{1.0}, // g_22 - FieldMetric{1.0}, // g_23 - FieldMetric{0.0}, // g_12 - FieldMetric{0.0}, // g_13 - FieldMetric{0.0}, // g_23 - FieldMetric{0.0}, // ShiftTorsion + FieldMetric{1.0}, // dx + FieldMetric{1.0}, // dy + FieldMetric{1.0}, // dz + FieldMetric{0.0}, // J + FieldMetric{0.0}, // Bxy + FieldMetric{0.0}, // g11 + FieldMetric{0.0}, // g22 + FieldMetric{0.0}, // g33 + FieldMetric{0.0}, // g12 + FieldMetric{0.0}, // g13 + FieldMetric{0.0}, // g23 + FieldMetric{1.0}, // g_11 + FieldMetric{1.0}, // g_22 + FieldMetric{1.0}, // g_23 + FieldMetric{0.0}, // g_12 + FieldMetric{0.0}, // g_13 + FieldMetric{0.0}, // g_23 + FieldMetric{0.0}, // ShiftTorsion FieldMetric{0.0}}; // IntShiftTorsion // No call to Coordinates::geometry() needed here @@ -250,7 +250,8 @@ TEST_F(CoordinatesTest, SmallMeshSpacing) { TEST_F(CoordinatesTest, ConstructWithDiagonalContravariantMetric) { static_cast(bout::globals::mesh) - ->setGridDataSource(new FakeGridDataSource({{"g11", 2.0}, {"g22", 3.2}, {"g33", 42}})); + ->setGridDataSource( + new FakeGridDataSource({{"g11", 2.0}, {"g22", 3.2}, {"g33", 42}})); output_info.disable(); output_warn.disable(); @@ -273,9 +274,9 @@ TEST_F(CoordinatesTest, ConstructWithDiagonalContravariantMetric) { // Covariant metric should be inverse // Note: Not calculated in corners - EXPECT_TRUE(IsFieldEqual(coords.g_11, 1./2.0, "RGN_NOCORNERS")); - EXPECT_TRUE(IsFieldEqual(coords.g_22, 1./3.2, "RGN_NOCORNERS")); - EXPECT_TRUE(IsFieldEqual(coords.g_33, 1./42, "RGN_NOCORNERS")); + EXPECT_TRUE(IsFieldEqual(coords.g_11, 1. / 2.0, "RGN_NOCORNERS")); + EXPECT_TRUE(IsFieldEqual(coords.g_22, 1. / 3.2, "RGN_NOCORNERS")); + EXPECT_TRUE(IsFieldEqual(coords.g_33, 1. / 42, "RGN_NOCORNERS")); EXPECT_TRUE(IsFieldEqual(coords.J, 1. / sqrt(2.0 * 3.2 * 42), "RGN_NOCORNERS")); EXPECT_TRUE(IsFieldEqual(coords.Bxy, sqrt(2.0 * 42), "RGN_NOCORNERS", 1e-10)); diff --git a/tests/unit/mesh/test_interpolation.cxx b/tests/unit/mesh/test_interpolation.cxx index 94bd181eab..1670c50692 100644 --- a/tests/unit/mesh/test_interpolation.cxx +++ b/tests/unit/mesh/test_interpolation.cxx @@ -1,27 +1,27 @@ #include "gtest/gtest.h" -#include "bout/mesh.hxx" -#include "boutexception.hxx" -#include "interpolation.hxx" -#include "output.hxx" +#include "bout/boutexception.hxx" +#include "bout/interpolation.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" +#include "bout/mesh.hxx" ////// delete these +#include "bout/boutexception.hxx" +#include "bout/field3d.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" -#include "boutexception.hxx" -#include "field3d.hxx" -#include "unused.hxx" -#include "utils.hxx" #include #include #include /////// /// Global mesh -namespace bout{ -namespace globals{ -extern Mesh *mesh; +namespace bout { +namespace globals { +extern Mesh* mesh; } // namespace globals } // namespace bout @@ -63,16 +63,19 @@ class Field3DInterpToTest : public ::testing::Test { // We need Coordinates so a parallel transform is available as // FieldFactory::create3D wants to un-field-align the result - for (const auto& location - : std::list{CELL_CENTRE, CELL_XLOW, CELL_YLOW, CELL_ZLOW}) { + for (const auto& location : + std::list{CELL_CENTRE, CELL_XLOW, CELL_YLOW, CELL_ZLOW}) { static_cast(mesh)->setCoordinates(nullptr, location); - static_cast(mesh)->setCoordinates(std::make_shared( - mesh, Field2D{1.0, mesh}, Field2D{1.0, mesh}, BoutReal{1.0}, Field2D{1.0, mesh}, - Field2D{0.0, mesh}, Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{1.0, mesh}, - Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{1.0, mesh}, - Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}, - Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}), + static_cast(mesh)->setCoordinates( + std::make_shared( + mesh, Field2D{1.0, mesh}, Field2D{1.0, mesh}, BoutReal{1.0}, + Field2D{1.0, mesh}, Field2D{0.0, mesh}, Field2D{1.0, mesh}, + Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{0.0, mesh}, + Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{1.0, mesh}, + Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{0.0, mesh}, + Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}, + Field2D{0.0, mesh}), location); // No call to Coordinates::geometry() needed here mesh->getCoordinates(location)->setParallelTransform( @@ -307,16 +310,19 @@ class Field2DInterpToTest : public ::testing::Test { // We need Coordinates so a parallel transform is available as // FieldFactory::create3D wants to un-field-align the result - for (const auto& location - : std::list{CELL_CENTRE, CELL_XLOW, CELL_YLOW, CELL_ZLOW}) { + for (const auto& location : + std::list{CELL_CENTRE, CELL_XLOW, CELL_YLOW, CELL_ZLOW}) { static_cast(mesh)->setCoordinates(nullptr, location); - static_cast(mesh)->setCoordinates(std::make_shared( - mesh, Field2D{1.0, mesh}, Field2D{1.0, mesh}, BoutReal{1.0}, Field2D{1.0, mesh}, - Field2D{0.0, mesh}, Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{1.0, mesh}, - Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{1.0, mesh}, - Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}, - Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}), + static_cast(mesh)->setCoordinates( + std::make_shared( + mesh, Field2D{1.0, mesh}, Field2D{1.0, mesh}, BoutReal{1.0}, + Field2D{1.0, mesh}, Field2D{0.0, mesh}, Field2D{1.0, mesh}, + Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{0.0, mesh}, + Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{1.0, mesh}, + Field2D{1.0, mesh}, Field2D{1.0, mesh}, Field2D{0.0, mesh}, + Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh}, + Field2D{0.0, mesh}), location); // No call to Coordinates::geometry() needed here mesh->getCoordinates(location)->setParallelTransform( diff --git a/tests/unit/mesh/test_mesh.cxx b/tests/unit/mesh/test_mesh.cxx index 2ed6c267c9..787831dd32 100644 --- a/tests/unit/mesh/test_mesh.cxx +++ b/tests/unit/mesh/test_mesh.cxx @@ -1,10 +1,10 @@ -#include "gtest/gtest.h" #include "gmock/gmock.h" +#include "gtest/gtest.h" +#include "bout/boutexception.hxx" +#include "bout/output.hxx" #include "bout/mesh.hxx" #include "bout/region.hxx" -#include "boutexception.hxx" -#include "output.hxx" #include "test_extras.hxx" @@ -159,7 +159,7 @@ TEST_F(MeshTest, MapInd3DTo2D) { TEST_F(MeshTest, IndPerpTo3D) { std::vector globalInds = {0, 1, 49, 50, 98, 99}; - for (const auto &i : globalInds) { + for (const auto& i : globalInds) { const auto tmp3D = Ind3D(i, ny, nz); const auto tmpPerp = IndPerp(tmp3D.x() * nz + tmp3D.z(), 1, nz); @@ -177,8 +177,8 @@ TEST_F(MeshTest, Ind3DToPerp) { 11, 12, 13, 14, 15, 16, 17, 18, 19, 20}; std::vector jyVals{0, 1, 2, 3, 4}; - for (const auto &jy : jyVals) { - for (const auto &i : perpInds) { + for (const auto& jy : jyVals) { + for (const auto& i : perpInds) { const auto tmpPerp = IndPerp(i, 1, nz); const auto tmp3D = Ind3D(tmpPerp.z() + nz * (jy + ny * tmpPerp.x()), ny, nz); @@ -287,7 +287,7 @@ TEST_F(MeshTest, MsgLen) { Field2D f2D_1(0., &localmesh); Field2D f2D_2(0., &localmesh); - std::vector var_list {&f3D_1, &f2D_1, &f3D_2, &f2D_2}; + std::vector var_list{&f3D_1, &f2D_1, &f3D_2, &f2D_2}; const int len = localmesh.msg_len(var_list, 0, nx, 0, ny); diff --git a/tests/unit/solver/test_solver.cxx b/tests/unit/solver/test_solver.cxx index 68d7040cb1..f99380e4dc 100644 --- a/tests/unit/solver/test_solver.cxx +++ b/tests/unit/solver/test_solver.cxx @@ -1,9 +1,9 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" -#include "boutexception.hxx" -#include "field2d.hxx" -#include "field3d.hxx" +#include "bout/boutexception.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" #include "test_extras.hxx" #include "test_fakesolver.hxx" #include "bout/physicsmodel.hxx" @@ -59,13 +59,11 @@ class MockPhysicsModel : public PhysicsModel { return static_cast(time + gamma + delta); } - int jacobian(BoutReal time) { - return static_cast(time); - } + int jacobian(BoutReal time) { return static_cast(time); } // Expose some protected methods to aid testing - using PhysicsModel::setPrecon; using PhysicsModel::setJacobian; + using PhysicsModel::setPrecon; using PhysicsModel::setSplitOperator; }; @@ -1199,4 +1197,3 @@ TEST_F(SolverTest, SolveFixDefaultTimestepLarger) { EXPECT_EQ(default_timestep.last_called, 9); EXPECT_EQ(smaller_timestep.last_called, 99); } - diff --git a/tests/unit/solver/test_solverfactory.cxx b/tests/unit/solver/test_solverfactory.cxx index 8a70e68d5c..694a4da3ff 100644 --- a/tests/unit/solver/test_solverfactory.cxx +++ b/tests/unit/solver/test_solverfactory.cxx @@ -1,6 +1,6 @@ #include "gtest/gtest.h" -#include "boutexception.hxx" +#include "bout/boutexception.hxx" #include "test_extras.hxx" #include "test_fakesolver.hxx" #include "bout/solver.hxx" diff --git a/tests/unit/src/test_bout++.cxx b/tests/unit/src/test_bout++.cxx index 33e701aa68..ec4de49e9c 100644 --- a/tests/unit/src/test_bout++.cxx +++ b/tests/unit/src/test_bout++.cxx @@ -2,10 +2,10 @@ #include "gtest/gtest.h" -#include "bout.hxx" -#include "boutexception.hxx" +#include "bout/bout.hxx" +#include "bout/boutexception.hxx" #include "test_extras.hxx" -#include "utils.hxx" +#include "bout/utils.hxx" #include "bout/version.hxx" #include @@ -199,7 +199,6 @@ TEST(ParseCommandLineArgs, VerbosityWithDataDir) { EXPECT_EQ(args.argv, expected_argv); } - TEST(ParseCommandLineArgs, VerbosityLong) { std::vector v_args{"test", "--verbose"}; auto v_args_copy = v_args; @@ -425,5 +424,6 @@ TEST(BoutInitialiseFunctions, SavePIDtoFile) { std::remove(filename.c_str()); - EXPECT_THROW(bout::experimental::savePIDtoFile("/does/likely/not/exists", 2), BoutException); + EXPECT_THROW(bout::experimental::savePIDtoFile("/does/likely/not/exists", 2), + BoutException); } diff --git a/tests/unit/sys/test_boutexception.cxx b/tests/unit/sys/test_boutexception.cxx index 9079657894..3a36ceb740 100644 --- a/tests/unit/sys/test_boutexception.cxx +++ b/tests/unit/sys/test_boutexception.cxx @@ -1,8 +1,8 @@ #include "bout/build_config.hxx" -#include "gtest/gtest.h" -#include "boutexception.hxx" +#include "bout/boutexception.hxx" #include "test_extras.hxx" +#include "gtest/gtest.h" #include #include @@ -15,23 +15,22 @@ TEST(BoutExceptionTest, What) { std::string test_message{"Test message"}; try { throw BoutException(test_message); - } catch (const BoutException &e) { + } catch (const BoutException& e) { EXPECT_EQ(e.what(), test_message); } try { throw BoutException("this is {}", "second"); - } catch (const BoutException &e) { + } catch (const BoutException& e) { std::string message(e.what()); EXPECT_EQ(message, "this is second"); } } - TEST(BoutExceptionTest, GetBacktrace) { std::string test_message{"Test message"}; try { throw BoutException(test_message); - } catch (const BoutException &e) { + } catch (const BoutException& e) { std::string expected_1{"[bt] #1"}; std::string expected_2{"serial_tests"}; #if BOUT_USE_BACKTRACE @@ -46,7 +45,6 @@ TEST(BoutExceptionTest, GetBacktrace) { } } - TEST(BoutRhsFailTest, ThrowCorrect) { EXPECT_THROW(throw BoutRhsFail("RHS Fail test"), BoutRhsFail); } diff --git a/tests/unit/sys/test_expressionparser.cxx b/tests/unit/sys/test_expressionparser.cxx index 4b9ff807b5..fd297d7b6a 100644 --- a/tests/unit/sys/test_expressionparser.cxx +++ b/tests/unit/sys/test_expressionparser.cxx @@ -1,9 +1,9 @@ #include "gtest/gtest.h" -#include "bout/sys/expressionparser.hxx" -#include "bout_types.hxx" -#include "unused.hxx" +#include "bout/bout_types.hxx" #include "test_extras.hxx" +#include "bout/unused.hxx" +#include "bout/sys/expressionparser.hxx" #include @@ -13,8 +13,8 @@ using bout::generator::Context; // protected parseString as a public method class ExpressionParserSubClass : public ExpressionParser { public: - using ExpressionParser::parseString; using ExpressionParser::fuzzyFind; + using ExpressionParser::parseString; }; class ExpressionParserTest : public ::testing::Test { @@ -75,9 +75,7 @@ class IncrementGenerator : public FieldGenerator { return std::make_shared(args.front()); } - BoutReal generate(const Context& ctx) override { - return gen->generate(ctx) + 1; - } + BoutReal generate(const Context& ctx) override { return gen->generate(ctx) + 1; } std::string str() const override { return std::string{"increment(" + gen->str() + ")"}; } @@ -102,9 +100,7 @@ class NullaryGenerator : public FieldGenerator { return std::make_shared(); } - BoutReal generate(const Context &) override { - return 4.0; - } + BoutReal generate(const Context&) override { return 4.0; } }; TEST_F(ExpressionParserTest, Parse2) { @@ -115,7 +111,7 @@ TEST_F(ExpressionParserTest, Parse2) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), 2); } } @@ -131,7 +127,7 @@ TEST_F(ExpressionParserTest, ParseX) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), x); } } @@ -147,8 +143,8 @@ TEST_F(ExpressionParserTest, ParseY) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); - EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), y); + auto ctx = LegacyContext(x, y, z, t); + EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), y); } } } @@ -163,7 +159,7 @@ TEST_F(ExpressionParserTest, ParseZ) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), z); } } @@ -179,7 +175,7 @@ TEST_F(ExpressionParserTest, ParseT) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), t); } } @@ -194,7 +190,7 @@ TEST_F(ExpressionParserTest, ParseXPlus2) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), x + 2); } } @@ -209,7 +205,7 @@ TEST_F(ExpressionParserTest, ParseXTimesMinus4) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), x * (-4)); } } @@ -224,7 +220,7 @@ TEST_F(ExpressionParserTest, ParseXDividedBy3e8) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), x / 3.e8); } } @@ -239,7 +235,7 @@ TEST_F(ExpressionParserTest, ParseXSquared) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), x * x); } } @@ -297,7 +293,7 @@ TEST_F(ExpressionParserTest, AddGenerator) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); + auto ctx = LegacyContext(x, y, z, t); EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), x + 1); } } @@ -358,9 +354,8 @@ TEST_F(ExpressionParserTest, CloneBinaryOp) { for (auto y : y_array) { for (auto z : z_array) { for (auto t : t_array) { - auto ctx = LegacyContext(x, y, z, t); - EXPECT_DOUBLE_EQ(actualFieldgen->generate(ctx), - clonedFieldgen->generate(ctx)); + auto ctx = LegacyContext(x, y, z, t); + EXPECT_DOUBLE_EQ(actualFieldgen->generate(ctx), clonedFieldgen->generate(ctx)); } } } @@ -377,7 +372,7 @@ TEST_F(ExpressionParserTest, BadBinaryOp) { // Refers to an unrecognised binary operator "?" parser.addBinaryOp('&', std::make_shared(nullptr, nullptr, '?'), 5); auto fieldgen = parser.parseString("2 & x + 3"); - auto ctx = LegacyContext(0,0,0,0); + auto ctx = LegacyContext(0, 0, 0, 0); EXPECT_THROW(fieldgen->generate(ctx), ParseException); } @@ -404,7 +399,7 @@ TEST_F(ExpressionParserTest, AddBinaryOp) { TEST(ParseExceptionTest, WhatTest) { try { throw ParseException("test message"); - } catch (ParseException &e) { + } catch (ParseException& e) { std::string message{e.what()}; EXPECT_NE(message.find("test message"), std::string::npos); } @@ -413,7 +408,7 @@ TEST(ParseExceptionTest, WhatTest) { TEST_F(ExpressionParserTest, EscapeSymbol) { auto fieldgen = parser.parseString("`x`"); EXPECT_EQ(fieldgen->str(), "x"); - + for (auto x : x_array) { for (auto y : y_array) { for (auto z : z_array) { @@ -507,7 +502,7 @@ TEST_F(ExpressionParserTest, ImplicitMultiply) { for (auto z : z_array) { for (auto t : t_array) { auto ctx = LegacyContext(x, y, z, t); - EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), 2*x + 3*y); + EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), 2 * x + 3 * y); } } } @@ -523,7 +518,7 @@ TEST_F(ExpressionParserTest, ImplicitMultiplyBracket) { for (auto z : z_array) { for (auto t : t_array) { auto ctx = LegacyContext(x, y, z, t); - EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), 2*(x + 3*y)); + EXPECT_DOUBLE_EQ(fieldgen->generate(ctx), 2 * (x + 3 * y)); } } } @@ -568,7 +563,8 @@ TEST_F(ExpressionParserTest, PassParameterImplicitMultiply) { for (auto z : z_array) { for (auto t : t_array) { auto ctx = LegacyContext(x, y, z, t); - EXPECT_DOUBLE_EQ(fieldgen->generate(ctx.set("value", 1 + y + z)), x - 3 * (1 + y + z)); + EXPECT_DOUBLE_EQ(fieldgen->generate(ctx.set("value", 1 + y + z)), + x - 3 * (1 + y + z)); } } } @@ -619,16 +615,15 @@ class GeneratorCloneCopy : public FieldGenerator { FieldGeneratorPtr clone(const std::list UNUSED(args)) override { return std::make_shared(expr); } - double generate(const Context& ctx) override { - return expr->generate(ctx); - } + double generate(const Context& ctx) override { return expr->generate(ctx); } + private: FieldGeneratorPtr expr; }; TEST_F(ExpressionParserTest, ContextFunction) { - parser.addGenerator("func", - std::make_shared(parser.parseString("2 * {x}"))); + parser.addGenerator( + "func", std::make_shared(parser.parseString("2 * {x}"))); auto fieldgen = parser.parseString("[x=3](func)"); EXPECT_DOUBLE_EQ(fieldgen->generate({}), 6); @@ -660,7 +655,8 @@ TEST_F(ExpressionParserTest, SumExpr) { } TEST_F(ExpressionParserTest, SumNestedScope) { - auto fieldgen = parser.parseString("sum(i, 3, sum(i, 2*{i}, {i}+1))"); // => (0) + (1 + 2) + (1 + 2 + 3 + 4) = 13 + auto fieldgen = parser.parseString( + "sum(i, 3, sum(i, 2*{i}, {i}+1))"); // => (0) + (1 + 2) + (1 + 2 + 3 + 4) = 13 EXPECT_DOUBLE_EQ(fieldgen->generate({}), 13); } diff --git a/tests/unit/sys/test_msg_stack.cxx b/tests/unit/sys/test_msg_stack.cxx index cb2d33d1f7..3e2c8e511b 100644 --- a/tests/unit/sys/test_msg_stack.cxx +++ b/tests/unit/sys/test_msg_stack.cxx @@ -1,9 +1,9 @@ // These tests rely on MsgStack::getDump, and so won't work without it #if BOUT_USE_MSGSTACK -#include "gtest/gtest.h" -#include "msg_stack.hxx" +#include "bout/msg_stack.hxx" #include "test_extras.hxx" +#include "gtest/gtest.h" #include #include @@ -133,7 +133,7 @@ TEST(MsgStackTest, DumpTest) { // Write cout to buffer instead of stdout std::stringstream buffer; // Save cout's buffer here - std::streambuf *sbuf(std::cout.rdbuf()); + std::streambuf* sbuf(std::cout.rdbuf()); std::cout.rdbuf(buffer.rdbuf()); MsgStack msg_stack; diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index 6079660912..a357923053 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -1,9 +1,9 @@ -#include "gtest/gtest.h" #include "test_extras.hxx" +#include "gtest/gtest.h" -#include "options.hxx" -#include "output.hxx" -#include +#include "bout/options.hxx" +#include "bout/output.hxx" +#include #include @@ -21,7 +21,7 @@ TEST_F(OptionsTest, IsSet) { Options options; ASSERT_FALSE(options.isSet("int_key")); - + options.set("int_key", 42, "code"); ASSERT_TRUE(options.isSet("int_key")); @@ -110,7 +110,7 @@ TEST_F(OptionsTest, SetGetIntFromReal) { options.set("int_key2", 12.5, "code"); EXPECT_THROW(options.get("int_key2", value, 99, false), BoutException); - + // value is not changed EXPECT_EQ(value, 42); } @@ -299,9 +299,9 @@ TEST_F(OptionsTest, InconsistentDefaultValueOptions) { EXPECT_EQ(options["int_key"].withDefault(42), 42); int value = 0; - EXPECT_THROW( - value = options["int_key"].withDefault(default_options["int_key"]).as(), - BoutException); + EXPECT_THROW(value = + options["int_key"].withDefault(default_options["int_key"]).as(), + BoutException); EXPECT_EQ(value, 0); } @@ -317,8 +317,8 @@ TEST_F(OptionsTest, OverrideDefaultValueOptions) { } TEST_F(OptionsTest, SingletonTest) { - Options *root = Options::getRoot(); - Options *second = Options::getRoot(); + Options* root = Options::getRoot(); + Options* second = Options::getRoot(); EXPECT_EQ(root, second); } @@ -339,12 +339,12 @@ TEST_F(OptionsTest, CheckUsed) { std::stringstream buffer; // Save cout's buffer here - std::streambuf *sbuf = std::cout.rdbuf(); + std::streambuf* sbuf = std::cout.rdbuf(); // Redirect cout to our stringstream buffer or any other ostream std::cout.rdbuf(buffer.rdbuf()); Options options; - Options *section1 = options.getSection("section1"); + Options* section1 = options.getSection("section1"); options.set("key1", "a", "code"); section1->set("key2", "b", "code"); options.set("key3", "c", "code"); @@ -391,14 +391,14 @@ TEST_F(OptionsTest, CheckUsed) { TEST_F(OptionsTest, GetEmptySection) { Options options; - Options *new_section = options.getSection(""); + Options* new_section = options.getSection(""); EXPECT_EQ(new_section, &options); } TEST_F(OptionsTest, MakeNewSection) { Options options; - Options *new_section = options.getSection("section1"); + Options* new_section = options.getSection("section1"); EXPECT_NE(new_section, &options); EXPECT_EQ(new_section->getParent(), &options); @@ -407,26 +407,26 @@ TEST_F(OptionsTest, MakeNewSection) { TEST_F(OptionsTest, GetExistingSection) { Options options; - Options *new_section = options.getSection("section1"); - Options *old_section = options.getSection("section1"); + Options* new_section = options.getSection("section1"); + Options* old_section = options.getSection("section1"); EXPECT_EQ(new_section, old_section); } TEST_F(OptionsTest, GetCorrectSection) { Options options; - Options *section1 = options.getSection("section1"); + Options* section1 = options.getSection("section1"); options.getSection("section2"); - Options *old_section = options.getSection("section1"); + Options* old_section = options.getSection("section1"); EXPECT_EQ(section1, old_section); } TEST_F(OptionsTest, MakeNestedSection) { Options options; - Options *section1 = options.getSection("section1"); - Options *section2 = section1->getSection("section2"); + Options* section1 = options.getSection("section1"); + Options* section2 = section1->getSection("section2"); EXPECT_NE(section2, section1); EXPECT_EQ(section2->getParent(), section1); @@ -436,11 +436,11 @@ TEST_F(OptionsTest, MakeNestedSection) { TEST_F(OptionsTest, SetSameOptionTwice) { Options options; options.set("key", "value", "code"); - EXPECT_THROW(options.set("key", "new value", "code"),BoutException); + EXPECT_THROW(options.set("key", "new value", "code"), BoutException); options.set("key", "value", "code"); EXPECT_NO_THROW(options.forceSet("key", "new value", "code")); - EXPECT_NO_THROW(options.set("key", "value", "code",true)); + EXPECT_NO_THROW(options.set("key", "value", "code", true)); } /// New interface @@ -484,12 +484,12 @@ TEST_F(OptionsTest, NewIsSet) { TEST_F(OptionsTest, NewSubSection) { Options options; - + options["sub-section"]["int_key"].assign(42, "code"); - + ASSERT_FALSE(options["int_key"].isSet()); ASSERT_TRUE(options["sub-section"]["int_key"].isSet()); - + int value = options["sub-section"]["int_key"].withDefault(99); EXPECT_EQ(value, 42); } @@ -622,7 +622,7 @@ TEST_F(OptionsTest, CopyOptionDistinct) { Options option2(option1); option1.force(23); - + EXPECT_EQ(option1.as(), 23); EXPECT_EQ(option2.as(), 42); } @@ -631,7 +631,7 @@ TEST_F(OptionsTest, CopyOptionDistinct) { TEST_F(OptionsTest, CopySection) { Options option1; - option1["key"] = 42; // option1 now a section + option1["key"] = 42; // option1 now a section Options option2(option1); @@ -645,15 +645,15 @@ TEST_F(OptionsTest, CopySectionParent) { option1["key"] = 42; Options option2(option1); - - EXPECT_TRUE( &option2["key"].parent() == &option2 ); + + EXPECT_TRUE(&option2["key"].parent() == &option2); } TEST_F(OptionsTest, AssignOption) { Options option1, option2; option1 = 42; - + option2 = option1; EXPECT_EQ(option2.as(), 42); @@ -663,7 +663,7 @@ TEST_F(OptionsTest, AssignSection) { Options option1, option2; option1["key"] = 42; - + option2 = option1; EXPECT_EQ(option2["key"].as(), 42); @@ -675,7 +675,7 @@ TEST_F(OptionsTest, AssignSectionReplace) { option1["key"] = 42; option2["key"] = 23; - + option2 = option1; EXPECT_EQ(option2["key"].as(), 42); @@ -685,17 +685,17 @@ TEST_F(OptionsTest, AssignSectionParent) { Options option1, option2; option1["key"] = 42; - + option2 = option1; - - EXPECT_TRUE( &option2["key"].parent() == &option2 ); + + EXPECT_TRUE(&option2["key"].parent() == &option2); } TEST_F(OptionsTest, AssignSubSection) { Options option1, option2; option1["key1"] = 42; - + option2["key2"] = option1; EXPECT_EQ(option2["key2"]["key1"].as(), 42); @@ -705,7 +705,7 @@ TEST_F(OptionsTest, AssignSubSectionParent) { Options option1, option2; option1["key1"] = 42; - + option2["key2"] = option1; EXPECT_EQ(&option2["key2"].parent(), &option2); @@ -820,7 +820,7 @@ TEST_F(OptionsTest, AttributeTimeDimension) { option = 3; EXPECT_EQ(option.as(), 3); - + option.attributes["time_dimension"] = "t"; option = 4; @@ -932,7 +932,7 @@ TEST_F(OptionsTest, WithDefaultIntThrow) { Options option; option = "4.32"; - + EXPECT_THROW(option.withDefault(0), BoutException); } @@ -976,7 +976,7 @@ TEST_F(OptionsTest, TypeAttributeField2D) { // Casting to Field2D should modify the "type" attribute Field2D value = option.withDefault(Field2D(-1, bout::globals::mesh)); - EXPECT_EQ(value(0,0), 42); + EXPECT_EQ(value(0, 0), 42); EXPECT_EQ(option.attributes["type"].as(), "Field2D"); } @@ -987,7 +987,7 @@ TEST_F(OptionsTest, TypeAttributeField3D) { // Casting to Field3D should modify the "type" attribute Field3D value = option.withDefault(Field3D(-1, bout::globals::mesh)); - EXPECT_EQ(value(0,0,0), 42); + EXPECT_EQ(value(0, 0, 0), 42); EXPECT_EQ(option.attributes["type"].as(), "Field3D"); } @@ -998,7 +998,7 @@ TEST_F(OptionsTest, TypeAttributeFieldPerp) { // Casting to FieldPerp should modify the "type" attribute FieldPerp value = option.withDefault(FieldPerp(-1, bout::globals::mesh)); - EXPECT_EQ(value(0,0,0), 36); + EXPECT_EQ(value(0, 0, 0), 36); EXPECT_EQ(option.attributes["type"].as(), "FieldPerp"); } @@ -1012,7 +1012,7 @@ TEST_F(OptionsTest, DocString) { TEST_F(OptionsTest, DocStringAssignTo) { Options option; - + option.doc("test string") = 42; EXPECT_EQ(option.attributes["doc"].as(), "test string"); @@ -1022,7 +1022,7 @@ TEST_F(OptionsTest, DocStringAssignTo) { TEST_F(OptionsTest, DocStringAssignFrom) { Options option; option = 42; - + int value = option.doc("test string"); EXPECT_EQ(option.attributes["doc"].as(), "test string"); @@ -1036,7 +1036,7 @@ TEST_F(OptionsTest, DocStringWithDefault) { int value = option.doc("some value").withDefault(2); EXPECT_EQ(value, 42); - EXPECT_EQ(option.attributes["doc"].as(), "some value"); + EXPECT_EQ(option.attributes["doc"].as(), "some value"); } TEST_F(OptionsTest, DocStringNotCopied) { @@ -1046,24 +1046,22 @@ TEST_F(OptionsTest, DocStringNotCopied) { Options option2 = option; int value = option2.doc("test value"); - + EXPECT_EQ(value, 32); EXPECT_EQ(option2.attributes["doc"].as(), "test value"); EXPECT_EQ(option.attributes.count("doc"), 0); } TEST_F(OptionsTest, InitializeInt) { - Options option {3}; + Options option{3}; EXPECT_EQ(option.as(), 3); } TEST_F(OptionsTest, InitialiseTree) { - Options option {{"section1", {{"value1", 42}, - {"value2", "hello"}}}, - {"section2", {{"subsection1", {{"value3", true}, - {"value4", 3.2}}}, - {"value5", 3}}}}; - + Options option{{"section1", {{"value1", 42}, {"value2", "hello"}}}, + {"section2", + {{"subsection1", {{"value3", true}, {"value4", 3.2}}}, {"value5", 3}}}}; + EXPECT_EQ(option["section1"]["value1"].as(), 42); EXPECT_EQ(option["section1"]["value2"].as(), "hello"); EXPECT_EQ(option["section2"]["subsection1"]["value3"].as(), true); @@ -1108,7 +1106,8 @@ TEST_F(OptionsTest, FormatValue) { options["value1"].doc("This is a value").assign(4, "some test"); options["value1"].attributes["type"] = "int"; - const std::string expected = "value1 = 4 # type: int, doc: This is a value, source: some test"; + const std::string expected = + "value1 = 4 # type: int, doc: This is a value, source: some test"; EXPECT_EQ(expected, fmt::format("{:ds}", options["value1"])); } @@ -1250,9 +1249,8 @@ TEST_F(OptionsTest, GetUnused) { MAYBE_UNUSED(auto value1) = option["section1"]["value1"].as(); MAYBE_UNUSED(auto value3) = option["section2"]["subsection1"]["value3"].as(); - Options expected_unused{ - {"section1", {{"value2", "hello"}}}, - {"section2", {{"subsection1", {{"value4", 3.2}}}}}}; + Options expected_unused{{"section1", {{"value2", "hello"}}}, + {"section2", {{"subsection1", {{"value4", 3.2}}}}}}; EXPECT_EQ(option.getUnused(), expected_unused); @@ -1278,10 +1276,11 @@ TEST_F(OptionsTest, SetConditionallyUsed) { } TEST_F(OptionsTest, FuzzyFind) { - Options option{{"value1", 21}, - {"section1", {{"value1", 42}, {"value2", "hello"}, {"not this", 1}}}, - {"section2", - {{"subsection1", {{"value3", true}, {"value4", 3.2}}}, {"value_5", 3}}}}; + Options option{ + {"value1", 21}, + {"section1", {{"value1", 42}, {"value2", "hello"}, {"not this", 1}}}, + {"section2", + {{"subsection1", {{"value3", true}, {"value4", 3.2}}}, {"value_5", 3}}}}; auto fuzzy_matches = option.fuzzyFind("value1"); EXPECT_EQ(fuzzy_matches.size(), 6); @@ -1351,7 +1350,7 @@ TEST_F(OptionsTest, CheckForUnusedOptionsGlobalRoot) { } class BoolTrueTestParametrized : public OptionsTest, - public ::testing::WithParamInterface {}; + public ::testing::WithParamInterface {}; TEST_P(BoolTrueTestParametrized, BoolTrueFromString) { std::string testval = GetParam(); @@ -1361,13 +1360,9 @@ TEST_P(BoolTrueTestParametrized, BoolTrueFromString) { ASSERT_TRUE(options["bool_key"].as()); } -INSTANTIATE_TEST_CASE_P( - BoolTrueTests, - BoolTrueTestParametrized, - ::testing::Values( - "y", "Y", "yes", "Yes", "yeS", "t", "true", "T", "True", "tRuE", "1" - ) -); +INSTANTIATE_TEST_CASE_P(BoolTrueTests, BoolTrueTestParametrized, + ::testing::Values("y", "Y", "yes", "Yes", "yeS", "t", "true", "T", + "True", "tRuE", "1")); class BoolFalseTestParametrized : public OptionsTest, public ::testing::WithParamInterface {}; @@ -1380,16 +1375,12 @@ TEST_P(BoolFalseTestParametrized, BoolFalseFromString) { ASSERT_FALSE(options["bool_key"].as()); } -INSTANTIATE_TEST_CASE_P( - BoolFalseTests, - BoolFalseTestParametrized, - ::testing::Values( - "n", "N", "no", "No", "nO", "f", "false", "F", "False", "fAlSe", "0" - ) -); +INSTANTIATE_TEST_CASE_P(BoolFalseTests, BoolFalseTestParametrized, + ::testing::Values("n", "N", "no", "No", "nO", "f", "false", "F", + "False", "fAlSe", "0")); class BoolInvalidTestParametrized : public OptionsTest, - public ::testing::WithParamInterface {}; + public ::testing::WithParamInterface {}; TEST_P(BoolInvalidTestParametrized, BoolInvalidFromString) { std::string testval = GetParam(); @@ -1399,11 +1390,7 @@ TEST_P(BoolInvalidTestParametrized, BoolInvalidFromString) { EXPECT_THROW(options["bool_key"].as(), BoutException); } -INSTANTIATE_TEST_CASE_P( - BoolInvalidTests, - BoolInvalidTestParametrized, - ::testing::Values( - "a", "B", "yellow", "Yogi", "test", "truelong", "Tim", "2", "not", "No bool", - "nOno", "falsebuttoolong", "-1" - ) -); +INSTANTIATE_TEST_CASE_P(BoolInvalidTests, BoolInvalidTestParametrized, + ::testing::Values("a", "B", "yellow", "Yogi", "test", "truelong", + "Tim", "2", "not", "No bool", "nOno", + "falsebuttoolong", "-1")); diff --git a/tests/unit/sys/test_options_fields.cxx b/tests/unit/sys/test_options_fields.cxx index df9464bab9..4858886d96 100644 --- a/tests/unit/sys/test_options_fields.cxx +++ b/tests/unit/sys/test_options_fields.cxx @@ -3,10 +3,10 @@ #include "gtest/gtest.h" -#include "bout/mesh.hxx" -#include "field3d.hxx" +#include "bout/field3d.hxx" #include "test_extras.hxx" -#include "unused.hxx" +#include "bout/unused.hxx" +#include "bout/mesh.hxx" /// Global mesh namespace bout { @@ -25,7 +25,7 @@ TEST_F(OptionsFieldTest, StoreField3D) { Options options; EXPECT_FALSE(options.isValue()); - + options = field; EXPECT_TRUE(options.isValue()); @@ -36,7 +36,7 @@ TEST_F(OptionsFieldTest, StoreField2D) { Options options; EXPECT_FALSE(options.isValue()); - + options = field; EXPECT_TRUE(options.isValue()); @@ -44,15 +44,15 @@ TEST_F(OptionsFieldTest, StoreField2D) { TEST_F(OptionsFieldTest, RetrieveField3D) { Field3D field = 1.0; - field(0,1,1) = 2.0; - + field(0, 1, 1) = 2.0; + Options options; options = field; Field3D other = options; - EXPECT_DOUBLE_EQ(other(0,1,0), 1.0); - EXPECT_DOUBLE_EQ(other(0,1,1), 2.0); + EXPECT_DOUBLE_EQ(other(0, 1, 0), 1.0); + EXPECT_DOUBLE_EQ(other(0, 1, 1), 2.0); } TEST_F(OptionsFieldTest, RetrieveField3DfromBoutReal) { @@ -61,8 +61,8 @@ TEST_F(OptionsFieldTest, RetrieveField3DfromBoutReal) { Field3D other = options; - EXPECT_DOUBLE_EQ(other(0,1,0), 1.2); - EXPECT_DOUBLE_EQ(other(0,0,1), 1.2); + EXPECT_DOUBLE_EQ(other(0, 1, 0), 1.2); + EXPECT_DOUBLE_EQ(other(0, 0, 1), 1.2); } TEST_F(OptionsFieldTest, RetrieveBoutRealfromField3D) { @@ -87,7 +87,7 @@ TEST_F(OptionsFieldTest, RetrieveField3DfromField2D) { options = field; Field3D value = options.as(); - EXPECT_DOUBLE_EQ(value(0,1,0), 1.2); + EXPECT_DOUBLE_EQ(value(0, 1, 0), 1.2); } TEST_F(OptionsFieldTest, RetrieveStringfromField3D) { @@ -116,8 +116,8 @@ TEST_F(OptionsFieldTest, RetrieveField3DfromString) { Field3D other = options.as(); - EXPECT_DOUBLE_EQ(other(0,1,0), 3.0); - EXPECT_DOUBLE_EQ(other(0,0,1), 3.0); + EXPECT_DOUBLE_EQ(other(0, 1, 0), 3.0); + EXPECT_DOUBLE_EQ(other(0, 0, 1), 3.0); } TEST_F(OptionsFieldTest, RetrieveField2DfromString) { @@ -126,8 +126,8 @@ TEST_F(OptionsFieldTest, RetrieveField2DfromString) { Field2D other = options.as(); - EXPECT_DOUBLE_EQ(other(0,1,0), 3.0); - EXPECT_DOUBLE_EQ(other(0,0,1), 3.0); + EXPECT_DOUBLE_EQ(other(0, 1, 0), 3.0); + EXPECT_DOUBLE_EQ(other(0, 0, 1), 3.0); } TEST_F(OptionsFieldTest, RetrieveField2DfromBadString) { @@ -136,4 +136,3 @@ TEST_F(OptionsFieldTest, RetrieveField2DfromBadString) { EXPECT_THROW(Field2D other = options.as(), ParseException); } - diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx index dc9f9c349a..fcab2bdb9a 100644 --- a/tests/unit/sys/test_options_netcdf.cxx +++ b/tests/unit/sys/test_options_netcdf.cxx @@ -6,10 +6,10 @@ #include "gtest/gtest.h" -#include "bout/mesh.hxx" -#include "field3d.hxx" +#include "bout/field3d.hxx" +#include "bout/options_netcdf.hxx" #include "test_extras.hxx" -#include "options_netcdf.hxx" +#include "bout/mesh.hxx" using bout::OptionsNetCDF; @@ -23,7 +23,7 @@ extern Mesh* mesh; } // namespace bout // Reuse the "standard" fixture for FakeMesh -class OptionsNetCDFTest: public FakeMeshFixture { +class OptionsNetCDFTest : public FakeMeshFixture { public: OptionsNetCDFTest() : FakeMeshFixture() {} ~OptionsNetCDFTest() override { std::remove(filename.c_str()); } @@ -56,7 +56,7 @@ TEST_F(OptionsNetCDFTest, ReadWriteString) { // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); @@ -67,48 +67,48 @@ TEST_F(OptionsNetCDFTest, ReadWriteField2D) { { Options options; options["test"] = Field2D(1.0); - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); Field2D value = data["test"].as(bout::globals::mesh); - - EXPECT_DOUBLE_EQ(value(0,1), 1.0); - EXPECT_DOUBLE_EQ(value(1,0), 1.0); + + EXPECT_DOUBLE_EQ(value(0, 1), 1.0); + EXPECT_DOUBLE_EQ(value(1, 0), 1.0); } TEST_F(OptionsNetCDFTest, ReadWriteField3D) { - { + { Options options; options["test"] = Field3D(2.4); - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); Field3D value = data["test"].as(bout::globals::mesh); - - EXPECT_DOUBLE_EQ(value(0,1,0), 2.4); - EXPECT_DOUBLE_EQ(value(1,0,1), 2.4); - EXPECT_DOUBLE_EQ(value(1,1,1), 2.4); + + EXPECT_DOUBLE_EQ(value(0, 1, 0), 2.4); + EXPECT_DOUBLE_EQ(value(1, 0, 1), 2.4); + EXPECT_DOUBLE_EQ(value(1, 1, 1), 2.4); } TEST_F(OptionsNetCDFTest, Groups) { { Options options; options["test"]["key"] = 42; - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); EXPECT_EQ(data["test"]["key"], 42); @@ -123,7 +123,7 @@ TEST_F(OptionsNetCDFTest, AttributeInt) { // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); EXPECT_EQ(data["test"].attributes["thing"].as(), 4); @@ -134,11 +134,11 @@ TEST_F(OptionsNetCDFTest, AttributeBoutReal) { Options options; options["test"] = 3; options["test"].attributes["thing"] = 3.14; - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); EXPECT_DOUBLE_EQ(data["test"].attributes["thing"].as(), 3.14); @@ -149,11 +149,11 @@ TEST_F(OptionsNetCDFTest, AttributeString) { Options options; options["test"] = 3; options["test"].attributes["thing"] = "hello"; - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); EXPECT_EQ(data["test"].attributes["thing"].as(), "hello"); @@ -163,60 +163,64 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellCentre) { { Options options; options["f2d"] = Field2D(2.0); - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); - EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), toString(CELL_CENTRE)); + EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), + toString(CELL_CENTRE)); } TEST_F(OptionsNetCDFTest, Field2DWriteCellYLow) { { Options options; options["f2d"] = Field2D(2.0, mesh_staggered).setLocation(CELL_YLOW); - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); - EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), toString(CELL_YLOW)); + EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), + toString(CELL_YLOW)); } TEST_F(OptionsNetCDFTest, Field3DWriteCellCentre) { { Options options; options["f3d"] = Field3D(2.0); - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); - EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), toString(CELL_CENTRE)); + EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), + toString(CELL_CENTRE)); } TEST_F(OptionsNetCDFTest, Field3DWriteCellYLow) { { Options options; options["f3d"] = Field3D(2.0, mesh_staggered).setLocation(CELL_YLOW); - + // Write file OptionsNetCDF(filename).write(options); } - + // Read file Options data = OptionsNetCDF(filename).read(); - EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), toString(CELL_YLOW)); + EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), + toString(CELL_YLOW)); } TEST_F(OptionsNetCDFTest, FieldPerpWriteCellCentre) { diff --git a/tests/unit/sys/test_optionsreader.cxx b/tests/unit/sys/test_optionsreader.cxx index dd0b267029..5d2859ea35 100644 --- a/tests/unit/sys/test_optionsreader.cxx +++ b/tests/unit/sys/test_optionsreader.cxx @@ -1,10 +1,10 @@ -#include "gtest/gtest.h" +#include "bout/optionsreader.hxx" #include "test_extras.hxx" -#include "optionsreader.hxx" +#include "gtest/gtest.h" -#include "boutexception.hxx" -#include "output.hxx" -#include "utils.hxx" +#include "bout/boutexception.hxx" +#include "bout/output.hxx" +#include "bout/utils.hxx" #include #include @@ -35,7 +35,7 @@ class OptionsReaderTest : public ::testing::Test { // Write cout to buffer instead of stdout std::stringstream buffer; // Save cout's buffer here - std::streambuf *sbuf; + std::streambuf* sbuf; WithQuietOutput quiet{output_info}; // A temporary filename @@ -90,8 +90,8 @@ TEST_F(OptionsReaderTest, ParseCommandLine) { } TEST_F(OptionsReaderTest, ParseCommandLineGlobalInstance) { - OptionsReader *reader = OptionsReader::getInstance(); - Options *options = Options::getRoot(); + OptionsReader* reader = OptionsReader::getInstance(); + Options* options = Options::getRoot(); std::vector argv{"prog", "int_key=42"}; @@ -109,7 +109,7 @@ TEST_F(OptionsReaderTest, ParseCommandLineGlobalInstance) { TEST_F(OptionsReaderTest, ParseCommandLineWithSpaces) { OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); std::vector argv{"prog", "int_key", "=", "42"}; @@ -125,7 +125,7 @@ TEST_F(OptionsReaderTest, ParseCommandLineWithSpaces) { TEST_F(OptionsReaderTest, ParseCommandLineWithTrailingSpace) { OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); std::vector argv{"prog", "int_key=", "42"}; @@ -141,7 +141,7 @@ TEST_F(OptionsReaderTest, ParseCommandLineWithTrailingSpace) { TEST_F(OptionsReaderTest, ParseCommandLineFlag) { OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); std::vector argv{"prog", "-flag", "command"}; @@ -162,7 +162,7 @@ TEST_F(OptionsReaderTest, ParseCommandLineFlag) { TEST_F(OptionsReaderTest, ParseCommandLineWithSection) { OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); std::vector argv{"prog", "subsection1:int_key=42"}; @@ -170,7 +170,7 @@ TEST_F(OptionsReaderTest, ParseCommandLineWithSection) { EXPECT_FALSE(options->isSet("int_key")); - Options *section1 = options->getSection("subsection1"); + Options* section1 = options->getSection("subsection1"); ASSERT_TRUE(section1->isSet("int_key")); @@ -195,7 +195,7 @@ bool_key = false test_file.close(); OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); reader.read(options, filename); ASSERT_TRUE(options->isSet("flag")); @@ -207,7 +207,7 @@ bool_key = false EXPECT_FALSE(options->isSet("int_key")); - Options *section1 = options->getSection("section1"); + Options* section1 = options->getSection("section1"); ASSERT_TRUE(section1->isSet("int_key")); @@ -223,7 +223,7 @@ bool_key = false EXPECT_DOUBLE_EQ(real_value, 42.34e-67); - Options *subsection2 = section1->getSection("subsection2"); + Options* subsection2 = section1->getSection("subsection2"); ASSERT_TRUE(subsection2->isSet("bool_key")); @@ -235,7 +235,7 @@ bool_key = false TEST_F(OptionsReaderTest, ReadBadFile) { OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); EXPECT_THROW(reader.read(options, filename), BoutException); } @@ -250,7 +250,7 @@ int_key = 34 test_file.close(); OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); EXPECT_THROW(reader.read(options, filename), BoutException); }; @@ -265,19 +265,19 @@ int_key = 34 test_file.close(); OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); EXPECT_THROW(reader.read(options, filename), BoutException); }; TEST_F(OptionsReaderTest, WriteFile) { OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); options->set("bool_key", true, "test"); - Options *section1 = options->getSection("section1"); + Options* section1 = options->getSection("section1"); section1->set("int_key", 17, "test"); section1->set("real_key", 6.17e23, "test"); - Options *subsection2 = section1->getSection("subsection2"); + Options* subsection2 = section1->getSection("subsection2"); subsection2->set("string_key", "BOUT++", "test"); reader.write(options, filename); @@ -291,7 +291,7 @@ TEST_F(OptionsReaderTest, WriteFile) { "int_key = 17", "real_key = 6.17e+23", "[section1:subsection2]", "string_key = BOUT++"}; - for (auto &result : expected) { + for (auto& result : expected) { EXPECT_TRUE(IsSubString(test_buffer.str(), result)); } } @@ -299,10 +299,10 @@ TEST_F(OptionsReaderTest, WriteFile) { TEST_F(OptionsReaderTest, WriteBadFile) { std::string filename1 = filename + std::tmpnam(nullptr); OptionsReader reader; - Options *options = Options::getRoot(); + Options* options = Options::getRoot(); options->set("bool_key", true, "test"); - Options *section1 = options->getSection("section1"); + Options* section1 = options->getSection("section1"); section1->set("int_key", 17, "test"); EXPECT_THROW(reader.write(options, filename1), BoutException); @@ -311,14 +311,14 @@ TEST_F(OptionsReaderTest, WriteBadFile) { } TEST_F(OptionsReaderTest, ReadEmptyString) { -const std::string text = R"( + const std::string text = R"( value = )"; std::ofstream test_file(filename, std::ios::out); test_file << text; test_file.close(); - + Options opt; OptionsReader reader; @@ -353,7 +353,7 @@ test6 = h2`+`:on`e-`more # Escape sequences in the middle reader.read(Options::getRoot(), filename); auto options = Options::root()["tests"]; - + EXPECT_EQ(options["test1"].as(), 3); EXPECT_EQ(options["test2"].as(), 15); EXPECT_EQ(options["test3"].as(), 4); @@ -375,7 +375,7 @@ some:value = 3 test_file.close(); OptionsReader reader; - + EXPECT_THROW(reader.read(Options::getRoot(), filename), BoutException); } @@ -399,9 +399,9 @@ twopi = 2 * π # Unicode symbol defined for pi reader.read(Options::getRoot(), filename); auto options = Options::root()["tests"]; - + EXPECT_EQ(options["結果"].as(), 8); - EXPECT_DOUBLE_EQ(options["value"].as(), 1.3*(1+3)); + EXPECT_DOUBLE_EQ(options["value"].as(), 1.3 * (1 + 3)); EXPECT_DOUBLE_EQ(options["twopi"].as(), 2 * 3.141592653589793); } diff --git a/tests/unit/sys/test_output.cxx b/tests/unit/sys/test_output.cxx index 9074d8f691..661e7bb1af 100644 --- a/tests/unit/sys/test_output.cxx +++ b/tests/unit/sys/test_output.cxx @@ -1,7 +1,7 @@ -#include "gtest/gtest.h" -#include "boutexception.hxx" -#include "output.hxx" +#include "bout/boutexception.hxx" +#include "bout/output.hxx" #include "bout/output_bout_types.hxx" +#include "gtest/gtest.h" #include #include @@ -26,7 +26,7 @@ class OutputTest : public ::testing::Test { // Write cout to buffer instead of stdout std::stringstream buffer; // Save cout's buffer here - std::streambuf *sbuf; + std::streambuf* sbuf; // A temporary filename std::string filename{std::tmpnam(nullptr)}; }; @@ -122,11 +122,11 @@ TEST_F(OutputTest, DisableEnableStdout) { } TEST_F(OutputTest, GetInstance) { - Output *local_output = Output::getInstance(); + Output* local_output = Output::getInstance(); EXPECT_NE(local_output, nullptr); - Output *new_output = Output::getInstance(); + Output* new_output = Output::getInstance(); EXPECT_EQ(local_output, new_output); } diff --git a/tests/unit/sys/test_raja.cxx b/tests/unit/sys/test_raja.cxx index 63a96aa599..b2935941cb 100644 --- a/tests/unit/sys/test_raja.cxx +++ b/tests/unit/sys/test_raja.cxx @@ -93,7 +93,7 @@ TEST(RajaTest, SimpleForall) { EXPECT_TRUE(match); } -#if 0 // disable temporarily until reconcile iteration space for parallel_forall under +#if 0 // disable temporarily until reconcile iteration space for parallel_forall under \ // nvcc TEST(RajaTest, ParallelForall) { // diff --git a/tests/unit/sys/test_range.cxx b/tests/unit/sys/test_range.cxx index 3a3d7496ca..279fccc846 100644 --- a/tests/unit/sys/test_range.cxx +++ b/tests/unit/sys/test_range.cxx @@ -1,5 +1,5 @@ -#include "gtest/gtest.h" #include "bout/sys/range.hxx" +#include "gtest/gtest.h" #include diff --git a/tests/unit/sys/test_timer.cxx b/tests/unit/sys/test_timer.cxx index 8196929b5b..4ec934658d 100644 --- a/tests/unit/sys/test_timer.cxx +++ b/tests/unit/sys/test_timer.cxx @@ -1,5 +1,5 @@ -#include "gtest/gtest.h" #include "gmock/gmock.h" +#include "gtest/gtest.h" #include "bout/sys/timer.hxx" diff --git a/tests/unit/sys/test_type_name.cxx b/tests/unit/sys/test_type_name.cxx index 91d9601908..cc3d7346c8 100644 --- a/tests/unit/sys/test_type_name.cxx +++ b/tests/unit/sys/test_type_name.cxx @@ -1,32 +1,20 @@ -#include "gtest/gtest.h" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" #include "bout/sys/type_name.hxx" -#include "field2d.hxx" -#include "field3d.hxx" +#include "gtest/gtest.h" #include using bout::utils::typeName; -TEST(TypeNameTest, BoolName) { - EXPECT_EQ(typeName(), "bool"); -} +TEST(TypeNameTest, BoolName) { EXPECT_EQ(typeName(), "bool"); } -TEST(TypeNameTest, IntName) { - EXPECT_EQ(typeName(), "int"); -} +TEST(TypeNameTest, IntName) { EXPECT_EQ(typeName(), "int"); } -TEST(TypeNameTest, StringName) { - EXPECT_EQ(typeName(), "string"); -} +TEST(TypeNameTest, StringName) { EXPECT_EQ(typeName(), "string"); } -TEST(TypeNameTest, BoutRealName) { - EXPECT_EQ(typeName(), "BoutReal"); -} +TEST(TypeNameTest, BoutRealName) { EXPECT_EQ(typeName(), "BoutReal"); } -TEST(TypeNameTest, Field2DName) { - EXPECT_EQ(typeName(), "Field2D"); -} +TEST(TypeNameTest, Field2DName) { EXPECT_EQ(typeName(), "Field2D"); } -TEST(TypeNameTest, Field3DName) { - EXPECT_EQ(typeName(), "Field3D"); -} +TEST(TypeNameTest, Field3DName) { EXPECT_EQ(typeName(), "Field3D"); } diff --git a/tests/unit/sys/test_utils.cxx b/tests/unit/sys/test_utils.cxx index 9cadd963d3..0826a742de 100644 --- a/tests/unit/sys/test_utils.cxx +++ b/tests/unit/sys/test_utils.cxx @@ -1,5 +1,5 @@ +#include "bout/utils.hxx" #include "gtest/gtest.h" -#include "utils.hxx" #include #include @@ -170,7 +170,8 @@ TEST(MatrixTest, GetData) { auto data = matrix.getData(); - EXPECT_TRUE(std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); + EXPECT_TRUE( + std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); data[0] = 4; @@ -183,8 +184,10 @@ TEST(MatrixTest, ConstGetData) { const auto data = matrix.getData(); - EXPECT_TRUE(std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); - EXPECT_TRUE(std::all_of(std::begin(matrix), std::end(matrix), [](int a) { return a == 3; })); + EXPECT_TRUE( + std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); + EXPECT_TRUE( + std::all_of(std::begin(matrix), std::end(matrix), [](int a) { return a == 3; })); } TEST(TensorTest, DefaultShape) { @@ -363,7 +366,8 @@ TEST(TensorTest, GetData) { auto data = tensor.getData(); - EXPECT_TRUE(std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); + EXPECT_TRUE( + std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); data[0] = 4; @@ -376,8 +380,10 @@ TEST(TensorTest, ConstGetData) { const auto data = tensor.getData(); - EXPECT_TRUE(std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); - EXPECT_TRUE(std::all_of(std::begin(tensor), std::end(tensor), [](int a) { return a == 3; })); + EXPECT_TRUE( + std::all_of(std::begin(data), std::end(data), [](int a) { return a == 3; })); + EXPECT_TRUE( + std::all_of(std::begin(tensor), std::end(tensor), [](int a) { return a == 3; })); } TEST(Invert3x3Test, Identity) { @@ -460,7 +466,8 @@ TEST(Invert3x3Test, BadCondition) { // Non-default small input = 0.; input(0, 0) = 1.0e-12; - input(1, 1) = 1.0; input(2, 2) = 1.0; + input(1, 1) = 1.0; + input(2, 2) = 1.0; EXPECT_NO_THROW(invert3x3(input, -1.0e-10)); } @@ -534,21 +541,15 @@ TEST(NumberUtilitiesTest, MinModInt) { } #if CHECK > 0 -TEST(NumberUtilitiesTest, CheckDataGood) { - EXPECT_NO_THROW(checkData(5.0)); -} +TEST(NumberUtilitiesTest, CheckDataGood) { EXPECT_NO_THROW(checkData(5.0)); } TEST(NumberUtilitiesTest, CheckDataBad) { EXPECT_THROW(checkData(nan("")), BoutException); } #else -TEST(NumberUtilitiesTest, CheckDataGoodDisabled) { - EXPECT_NO_THROW(checkData(5.0)); -} +TEST(NumberUtilitiesTest, CheckDataGoodDisabled) { EXPECT_NO_THROW(checkData(5.0)); } -TEST(NumberUtilitiesTest, CheckDataBadDisabled) { - EXPECT_NO_THROW(checkData(nan(""))); -} +TEST(NumberUtilitiesTest, CheckDataBadDisabled) { EXPECT_NO_THROW(checkData(nan(""))); } #endif TEST(StringUtilitiesTest, CopyString) { @@ -622,7 +623,7 @@ TEST(StringUtilitiesTest, ConstCharToString) { TEST(StringUtilitiesTest, StringToString) { std::string test_string = "dlkjl872kj"; - EXPECT_EQ( test_string, toString(test_string) ); + EXPECT_EQ(test_string, toString(test_string)); } TEST(StringUtilitiesTest, IntToString) { @@ -680,12 +681,12 @@ TEST(StringUtilitiesTest, EditDistance) { EXPECT_EQ(editDistance("Hello World", "hello world"), 2); // two substitutions EXPECT_EQ(editDistance("hello world", "Hello World"), 2); // transitive // Following might be affected by encoding, so should be at least two - EXPECT_GE(editDistance("très tôt", "tres tot"), 2); // non-ASCII + EXPECT_GE(editDistance("très tôt", "tres tot"), 2); // non-ASCII } namespace { -using function_typedef = int(*)(char, int, double); -int function_pointer(double, char) {return 0;}; +using function_typedef = int (*)(char, int, double); +int function_pointer(double, char) { return 0; }; template void function_template(T) {} } // namespace @@ -751,23 +752,23 @@ TEST(FunctionTraitsTest, SecondArg) { #ifndef __cpp_lib_erase_if TEST(StdLibBackPorts, EraseIfMultiset) { - std::multiset data { 3, 3, 4, 5, 5, 6, 6, 7, 2, 1, 0 }; + std::multiset data{3, 3, 4, 5, 5, 6, 6, 7, 2, 1, 0}; auto divisible_by_3 = [](auto const& x) { return (x % 3) == 0; }; bout::utils::erase_if(data, divisible_by_3); - std::multiset expected { 1, 2, 4, 5, 5, 7 }; + std::multiset expected{1, 2, 4, 5, 5, 7}; EXPECT_EQ(data, expected); } TEST(StdLibBackPorts, EraseIfSet) { - std::set data { 3, 4, 5, 6, 7, 2, 1, 0 }; + std::set data{3, 4, 5, 6, 7, 2, 1, 0}; auto divisible_by_3 = [](auto const& x) { return (x % 3) == 0; }; bout::utils::erase_if(data, divisible_by_3); - std::set expected { 1, 2, 4, 5, 7 }; + std::set expected{1, 2, 4, 5, 7}; EXPECT_EQ(data, expected); } diff --git a/tests/unit/test_extras.cxx b/tests/unit/test_extras.cxx index 8d34359418..a4c51ac3c4 100644 --- a/tests/unit/test_extras.cxx +++ b/tests/unit/test_extras.cxx @@ -1,5 +1,5 @@ -#include "gtest/gtest.h" #include "test_extras.hxx" +#include "gtest/gtest.h" #include @@ -8,8 +8,8 @@ constexpr int FakeMeshFixture::nx; constexpr int FakeMeshFixture::ny; constexpr int FakeMeshFixture::nz; -::testing::AssertionResult IsSubString(const std::string &str, - const std::string &substring) { +::testing::AssertionResult IsSubString(const std::string& str, + const std::string& substring) { if (str.find(substring) != std::string::npos) { return ::testing::AssertionSuccess(); } else { diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 1ad94ddc0e..8b8e3a3f4e 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -3,15 +3,15 @@ #include "gtest/gtest.h" -#include #include #include +#include #include -#include "boundary_region.hxx" -#include "boutcomm.hxx" -#include "field3d.hxx" -#include "unused.hxx" +#include "bout/boundary_region.hxx" +#include "bout/boutcomm.hxx" +#include "bout/field3d.hxx" +#include "bout/unused.hxx" #include "bout/coordinates.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" @@ -22,8 +22,8 @@ static constexpr BoutReal BoutRealTolerance{1e-15}; static constexpr BoutReal FFTTolerance{1.e-12}; /// Does \p str contain \p substring? -::testing::AssertionResult IsSubString(const std::string &str, - const std::string &substring); +::testing::AssertionResult IsSubString(const std::string& str, + const std::string& substring); void fillField(Field3D& f, std::vector>> values); void fillField(Field2D& f, std::vector> values); @@ -46,8 +46,8 @@ T makeField(const std::function& fill_function, } /// Teach googletest how to print SpecificInds -template -inline std::ostream& operator<< (std::ostream &out, const SpecificInd &index) { +template +inline std::ostream& operator<<(std::ostream& out, const SpecificInd& index) { return out << index.ind; } @@ -147,8 +147,8 @@ public: zstart = 0; zend = nz - 1; - StaggerGrids=false; - + StaggerGrids = false; + // Unused variables periodicX = false; NXPE = 1; @@ -161,13 +161,12 @@ public: mpi = bout::globals::mpi; } - void setCoordinates(std::shared_ptr coords, CELL_LOC location = CELL_CENTRE) { + void setCoordinates(std::shared_ptr coords, + CELL_LOC location = CELL_CENTRE) { coords_map[location] = coords; } - void setGridDataSource(GridDataSource* source_in) { - source = source_in; - } + void setGridDataSource(GridDataSource* source_in) { source = source_in; } // Use this if the FakeMesh needs x- and y-boundaries void createBoundaries() { @@ -182,8 +181,8 @@ public: bool UNUSED(disable_corners) = false) override { return nullptr; } - comm_handle sendY(FieldGroup& UNUSED(g), comm_handle UNUSED(handle) = nullptr) override - { + comm_handle sendY(FieldGroup& UNUSED(g), + comm_handle UNUSED(handle) = nullptr) override { return nullptr; } int wait(comm_handle UNUSED(handle)) override { return 0; } @@ -254,8 +253,8 @@ public: int getLocalZIndex(int) const override { return 0; } int getLocalZIndexNoBoundaries(int) const override { return 0; } - void initDerivs(Options * opt){ - StaggerGrids=true; + void initDerivs(Options* opt) { + StaggerGrids = true; derivs_init(opt); } @@ -323,7 +322,7 @@ public: using Mesh::msg_len; private: - std::vector boundaries; + std::vector boundaries; }; /// FakeGridDataSource provides a non-null GridDataSource* source to use with FakeMesh, to @@ -413,6 +412,7 @@ public: bool hasXBoundaryGuards(Mesh* UNUSED(m)) override { return true; } bool hasYBoundaryGuards() override { return true; } + private: Options values; ///< Store values to be returned by get() }; @@ -456,8 +456,8 @@ public: // No call to Coordinates::geometry() needed here static_cast(bout::globals::mesh)->setCoordinates(test_coords); - static_cast(bout::globals::mesh)->setGridDataSource( - new FakeGridDataSource()); + static_cast(bout::globals::mesh) + ->setGridDataSource(new FakeGridDataSource()); // May need a ParallelTransform to create fields, because create3D calls // fromFieldAligned test_coords->setParallelTransform( diff --git a/tools/archiving/dumpsample/pdbsample.cxx b/tools/archiving/dumpsample/pdbsample.cxx index 7fdc023401..90ea69adb2 100644 --- a/tools/archiving/dumpsample/pdbsample.cxx +++ b/tools/archiving/dumpsample/pdbsample.cxx @@ -11,219 +11,222 @@ // The PDB library (C) #include "pdb.h" -int main(int argc, char** argv) -{ - if(argc < 4) { +int main(int argc, char** argv) { + if (argc < 4) { fprintf(stderr, "Useage: %s \n", argv[0]); return 1; } int tstride; - if(sscanf(argv[3], "%d", &tstride) != 1) { + if (sscanf(argv[3], "%d", &tstride) != 1) { fprintf(stderr, "\tERROR: t stride must be an integer\n"); return 1; } // Open input file - PDBfile *in; - if((in = PD_open(argv[1], "r")) == NULL) { + PDBfile* in; + if ((in = PD_open(argv[1], "r")) == NULL) { fprintf(stderr, "\tERROR: Could not open input file '%s'\n", argv[1]); return 1; } // Open output file - PDBfile *out; - if((out = PD_open(argv[2], "w")) == NULL) { + PDBfile* out; + if ((out = PD_open(argv[2], "w")) == NULL) { fprintf(stderr, "\tERROR: Could not open output file '%s'\n", argv[2]); return 1; } // Get list of variables - + int nvars; - char **var_names = PD_ls(in, NULL, NULL, &nvars); - if((var_names == (char**) NULL) || (nvars < 1)) { + char** var_names = PD_ls(in, NULL, NULL, &nvars); + if ((var_names == (char**)NULL) || (nvars < 1)) { fprintf(stderr, "\tERROR: No variables\n"); return 1; } - + // Go through the variables - char *varname; - for(int var=0;varindex_min; max = dims->index_max; - - if(nd > 3) { - fprintf(stderr, "\tERROR: Can't handle variable '%s': more than 4D\n", varname); - return 2; + + if (nd > 3) { + fprintf(stderr, "\tERROR: Can't handle variable '%s': more than 4D\n", varname); + return 2; } - inds[3*nd] = min; inds[3*nd + 1] = max; inds[3*nd + 2] = 1L; - + inds[3 * nd] = min; + inds[3 * nd + 1] = max; + inds[3 * nd + 2] = 1L; + varsize *= max - min + 1; nd++; dims = dims->next; } - + // Get variable type - char *typ; + char* typ; typ = PD_entry_type(ep); - if((strcmp(varname, "t_array") == 0) && (nd == 1)) { - float *fdata = new float[varsize]; + if ((strcmp(varname, "t_array") == 0) && (nd == 1)) { + float* fdata = new float[varsize]; // Read the data from the PDB file inds[2] = tstride; int nread; - if( (nread = PD_read_as_alt(in, varname, "float", fdata, inds)) == 0) { - fprintf(stderr, "\tWARNING: Could not read t_array. Ignoring\n"); - delete[] fdata; - continue; + if ((nread = PD_read_as_alt(in, varname, "float", fdata, inds)) == 0) { + fprintf(stderr, "\tWARNING: Could not read t_array. Ignoring\n"); + delete[] fdata; + continue; } - + inds[0] = 0L; - inds[1] = nread-1; + inds[1] = nread - 1; inds[2] = 1L; - - if(PD_write_alt(out, varname, "float", fdata, 1, inds) == FALSE) { - fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname); + + if (PD_write_alt(out, varname, "float", fdata, 1, inds) == FALSE) { + fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname); } delete[] fdata; - }else if(nd == 4) { + } else if (nd == 4) { // Reducing time resolution - - if(strcasecmp(typ, "integer") == 0) { - int *idata = new int[varsize]; - - // Read the data from the PDB file - inds[2] = tstride; - int nread; - if( (nread = PD_read_as_alt(in, varname, "integer", idata, inds)) == 0) { - fprintf(stderr, "\tWARNING: Could not read '%s'. Ignoring\n", varname); - delete[] idata; - continue; - } - - if( nread % (varsize / (inds[1] - inds[0] + 1)) != 0 ) { - fprintf(stderr, "ERROR: Accounting error: (%ld, %ld), %d, %d\n", inds[0], inds[1], varsize, nread); - delete[] idata; - continue; - } - - nread = nread / (varsize / (inds[1] - inds[0] + 1)); - - inds[0] = 0L; - inds[1] = nread - 1; - inds[2] = 1L; - - if(PD_write_alt(out, varname, "integer", idata, 4, inds) == FALSE) { - fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname); - } - - delete[] idata; - - }else if( (strcasecmp(typ, "float") == 0) || - (strcasecmp(typ, "double") == 0) ) { - // Convert doubles to floats - - float *fdata = new float[varsize]; - - // Read the data from the PDB file - inds[2] = tstride; - int nread; - if( (nread = PD_read_as_alt(in, varname, "float", fdata, inds)) == 0) { - fprintf(stderr, "\tWARNING: Could not read '%s'. Ignoring\n", varname); - delete[] fdata; - continue; - } - - if( nread % (varsize / (inds[1] - inds[0] + 1)) != 0 ) { - fprintf(stderr, "ERROR: Accounting error: (%ld, %ld), %d, %d\n", inds[0], inds[1], varsize, nread); - delete[] fdata; - continue; - } - - nread = nread / (varsize / (inds[1] - inds[0] + 1)); - - inds[0] = 0L; - inds[1] = nread - 1; - inds[2] = 1L; - - if(PD_write_alt(out, varname, "float", fdata, 4, inds) == FALSE) { - fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname); - } - - delete[] fdata; - - }else { - fprintf(stderr, "\tWARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, typ); + + if (strcasecmp(typ, "integer") == 0) { + int* idata = new int[varsize]; + + // Read the data from the PDB file + inds[2] = tstride; + int nread; + if ((nread = PD_read_as_alt(in, varname, "integer", idata, inds)) == 0) { + fprintf(stderr, "\tWARNING: Could not read '%s'. Ignoring\n", varname); + delete[] idata; + continue; + } + + if (nread % (varsize / (inds[1] - inds[0] + 1)) != 0) { + fprintf(stderr, "ERROR: Accounting error: (%ld, %ld), %d, %d\n", inds[0], + inds[1], varsize, nread); + delete[] idata; + continue; + } + + nread = nread / (varsize / (inds[1] - inds[0] + 1)); + + inds[0] = 0L; + inds[1] = nread - 1; + inds[2] = 1L; + + if (PD_write_alt(out, varname, "integer", idata, 4, inds) == FALSE) { + fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname); + } + + delete[] idata; + + } else if ((strcasecmp(typ, "float") == 0) || (strcasecmp(typ, "double") == 0)) { + // Convert doubles to floats + + float* fdata = new float[varsize]; + + // Read the data from the PDB file + inds[2] = tstride; + int nread; + if ((nread = PD_read_as_alt(in, varname, "float", fdata, inds)) == 0) { + fprintf(stderr, "\tWARNING: Could not read '%s'. Ignoring\n", varname); + delete[] fdata; + continue; + } + + if (nread % (varsize / (inds[1] - inds[0] + 1)) != 0) { + fprintf(stderr, "ERROR: Accounting error: (%ld, %ld), %d, %d\n", inds[0], + inds[1], varsize, nread); + delete[] fdata; + continue; + } + + nread = nread / (varsize / (inds[1] - inds[0] + 1)); + + inds[0] = 0L; + inds[1] = nread - 1; + inds[2] = 1L; + + if (PD_write_alt(out, varname, "float", fdata, 4, inds) == FALSE) { + fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname); + } + + delete[] fdata; + + } else { + fprintf(stderr, "\tWARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, + typ); } - }else { + } else { // Just copy the data across - - if(strcasecmp(typ, "integer") == 0) { - - int *idata = new int[varsize]; - - // Read the data from the PDB file - if (PD_read_as(in, varname, "integer", idata) == 0) { - fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); - delete[] idata; - continue; - } - - if(PD_write_alt(out, varname, "integer", idata, nd, inds) == FALSE) { - fprintf(stderr, "\tWARNING: Could not write variable '%s'\n", varname); - } - - delete[] idata; - - }else if( (strcasecmp(typ, "float") == 0) || - (strcasecmp(typ, "double") == 0) ) { - // Convert doubles to floats - - float *fdata = new float[varsize]; - - // Read the data from the PDB file - if (PD_read_as(in, varname, "float", fdata) == 0) { - fprintf(stderr, "\tWARNING: Could not read variable '%s'. Ignoring\n", varname); - delete[] fdata; - continue; - } - - if(PD_write_alt(out, varname, "float", fdata, nd, inds) == FALSE) { - fprintf(stderr, "\tWARNING: Could not write variable '%s'\n", varname); - } - - delete[] fdata; - }else { - fprintf(stderr, "WARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, typ); + + if (strcasecmp(typ, "integer") == 0) { + + int* idata = new int[varsize]; + + // Read the data from the PDB file + if (PD_read_as(in, varname, "integer", idata) == 0) { + fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); + delete[] idata; + continue; + } + + if (PD_write_alt(out, varname, "integer", idata, nd, inds) == FALSE) { + fprintf(stderr, "\tWARNING: Could not write variable '%s'\n", varname); + } + + delete[] idata; + + } else if ((strcasecmp(typ, "float") == 0) || (strcasecmp(typ, "double") == 0)) { + // Convert doubles to floats + + float* fdata = new float[varsize]; + + // Read the data from the PDB file + if (PD_read_as(in, varname, "float", fdata) == 0) { + fprintf(stderr, "\tWARNING: Could not read variable '%s'. Ignoring\n", varname); + delete[] fdata; + continue; + } + + if (PD_write_alt(out, varname, "float", fdata, nd, inds) == FALSE) { + fprintf(stderr, "\tWARNING: Could not write variable '%s'\n", varname); + } + + delete[] fdata; + } else { + fprintf(stderr, "WARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, + typ); } } } - + PD_close(in); PD_close(out); - + return 0; } diff --git a/tools/archiving/pdb2cdf/pdb2cdf.cxx b/tools/archiving/pdb2cdf/pdb2cdf.cxx index 7904e51ba2..ac8bc85de6 100644 --- a/tools/archiving/pdb2cdf/pdb2cdf.cxx +++ b/tools/archiving/pdb2cdf/pdb2cdf.cxx @@ -16,63 +16,57 @@ // Dimension struct TDim { char* label; // Label for the dimension - int size; + int size; int min, max; // Minimum, maximum index - NcDim* nDim; // netCDF dimension + NcDim* nDim; // netCDF dimension }; // List of dimensions. Handles up to 3 -static TDim dimlist3d[] = {{"x", 0}, - {"y", 0}, - {"z", 0}}; +static TDim dimlist3d[] = {{"x", 0}, {"y", 0}, {"z", 0}}; // Special case for 4D -static TDim dimlist4d[] = {{"t", 0}, - {"x", 0}, - {"y", 0}, - {"z", 0}}; - -int main(int argc, char** argv) -{ - TDim *dimlist; - - if(argc < 2) { +static TDim dimlist4d[] = {{"t", 0}, {"x", 0}, {"y", 0}, {"z", 0}}; + +int main(int argc, char** argv) { + TDim* dimlist; + + if (argc < 2) { fprintf(stderr, "Useage: %s file1 file2 ...\n", argv[0]); return 1; } - for(int i=1;inext; + while (dims != (dimdes*)NULL) { + nd++; + dims = dims->next; } - if(nd > maxdims) { - maxdims = nd; - maxdimvar = var; + if (nd > maxdims) { + maxdims = nd; + maxdimvar = var; } } printf("%d dimensions\n", maxdims); - - if(maxdims < 4) { + + if (maxdims < 4) { dimlist = dimlist3d; - }else + } else { dimlist = dimlist4d; - - if(maxdims > 4) { + } + + if (maxdims > 4) { fprintf(stderr, "ERROR: Can only handle up to 4D variables\n"); return 1; } - + // Get the size of each dimension varname = var_names[maxdimvar]; - if((ep = PD_query_entry(in, varname, NULL)) == (syment*) NULL) { + if ((ep = PD_query_entry(in, varname, NULL)) == (syment*)NULL) { fprintf(stderr, "Error querying variable %s\n", varname); return 1; } dims = PD_entry_dimensions(ep); - - for(int d=0;dindex_min; dimlist[d].max = dims->index_max; dimlist[d].size = dims->index_max - dims->index_min + 1; - + // Create a netCDF dimension dimlist[d].nDim = dataFile.add_dim(dimlist[d].label, dimlist[d].size); - - printf("\t\t%s: %d -> %d (%d)\n", dimlist[d].label, dimlist[d].min, dimlist[d].max, dimlist[d].size); + + printf("\t\t%s: %d -> %d (%d)\n", dimlist[d].label, dimlist[d].min, dimlist[d].max, + dimlist[d].size); dims = dims->next; } // Go through each variable - for(int var=0;varindex_min; - max = dims->index_max; - - varsize *= max - min + 1; - - vardim[nd] = -1; - // Find which dimension this corresponds to - for(int d = lastdim+1;d %d]\n", varname, nd+1, min, max); - gotdims = false; - break; - } - - nd++; - dims = dims->next; + while (dims != (dimdes*)NULL) { + int min, max; + min = dims->index_min; + max = dims->index_max; + + varsize *= max - min + 1; + + vardim[nd] = -1; + // Find which dimension this corresponds to + for (int d = lastdim + 1; d < maxdims; d++) { + if ((dimlist[d].min == min) && (dimlist[d].max == max)) { + if (lastdim == -1) { + printf("[%s", dimlist[d].label); + } else { + printf(",%s", dimlist[d].label); + } + vardim[nd] = d; + lastdim = d; + break; + } + } + if (vardim[nd] == -1) { + // Not an existing dimension. Should create a new dimension + fprintf(stderr, "ERROR: %s has an unrecognised %d dimension [%d -> %d]\n", + varname, nd + 1, min, max); + gotdims = false; + break; + } + + nd++; + dims = dims->next; } - - if(!gotdims) - continue; // Skip this variable - if(lastdim != -1) - printf("] (%d elements) ", varsize); + if (!gotdims) { + continue; // Skip this variable + } + + if (lastdim != -1) { + printf("] (%d elements) ", varsize); + } // Now know number of dimensions nd, and a list of dimension indices vardim // Get variable type - char *typ; + char* typ; typ = PD_entry_type(ep); printf(" Type: %s ", typ); fflush(stdout); - if(strcasecmp(typ, "integer") == 0) { - - int *idata = new int[varsize]; - - // Read the data from the PDB file - if (PD_read_as(in, varname, "integer", idata) == FALSE) { - fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); - continue; - } - switch(nd) { - case 0: { - // Add a 0-D variable to the netCDF file - NcVar *ncdata = dataFile.add_var(varname, ncInt); - - // Write data - ncdata->put(idata); - break; - } - case 1: { - NcVar *ncdata = dataFile.add_var(varname, ncInt, dimlist[vardim[0]].nDim); - ncdata->put(idata, varsize); - break; - } - case 2: { - NcVar *ncdata = dataFile.add_var(varname, ncInt, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim); - ncdata->put(idata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size); - break; - } - case 3: { - NcVar *ncdata = dataFile.add_var(varname, ncInt, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim, - dimlist[vardim[2]].nDim); - ncdata->put(idata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size, - dimlist[vardim[2]].size); - break; - } - case 4: { - NcVar *ncdata = dataFile.add_var(varname, ncInt, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim, - dimlist[vardim[2]].nDim, - dimlist[vardim[3]].nDim); - ncdata->put(idata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size, - dimlist[vardim[2]].size, - dimlist[vardim[3]].size); - break; - } - default: { - fprintf(stderr, "\t\tWARNING: Cannot yet handle %d-D integers. Ignoring\n", nd); - } - } - delete[] idata; - - ////////////////////////////////////////////////////////////////// - - }else if(strcasecmp(typ, "float") == 0) { - - float *fdata = new float[varsize]; - - // Read the data from the PDB file - if (PD_read_as(in, varname, "float", fdata) == FALSE) { - fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); - continue; - } - switch(nd) { - case 0: { - NcVar *ncdata = dataFile.add_var(varname, ncFloat); - - // Write data - ncdata->put(fdata); - break; - } - case 1: { - NcVar *ncdata = dataFile.add_var(varname, ncFloat, dimlist[vardim[0]].nDim); - ncdata->put(fdata, varsize); - break; - } - case 2: { - NcVar *ncdata = dataFile.add_var(varname, ncFloat, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim); - ncdata->put(fdata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size); - break; - } - case 3: { - NcVar *ncdata = dataFile.add_var(varname, ncFloat, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim, - dimlist[vardim[2]].nDim); - ncdata->put(fdata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size, - dimlist[vardim[2]].size); - break; - } - case 4: { - NcVar *ncdata = dataFile.add_var(varname, ncFloat, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim, - dimlist[vardim[2]].nDim, - dimlist[vardim[3]].nDim); - ncdata->put(fdata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size, - dimlist[vardim[2]].size, - dimlist[vardim[3]].size); - break; - } - default: { - fprintf(stderr, "\t\tWARNING: Cannot yet handle %d-D floats. Ignoring\n", nd); - } - } - delete[] fdata; - - ////////////////////////////////////////////////////////////////// - - }else if(strcasecmp(typ, "double") == 0) { - - double *ddata = new double[varsize]; - - // Read the data from the PDB file - if (PD_read_as(in, varname, "double", ddata) == FALSE) { - fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); - continue; - } - switch(nd) { - case 0: { - NcVar *ncdata = dataFile.add_var(varname, ncDouble); - - // Write data - ncdata->put(ddata); - break; - } - case 1: { - NcVar *ncdata = dataFile.add_var(varname, ncDouble, dimlist[vardim[0]].nDim); - ncdata->put(ddata, varsize); - break; - } - case 2: { - NcVar *ncdata = dataFile.add_var(varname, ncDouble, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim); - ncdata->put(ddata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size); - break; - } - case 3: { - NcVar *ncdata = dataFile.add_var(varname, ncDouble, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim, - dimlist[vardim[2]].nDim); - ncdata->put(ddata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size, - dimlist[vardim[2]].size); - break; - } - case 4: { - NcVar *ncdata = dataFile.add_var(varname, ncDouble, - dimlist[vardim[0]].nDim, - dimlist[vardim[1]].nDim, - dimlist[vardim[2]].nDim, - dimlist[vardim[3]].nDim); - ncdata->put(ddata, - dimlist[vardim[0]].size, - dimlist[vardim[1]].size, - dimlist[vardim[2]].size, - dimlist[vardim[3]].size); - break; - } - default: { - fprintf(stderr, "\t\tWARNING: Cannot yet handle %d-D doubles. Ignoring\n", nd); - } - } - delete[] ddata; - }else { - fprintf(stderr, "\tWARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, typ); + if (strcasecmp(typ, "integer") == 0) { + + int* idata = new int[varsize]; + + // Read the data from the PDB file + if (PD_read_as(in, varname, "integer", idata) == FALSE) { + fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); + continue; + } + switch (nd) { + case 0: { + // Add a 0-D variable to the netCDF file + NcVar* ncdata = dataFile.add_var(varname, ncInt); + + // Write data + ncdata->put(idata); + break; + } + case 1: { + NcVar* ncdata = dataFile.add_var(varname, ncInt, dimlist[vardim[0]].nDim); + ncdata->put(idata, varsize); + break; + } + case 2: { + NcVar* ncdata = dataFile.add_var(varname, ncInt, dimlist[vardim[0]].nDim, + dimlist[vardim[1]].nDim); + ncdata->put(idata, dimlist[vardim[0]].size, dimlist[vardim[1]].size); + break; + } + case 3: { + NcVar* ncdata = + dataFile.add_var(varname, ncInt, dimlist[vardim[0]].nDim, + dimlist[vardim[1]].nDim, dimlist[vardim[2]].nDim); + ncdata->put(idata, dimlist[vardim[0]].size, dimlist[vardim[1]].size, + dimlist[vardim[2]].size); + break; + } + case 4: { + NcVar* ncdata = dataFile.add_var( + varname, ncInt, dimlist[vardim[0]].nDim, dimlist[vardim[1]].nDim, + dimlist[vardim[2]].nDim, dimlist[vardim[3]].nDim); + ncdata->put(idata, dimlist[vardim[0]].size, dimlist[vardim[1]].size, + dimlist[vardim[2]].size, dimlist[vardim[3]].size); + break; + } + default: { + fprintf(stderr, "\t\tWARNING: Cannot yet handle %d-D integers. Ignoring\n", nd); + } + } + delete[] idata; + + ////////////////////////////////////////////////////////////////// + + } else if (strcasecmp(typ, "float") == 0) { + + float* fdata = new float[varsize]; + + // Read the data from the PDB file + if (PD_read_as(in, varname, "float", fdata) == FALSE) { + fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); + continue; + } + switch (nd) { + case 0: { + NcVar* ncdata = dataFile.add_var(varname, ncFloat); + + // Write data + ncdata->put(fdata); + break; + } + case 1: { + NcVar* ncdata = dataFile.add_var(varname, ncFloat, dimlist[vardim[0]].nDim); + ncdata->put(fdata, varsize); + break; + } + case 2: { + NcVar* ncdata = dataFile.add_var(varname, ncFloat, dimlist[vardim[0]].nDim, + dimlist[vardim[1]].nDim); + ncdata->put(fdata, dimlist[vardim[0]].size, dimlist[vardim[1]].size); + break; + } + case 3: { + NcVar* ncdata = + dataFile.add_var(varname, ncFloat, dimlist[vardim[0]].nDim, + dimlist[vardim[1]].nDim, dimlist[vardim[2]].nDim); + ncdata->put(fdata, dimlist[vardim[0]].size, dimlist[vardim[1]].size, + dimlist[vardim[2]].size); + break; + } + case 4: { + NcVar* ncdata = dataFile.add_var( + varname, ncFloat, dimlist[vardim[0]].nDim, dimlist[vardim[1]].nDim, + dimlist[vardim[2]].nDim, dimlist[vardim[3]].nDim); + ncdata->put(fdata, dimlist[vardim[0]].size, dimlist[vardim[1]].size, + dimlist[vardim[2]].size, dimlist[vardim[3]].size); + break; + } + default: { + fprintf(stderr, "\t\tWARNING: Cannot yet handle %d-D floats. Ignoring\n", nd); + } + } + delete[] fdata; + + ////////////////////////////////////////////////////////////////// + + } else if (strcasecmp(typ, "double") == 0) { + + double* ddata = new double[varsize]; + + // Read the data from the PDB file + if (PD_read_as(in, varname, "double", ddata) == FALSE) { + fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n"); + continue; + } + switch (nd) { + case 0: { + NcVar* ncdata = dataFile.add_var(varname, ncDouble); + + // Write data + ncdata->put(ddata); + break; + } + case 1: { + NcVar* ncdata = dataFile.add_var(varname, ncDouble, dimlist[vardim[0]].nDim); + ncdata->put(ddata, varsize); + break; + } + case 2: { + NcVar* ncdata = dataFile.add_var(varname, ncDouble, dimlist[vardim[0]].nDim, + dimlist[vardim[1]].nDim); + ncdata->put(ddata, dimlist[vardim[0]].size, dimlist[vardim[1]].size); + break; + } + case 3: { + NcVar* ncdata = + dataFile.add_var(varname, ncDouble, dimlist[vardim[0]].nDim, + dimlist[vardim[1]].nDim, dimlist[vardim[2]].nDim); + ncdata->put(ddata, dimlist[vardim[0]].size, dimlist[vardim[1]].size, + dimlist[vardim[2]].size); + break; + } + case 4: { + NcVar* ncdata = dataFile.add_var( + varname, ncDouble, dimlist[vardim[0]].nDim, dimlist[vardim[1]].nDim, + dimlist[vardim[2]].nDim, dimlist[vardim[3]].nDim); + ncdata->put(ddata, dimlist[vardim[0]].size, dimlist[vardim[1]].size, + dimlist[vardim[2]].size, dimlist[vardim[3]].size); + break; + } + default: { + fprintf(stderr, "\t\tWARNING: Cannot yet handle %d-D doubles. Ignoring\n", nd); + } + } + delete[] ddata; + } else { + fprintf(stderr, "\tWARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, + typ); } printf("\n"); } - - delete[] outname; + + delete[] outname; dataFile.close(); // Close the output file. Probably optional. } - + return 0; } - diff --git a/tools/pylib/_boutpp_build/boutexception_helper.cxx b/tools/pylib/_boutpp_build/boutexception_helper.cxx index 09d8249f44..650ec3e546 100644 --- a/tools/pylib/_boutpp_build/boutexception_helper.cxx +++ b/tools/pylib/_boutpp_build/boutexception_helper.cxx @@ -1,4 +1,4 @@ -#include "boutexception.hxx" +#include "bout/boutexception.hxx" #include void raise_bout_py_error() { diff --git a/tools/pylib/_boutpp_build/boutpp_openmpi_compat.hxx b/tools/pylib/_boutpp_build/boutpp_openmpi_compat.hxx index 890cf3770d..f17cf5bf54 100644 --- a/tools/pylib/_boutpp_build/boutpp_openmpi_compat.hxx +++ b/tools/pylib/_boutpp_build/boutpp_openmpi_compat.hxx @@ -101,24 +101,30 @@ static void PyMPI_OPENMPI_dlopen_libmpi(void) { #endif #if defined(OMPI_MAJOR_VERSION) #if OMPI_MAJOR_VERSION == 3 - if (!handle) + if (!handle) { handle = dlopen("libmpi.40.dylib", mode); + } #elif OMPI_MAJOR_VERSION == 2 - if (!handle) + if (!handle) { handle = dlopen("libmpi.20.dylib", mode); + } #elif OMPI_MAJOR_VERSION == 1 && OMPI_MINOR_VERSION >= 10 - if (!handle) + if (!handle) { handle = dlopen("libmpi.12.dylib", mode); + } #elif OMPI_MAJOR_VERSION == 1 && OMPI_MINOR_VERSION >= 6 - if (!handle) + if (!handle) { handle = dlopen("libmpi.1.dylib", mode); + } #elif OMPI_MAJOR_VERSION == 1 - if (!handle) + if (!handle) { handle = dlopen("libmpi.0.dylib", mode); + } #endif #endif - if (!handle) + if (!handle) { handle = dlopen("libmpi.dylib", mode); + } #else /* GNU/Linux and others */ #ifdef RTLD_NOLOAD @@ -126,31 +132,40 @@ static void PyMPI_OPENMPI_dlopen_libmpi(void) { #endif #if defined(OMPI_MAJOR_VERSION) #if OMPI_MAJOR_VERSION >= 10 /* IBM Spectrum MPI */ - if (!handle) + if (!handle) { handle = dlopen("libmpi_ibm.so.2", mode); - if (!handle) + } + if (!handle) { handle = dlopen("libmpi_ibm.so.1", mode); - if (!handle) + } + if (!handle) { handle = dlopen("libmpi_ibm.so", mode); + } #elif OMPI_MAJOR_VERSION == 3 - if (!handle) + if (!handle) { handle = dlopen("libmpi.so.40", mode); + } #elif OMPI_MAJOR_VERSION == 2 - if (!handle) + if (!handle) { handle = dlopen("libmpi.so.20", mode); + } #elif OMPI_MAJOR_VERSION == 1 && OMPI_MINOR_VERSION >= 10 - if (!handle) + if (!handle) { handle = dlopen("libmpi.so.12", mode); + } #elif OMPI_MAJOR_VERSION == 1 && OMPI_MINOR_VERSION >= 6 - if (!handle) + if (!handle) { handle = dlopen("libmpi.so.1", mode); + } #elif OMPI_MAJOR_VERSION == 1 - if (!handle) + if (!handle) { handle = dlopen("libmpi.so.0", mode); + } #endif #endif - if (!handle) + if (!handle) { handle = dlopen("libmpi.so", mode); + } #endif } diff --git a/tools/tokamak_grids/coils/coils.cxx b/tools/tokamak_grids/coils/coils.cxx index 0415f3c9d6..caf7084387 100644 --- a/tools/tokamak_grids/coils/coils.cxx +++ b/tools/tokamak_grids/coils/coils.cxx @@ -4,9 +4,9 @@ #include "coils.h" #include -#include -#include #include +#include +#include using namespace std; @@ -15,88 +15,64 @@ const double PI = 3.1415926; ///////////////////////////////////////////////////////////// // Point implementation -double Point::norm() const -{ - return sqrt(x*x + y*y + z*z); -} +double Point::norm() const { return sqrt(x * x + y * y + z * z); } -double Point::distanceTo(const Point &p) -{ - return (*this - p).norm(); -} +double Point::distanceTo(const Point& p) { return (*this - p).norm(); } -const Point Point::operator+() const -{ - return *this; -} +const Point Point::operator+() const { return *this; } -const Point Point::operator+(const Point &p) const -{ - return Point(x+p.x, y+p.y, z+p.z); +const Point Point::operator+(const Point& p) const { + return Point(x + p.x, y + p.y, z + p.z); } -Point & Point::operator+=(const Point &p) -{ +Point& Point::operator+=(const Point& p) { x += p.x; y += p.y; z += p.z; return *this; } -const Point Point::operator-() const -{ - return Point(-x, -y, -z); -} +const Point Point::operator-() const { return Point(-x, -y, -z); } -const Point Point::operator-(const Point &p) const -{ - return Point(x+p.x, y+p.y, z+p.z); +const Point Point::operator-(const Point& p) const { + return Point(x + p.x, y + p.y, z + p.z); } -Point & Point::operator-=(const Point &p) -{ +Point& Point::operator-=(const Point& p) { x -= p.x; y -= p.y; z -= p.z; return *this; } -const Point Point::operator/(double val) const -{ - return Point(x/val, y/val, z/val); +const Point Point::operator/(double val) const { + return Point(x / val, y / val, z / val); } -Point & Point::operator/=(double val) -{ +Point& Point::operator/=(double val) { x /= val; y /= val; z /= val; return *this; } -const Point Point::operator*(double val) const -{ - return Point(x*val, y*val, z*val); +const Point Point::operator*(double val) const { + return Point(x * val, y * val, z * val); } -Point & Point::operator*=(double val) -{ +Point& Point::operator*=(double val) { x *= val; y *= val; z *= val; return *this; } -const Point operator*(const double lhs, const Point &rhs) -{ - return rhs * lhs; -} +const Point operator*(const double lhs, const Point& rhs) { return rhs * lhs; } ///////////////////////////////////////////////////////////// // Vector implementation -Vector & Vector::operator+=(const Vector &v) -{ +Vector& Vector::operator+=(const Vector& v) { direction += v.direction; return *this; } @@ -104,164 +80,163 @@ Vector & Vector::operator+=(const Vector &v) ///////////////////////////////////////////////////////////// // Calculate vector potential from a line at given position -const Point AfromLine(Point start, Point end, double current, Point pos) -{ +const Point AfromLine(Point start, Point end, double current, Point pos) { double len = start.distanceTo(end); - + Point ivec = current * (end - start) / len; // Current vector - + // Integrate ivec * 1/d over wire double integral = 0., last; int n = 1; do { last = integral; n *= 2; - + // Use Simpson's rule to integrate - double h = len / ((double) n); - + double h = len / ((double)n); + integral = 0.; - for(int i=0;i<=n;i++) { - double frac = ((double) i) / ((double) (n-1)); - double d = pos.distanceTo( frac*start + (1.-frac)*end ); - - if( (i == 0) || (i == (n-1)) ) { + for (int i = 0; i <= n; i++) { + double frac = ((double)i) / ((double)(n - 1)); + double d = pos.distanceTo(frac * start + (1. - frac) * end); + + if ((i == 0) || (i == (n - 1))) { integral += 1. / d; - }else if( i % 2 == 1 ){ + } else if (i % 2 == 1) { integral += 4. / d; - }else + } else { integral += 2. / d; + } integral *= h / 3.; } - }while(abs( (integral - last) / (integral + last) ) > 1.e-3); - + } while (abs((integral - last) / (integral + last)) > 1.e-3); + return ivec * integral; } -const Point AfromCoil(vector corners, double current, Point pos) -{ +const Point AfromCoil(vector corners, double current, Point pos) { Point A; - - for(int i=0;iget_var(name); - if(!var) { +int readInteger(NcFile* dataFile, const char* name) { + NcVar* var = dataFile->get_var(name); + if (!var) { cout << "ERROR: Couldn't read " << string(name) << endl; return NULL; } - if(!var->is_valid()) { + if (!var->is_valid()) { cout << "ERROR: Couldn't read " << string(name) << endl; return NULL; } - + int result; - var->get(&result,1); + var->get(&result, 1); return result; } -double** readMatrix(NcFile *dataFile, const char *name, int &nx, int &ny) -{ - NcVar *var = dataFile->get_var(name); - if(!var) { +double** readMatrix(NcFile* dataFile, const char* name, int& nx, int& ny) { + NcVar* var = dataFile->get_var(name); + if (!var) { cout << "ERROR: Couldn't read " << string(name) << endl; return NULL; } - if(!var->is_valid()) { + if (!var->is_valid()) { cout << "ERROR: Couldn't read " << string(name) << endl; return NULL; } - if(var->num_dims() != 2) { + if (var->num_dims() != 2) { cout << "ERROR: " << string(name) << " must be 2D" << endl; return NULL; } - + NcDim *xDim, *yDim; xDim = var->get_dim(0); yDim = var->get_dim(1); - + nx = xDim->size(); ny = yDim->size(); - double **m = matrix(nx, ny); + double** m = matrix(nx, ny); var->get(m[0], nx, ny); - + return m; } -int main(int argc, char **argv) -{ - char *name; - +int main(int argc, char** argv) { + char* name; + // Check command-line arguments - - if(argc == 1) { + + if (argc == 1) { cout << "Useage: " << string(argv[0]) << " " << endl; return 1; } name = argv[1]; - NcFile *dataFile; + NcFile* dataFile; NcDim *xDim, *yDim; - + NcError err(NcError::verbose_nonfatal); dataFile = new NcFile(name, NcFile::ReadOnly); - if(!dataFile->is_valid()) { + if (!dataFile->is_valid()) { delete dataFile; cout << "ERROR: Couldn't open grid file" << endl; return 1; } - if(!(xDim = dataFile->get_dim("x"))) { + if (!(xDim = dataFile->get_dim("x"))) { cout << "ERROR: Grid file doesn't have an x dimension" << endl; return 1; } - if(!(yDim = dataFile->get_dim("y"))) { + if (!(yDim = dataFile->get_dim("y"))) { cout << "ERROR: Grid file doesn't have a y dimension" << endl; return 1; } - + int nx, ny; - - double **Rxy = readMatrix(dataFile, "Rxy", nx, ny); - if(!Rxy) + + double** Rxy = readMatrix(dataFile, "Rxy", nx, ny); + if (!Rxy) { return 1; - double **Zxy = readMatrix(dataFile, "Zxy", nx, ny); - if(!Zxy) + } + double** Zxy = readMatrix(dataFile, "Zxy", nx, ny); + if (!Zxy) { return 1; - - int nz = 16; // Number of points to use in Z + } + + int nz = 16; // Number of points to use in Z // Loop over the grid points - for(int x=0; x < nx; x++) - for(int y=0;y Date: Mon, 20 Feb 2023 11:44:53 +0100 Subject: [PATCH 060/412] get script from next --- .clang-format | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.clang-format b/.clang-format index eb5e7992cb..b049b1a473 100644 --- a/.clang-format +++ b/.clang-format @@ -61,7 +61,6 @@ ForEachMacros: - foreach - Q_FOREACH - BOOST_FOREACH - - BOUT_FOR # IncludeBlocks: Regroup IncludeCategories: - Regex: '^(<|")bout/' @@ -77,8 +76,7 @@ IndentCaseLabels: false # IndentPPDirectives: None IndentWidth: 2 IndentWrappedFunctionNames: false -# requires clang-format 15+ -# InsertBraces: true +InsertBraces: true KeepEmptyLinesAtTheStartOfBlocks: true MacroBlockBegin: '' MacroBlockEnd: '' @@ -108,7 +106,7 @@ SpacesInContainerLiterals: true SpacesInCStyleCastParentheses: false SpacesInParentheses: false SpacesInSquareBrackets: false -StatementAttributeLikeMacros: +StatementMacros: - BOUT_OMP Standard: c++14 TabWidth: 8 From c2eb56db287c0ce463ced6ea6c0df72bbdb11fb7 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 11:44:53 +0100 Subject: [PATCH 061/412] Update all files for new headers --- examples/2Dturbulence_multigrid/esel.cxx | 2 +- examples/6field-simple/elm_6f.cxx | 4 +- examples/IMEX/advection-diffusion/imex.cxx | 2 +- .../advection-reaction/split_operator.cxx | 2 +- examples/IMEX/diffusion-nl/diffusion-nl.cxx | 2 +- examples/advdiff/advdiff.cxx | 2 +- examples/advdiff2/init.cxx | 2 +- examples/backtrace/backtrace.cxx | 2 +- examples/blob2d-laplacexz/blob2d.cxx | 4 +- examples/blob2d-outerloop/blob2d.cxx | 6 +- examples/blob2d/blob2d.cxx | 6 +- examples/conduction-snb/conduction-snb.cxx | 2 +- examples/constraints/alfven-wave/alfven.cxx | 4 +- .../constraints/laplace-dae/laplace_dae.cxx | 2 +- examples/dalf3/dalf3.cxx | 4 +- examples/eigen-box/eigen-box.cxx | 2 +- .../elm-pb-outerloop/elm_pb_outerloop.cxx | 8 +- examples/elm-pb/elm_pb.cxx | 4 +- examples/hasegawa-wakatani-3d/hw.cxx | 2 +- examples/hasegawa-wakatani/hw.cxx | 2 +- .../invertable_operator.cxx | 2 +- examples/laplacexy/alfven-wave/alfven.cxx | 4 +- examples/laplacexy/laplace_perp/test.cxx | 2 +- .../simple-hypre/test-laplacexy-hypre.cxx | 2 +- examples/laplacexy/simple/test-laplacexy.cxx | 2 +- examples/monitor/monitor.cxx | 2 +- .../communications/communications.cxx | 2 +- examples/performance/iterator/iterator.cxx | 2 +- .../tuning_regionblocksize.cxx | 2 +- examples/preconditioning/wave/test_precon.cxx | 2 +- examples/staggered_grid/test_staggered.cxx | 2 +- examples/subsampling/monitor.cxx | 2 +- examples/uedge-benchmark/ue_bmark.cxx | 2 +- include/bout/array.hxx | 3 +- include/bout/bout.hxx | 8 +- include/bout/bout_enum_class.hxx | 2 +- include/bout/coordinates.hxx | 2 +- include/bout/cyclic_reduction.hxx | 2 +- include/bout/expr.hxx | 2 +- include/bout/field.hxx | 48 +- include/bout/field2d.hxx | 2 +- include/bout/field_accessor.hxx | 6 +- include/bout/fv_ops.hxx | 4 +- include/bout/globalindexer.hxx | 6 +- include/bout/griddata.hxx | 2 +- include/bout/hypre_interface.hxx | 6 +- include/bout/index_derivs.hxx | 6 +- include/bout/index_derivs_interface.hxx | 2 +- include/bout/interpolation.hxx | 12 +- include/bout/invert/laplacexy.hxx | 4 +- include/bout/invert/laplacexy2.hxx | 4 +- include/bout/invert/laplacexy2_hypre.hxx | 2 +- include/bout/invert/laplacexz.hxx | 2 +- include/bout/invert_laplace.hxx | 2 +- include/bout/invert_parderiv.hxx | 2 +- include/bout/invert_pardiv.hxx | 2 +- include/bout/invertable_operator.hxx | 4 +- include/bout/mask.hxx | 2 +- include/bout/monitor.hxx | 2 +- include/bout/msg_stack.hxx | 2 +- include/bout/options.hxx | 4 +- include/bout/optionsreader.hxx | 2 +- include/bout/output.hxx | 4 +- include/bout/petsc_interface.hxx | 4 +- include/bout/physicsmodel.hxx | 6 +- include/bout/rajalib.hxx | 2 +- include/bout/region.hxx | 2 +- include/bout/snb.hxx | 2 +- include/bout/solver.hxx | 4 +- include/bout/sys/expressionparser.hxx | 2 +- include/bout/utils.hxx | 4 +- include/bout/vecops.hxx | 2 +- include/bout/where.hxx | 8 +- src/bout++.cxx | 12 +- src/field/field.cxx | 4 +- src/field/field2d.cxx | 14 +- src/field/field3d.cxx | 30 +- src/field/field_data.cxx | 2 +- src/field/field_factory.cxx | 6 +- src/field/fieldperp.cxx | 14 +- src/field/generated_fieldops.cxx | 292 ++-- src/field/globalfield.cxx | 2 +- src/field/initialprofiles.cxx | 2 +- src/field/vecops.cxx | 12 +- src/field/vector2d.cxx | 10 +- src/field/vector3d.cxx | 10 +- .../laplace/impls/cyclic/cyclic_laplace.cxx | 30 +- .../laplace/impls/cyclic/cyclic_laplace.hxx | 2 +- .../laplace/impls/hypre3d/hypre3d_laplace.cxx | 30 +- .../laplace/impls/hypre3d/hypre3d_laplace.hxx | 6 +- .../iterative_parallel_tri.cxx | 8 +- .../iterative_parallel_tri.hxx | 2 +- .../laplace/impls/multigrid/multigrid_alg.cxx | 1219 +++++++++-------- .../impls/multigrid/multigrid_laplace.cxx | 9 +- .../impls/multigrid/multigrid_laplace.hxx | 2 +- .../impls/multigrid/multigrid_solver.cxx | 36 +- .../laplace/impls/naulin/naulin_laplace.cxx | 6 +- src/invert/laplace/impls/pcr/pcr.cxx | 32 +- .../laplace/impls/pcr_thomas/pcr_thomas.cxx | 32 +- .../laplace/impls/petsc/petsc_laplace.cxx | 2 +- .../laplace/impls/petsc/petsc_laplace.hxx | 4 +- .../laplace/impls/petsc3damg/petsc3damg.cxx | 22 +- .../laplace/impls/petsc3damg/petsc3damg.hxx | 8 +- .../laplace/impls/serial_band/serial_band.cxx | 6 +- .../laplace/impls/serial_band/serial_band.hxx | 2 +- .../laplace/impls/serial_tri/serial_tri.cxx | 8 +- src/invert/laplace/impls/spt/spt.cxx | 6 +- src/invert/laplace/impls/spt/spt.hxx | 2 +- src/invert/laplace/invert_laplace.cxx | 12 +- src/invert/laplacexy/laplacexy.cxx | 2 +- src/invert/laplacexy2/laplacexy2.cxx | 2 +- src/invert/laplacexy2/laplacexy2_hypre.cxx | 6 +- .../impls/cyclic/laplacexz-cyclic.cxx | 2 +- src/invert/parderiv/impls/cyclic/cyclic.cxx | 2 +- src/invert/parderiv/impls/cyclic/cyclic.hxx | 2 +- .../pardiv/impls/cyclic/pardiv_cyclic.cxx | 2 +- src/mesh/boundary_region.cxx | 2 +- 117 files changed, 1091 insertions(+), 1104 deletions(-) diff --git a/examples/2Dturbulence_multigrid/esel.cxx b/examples/2Dturbulence_multigrid/esel.cxx index 55a773df45..810e1aa018 100644 --- a/examples/2Dturbulence_multigrid/esel.cxx +++ b/examples/2Dturbulence_multigrid/esel.cxx @@ -1,7 +1,7 @@ -#include #include #include #include +#include #include class ESEL : public PhysicsModel { diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx index 651aa8cdb8..40e4f7b3b3 100644 --- a/examples/6field-simple/elm_6f.cxx +++ b/examples/6field-simple/elm_6f.cxx @@ -7,15 +7,15 @@ *******************************************************************************/ #include "bout/bout.hxx" +#include "bout/constants.hxx" #include "bout/derivs.hxx" #include "bout/initialprofiles.hxx" #include "bout/interpolation_xz.hxx" #include "bout/invert_laplace.hxx" #include "bout/invert_parderiv.hxx" #include "bout/msg_stack.hxx" -#include "bout/sourcex.hxx" -#include "bout/constants.hxx" #include "bout/physicsmodel.hxx" +#include "bout/sourcex.hxx" #include diff --git a/examples/IMEX/advection-diffusion/imex.cxx b/examples/IMEX/advection-diffusion/imex.cxx index 7ec927e471..db3050fcdb 100644 --- a/examples/IMEX/advection-diffusion/imex.cxx +++ b/examples/IMEX/advection-diffusion/imex.cxx @@ -7,8 +7,8 @@ * * *******************************************************************/ -#include #include +#include class IMEXexample : public PhysicsModel { private: diff --git a/examples/IMEX/advection-reaction/split_operator.cxx b/examples/IMEX/advection-reaction/split_operator.cxx index c847e47ee6..33c3e5feb9 100644 --- a/examples/IMEX/advection-reaction/split_operator.cxx +++ b/examples/IMEX/advection-reaction/split_operator.cxx @@ -19,9 +19,9 @@ * *************************************************************/ -#include #include #include +#include class Split_operator : public PhysicsModel { Field3D U; // Evolving variable diff --git a/examples/IMEX/diffusion-nl/diffusion-nl.cxx b/examples/IMEX/diffusion-nl/diffusion-nl.cxx index fcb6aa165d..6e032fbbe4 100644 --- a/examples/IMEX/diffusion-nl/diffusion-nl.cxx +++ b/examples/IMEX/diffusion-nl/diffusion-nl.cxx @@ -16,8 +16,8 @@ */ #include -#include #include +#include class DiffusionNL : public PhysicsModel { protected: diff --git a/examples/advdiff/advdiff.cxx b/examples/advdiff/advdiff.cxx index 063d5076de..2e7d3748fc 100644 --- a/examples/advdiff/advdiff.cxx +++ b/examples/advdiff/advdiff.cxx @@ -4,8 +4,8 @@ * MVU 19-july-2011 *******************************************************************/ -#include #include +#include class AdvDiff : public PhysicsModel { private: diff --git a/examples/advdiff2/init.cxx b/examples/advdiff2/init.cxx index 196e261c6c..7954f7b543 100644 --- a/examples/advdiff2/init.cxx +++ b/examples/advdiff2/init.cxx @@ -1,5 +1,5 @@ -#include #include +#include #include "header.hxx" diff --git a/examples/backtrace/backtrace.cxx b/examples/backtrace/backtrace.cxx index 116120f8a9..1a096704e9 100644 --- a/examples/backtrace/backtrace.cxx +++ b/examples/backtrace/backtrace.cxx @@ -2,8 +2,8 @@ * Check for backtrace after throw */ -#include #include +#include void f1() { BoutReal a = 1; diff --git a/examples/blob2d-laplacexz/blob2d.cxx b/examples/blob2d-laplacexz/blob2d.cxx index e51019a8c6..3c88740775 100644 --- a/examples/blob2d-laplacexz/blob2d.cxx +++ b/examples/blob2d-laplacexz/blob2d.cxx @@ -4,8 +4,8 @@ NR Walkden, B Dudson 20 January 2012 *******************************************************************/ -#include "bout/bout.hxx" // Commonly used BOUT++ components -#include "bout/derivs.hxx" // To use DDZ() +#include "bout/bout.hxx" // Commonly used BOUT++ components +#include "bout/derivs.hxx" // To use DDZ() #include "bout/invert/laplacexz.hxx" // Laplacian inversion class Blob2D : public PhysicsModel { diff --git a/examples/blob2d-outerloop/blob2d.cxx b/examples/blob2d-outerloop/blob2d.cxx index c52984e2f1..f5db9d5b34 100644 --- a/examples/blob2d-outerloop/blob2d.cxx +++ b/examples/blob2d-outerloop/blob2d.cxx @@ -6,9 +6,9 @@ * NR Walkden, B Dudson 20 January 2012 *******************************************************************/ -#include // Commonly used BOUT++ components -#include // To use DDZ() -#include // Laplacian inversion +#include // To use DDZ() +#include // Laplacian inversion +#include // Commonly used BOUT++ components #include "bout/single_index_ops.hxx" // Operators at a single index diff --git a/examples/blob2d/blob2d.cxx b/examples/blob2d/blob2d.cxx index f48e3bc03a..f41f857d46 100644 --- a/examples/blob2d/blob2d.cxx +++ b/examples/blob2d/blob2d.cxx @@ -6,9 +6,9 @@ * NR Walkden, B Dudson 20 January 2012 *******************************************************************/ -#include // Commonly used BOUT++ components -#include // To use DDZ() -#include // Laplacian inversion +#include // To use DDZ() +#include // Laplacian inversion +#include // Commonly used BOUT++ components /// 2D drift-reduced model, mainly used for blob studies /// diff --git a/examples/conduction-snb/conduction-snb.cxx b/examples/conduction-snb/conduction-snb.cxx index 6ebb853c83..a5ff7fd804 100644 --- a/examples/conduction-snb/conduction-snb.cxx +++ b/examples/conduction-snb/conduction-snb.cxx @@ -1,7 +1,7 @@ // SNB heat conduction model -#include #include +#include int main(int argc, char** argv) { using bout::HeatFluxSNB; diff --git a/examples/constraints/alfven-wave/alfven.cxx b/examples/constraints/alfven-wave/alfven.cxx index 8d74794cf2..3e643331a1 100644 --- a/examples/constraints/alfven-wave/alfven.cxx +++ b/examples/constraints/alfven-wave/alfven.cxx @@ -1,8 +1,8 @@ -#include -#include #include +#include #include +#include /// Fundamental constants const BoutReal PI = 3.14159265; diff --git a/examples/constraints/laplace-dae/laplace_dae.cxx b/examples/constraints/laplace-dae/laplace_dae.cxx index 20a9ffdbd8..a5a614d5b2 100644 --- a/examples/constraints/laplace-dae/laplace_dae.cxx +++ b/examples/constraints/laplace-dae/laplace_dae.cxx @@ -3,11 +3,11 @@ * *************************************************************/ -#include #include #include #include #include +#include class Laplace_dae : public PhysicsModel { Field3D U, Apar; // Evolving variables diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx index 7f9422a60f..246cda7b74 100644 --- a/examples/dalf3/dalf3.cxx +++ b/examples/dalf3/dalf3.cxx @@ -20,11 +20,11 @@ #include -#include #include +#include #include -#include #include +#include #include diff --git a/examples/eigen-box/eigen-box.cxx b/examples/eigen-box/eigen-box.cxx index c3eb738f8a..f870f175de 100644 --- a/examples/eigen-box/eigen-box.cxx +++ b/examples/eigen-box/eigen-box.cxx @@ -5,8 +5,8 @@ * d^2f/dt^2 = d^2f/dx^2 */ -#include #include +#include class EigenBox : public PhysicsModel { protected: diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx index 41dcc75eda..144691be3a 100644 --- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx +++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx @@ -28,12 +28,12 @@ /*******************************************************************************/ -#include -#include #include +#include #include #include #include +#include #include #include #include @@ -42,10 +42,10 @@ #include -#include -#include #include #include +#include +#include #include #include // Defines BOUT_FOR_RAJA diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index 78042ae364..6232c72d52 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -5,12 +5,12 @@ * Can also include the Vpar compressional term *******************************************************************************/ -#include -#include #include +#include #include #include #include +#include #include #include #include diff --git a/examples/hasegawa-wakatani-3d/hw.cxx b/examples/hasegawa-wakatani-3d/hw.cxx index 0405d1dbe3..f2de708814 100644 --- a/examples/hasegawa-wakatani-3d/hw.cxx +++ b/examples/hasegawa-wakatani-3d/hw.cxx @@ -9,9 +9,9 @@ #include +#include #include #include -#include #define DISABLE_RAJA 0 #include diff --git a/examples/hasegawa-wakatani/hw.cxx b/examples/hasegawa-wakatani/hw.cxx index dcd7533f35..23f93d5eb7 100644 --- a/examples/hasegawa-wakatani/hw.cxx +++ b/examples/hasegawa-wakatani/hw.cxx @@ -1,7 +1,7 @@ -#include #include #include +#include #include class HW : public PhysicsModel { diff --git a/examples/invertable_operator/invertable_operator.cxx b/examples/invertable_operator/invertable_operator.cxx index 064cc1719c..57f9e24b08 100644 --- a/examples/invertable_operator/invertable_operator.cxx +++ b/examples/invertable_operator/invertable_operator.cxx @@ -1,10 +1,10 @@ #include #include +#include #include #include #include -#include #include diff --git a/examples/laplacexy/alfven-wave/alfven.cxx b/examples/laplacexy/alfven-wave/alfven.cxx index 4f7de495ea..e7a945b3f4 100644 --- a/examples/laplacexy/alfven-wave/alfven.cxx +++ b/examples/laplacexy/alfven-wave/alfven.cxx @@ -1,9 +1,9 @@ +#include #include #include -#include -#include #include +#include /// Fundamental constants const BoutReal PI = 3.14159265; diff --git a/examples/laplacexy/laplace_perp/test.cxx b/examples/laplacexy/laplace_perp/test.cxx index 104aaedf10..7881f4ab82 100644 --- a/examples/laplacexy/laplace_perp/test.cxx +++ b/examples/laplacexy/laplace_perp/test.cxx @@ -1,8 +1,8 @@ #include -#include #include #include +#include using bout::globals::mesh; diff --git a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx b/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx index e90ccfc2e9..68caa2222b 100644 --- a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx +++ b/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx @@ -1,6 +1,6 @@ -#include #include #include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/examples/laplacexy/simple/test-laplacexy.cxx b/examples/laplacexy/simple/test-laplacexy.cxx index c21d47d947..c033eb68e3 100644 --- a/examples/laplacexy/simple/test-laplacexy.cxx +++ b/examples/laplacexy/simple/test-laplacexy.cxx @@ -1,7 +1,7 @@ -#include #include #include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/examples/monitor/monitor.cxx b/examples/monitor/monitor.cxx index 8a8825bad1..37825e5ce9 100644 --- a/examples/monitor/monitor.cxx +++ b/examples/monitor/monitor.cxx @@ -1,8 +1,8 @@ /* */ -#include #include +#include /// Create a function to be called every timestep int my_timestep_monitor(Solver* UNUSED(solver), BoutReal simtime, BoutReal dt) { diff --git a/examples/performance/communications/communications.cxx b/examples/performance/communications/communications.cxx index 1360f45e77..610caaf65e 100644 --- a/examples/performance/communications/communications.cxx +++ b/examples/performance/communications/communications.cxx @@ -1,6 +1,6 @@ -#include #include #include +#include int main(int argc, char** argv) { diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx index 5e8df511d7..7f9eb7ce1f 100644 --- a/examples/performance/iterator/iterator.cxx +++ b/examples/performance/iterator/iterator.cxx @@ -108,7 +108,7 @@ int main(int argc, char** argv) { #if BOUT_USE_OPENMP ITERATOR_TEST_BLOCK( "Region (omp)", - BOUT_FOR (i, mesh->getRegion("RGN_ALL")) { result[i] = a[i] + b[i]; }); + BOUT_FOR(i, mesh->getRegion("RGN_ALL")) { result[i] = a[i] + b[i]; }); #endif if (profileMode) { diff --git a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx index aa8fa7fe52..521ffede74 100644 --- a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx +++ b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx @@ -61,7 +61,7 @@ int main(int argc, char** argv) { mesh->LocalNy, mesh->LocalNz, blocksize); ITERATOR_TEST_BLOCK( - name, BOUT_FOR (i, region) { result[i] = a[i] + b[i]; }); + name, BOUT_FOR(i, region) { result[i] = a[i] + b[i]; }); } // Report diff --git a/examples/preconditioning/wave/test_precon.cxx b/examples/preconditioning/wave/test_precon.cxx index 639bbed344..e27759824c 100644 --- a/examples/preconditioning/wave/test_precon.cxx +++ b/examples/preconditioning/wave/test_precon.cxx @@ -6,9 +6,9 @@ * solver:type=petsc -ts_type theta -ts_theta_theta 0.5 -{ksp,snes,ts}_monitor */ -#include #include #include +#include class Test_precon : public PhysicsModel { Field3D u, v; // Evolving variables diff --git a/examples/staggered_grid/test_staggered.cxx b/examples/staggered_grid/test_staggered.cxx index f6e368f20a..52a406d9da 100644 --- a/examples/staggered_grid/test_staggered.cxx +++ b/examples/staggered_grid/test_staggered.cxx @@ -2,9 +2,9 @@ * Demonstrates how to use staggered grids with boundary conditions */ -#include #include #include +#include class TestStaggered : public PhysicsModel { Field3D n, v; diff --git a/examples/subsampling/monitor.cxx b/examples/subsampling/monitor.cxx index c06886c26a..981ff8b235 100644 --- a/examples/subsampling/monitor.cxx +++ b/examples/subsampling/monitor.cxx @@ -1,7 +1,7 @@ /* */ -#include #include +#include #include diff --git a/examples/uedge-benchmark/ue_bmark.cxx b/examples/uedge-benchmark/ue_bmark.cxx index 969b4fc5db..2d03885c45 100644 --- a/examples/uedge-benchmark/ue_bmark.cxx +++ b/examples/uedge-benchmark/ue_bmark.cxx @@ -10,9 +10,9 @@ * *******************************************************************************/ -#include #include #include +#include #include diff --git a/include/bout/array.hxx b/include/bout/array.hxx index e258f235b4..68607e6b58 100644 --- a/include/bout/array.hxx +++ b/include/bout/array.hxx @@ -390,7 +390,8 @@ private: // Clean by deleting all data -- possible that just stores.clear() is // sufficient rather than looping over each entry. - BOUT_OMP(single) { + BOUT_OMP(single) + { for (auto& stores : arena) { for (auto& p : stores) { auto& v = p.second; diff --git a/include/bout/bout.hxx b/include/bout/bout.hxx index b1845b8f1b..5e718dde33 100644 --- a/include/bout/bout.hxx +++ b/include/bout/bout.hxx @@ -43,18 +43,18 @@ #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/globals.hxx" +#include "bout/mesh.hxx" #include "bout/options_netcdf.hxx" #include "bout/output.hxx" #include "bout/smoothing.hxx" // Smoothing functions -#include "bout/sourcex.hxx" // source and mask functions +#include "bout/solver.hxx" +#include "bout/sourcex.hxx" // source and mask functions #include "bout/utils.hxx" #include "bout/vecops.hxx" // Vector differential operations #include "bout/vector2d.hxx" #include "bout/vector3d.hxx" -#include "bout/where.hxx" -#include "bout/mesh.hxx" -#include "bout/solver.hxx" #include "bout/version.hxx" +#include "bout/where.hxx" // BOUT++ main functions diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx index 451d97ccf1..ef251b4c2f 100644 --- a/include/bout/bout_enum_class.hxx +++ b/include/bout/bout_enum_class.hxx @@ -23,9 +23,9 @@ #define __BOUT_ENUM_CLASS_H__ #include "bout/boutexception.hxx" +#include "bout/macro_for_each.hxx" #include "bout/msg_stack.hxx" #include "bout/options.hxx" -#include "bout/macro_for_each.hxx" #include #include diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx index 625c07ec2e..e9544fff38 100644 --- a/include/bout/coordinates.hxx +++ b/include/bout/coordinates.hxx @@ -35,8 +35,8 @@ #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "bout/utils.hxx" #include "bout/paralleltransform.hxx" +#include "bout/utils.hxx" #include class Datafile; diff --git a/include/bout/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx index 82ef283476..d4ef958e93 100644 --- a/include/bout/cyclic_reduction.hxx +++ b/include/bout/cyclic_reduction.hxx @@ -51,8 +51,8 @@ #include "bout/utils.hxx" #include -#include "bout/boutexception.hxx" #include "bout/assert.hxx" +#include "bout/boutexception.hxx" #include "bout/output.hxx" diff --git a/include/bout/expr.hxx b/include/bout/expr.hxx index f2de9c3b62..e03c07aa49 100644 --- a/include/bout/expr.hxx +++ b/include/bout/expr.hxx @@ -14,9 +14,9 @@ #warning expr.hxx is deprecated. Do not use! -#include #include #include +#include /// Literal class to capture BoutReal values in expressions class Literal { diff --git a/include/bout/field.hxx b/include/bout/field.hxx index 6b14d6a3a2..97b98fee13 100644 --- a/include/bout/field.hxx +++ b/include/bout/field.hxx @@ -42,12 +42,12 @@ class Field; #include "bout/boutcomm.hxx" #include "bout/boutexception.hxx" #include "bout/msg_stack.hxx" -#include "bout/stencils.hxx" -#include "bout/utils.hxx" #include "bout/region.hxx" +#include "bout/stencils.hxx" #include "bout/traits.hxx" -#include +#include "bout/utils.hxx" #include +#include #include "bout/unused.hxx" @@ -219,9 +219,7 @@ template < inline T filledFrom(const T& f, Function func, std::string region_string = "RGN_ALL") { static_assert(bout::utils::is_Field::value, "filledFrom only works on Fields"); T result{emptyFrom(f)}; - BOUT_FOR (i, result.getRegion(region_string)) { - result[i] = func(i); - } + BOUT_FOR(i, result.getRegion(region_string)) { result[i] = func(i); } return result; } @@ -462,9 +460,7 @@ T pow(const T& lhs, const T& rhs, const std::string& rgn = "RGN_ALL") { T result{emptyFrom(lhs)}; - BOUT_FOR (i, result.getRegion(rgn)) { - result[i] = ::pow(lhs[i], rhs[i]); - } + BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); } checkData(result); return result; @@ -480,9 +476,7 @@ T pow(const T& lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") { T result{emptyFrom(lhs)}; - BOUT_FOR (i, result.getRegion(rgn)) { - result[i] = ::pow(lhs[i], rhs); - } + BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs); } checkData(result); return result; @@ -499,9 +493,7 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") { // Define and allocate the output result T result{emptyFrom(rhs)}; - BOUT_FOR (i, result.getRegion(rgn)) { - result[i] = ::pow(lhs, rhs[i]); - } + BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs, rhs[i]); } checkData(result); return result; @@ -526,19 +518,17 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") { #ifdef FIELD_FUNC #error This macro has already been defined #else -#define FIELD_FUNC(name, func) \ - template > \ - inline T name(const T& f, const std::string& rgn = "RGN_ALL") { \ - AUTO_TRACE(); \ - /* Check if the input is allocated */ \ - checkData(f); \ - /* Define and allocate the output result */ \ - T result{emptyFrom(f)}; \ - BOUT_FOR (d, result.getRegion(rgn)) { \ - result[d] = func(f[d]); \ - } \ - checkData(result); \ - return result; \ +#define FIELD_FUNC(name, func) \ + template > \ + inline T name(const T& f, const std::string& rgn = "RGN_ALL") { \ + AUTO_TRACE(); \ + /* Check if the input is allocated */ \ + checkData(f); \ + /* Define and allocate the output result */ \ + T result{emptyFrom(f)}; \ + BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); } \ + checkData(result); \ + return result; \ } #endif @@ -674,7 +664,7 @@ inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") { checkData(var); T result = copy(var); - BOUT_FOR (d, var.getRegion(rgn)) { + BOUT_FOR(d, var.getRegion(rgn)) { if (result[d] < f) { result[d] = f; } diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index f00cd1ea69..783eb79e9e 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -37,9 +37,9 @@ class Field3D; //#include "bout/field3d.hxx" #include "bout/fieldperp.hxx" #include "bout/stencils.hxx" -#include "bout/utils.hxx" #include "bout/array.hxx" #include "bout/region.hxx" +#include "bout/utils.hxx" #include "bout/unused.hxx" diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx index d6d203d7f7..16661a0e75 100644 --- a/include/bout/field_accessor.hxx +++ b/include/bout/field_accessor.hxx @@ -7,13 +7,13 @@ #ifndef FIELD_ACCESSOR_H__ #define FIELD_ACCESSOR_H__ +#include "build_config.hxx" +#include "coordinates.hxx" +#include "coordinates_accessor.hxx" #include "bout/bout_types.hxx" #include "bout/field.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "build_config.hxx" -#include "coordinates.hxx" -#include "coordinates_accessor.hxx" /// Simple wrapper around a BoutReal* 1D array /// diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx index d2886775d8..5f1e688bd8 100644 --- a/include/bout/fv_ops.hxx +++ b/include/bout/fv_ops.hxx @@ -404,7 +404,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) { Field3D vz = v.z; Field3D n = n_in; - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Calculate velocities BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]); BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]); @@ -505,7 +505,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) { Field3D yresult = 0.0; yresult.setDirectionY(YDirectionType::Aligned); - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Y velocities on y boundaries BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]); BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]); diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index a6d0c2f676..a061f387dc 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -1,13 +1,13 @@ #ifndef BOUT_GLOBALINDEXER_H #define BOUT_GLOBALINDEXER_H +#include +#include #include #include #include #include #include -#include -#include template class GlobalIndexer; @@ -183,7 +183,7 @@ private: numOffDiagonal = std::vector(size(), 0); // Set initial guess for number of on-diagonal elements - BOUT_FOR (i, regionAll) { + BOUT_FOR(i, regionAll) { numDiagonal[getGlobal(i) - globalStart] = stencils.getStencilSize(i); } diff --git a/include/bout/griddata.hxx b/include/bout/griddata.hxx index 952d241692..875cb07d7a 100644 --- a/include/bout/griddata.hxx +++ b/include/bout/griddata.hxx @@ -28,8 +28,8 @@ class GridDataSource; #ifndef __GRIDDATA_H__ #define __GRIDDATA_H__ -#include "bout/bout_types.hxx" #include "mesh.hxx" +#include "bout/bout_types.hxx" #include "bout/options.hxx" #include diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx index 9e049ecdde..7f6271865a 100644 --- a/include/bout/hypre_interface.hxx +++ b/include/bout/hypre_interface.hxx @@ -5,13 +5,13 @@ #if BOUT_HAS_HYPRE -#include "bout/boutcomm.hxx" -#include "bout/field.hxx" -#include "bout/utils.hxx" #include "bout/bout_enum_class.hxx" +#include "bout/boutcomm.hxx" #include "bout/caliper_wrapper.hxx" +#include "bout/field.hxx" #include "bout/globalindexer.hxx" #include "bout/hyprelib.hxx" +#include "bout/utils.hxx" #include "HYPRE.h" #include "HYPRE_IJ_mv.h" diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx index 7d36143732..8cb5c88aff 100644 --- a/include/bout/index_derivs.hxx +++ b/include/bout/index_derivs.hxx @@ -89,7 +89,7 @@ public: || meta.derivType == DERIV::StandardFourth) ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); - BOUT_FOR (i, var.getRegion(region)) { + BOUT_FOR(i, var.getRegion(region)) { result[i] = apply(populateStencil(var, i)); } return; @@ -103,12 +103,12 @@ public: ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); if (meta.derivType == DERIV::Flux || stagger != STAGGER::None) { - BOUT_FOR (i, var.getRegion(region)) { + BOUT_FOR(i, var.getRegion(region)) { result[i] = apply(populateStencil(vel, i), populateStencil(var, i)); } } else { - BOUT_FOR (i, var.getRegion(region)) { + BOUT_FOR(i, var.getRegion(region)) { result[i] = apply(vel[i], populateStencil(var, i)); } diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx index 8866abe180..1f6e8bfbe9 100644 --- a/include/bout/index_derivs_interface.hxx +++ b/include/bout/index_derivs_interface.hxx @@ -30,8 +30,8 @@ #define __INDEX_DERIVS_INTERFACE_HXX__ #include "bout/traits.hxx" -#include #include +#include #include class Field3D; diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx index debd52c046..71fbd19e90 100644 --- a/include/bout/interpolation.hxx +++ b/include/bout/interpolation.hxx @@ -101,12 +101,12 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL ASSERT0(fieldmesh->xstart >= 2); if ((location == CELL_CENTRE) && (loc == CELL_XLOW)) { // C2L - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Producing a stencil centred around a lower X value result[i] = interp(populateStencil(var, i)); } } else if (location == CELL_XLOW) { // L2C - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Stencil centred around a cell centre result[i] = interp(populateStencil(var, i)); } @@ -146,13 +146,13 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL } if ((location == CELL_CENTRE) && (loc == CELL_YLOW)) { // C2L - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Producing a stencil centred around a lower X value result[i] = interp(populateStencil(var_fa, i)); } } else if (location == CELL_YLOW) { // L2C - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Stencil centred around a cell centre result[i] = interp(populateStencil(var_fa, i)); @@ -168,12 +168,12 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL case CELL_ZLOW: { if ((location == CELL_CENTRE) && (loc == CELL_ZLOW)) { // C2L - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Producing a stencil centred around a lower X value result[i] = interp(populateStencil(var, i)); } } else if (location == CELL_ZLOW) { // L2C - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Stencil centred around a cell centre result[i] = interp(populateStencil(var, i)); } diff --git a/include/bout/invert/laplacexy.hxx b/include/bout/invert/laplacexy.hxx index c4c4ef4f52..41fccf30ed 100644 --- a/include/bout/invert/laplacexy.hxx +++ b/include/bout/invert/laplacexy.hxx @@ -81,11 +81,11 @@ public: #undef MPI_Waitall #undef MPI_Waitany -#include "bout/utils.hxx" #include "bout/solver.hxx" +#include "bout/utils.hxx" +#include #include #include -#include class Options; class Solver; diff --git a/include/bout/invert/laplacexy2.hxx b/include/bout/invert/laplacexy2.hxx index 86df7433d3..c64f89d743 100644 --- a/include/bout/invert/laplacexy2.hxx +++ b/include/bout/invert/laplacexy2.hxx @@ -40,8 +40,8 @@ #warning LaplaceXY2 requires PETSc and 2D metrics. No LaplaceXY2 available -#include #include +#include #include /*! @@ -78,10 +78,10 @@ public: #undef MPI_Waitany #include "bout/utils.hxx" +#include #include #include #include -#include class LaplaceXY2 { public: diff --git a/include/bout/invert/laplacexy2_hypre.hxx b/include/bout/invert/laplacexy2_hypre.hxx index ea3b6c4440..6a552e6b6e 100644 --- a/include/bout/invert/laplacexy2_hypre.hxx +++ b/include/bout/invert/laplacexy2_hypre.hxx @@ -41,8 +41,8 @@ #warning LaplaceXY requires Hypre. No LaplaceXY available #include "bout/globalindexer.hxx" -#include #include +#include #include /*! diff --git a/include/bout/invert/laplacexz.hxx b/include/bout/invert/laplacexz.hxx index 800b8cc1c4..1b1ebef832 100644 --- a/include/bout/invert/laplacexz.hxx +++ b/include/bout/invert/laplacexz.hxx @@ -31,9 +31,9 @@ #ifndef __LAPLACEXZ_H__ #define __LAPLACEXZ_H__ +#include #include #include -#include #include #include diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index be4b5b44ee..5dd3568575 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -43,9 +43,9 @@ class Laplacian; #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/fieldperp.hxx" -#include "bout/unused.hxx" #include "bout/generic_factory.hxx" #include "bout/monitor.hxx" +#include "bout/unused.hxx" #include #include "bout/dcomplex.hxx" diff --git a/include/bout/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx index 8273690a72..5a83a7f4e8 100644 --- a/include/bout/invert_parderiv.hxx +++ b/include/bout/invert_parderiv.hxx @@ -33,9 +33,9 @@ #include "bout/field2d.hxx" #include "bout/field3d.hxx" +#include "bout/generic_factory.hxx" #include "bout/options.hxx" #include "bout/unused.hxx" -#include "bout/generic_factory.hxx" // Parderiv implementations constexpr auto PARDERIVCYCLIC = "cyclic"; diff --git a/include/bout/invert_pardiv.hxx b/include/bout/invert_pardiv.hxx index 74827c7303..0153cc1987 100644 --- a/include/bout/invert_pardiv.hxx +++ b/include/bout/invert_pardiv.hxx @@ -33,9 +33,9 @@ #include "bout/field2d.hxx" #include "bout/field3d.hxx" +#include "bout/generic_factory.hxx" #include "bout/options.hxx" #include "bout/unused.hxx" -#include "bout/generic_factory.hxx" // Pardivergence implementations constexpr auto PARDIVCYCLIC = "cyclic"; diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx index 10c1e813cc..49b254187a 100644 --- a/include/bout/invertable_operator.hxx +++ b/include/bout/invertable_operator.hxx @@ -38,14 +38,14 @@ class InvertableOperator; #if BOUT_HAS_PETSC #include "bout/traits.hxx" -#include -#include #include #include #include +#include #include #include #include +#include #include diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx index d36f8446c5..19c8ea86fd 100644 --- a/include/bout/mask.hxx +++ b/include/bout/mask.hxx @@ -25,8 +25,8 @@ #include #include "bout/globals.hxx" -#include "bout/msg_stack.hxx" #include "bout/mesh.hxx" +#include "bout/msg_stack.hxx" /** * 3D array of bools to mask Field3Ds diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx index 339aae031e..eb86c01554 100644 --- a/include/bout/monitor.hxx +++ b/include/bout/monitor.hxx @@ -1,9 +1,9 @@ #ifndef __MONITOR_H__ #define __MONITOR_H__ +#include "bout/assert.hxx" #include "bout/bout_types.hxx" #include "bout/utils.hxx" -#include "bout/assert.hxx" #include diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx index fc0f98c952..cc19a7b9f6 100644 --- a/include/bout/msg_stack.hxx +++ b/include/bout/msg_stack.hxx @@ -31,8 +31,8 @@ class MsgStack; #include "bout/build_config.hxx" -#include "bout/unused.hxx" #include "bout/format.hxx" +#include "bout/unused.hxx" #include "fmt/core.h" diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 39e870ea2e..bf1704100f 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -44,11 +44,11 @@ class Options; #include "bout/field3d.hxx" #include "bout/fieldperp.hxx" #include "bout/output.hxx" -#include "bout/unused.hxx" -#include "bout/utils.hxx" #include "bout/sys/type_name.hxx" #include "bout/sys/variant.hxx" #include "bout/traits.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" #include diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx index 900c3aedaa..428c7a8c8f 100644 --- a/include/bout/optionsreader.hxx +++ b/include/bout/optionsreader.hxx @@ -34,8 +34,8 @@ class OptionsReader; #ifndef __OPTIONSREADER_H__ #define __OPTIONSREADER_H__ -#include "bout/options.hxx" #include "bout/format.hxx" +#include "bout/options.hxx" #include "fmt/core.h" diff --git a/include/bout/output.hxx b/include/bout/output.hxx index 986fd94537..914d461fab 100644 --- a/include/bout/output.hxx +++ b/include/bout/output.hxx @@ -35,11 +35,11 @@ class Output; #include #include -#include "bout/boutexception.hxx" -#include "bout/unused.hxx" #include "bout/assert.hxx" +#include "bout/boutexception.hxx" #include "bout/format.hxx" #include "bout/sys/gettext.hxx" // for gettext _() macro +#include "bout/unused.hxx" #include "fmt/core.h" diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 01af336d75..8e7d44c67d 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -37,6 +37,8 @@ #include #include +#include +#include #include #include #include @@ -44,8 +46,6 @@ #include #include #include -#include -#include #if BOUT_HAS_PETSC diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index f17282b38b..3f6ba26ce7 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -37,15 +37,15 @@ class PhysicsModel; #ifndef __PHYSICS_MODEL_H__ #define __PHYSICS_MODEL_H__ +#include "solver.hxx" #include "bout/bout.hxx" +#include "bout/macro_for_each.hxx" #include "bout/msg_stack.hxx" #include "bout/options.hxx" #include "bout/options_netcdf.hxx" -#include "solver.hxx" +#include "bout/sys/variant.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/macro_for_each.hxx" -#include "bout/sys/variant.hxx" #include #include diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx index db19573f02..b9f6913459 100644 --- a/include/bout/rajalib.hxx +++ b/include/bout/rajalib.hxx @@ -136,7 +136,7 @@ private: /// If no RAJA, BOUT_FOR_RAJA reverts to BOUT_FOR /// Note: Redundant ';' after closing brace should be ignored by compiler /// Ignores any additional arguments -#define BOUT_FOR_RAJA(index, region, ...) BOUT_FOR (index, region) +#define BOUT_FOR_RAJA(index, region, ...) BOUT_FOR(index, region) /// If not using RAJA, CAPTURE doesn't do anything #define CAPTURE(...) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 1ff118bd56..e4313f8256 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -48,8 +48,8 @@ #include #include -#include "bout/bout_types.hxx" #include "bout/assert.hxx" +#include "bout/bout_types.hxx" #include "bout/openmpwrap.hxx" /// The MAXREGIONBLOCKSIZE value can be tuned to try to optimise diff --git a/include/bout/snb.hxx b/include/bout/snb.hxx index 880477c09c..1644e0059c 100644 --- a/include/bout/snb.hxx +++ b/include/bout/snb.hxx @@ -1,5 +1,5 @@ -#include "bout/options.hxx" #include "bout/invert_pardiv.hxx" +#include "bout/options.hxx" #include diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index 3862a24309..5aa8493124 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -40,9 +40,9 @@ #include "bout/bout_types.hxx" #include "bout/boutexception.hxx" +#include "bout/monitor.hxx" #include "bout/options.hxx" #include "bout/unused.hxx" -#include "bout/monitor.hxx" #include @@ -66,9 +66,9 @@ using TimestepMonitorFunc = int (*)(Solver* solver, BoutReal simtime, BoutReal l //#include "bout/globals.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" +#include "bout/generic_factory.hxx" #include "bout/vector2d.hxx" #include "bout/vector3d.hxx" -#include "bout/generic_factory.hxx" #define BOUT_NO_USING_NAMESPACE_BOUTGLOBALS #include "physicsmodel.hxx" diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx index 25ad3abe1e..0ee3a7f97b 100644 --- a/include/bout/sys/expressionparser.hxx +++ b/include/bout/sys/expressionparser.hxx @@ -27,8 +27,8 @@ #ifndef __EXPRESSION_PARSER_H__ #define __EXPRESSION_PARSER_H__ -#include "bout/unused.hxx" #include "bout/format.hxx" +#include "bout/unused.hxx" #include "fmt/core.h" diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 960a45849c..d221abcbad 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -33,11 +33,11 @@ #include "bout/boutexception.hxx" #include "bout/dcomplex.hxx" -#include "bout/msg_stack.hxx" -#include "bout/unused.hxx" #include "bout/array.hxx" #include "bout/assert.hxx" #include "bout/build_config.hxx" +#include "bout/msg_stack.hxx" +#include "bout/unused.hxx" #include #include diff --git a/include/bout/vecops.hxx b/include/bout/vecops.hxx index 8dc16d26f4..4a03d06b5e 100644 --- a/include/bout/vecops.hxx +++ b/include/bout/vecops.hxx @@ -30,11 +30,11 @@ #define __VECOPS_H__ #include "bout/bout_types.hxx" +#include "bout/coordinates.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/vector2d.hxx" #include "bout/vector3d.hxx" -#include "bout/coordinates.hxx" /// Gradient of scalar field \p f, returning a covariant vector /// diff --git a/include/bout/where.hxx b/include/bout/where.hxx index 4b1d8090d0..504dc028b1 100644 --- a/include/bout/where.hxx +++ b/include/bout/where.hxx @@ -45,7 +45,7 @@ auto where(const T& test, const U& gt0, const V& le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = (test[i] > 0.0) ? gt0[i] : le0[i]; } return result; @@ -57,7 +57,7 @@ auto where(const T& test, const U& gt0, BoutReal le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { // clang-format: ignore + BOUT_FOR(i, result.getRegion("RGN_ALL")) { // clang-format: ignore result[i] = (test[i] > 0.0) ? gt0[i] : le0; } return result; @@ -69,7 +69,7 @@ auto where(const T& test, BoutReal gt0, const V& le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { // clang-format: ignore + BOUT_FOR(i, result.getRegion("RGN_ALL")) { // clang-format: ignore result[i] = (test[i] > 0.0) ? gt0 : le0[i]; } return result; @@ -79,7 +79,7 @@ template auto where(const T& test, BoutReal gt0, BoutReal le0) -> ResultType { ResultType result{emptyFrom(test)}; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { // clang-format: ignore + BOUT_FOR(i, result.getRegion("RGN_ALL")) { // clang-format: ignore result[i] = (test[i] > 0.0) ? gt0 : le0; } return result; diff --git a/src/bout++.cxx b/src/bout++.cxx index 4659194f9b..983be46ef2 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -31,22 +31,22 @@ const char DEFAULT_DIR[] = "data"; #define GLOBALORIGIN -#include "bout/boundary_factory.hxx" #include "bout++-time.hxx" +#include "bout/boundary_factory.hxx" #include "bout/boutcomm.hxx" #include "bout/boutexception.hxx" +#include "bout/coordinates_accessor.hxx" +#include "bout/hyprelib.hxx" #include "bout/interpolation_xz.hxx" #include "bout/interpolation_z.hxx" +#include "bout/invert/laplacexz.hxx" #include "bout/invert_laplace.hxx" #include "bout/invert_parderiv.hxx" +#include "bout/mpi_wrapper.hxx" #include "bout/msg_stack.hxx" +#include "bout/openmpwrap.hxx" #include "bout/optionsreader.hxx" #include "bout/output.hxx" -#include "bout/coordinates_accessor.hxx" -#include "bout/hyprelib.hxx" -#include "bout/invert/laplacexz.hxx" -#include "bout/mpi_wrapper.hxx" -#include "bout/openmpwrap.hxx" #include "bout/petsclib.hxx" #include "bout/revision.hxx" #include "bout/rkscheme.hxx" diff --git a/src/field/field.cxx b/src/field/field.cxx index 34be778d8f..54883c506c 100644 --- a/src/field/field.cxx +++ b/src/field/field.cxx @@ -25,10 +25,10 @@ //#include -#include -#include #include +#include #include +#include #include #include #include diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx index 953d27953b..6a6740669b 100644 --- a/src/field/field2d.cxx +++ b/src/field/field2d.cxx @@ -27,8 +27,8 @@ #include "bout/build_config.hxx" -#include #include +#include #include // for mesh @@ -39,12 +39,12 @@ #include #include -#include #include +#include #include -#include #include +#include #include @@ -188,9 +188,7 @@ Field2D& Field2D::operator=(const BoutReal rhs) { TRACE("Field2D = BoutReal"); allocate(); - BOUT_FOR (i, getRegion("RGN_ALL")) { - (*this)[i] = rhs; - } + BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = rhs; } return *this; } @@ -383,9 +381,7 @@ void checkData(const Field2D& f, const std::string& region) { #if CHECK > 2 void invalidateGuards(Field2D& var) { - BOUT_FOR (i, var.getRegion("RGN_GUARDS")) { - var[i] = BoutNaN; - } + BOUT_FOR(i, var.getRegion("RGN_GUARDS")) { var[i] = BoutNaN; } } #endif diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 4347c7942d..4df23752ba 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -35,10 +35,10 @@ #include "bout/parallel_boundary_op.hxx" #include "bout/parallel_boundary_region.hxx" #include -#include #include #include #include +#include #include #include #include @@ -300,7 +300,7 @@ Field3D& Field3D::operator=(const Field2D& rhs) { ASSERT1_FIELDS_COMPATIBLE(*this, rhs); /// Copy data - BOUT_FOR (i, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(i, rhs.getRegion("RGN_ALL")) { for (int iz = 0; iz < nz; iz++) { (*this)(i, iz) = rhs[i]; } @@ -324,9 +324,7 @@ void Field3D::operator=(const FieldPerp& rhs) { allocate(); /// Copy data - BOUT_FOR (i, rhs.getRegion("RGN_ALL")) { - (*this)(i, rhs.getIndex()) = rhs[i]; - } + BOUT_FOR(i, rhs.getRegion("RGN_ALL")) { (*this)(i, rhs.getIndex()) = rhs[i]; } } Field3D& Field3D::operator=(const BoutReal val) { @@ -338,9 +336,7 @@ Field3D& Field3D::operator=(const BoutReal val) { allocate(); - BOUT_FOR (i, getRegion("RGN_ALL")) { - (*this)[i] = val; - } + BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = val; } return *this; } @@ -581,9 +577,7 @@ Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn) { // Define and allocate the output result Field3D result{emptyFrom(lhs)}; - BOUT_FOR (i, result.getRegion(rgn)) { - result[i] = ::pow(lhs[i], rhs[i]); - } + BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); } checkData(result); return result; @@ -598,7 +592,7 @@ FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn) FieldPerp result{emptyFrom(rhs)}; - BOUT_FOR (i, result.getRegion(rgn)) { + BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs(i, rhs.getIndex()), rhs[i]); } @@ -626,7 +620,8 @@ Field3D filter(const Field3D& var, int N0, const std::string& rgn) { const Region& region = var.getRegion2D(region_str); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { Array f(ncz / 2 + 1); BOUT_FOR_INNER(i, region) { @@ -675,7 +670,8 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string const Region& region = var.getRegion2D(region_str); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { Array f(ncz / 2 + 1); BOUT_FOR_INNER(i, region) { @@ -781,7 +777,7 @@ Field2D DC(const Field3D& f, const std::string& rgn) { Field2D result(localmesh, f.getLocation()); result.allocate(); - BOUT_FOR (i, result.getRegion(rgn)) { + BOUT_FOR(i, result.getRegion(rgn)) { result[i] = 0.0; for (int k = 0; k < localmesh->LocalNz; k++) { result[i] += f[localmesh->ind2Dto3D(i, k)]; @@ -795,9 +791,7 @@ Field2D DC(const Field3D& f, const std::string& rgn) { #if CHECK > 2 void invalidateGuards(Field3D& var) { - BOUT_FOR (i, var.getRegion("RGN_GUARDS")) { - var[i] = BoutNaN; - } + BOUT_FOR(i, var.getRegion("RGN_GUARDS")) { var[i] = BoutNaN; } } #endif diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx index 689f2549c3..88de80cec6 100644 --- a/src/field/field_data.cxx +++ b/src/field/field_data.cxx @@ -2,11 +2,11 @@ #include "bout/parallel_boundary_op.hxx" #include "bout/parallel_boundary_region.hxx" #include "bout/unused.hxx" -#include #include #include #include #include +#include #include namespace bout { diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx index 685a1a9727..fb03c3b174 100644 --- a/src/field/field_factory.cxx +++ b/src/field/field_factory.cxx @@ -183,7 +183,7 @@ Field2D FieldFactory::create2D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC result.allocate(); result.setLocation(loc); - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = gen->generate(Context(i, loc, localmesh, t)); }; @@ -215,7 +215,7 @@ Field3D FieldFactory::create3D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC auto result = Field3D(localmesh).setLocation(loc).setDirectionY(y_direction).allocate(); - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = gen->generate(Context(i, loc, localmesh, t)); }; @@ -267,7 +267,7 @@ FieldPerp FieldFactory::createPerp(FieldGeneratorPtr gen, Mesh* localmesh, CELL_ auto result = FieldPerp(localmesh).setLocation(loc).setDirectionY(y_direction).allocate(); - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = gen->generate(Context(i, loc, localmesh, t)); }; diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx index 23c47e762c..22e8aa994e 100644 --- a/src/field/fieldperp.cxx +++ b/src/field/fieldperp.cxx @@ -28,9 +28,9 @@ #include -#include #include #include +#include #include #include @@ -101,9 +101,7 @@ FieldPerp& FieldPerp::operator=(const BoutReal rhs) { allocate(); - BOUT_FOR (i, getRegion("RGN_ALL")) { - (*this)[i] = rhs; - } + BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = rhs; } return *this; } @@ -167,9 +165,7 @@ const FieldPerp sliceXZ(const Field3D& f, int y) { // Allocate memory result.allocate(); - BOUT_FOR (i, result.getRegion("RGN_ALL")) { - result[i] = f(i, y); - } + BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = f(i, y); } checkData(result); return result; @@ -205,9 +201,7 @@ void checkData(const FieldPerp& f, const std::string& region) { #if CHECK > 2 void invalidateGuards(FieldPerp& var) { - BOUT_FOR (i, var.getRegion("RGN_GUARDS")) { - var[i] = BoutNaN; - } + BOUT_FOR(i, var.getRegion("RGN_GUARDS")) { var[i] = BoutNaN; } } #endif diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx index b2b3e32ef9..a3613eca3e 100644 --- a/src/field/generated_fieldops.cxx +++ b/src/field/generated_fieldops.cxx @@ -1,10 +1,10 @@ // This file is autogenerated - see gen_fieldops.py -#include -#include #include #include #include #include +#include +#include // Provide the C++ wrapper for multiplication of Field3D and Field3D Field3D operator*(const Field3D& lhs, const Field3D& rhs) { @@ -14,7 +14,7 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -36,9 +36,7 @@ Field3D& Field3D::operator*=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } checkData(*this); @@ -56,7 +54,7 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -78,9 +76,7 @@ Field3D& Field3D::operator/=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] /= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } checkData(*this); @@ -98,7 +94,7 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -120,9 +116,7 @@ Field3D& Field3D::operator+=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] += rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } checkData(*this); @@ -140,7 +134,7 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -162,9 +156,7 @@ Field3D& Field3D::operator-=(const Field3D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] -= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } checkData(*this); @@ -184,7 +176,7 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[base_ind + jz] * rhs[index]; @@ -209,7 +201,7 @@ Field3D& Field3D::operator*=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { (*this)[base_ind + jz] *= rhs[index]; @@ -234,7 +226,7 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); const auto tmp = 1.0 / rhs[index]; for (int jz = 0; jz < localmesh->LocalNz; ++jz) { @@ -260,7 +252,7 @@ Field3D& Field3D::operator/=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); const auto tmp = 1.0 / rhs[index]; for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { @@ -286,7 +278,7 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[base_ind + jz] + rhs[index]; @@ -311,7 +303,7 @@ Field3D& Field3D::operator+=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { (*this)[base_ind + jz] += rhs[index]; @@ -336,7 +328,7 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[base_ind + jz] - rhs[index]; @@ -361,7 +353,7 @@ Field3D& Field3D::operator-=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, rhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, rhs.getRegion("RGN_ALL")) { const auto base_ind = fieldmesh->ind2Dto3D(index); for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) { (*this)[base_ind + jz] -= rhs[index]; @@ -386,7 +378,7 @@ FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] * rhs[index]; @@ -406,7 +398,7 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] / rhs[index]; @@ -426,7 +418,7 @@ FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] + rhs[index]; @@ -446,7 +438,7 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] - rhs[index]; @@ -463,9 +455,7 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] * rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } checkData(result); return result; @@ -484,9 +474,7 @@ Field3D& Field3D::operator*=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; } checkData(*this); @@ -504,9 +492,7 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] * tmp; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } checkData(result); return result; @@ -526,9 +512,7 @@ Field3D& Field3D::operator/=(const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= tmp; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; } checkData(*this); @@ -545,9 +529,7 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] + rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } checkData(result); return result; @@ -566,9 +548,7 @@ Field3D& Field3D::operator+=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] += rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; } checkData(*this); @@ -585,9 +565,7 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] - rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } checkData(result); return result; @@ -606,9 +584,7 @@ Field3D& Field3D::operator-=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] -= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; } checkData(*this); @@ -628,7 +604,7 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] * rhs[base_ind + jz]; @@ -649,7 +625,7 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] / rhs[base_ind + jz]; @@ -670,7 +646,7 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] + rhs[base_ind + jz]; @@ -691,7 +667,7 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, lhs.getRegion("RGN_ALL")) { + BOUT_FOR(index, lhs.getRegion("RGN_ALL")) { const auto base_ind = localmesh->ind2Dto3D(index); for (int jz = 0; jz < localmesh->LocalNz; ++jz) { result[base_ind + jz] = lhs[index] - rhs[base_ind + jz]; @@ -710,7 +686,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -728,9 +704,7 @@ Field2D& Field2D::operator*=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } checkData(*this); @@ -748,7 +722,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -766,9 +740,7 @@ Field2D& Field2D::operator/=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] /= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } checkData(*this); @@ -786,7 +758,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -804,9 +776,7 @@ Field2D& Field2D::operator+=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] += rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } checkData(*this); @@ -824,7 +794,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -842,9 +812,7 @@ Field2D& Field2D::operator-=(const Field2D& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] -= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } checkData(*this); @@ -864,7 +832,7 @@ FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] * rhs[index]; @@ -884,7 +852,7 @@ FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] / rhs[index]; @@ -904,7 +872,7 @@ FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] + rhs[index]; @@ -924,7 +892,7 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = rhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[base_ind] - rhs[index]; @@ -941,9 +909,7 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] * rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } checkData(result); return result; @@ -958,9 +924,7 @@ Field2D& Field2D::operator*=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; } checkData(*this); @@ -978,9 +942,7 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] * tmp; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } checkData(result); return result; @@ -996,9 +958,7 @@ Field2D& Field2D::operator/=(const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= tmp; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; } checkData(*this); @@ -1015,9 +975,7 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] + rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } checkData(result); return result; @@ -1032,9 +990,7 @@ Field2D& Field2D::operator+=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] += rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; } checkData(*this); @@ -1051,9 +1007,7 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] - rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } checkData(result); return result; @@ -1068,9 +1022,7 @@ Field2D& Field2D::operator-=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] -= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; } checkData(*this); @@ -1090,7 +1042,7 @@ FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] * rhs[base_ind]; @@ -1112,7 +1064,7 @@ FieldPerp& FieldPerp::operator*=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] *= rhs[base_ind]; @@ -1136,7 +1088,7 @@ FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] / rhs[base_ind]; @@ -1158,7 +1110,7 @@ FieldPerp& FieldPerp::operator/=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] /= rhs[base_ind]; @@ -1182,7 +1134,7 @@ FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] + rhs[base_ind]; @@ -1204,7 +1156,7 @@ FieldPerp& FieldPerp::operator+=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] += rhs[base_ind]; @@ -1228,7 +1180,7 @@ FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] - rhs[base_ind]; @@ -1250,7 +1202,7 @@ FieldPerp& FieldPerp::operator-=(const Field3D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] -= rhs[base_ind]; @@ -1274,7 +1226,7 @@ FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] * rhs[base_ind]; @@ -1296,7 +1248,7 @@ FieldPerp& FieldPerp::operator*=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] *= rhs[base_ind]; @@ -1320,7 +1272,7 @@ FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] / rhs[base_ind]; @@ -1342,7 +1294,7 @@ FieldPerp& FieldPerp::operator/=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] /= rhs[base_ind]; @@ -1366,7 +1318,7 @@ FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] + rhs[base_ind]; @@ -1388,7 +1340,7 @@ FieldPerp& FieldPerp::operator+=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] += rhs[base_ind]; @@ -1412,7 +1364,7 @@ FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs) { Mesh* localmesh = lhs.getMesh(); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { int yind = lhs.getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); result[index] = lhs[index] - rhs[base_ind]; @@ -1434,7 +1386,7 @@ FieldPerp& FieldPerp::operator-=(const Field2D& rhs) { Mesh* localmesh = this->getMesh(); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { + BOUT_FOR(index, this->getRegion("RGN_ALL")) { int yind = this->getIndex(); const auto base_ind = localmesh->indPerpto3D(index, yind); (*this)[index] -= rhs[base_ind]; @@ -1456,7 +1408,7 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -1474,9 +1426,7 @@ FieldPerp& FieldPerp::operator*=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; } checkData(*this); @@ -1494,7 +1444,7 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -1512,9 +1462,7 @@ FieldPerp& FieldPerp::operator/=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] /= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; } checkData(*this); @@ -1532,7 +1480,7 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -1550,9 +1498,7 @@ FieldPerp& FieldPerp::operator+=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] += rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; } checkData(*this); @@ -1570,7 +1516,7 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -1588,9 +1534,7 @@ FieldPerp& FieldPerp::operator-=(const FieldPerp& rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] -= rhs[index]; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; } checkData(*this); @@ -1607,9 +1551,7 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] * rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; } checkData(result); return result; @@ -1624,9 +1566,7 @@ FieldPerp& FieldPerp::operator*=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] *= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; } checkData(*this); @@ -1644,9 +1584,7 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] * tmp; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; } checkData(result); return result; @@ -1661,9 +1599,7 @@ FieldPerp& FieldPerp::operator/=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] /= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs; } checkData(*this); @@ -1680,9 +1616,7 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] + rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; } checkData(result); return result; @@ -1697,9 +1631,7 @@ FieldPerp& FieldPerp::operator+=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] += rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; } checkData(*this); @@ -1716,9 +1648,7 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs[index] - rhs; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; } checkData(result); return result; @@ -1733,9 +1663,7 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) { checkData(*this); checkData(rhs); - BOUT_FOR (index, this->getRegion("RGN_ALL")) { - (*this)[index] -= rhs; - } + BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; } checkData(*this); @@ -1752,9 +1680,7 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs * rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } checkData(result); return result; @@ -1767,9 +1693,7 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs / rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } checkData(result); return result; @@ -1782,9 +1706,7 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs + rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } checkData(result); return result; @@ -1797,9 +1719,7 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs - rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } checkData(result); return result; @@ -1812,9 +1732,7 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs * rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } checkData(result); return result; @@ -1827,9 +1745,7 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs / rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } checkData(result); return result; @@ -1842,9 +1758,7 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs + rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } checkData(result); return result; @@ -1857,9 +1771,7 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs - rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } checkData(result); return result; @@ -1872,9 +1784,7 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs * rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; } checkData(result); return result; @@ -1887,9 +1797,7 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs / rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; } checkData(result); return result; @@ -1902,9 +1810,7 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs + rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; } checkData(result); return result; @@ -1917,9 +1823,7 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR (index, result.getRegion("RGN_ALL")) { - result[index] = lhs - rhs[index]; - } + BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; } checkData(result); return result; diff --git a/src/field/globalfield.cxx b/src/field/globalfield.cxx index d98a0660e1..6bd2fd4dbf 100644 --- a/src/field/globalfield.cxx +++ b/src/field/globalfield.cxx @@ -1,7 +1,7 @@ -#include #include #include +#include GlobalField::GlobalField(Mesh* m, int proc, int xsize, int ysize, int zsize) : mesh(m), data_on_proc(proc), nx(xsize), ny(ysize), nz(zsize) { diff --git a/src/field/initialprofiles.cxx b/src/field/initialprofiles.cxx index b9e78d9deb..ded5aa9882 100644 --- a/src/field/initialprofiles.cxx +++ b/src/field/initialprofiles.cxx @@ -36,12 +36,12 @@ * **************************************************************************/ -#include #include #include #include #include #include +#include #include void initial_profile(const std::string& name, Field3D& var) { diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx index c4cfefa829..5f34e2af02 100644 --- a/src/field/vecops.cxx +++ b/src/field/vecops.cxx @@ -388,7 +388,7 @@ R V_dot_Grad(const T& v, const F& a) { if (a.covariant) { result.x = VDDX(vcn.x, a.x) + VDDY(vcn.y, a.x) + VDDZ(vcn.z, a.x); - BOUT_FOR (i, result.x.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.x.getRegion("RGN_ALL")) { result.x[i] -= vcn.x[i] * (metric->G1_11[i] * a.x[i] + metric->G2_11[i] * a.y[i] + metric->G3_11[i] * a.z[i]); @@ -401,7 +401,7 @@ R V_dot_Grad(const T& v, const F& a) { } result.y = VDDX(vcn.x, a.y) + VDDY(vcn.y, a.y) + VDDZ(vcn.z, a.y); - BOUT_FOR (i, result.y.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.y.getRegion("RGN_ALL")) { result.y[i] -= vcn.x[i] * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i] + metric->G3_12[i] * a.z[i]); @@ -414,7 +414,7 @@ R V_dot_Grad(const T& v, const F& a) { } result.z = VDDX(vcn.x, a.z) + VDDY(vcn.y, a.z) + VDDZ(vcn.z, a.z); - BOUT_FOR (i, result.z.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.z.getRegion("RGN_ALL")) { result.z[i] -= vcn.x[i] * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i] + metric->G3_13[i] * a.z[i]); @@ -428,7 +428,7 @@ R V_dot_Grad(const T& v, const F& a) { result.covariant = true; } else { result.x = VDDX(vcn.x, a.x) + VDDY(vcn.y, a.x) + VDDZ(vcn.z, a.x); - BOUT_FOR (i, result.x.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.x.getRegion("RGN_ALL")) { result.x[i] += vcn.x[i] * (metric->G1_11[i] * a.x[i] + metric->G1_12[i] * a.y[i] + metric->G1_13[i] * a.z[i]); @@ -441,7 +441,7 @@ R V_dot_Grad(const T& v, const F& a) { } result.y = VDDX(vcn.x, a.y) + VDDY(vcn.y, a.y) + VDDZ(vcn.z, a.y); - BOUT_FOR (i, result.y.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.y.getRegion("RGN_ALL")) { result.y[i] += vcn.x[i] * (metric->G2_11[i] * a.x[i] + metric->G2_12[i] * a.y[i] + metric->G2_13[i] * a.z[i]); @@ -454,7 +454,7 @@ R V_dot_Grad(const T& v, const F& a) { } result.z = VDDX(vcn.x, a.z) + VDDY(vcn.y, a.z) + VDDZ(vcn.z, a.z); - BOUT_FOR (i, result.z.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.z.getRegion("RGN_ALL")) { result.z[i] += vcn.x[i] * (metric->G3_11[i] * a.x[i] + metric->G3_12[i] * a.y[i] + metric->G3_13[i] * a.z[i]); diff --git a/src/field/vector2d.cxx b/src/field/vector2d.cxx index 2be11e4117..74d3a88a22 100644 --- a/src/field/vector2d.cxx +++ b/src/field/vector2d.cxx @@ -30,10 +30,10 @@ #include -#include #include #include #include +#include #include Vector2D::Vector2D(const Vector2D& f) @@ -85,7 +85,7 @@ void Vector2D::toCovariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR (i, x.getRegion("RGN_ALL")) { + BOUT_FOR(i, x.getRegion("RGN_ALL")) { x[i] = metric_x->g_11[i] * x[i] + metric_x->g_12[i] * y_at_x[i] + metric_x->g_13[i] * z_at_x[i]; y[i] = metric_y->g_22[i] * y[i] + metric_y->g_12[i] * x_at_y[i] @@ -99,7 +99,7 @@ void Vector2D::toCovariant() { // Need to use temporary arrays to store result Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR (i, x.getRegion("RGN_ALL")) { + BOUT_FOR(i, x.getRegion("RGN_ALL")) { gx[i] = metric->g_11[i] * x[i] + metric->g_12[i] * y[i] + metric->g_13[i] * z[i]; gy[i] = metric->g_22[i] * y[i] + metric->g_12[i] * x[i] + metric->g_23[i] * z[i]; gz[i] = metric->g_33[i] * z[i] + metric->g_13[i] * x[i] + metric->g_23[i] * y[i]; @@ -139,7 +139,7 @@ void Vector2D::toContravariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR (i, x.getRegion("RGN_ALL")) { + BOUT_FOR(i, x.getRegion("RGN_ALL")) { x[i] = metric_x->g11[i] * x[i] + metric_x->g12[i] * y_at_x[i] + metric_x->g13[i] * z_at_x[i]; y[i] = metric_y->g22[i] * y[i] + metric_y->g12[i] * x_at_y[i] @@ -154,7 +154,7 @@ void Vector2D::toContravariant() { // Need to use temporary arrays to store result Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR (i, x.getRegion("RGN_ALL")) { + BOUT_FOR(i, x.getRegion("RGN_ALL")) { gx[i] = metric->g11[i] * x[i] + metric->g12[i] * y[i] + metric->g13[i] * z[i]; gy[i] = metric->g22[i] * y[i] + metric->g12[i] * x[i] + metric->g23[i] * z[i]; gz[i] = metric->g33[i] * z[i] + metric->g13[i] * x[i] + metric->g23[i] * y[i]; diff --git a/src/field/vector3d.cxx b/src/field/vector3d.cxx index 2a9ac86066..56124595b3 100644 --- a/src/field/vector3d.cxx +++ b/src/field/vector3d.cxx @@ -31,10 +31,10 @@ #include #include -#include #include #include #include +#include #include Vector3D::Vector3D(const Vector3D& f) @@ -86,7 +86,7 @@ void Vector3D::toCovariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) { x[i] = metric_x->g_11[i] * x[i] + metric_x->g_12[i] * y_at_x[i] + metric_x->g_13[i] * z_at_x[i]; y[i] = metric_y->g_22[i] * y[i] + metric_y->g_12[i] * x_at_y[i] @@ -100,7 +100,7 @@ void Vector3D::toCovariant() { // Need to use temporary arrays to store result Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) { gx[i] = metric->g_11[i] * x[i] + metric->g_12[i] * y[i] + metric->g_13[i] * z[i]; gy[i] = metric->g_22[i] * y[i] + metric->g_12[i] * x[i] + metric->g_23[i] * z[i]; gz[i] = metric->g_33[i] * z[i] + metric->g_13[i] * x[i] + metric->g_23[i] * y[i]; @@ -140,7 +140,7 @@ void Vector3D::toContravariant() { const auto y_at_z = interp_to(y, z.getLocation()); // multiply by g_{ij} - BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) { x[i] = metric_x->g11[i] * x[i] + metric_x->g12[i] * y_at_x[i] + metric_x->g13[i] * z_at_x[i]; y[i] = metric_y->g22[i] * y[i] + metric_y->g12[i] * x_at_y[i] @@ -155,7 +155,7 @@ void Vector3D::toContravariant() { // Need to use temporary arrays to store result Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)}; - BOUT_FOR (i, localmesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) { gx[i] = metric->g11[i] * x[i] + metric->g12[i] * y[i] + metric->g13[i] * z[i]; gy[i] = metric->g22[i] * y[i] + metric->g12[i] * x[i] + metric->g23[i] * z[i]; gz[i] = metric->g33[i] * z[i] + metric->g13[i] * x[i] + metric->g23[i] * y[i]; diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx index a9ce985289..d51474a8ab 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx @@ -38,13 +38,13 @@ #if not BOUT_USE_METRIC_3D -#include -#include -#include #include +#include #include #include +#include #include +#include #include #include "cyclic_laplace.hxx" @@ -131,7 +131,8 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } if (dst) { - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -180,7 +181,8 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { cr->solve(bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array // ZFFT routine expects input of this length @@ -204,7 +206,8 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array // ZFFT routine expects input of this length auto k1d = Array((localmesh->LocalNz) / 2 + 1); @@ -266,7 +269,8 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array // ZFFT routine expects input of this length auto k1d = Array((localmesh->LocalNz) / 2 + 1); @@ -354,7 +358,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { auto bcmplx3D = Matrix(nsys, nx); if (dst) { - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array // ZFFT routine expects input of this length auto k1d = Array(localmesh->LocalNz); @@ -412,7 +417,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { cr->solve(bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array // ZFFT routine expects input of length LocalNz auto k1d = Array(localmesh->LocalNz); @@ -439,7 +445,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array // ZFFT routine expects input of this length auto k1d = Array(localmesh->LocalNz / 2 + 1); @@ -517,7 +524,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { } // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx index 314f9942ed..302fa0f7b4 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx @@ -31,8 +31,8 @@ class LaplaceCyclic; #ifndef __LAP_CYCLIC_H__ #define __LAP_CYCLIC_H__ -#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" +#include "bout/invert_laplace.hxx" #if BOUT_USE_METRIC_3D diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx index 99946a64dd..831524aba0 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx @@ -30,16 +30,16 @@ #include "hypre3d_laplace.hxx" #include +#include #include +#include #include #include #include #include #include -#include -#include -#include #include +#include LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* solver, Datafile* dump) @@ -249,28 +249,16 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) { Field3D result = solution.toField(); localmesh->communicate(result); if (result.hasParallelSlices()) { - BOUT_FOR (i, indexer->getRegionLowerY()) { - result.ydown()[i] = result[i]; - } - BOUT_FOR (i, indexer->getRegionUpperY()) { - result.yup()[i] = result[i]; - } + BOUT_FOR(i, indexer->getRegionLowerY()) { result.ydown()[i] = result[i]; } + BOUT_FOR(i, indexer->getRegionUpperY()) { result.yup()[i] = result[i]; } for (int b = 1; b < localmesh->ystart; b++) { - BOUT_FOR (i, indexer->getRegionLowerY()) { - result.ydown(b)[i.ym(b)] = result[i]; - } - BOUT_FOR (i, indexer->getRegionUpperY()) { - result.yup(b)[i.yp(b)] = result[i]; - } + BOUT_FOR(i, indexer->getRegionLowerY()) { result.ydown(b)[i.ym(b)] = result[i]; } + BOUT_FOR(i, indexer->getRegionUpperY()) { result.yup(b)[i.yp(b)] = result[i]; } } } for (int b = 1; b < localmesh->xstart; b++) { - BOUT_FOR (i, indexer->getRegionInnerX()) { - result[i.xm(b)] = result[i]; - } - BOUT_FOR (i, indexer->getRegionOuterX()) { - result[i.xp(b)] = result[i]; - } + BOUT_FOR(i, indexer->getRegionInnerX()) { result[i.xm(b)] = result[i]; } + BOUT_FOR(i, indexer->getRegionOuterX()) { result[i.xp(b)] = result[i]; } } CALI_MARK_END("LaplaceHypre3d_solve:createField"); diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx index 9fc2864f84..fdd9d99b0b 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx @@ -35,12 +35,12 @@ class LaplaceHypre3d; #if BOUT_HAS_HYPRE -#include -#include -#include #include #include +#include #include +#include +#include #include #include diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx index 261ea2089a..3652371b65 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx @@ -31,16 +31,16 @@ #include "bout/globals.hxx" +#include #include +#include +#include #include #include #include #include -#include -#include -#include -#include #include +#include #include "bout/boutcomm.hxx" #include diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx index 5f78ac89d1..3380d25391 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx @@ -29,8 +29,8 @@ class LaplaceIPT; #ifndef __IPT_H__ #define __IPT_H__ -#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" +#include "bout/invert_laplace.hxx" #if BOUT_USE_METRIC_3D diff --git a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx index 3670b314c7..14893d3103 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx @@ -32,8 +32,8 @@ #if not BOUT_USE_METRIC_3D #include "multigrid_laplace.hxx" -#include #include "bout/unused.hxx" +#include // Define basic multigrid algorithm @@ -41,7 +41,9 @@ MultigridAlg::MultigridAlg(int level, int lx, int lz, int gx, int gz, MPI_Comm c int check) : mglevel(level), pcheck(check), commMG(comm) { - if(pcheck > 0) output<<"Construct MG "< 0) { + output << "Construct MG " << level << endl; + } // Memory allocate for Multigrid gnx.reallocate(mglevel); @@ -49,79 +51,85 @@ MultigridAlg::MultigridAlg(int level, int lx, int lz, int gx, int gz, MPI_Comm c lnx.reallocate(mglevel); lnz.reallocate(mglevel); - gnx[mglevel-1] = gx; - gnz[mglevel-1] = gz; - lnx[mglevel-1] = lx; - lnz[mglevel-1] = lz; - if(mglevel > 1) { - for(int i=mglevel-1;i>0;i--) { - gnx[i-1] = gnx[i]/2; - gnz[i-1] = gnz[i]/2; - lnx[i-1] = lnx[i]/2; - lnz[i-1] = lnz[i]/2; + gnx[mglevel - 1] = gx; + gnz[mglevel - 1] = gz; + lnx[mglevel - 1] = lx; + lnz[mglevel - 1] = lz; + if (mglevel > 1) { + for (int i = mglevel - 1; i > 0; i--) { + gnx[i - 1] = gnx[i] / 2; + gnz[i - 1] = gnz[i] / 2; + lnx[i - 1] = lnx[i] / 2; + lnz[i - 1] = lnz[i] / 2; } } // Could be replaced with a Matrix - matmg = new BoutReal *[mglevel]; - for(int i = 0;i 1) { - int level = mglevel-1; - int ldim = (lnx[level]+2)*(lnz[level]+2); + if (mglevel == 1) { + pGMRES(x, b, mglevel - 1, 1); + } else if (mgplag == 1) { + pGMRES(x, b, mglevel - 1, 1); + } else { + solveMG(x, b, mglevel - 1); + } + } else { + cycleMG(mglevel - 1, x, b); + if (flag > 1) { + int level = mglevel - 1; + int ldim = (lnx[level] + 2) * (lnz[level] + 2); Array y(ldim); Array r(ldim); - for(int n = 1;n r((lnx[level] + 2) * (lnz[level] + 2)); Array pr((lnx[level - 1] + 2) * (lnz[level - 1] + 2)); Array y((lnx[level - 1] + 2) * (lnz[level - 1] + 2)); Array iy((lnx[level] + 2) * (lnz[level] + 2)); - smoothings(level,sol,rhs); + smoothings(level, sol, rhs); residualVec(level, sol, rhs, std::begin(r)); @@ -129,149 +137,172 @@ void MultigridAlg::cycleMG(int level,BoutReal *sol,BoutReal *rhs) BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i=0;i<(lnx[level-1]+2)*(lnz[level-1]+2);i++) y[i] = 0.0; +for (int i = 0; i < (lnx[level - 1] + 2) * (lnz[level - 1] + 2); i++) { + y[i] = 0.0; +} - cycleMG(level - 1, std::begin(y), std::begin(pr)); +cycleMG(level - 1, std::begin(y), std::begin(pr)); - prolongation(level - 1, std::begin(y), std::begin(iy)); - BOUT_OMP(parallel default(shared)) +prolongation(level - 1, std::begin(y), std::begin(iy)); +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i=0;i<(lnx[level]+2)*(lnz[level]+2);i++) - sol[i] += iy[i]; +for (int i = 0; i < (lnx[level] + 2) * (lnz[level] + 2); i++) { + sol[i] += iy[i]; +} - smoothings(level,sol,rhs); +smoothings(level, sol, rhs); } } -void MultigridAlg::projection(int level,BoutReal *r,BoutReal *pr) -{ +void MultigridAlg::projection(int level, BoutReal* r, BoutReal* pr) { -BOUT_OMP(parallel default(shared)) + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i=0;i<(lnx[level-1]+2)*(lnz[level-1]+2);i++) pr[i] = 0.; - int xend = lnx[level-1]+1; - int zend = lnz[level-1]+1; +for (int i = 0; i < (lnx[level - 1] + 2) * (lnz[level - 1] + 2); i++) { + pr[i] = 0.; +} +int xend = lnx[level - 1] + 1; +int zend = lnz[level - 1] + 1; BOUT_OMP(for collapse(2)) - for (int i=1; i< xend; i++) { - for (int k=1; k< zend; k++) { - int i2 = 2*i-1; - int k2 = 2*k-1; - int nn = i*(lnz[level-1]+2)+k; - int n0 = i2*(lnz[level]+2)+k2; - int n1 = n0 + 1; - int n2 = n0 + lnz[level]+2; - int n3 = n2 + 1; - pr[nn] = (r[n0]+r[n1]+r[n2]+r[n3])/4.0; - } - } +for (int i = 1; i < xend; i++) { + for (int k = 1; k < zend; k++) { +int i2 = 2 * i - 1; +int k2 = 2 * k - 1; +int nn = i * (lnz[level - 1] + 2) + k; +int n0 = i2 * (lnz[level] + 2) + k2; +int n1 = n0 + 1; +int n2 = n0 + lnz[level] + 2; +int n3 = n2 + 1; +pr[nn] = (r[n0] + r[n1] + r[n2] + r[n3]) / 4.0; } - communications(pr,level-1); +} + } + communications(pr, level - 1); } -void MultigridAlg::prolongation(int level,BoutReal *x,BoutReal *ix) { +void MultigridAlg::prolongation(int level, BoutReal* x, BoutReal* ix) { -BOUT_OMP(parallel default(shared)) + BOUT_OMP(parallel default(shared)) { BOUT_OMP(for) - for(int i=0;i<(lnx[level+1]+2)*(lnz[level+1]+2);i++) ix[i] = 0.; +for (int i = 0; i < (lnx[level + 1] + 2) * (lnz[level + 1] + 2); i++) { + ix[i] = 0.; +} - int xend = lnx[level]+1; - int zend = lnz[level]+1; +int xend = lnx[level] + 1; +int zend = lnz[level] + 1; BOUT_OMP(for collapse(2)) - for (int i=1; i< xend; i++) { - for (int k=1; k< zend; k++) { - int i2 = 2*i-1; - int k2 = 2*k-1; - int nn = i*(lnz[level]+2)+k; - int n0 = i2*(lnz[level+1]+2)+k2; - int n1 = n0 + 1; - int n2 = n0 + lnz[level+1]+2; - int n3 = n2 +1; - ix[n0] = x[nn]; - ix[n1] = x[nn]; - ix[n2] = x[nn]; - ix[n3] = x[nn]; - } - } +for (int i = 1; i < xend; i++) { + for (int k = 1; k < zend; k++) { +int i2 = 2 * i - 1; +int k2 = 2 * k - 1; +int nn = i * (lnz[level] + 2) + k; +int n0 = i2 * (lnz[level + 1] + 2) + k2; +int n1 = n0 + 1; +int n2 = n0 + lnz[level + 1] + 2; +int n3 = n2 + 1; +ix[n0] = x[nn]; +ix[n1] = x[nn]; +ix[n2] = x[nn]; +ix[n3] = x[nn]; } - communications(ix,level+1); +} + } + communications(ix, level + 1); } -void MultigridAlg::smoothings(int level, BoutReal *x, BoutReal *b) { +void MultigridAlg::smoothings(int level, BoutReal* x, BoutReal* b) { int dim; - int mm = lnz[level]+2; - dim = mm*(lnx[level]+2); - if(mgsm == 0) { - Array x0(dim); + int mm = lnz[level] + 2; + dim = mm * (lnx[level] + 2); + if (mgsm == 0) { +Array x0(dim); BOUT_OMP(parallel default(shared)) - for(int num =0;num < 2;num++) { +for (int num = 0; num < 2; num++) { BOUT_OMP(for) - for(int i = 0;i0;i--) - for(int k= lnz[level];k>0;k--) { - int nn = i*mm+k; - BoutReal val = b[nn] - matmg[level][nn*9+3]*x[nn-1] - - matmg[level][nn*9+5]*x[nn+1] - matmg[level][nn*9+1]*x[nn-mm] - - matmg[level][nn*9+7]*x[nn+mm] - matmg[level][nn*9]*x[nn-mm-1] - - matmg[level][nn*9+2]*x[nn-mm+1] - matmg[level][nn*9+6]*x[nn+mm-1] - - matmg[level][nn*9+8]*x[nn+mm+1]; - if(fabs(matmg[level][nn*9+4]) 0; i--) { +for (int k = lnz[level]; k > 0; k--) { +int nn = i * mm + k; +BoutReal val = + b[nn] - matmg[level][nn * 9 + 3] * x[nn - 1] - matmg[level][nn * 9 + 5] * x[nn + 1] + - matmg[level][nn * 9 + 1] * x[nn - mm] - matmg[level][nn * 9 + 7] * x[nn + mm] + - matmg[level][nn * 9] * x[nn - mm - 1] - matmg[level][nn * 9 + 2] * x[nn - mm + 1] + - matmg[level][nn * 9 + 6] * x[nn + mm - 1] + - matmg[level][nn * 9 + 8] * x[nn + mm + 1]; +if (fabs(matmg[level][nn * 9 + 4]) < atol) { + throw BoutException("Error at matmg({:d}-{:d})", level, nn); +} +x[nn] = val / matmg[level][nn * 9 + 4]; +} +} +communications(x, level); } } -void MultigridAlg::pGMRES(BoutReal *sol,BoutReal *rhs,int level,int iplag) { - int it,etest = 1,MAXIT; - BoutReal ini_e,error,a0,a1,rederr,perror; - BoutReal **v; - BoutReal c[MAXGM+1],s[MAXGM+1],y[MAXGM+1],g[MAXGM+1],h[MAXGM+1][MAXGM+1]; +void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { + int it, etest = 1, MAXIT; + BoutReal ini_e, error, a0, a1, rederr, perror; + BoutReal** v; + BoutReal c[MAXGM + 1], s[MAXGM + 1], y[MAXGM + 1], g[MAXGM + 1], + h[MAXGM + 1][MAXGM + 1]; - if((level == 0) || (iplag == 0)) MAXIT = 40000; - else MAXIT = 500; + if ((level == 0) || (iplag == 0)) { +MAXIT = 40000; + } else { +MAXIT = 500; + } - int ldim = (lnx[level]+2)*(lnz[level]+2); + int ldim = (lnx[level] + 2) * (lnz[level] + 2); // Could we use a Matrix here? - v = new BoutReal *[MAXGM+1]; - for(int i=0;i p(ldim); Array q(ldim); @@ -279,490 +310,550 @@ void MultigridAlg::pGMRES(BoutReal *sol,BoutReal *rhs,int level,int iplag) { BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i = 0;i 9) { - output< 9) { +output << num << " Second a1 in GMRES is wrong at level " << level << ": " << a1 << endl; +} +a0 = 1.0 / a1; +h[it + 1][it] = a1; BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i=0;i=0;i--) { - y[i] = g[i]; - for(int j=i+1;j<=it;j++) y[i] -= h[i][j]*y[j]; - y[i] = y[i]/h[i][i]; - } +for (int i = 0; i < it; i++) { +a0 = c[i] * h[i][it] - s[i] * h[i + 1][it]; +a1 = s[i] * h[i][it] + c[i] * h[i + 1][it]; +h[i][it] = a0; +h[i + 1][it] = a1; +} +a0 = h[it][it] * h[it][it] + h[it + 1][it] * h[it + 1][it]; +if (a0 < 0.0) { +throw BoutException("a0 in GMRES is negative \n"); +} +a0 = sqrt(a0); +if (fabs(a0) < atol * rtol) { +throw BoutException("a0 in GMRES is wrong \n"); +} +c[it] = h[it][it] / a0; +s[it] = -h[it + 1][it] / a0; +h[it][it] = a0; +h[it + 1][it] = 0.0; +a0 = c[it] * g[it] - s[it] * g[it + 1]; +a1 = s[it] * g[it] + c[it] * g[it + 1]; +g[it] = a0; +g[it + 1] = a1; + +/* Get solution y and x_m*/ +for (int i = it; i >= 0; i--) { +y[i] = g[i]; +for (int j = i + 1; j <= it; j++) { + y[i] -= h[i][j] * y[j]; +} +y[i] = y[i] / h[i][i]; +} BOUT_OMP(parallel default(shared)) - { +{ BOUT_OMP(for) - for(int i=0;i dtol) - throw BoutException("GMRES reached dtol with error {:16.10f} at iteration {:d}\n", - error, num); - if(num > MAXIT) - throw BoutException( - "GMRES reached MAXIT with error {:16.10f} at iteration {:d}\n", error, num); - if(error <= rtol*ini_e+atol) { - etest = 0; - break; - } - // J. Omotani, 27/2/2018: I think this test is intended to check for slow - // convergence of the GMRES solve, and 'abort' if it is converging - // slowly. This is OK on a coarse level solver, because at worst it means - // the top-level iteration will have to continue but the top level - // iteration should only be stopped by the previous test against the - // tolerance. - // Therefore, check that this is not the top-level solver before applying - // this test. - if( (level < mglevel-1) && (fabs(perror-error)/error < rtol) ) { - if(it == 0) etest = 0; - num -= 1; - break; - } - perror = error; - } - /* Restart with new initial */ +/* Get r_m and test convergence.*/ +residualVec(level, std::begin(p), rhs, std::begin(r)); +error = sqrt(vectorProd(level, std::begin(r), std::begin(r))); +num += 1; +if (error > dtol) { +throw BoutException("GMRES reached dtol with error {:16.10f} at iteration {:d}\n", error, + num); +} +if (num > MAXIT) { +throw BoutException("GMRES reached MAXIT with error {:16.10f} at iteration {:d}\n", error, + num); +} +if (error <= rtol * ini_e + atol) { +etest = 0; +break; +} +// J. Omotani, 27/2/2018: I think this test is intended to check for slow +// convergence of the GMRES solve, and 'abort' if it is converging +// slowly. This is OK on a coarse level solver, because at worst it means +// the top-level iteration will have to continue but the top level +// iteration should only be stopped by the previous test against the +// tolerance. +// Therefore, check that this is not the top-level solver before applying +// this test. +if ((level < mglevel - 1) && (fabs(perror - error) / error < rtol)) { +if (it == 0) { + etest = 0; +} +num -= 1; +break; +} +perror = error; +} +/* Restart with new initial */ BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i = 0;iMAXIT) - throw BoutException(" GMRES Iteration limit.\n"); - // if((etest == 1) & (xProcI == 0)) - // printf("Restart GMRES %d | %20.14f\n",num,error/ini_e); - } while(etest == 1); - - if(level == 0) { - if((rProcI == 0) && (pcheck == 1)) { - rederr = log(error / ini_e) / static_cast(num); - rederr = exp(rederr); - printf("The average error reduction of GMRES %d: %14.8f(%18.10f)\n",num,rederr,error); - fflush(stdout); - } - } - else { - if((rProcI == 0) && (pcheck == 1)) { - rederr = log(error / ini_e) / static_cast(num); - rederr = exp(rederr); - printf("The average error reduction of PGMRES %d: %14.8f(%18.10f)\n",num,rederr,error); - fflush(stdout); - } - } - for(int i=0;i MAXIT) { +throw BoutException(" GMRES Iteration limit.\n"); +} +// if((etest == 1) & (xProcI == 0)) +// printf("Restart GMRES %d | %20.14f\n",num,error/ini_e); +} while (etest == 1); + +if (level == 0) { +if ((rProcI == 0) && (pcheck == 1)) { +rederr = log(error / ini_e) / static_cast(num); +rederr = exp(rederr); +printf("The average error reduction of GMRES %d: %14.8f(%18.10f)\n", num, rederr, error); +fflush(stdout); +} +} else { +if ((rProcI == 0) && (pcheck == 1)) { +rederr = log(error / ini_e) / static_cast(num); +rederr = exp(rederr); +printf("The average error reduction of PGMRES %d: %14.8f(%18.10f)\n", num, rederr, error); +fflush(stdout); +} +} +for (int i = 0; i < MAXGM + 1; i++) { +delete[] v[i]; +} +delete[] v; } void MultigridAlg::setMultigridC(int UNUSED(plag)) { - int level = mglevel - 1; - for(int n = level;n>0;n--) { - setMatrixC(n); - if(pcheck == 2) { - output< 0; n--) { +setMatrixC(n); +if (pcheck == 2) { +output << n << "matrix in Alg = " << lnx[n] << "," << lnz[n] << endl; +output << gnx[n] << "," << gnz[n] << endl; +} +} } -void MultigridAlg::lowestSolver(BoutReal *x, BoutReal *b, int UNUSED(plag)) { - pGMRES(x, b, 0, 0); +void MultigridAlg::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { +pGMRES(x, b, 0, 0); } -BoutReal MultigridAlg::vectorProd(int level,BoutReal* x,BoutReal* y) { - // nx does not include guard cells - - BoutReal val; - BoutReal ini_e = 0.0; -BOUT_OMP(parallel default(shared) ) - { - int xend = lnx[level]+1; - int zend = lnz[level]+1; +BoutReal MultigridAlg::vectorProd(int level, BoutReal* x, BoutReal* y) { +// nx does not include guard cells + +BoutReal val; +BoutReal ini_e = 0.0; +BOUT_OMP(parallel default(shared)) +{ +int xend = lnx[level] + 1; +int zend = lnz[level] + 1; BOUT_OMP(for reduction(+:ini_e) collapse(2)) - for(int i= 1;i 1) - bout::globals::mpi->MPI_Allreduce(&ini_e, &val, 1, MPI_DOUBLE, MPI_SUM, commMG); - else val = ini_e; +for (int i = 1; i < xend; i++) { +for (int k = 1; k < zend; k++) { +int ii = i * (lnz[level] + 2) + k; +ini_e += x[ii] * y[ii]; +} +} +} +if (numP > 1) { +bout::globals::mpi->MPI_Allreduce(&ini_e, &val, 1, MPI_DOUBLE, MPI_SUM, commMG); +} else { +val = ini_e; +} - return(val); +return (val); } -void MultigridAlg::multiAVec(int level, BoutReal *x, BoutReal *b) { +void MultigridAlg::multiAVec(int level, BoutReal* x, BoutReal* b) { - int mm = lnz[level]+2; +int mm = lnz[level] + 2; BOUT_OMP(parallel default(shared)) - { +{ BOUT_OMP(for) - for(int i = 0;i1 and xNP>1 (with a single - // MPI_Waitall after all the MPI_Isend and MPI_Irecv calls, instead of the two - // MPI_Waitalls there are now. As there are never any z-communications at the moment, it - // is not worth implementing for now. - - MPI_Status status[4]; - int stag, rtag; - MAYBE_UNUSED(int ierr); - - if(zNP > 1) { - MPI_Request requests[] = {MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL}; - MPI_Datatype xvector; - - // Create datatype to hold z-direction guard cells, which are not continuous in memory - ierr = MPI_Type_vector(lnx[level], 1, lnz[level]+2, MPI_DOUBLE, &xvector); - ASSERT1(ierr == MPI_SUCCESS); - - ierr = MPI_Type_commit(&xvector); - ASSERT1(ierr == MPI_SUCCESS); - - // Receive from z- - rtag = zProcM; - ierr = bout::globals::mpi->MPI_Irecv(&x[lnz[level] + 2], 1, xvector, zProcM, rtag, - commMG, &requests[2]); - ASSERT1(ierr == MPI_SUCCESS); - - // Receive from z+ - rtag = zProcP+numP; - ierr = bout::globals::mpi->MPI_Irecv(&x[2 * (lnz[level] + 2) - 1], 1, xvector, zProcP, - rtag, commMG, &requests[3]); - ASSERT1(ierr == MPI_SUCCESS); - - // Send to z+ - stag = rProcI; - ierr = bout::globals::mpi->MPI_Isend(&x[2 * (lnz[level] + 2) - 2], 1, xvector, zProcP, - stag, commMG, &requests[0]); - ASSERT1(ierr == MPI_SUCCESS); - - // Send to z- - stag = rProcI+numP; - ierr = bout::globals::mpi->MPI_Isend(&x[lnz[level] + 3], 1, xvector, zProcM, stag, - commMG, &requests[1]); - ASSERT1(ierr == MPI_SUCCESS); - - // Wait for communications to complete - ierr = bout::globals::mpi->MPI_Waitall(4, requests, status); - ASSERT1(ierr == MPI_SUCCESS); - - ierr = MPI_Type_free(&xvector); - ASSERT1(ierr == MPI_SUCCESS); - } else { - for (int i=1;i 1) { - // Note: periodic x-direction not handled here - - MPI_Request requests[] = {MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL}; - - if (xProcI > 0) { - // Receive from x- - rtag = xProcM; - ierr = bout::globals::mpi->MPI_Irecv(&x[0], lnz[level] + 2, MPI_DOUBLE, xProcM, - rtag, commMG, &requests[2]); - ASSERT1(ierr == MPI_SUCCESS); - } - - if (xProcI < xNP - 1) { - // Receive from x+ - rtag = xProcP+xNP;; - ierr = bout::globals::mpi->MPI_Irecv(&x[(lnx[level] + 1) * (lnz[level] + 2)], - lnz[level] + 2, MPI_DOUBLE, xProcP, rtag, - commMG, &requests[3]); - ASSERT1(ierr == MPI_SUCCESS); - - // Send to x+ - stag = rProcI; - ierr = - bout::globals::mpi->MPI_Isend(&x[lnx[level] * (lnz[level] + 2)], lnz[level] + 2, - MPI_DOUBLE, xProcP, stag, commMG, &requests[0]); - ASSERT1(ierr == MPI_SUCCESS); - } +// Note: currently z-direction communications and x-direction communications are done +// independently. They should really be done together if zNP>1 and xNP>1 (with a single +// MPI_Waitall after all the MPI_Isend and MPI_Irecv calls, instead of the two +// MPI_Waitalls there are now. As there are never any z-communications at the moment, it +// is not worth implementing for now. + +MPI_Status status[4]; +int stag, rtag; +MAYBE_UNUSED(int ierr); + +if (zNP > 1) { +MPI_Request requests[] = {MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL, + MPI_REQUEST_NULL}; +MPI_Datatype xvector; + +// Create datatype to hold z-direction guard cells, which are not continuous in memory +ierr = MPI_Type_vector(lnx[level], 1, lnz[level] + 2, MPI_DOUBLE, &xvector); +ASSERT1(ierr == MPI_SUCCESS); + +ierr = MPI_Type_commit(&xvector); +ASSERT1(ierr == MPI_SUCCESS); + +// Receive from z- +rtag = zProcM; +ierr = bout::globals::mpi->MPI_Irecv(&x[lnz[level] + 2], 1, xvector, zProcM, rtag, commMG, + &requests[2]); +ASSERT1(ierr == MPI_SUCCESS); + +// Receive from z+ +rtag = zProcP + numP; +ierr = bout::globals::mpi->MPI_Irecv(&x[2 * (lnz[level] + 2) - 1], 1, xvector, zProcP, + rtag, commMG, &requests[3]); +ASSERT1(ierr == MPI_SUCCESS); + +// Send to z+ +stag = rProcI; +ierr = bout::globals::mpi->MPI_Isend(&x[2 * (lnz[level] + 2) - 2], 1, xvector, zProcP, + stag, commMG, &requests[0]); +ASSERT1(ierr == MPI_SUCCESS); + +// Send to z- +stag = rProcI + numP; +ierr = bout::globals::mpi->MPI_Isend(&x[lnz[level] + 3], 1, xvector, zProcM, stag, commMG, + &requests[1]); +ASSERT1(ierr == MPI_SUCCESS); + +// Wait for communications to complete +ierr = bout::globals::mpi->MPI_Waitall(4, requests, status); +ASSERT1(ierr == MPI_SUCCESS); + +ierr = MPI_Type_free(&xvector); +ASSERT1(ierr == MPI_SUCCESS); +} else { +for (int i = 1; i < lnx[level] + 1; i++) { +x[i * (lnz[level] + 2)] = x[(i + 1) * (lnz[level] + 2) - 2]; +x[(i + 1) * (lnz[level] + 2) - 1] = x[i * (lnz[level] + 2) + 1]; +} +} +if (xNP > 1) { +// Note: periodic x-direction not handled here + +MPI_Request requests[] = {MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL, + MPI_REQUEST_NULL}; + +if (xProcI > 0) { +// Receive from x- +rtag = xProcM; +ierr = bout::globals::mpi->MPI_Irecv(&x[0], lnz[level] + 2, MPI_DOUBLE, xProcM, rtag, + commMG, &requests[2]); +ASSERT1(ierr == MPI_SUCCESS); +} - if (xProcI > 0) { - // Send to x- - stag = rProcI+xNP; - ierr = bout::globals::mpi->MPI_Isend(&x[lnz[level] + 2], lnz[level] + 2, MPI_DOUBLE, - xProcM, stag, commMG, &requests[1]); - ASSERT1(ierr == MPI_SUCCESS); - } +if (xProcI < xNP - 1) { +// Receive from x+ +rtag = xProcP + xNP; +; +ierr = + bout::globals::mpi->MPI_Irecv(&x[(lnx[level] + 1) * (lnz[level] + 2)], lnz[level] + 2, + MPI_DOUBLE, xProcP, rtag, commMG, &requests[3]); +ASSERT1(ierr == MPI_SUCCESS); + +// Send to x+ +stag = rProcI; +ierr = bout::globals::mpi->MPI_Isend(&x[lnx[level] * (lnz[level] + 2)], lnz[level] + 2, + MPI_DOUBLE, xProcP, stag, commMG, &requests[0]); +ASSERT1(ierr == MPI_SUCCESS); +} - // Wait for communications to complete - ierr = bout::globals::mpi->MPI_Waitall(4, requests, status); - ASSERT1(ierr == MPI_SUCCESS); - } else { - for (int i=0;i 0) { +// Send to x- +stag = rProcI + xNP; +ierr = bout::globals::mpi->MPI_Isend(&x[lnz[level] + 2], lnz[level] + 2, MPI_DOUBLE, + xProcM, stag, commMG, &requests[1]); +ASSERT1(ierr == MPI_SUCCESS); } +// Wait for communications to complete +ierr = bout::globals::mpi->MPI_Waitall(4, requests, status); +ASSERT1(ierr == MPI_SUCCESS); +} else { +for (int i = 0; i < lnz[level] + 2; i++) { +x[i] = x[lnx[level] * (lnz[level] + 2) + i]; +x[(lnx[level] + 1) * (lnz[level] + 2) + i] = x[(lnz[level] + 2) + i]; +} +} +} -void MultigridAlg::solveMG(BoutReal *sol,BoutReal *rhs,int level) { - int m,MAXIT = 150; - BoutReal ini_e,perror,error,rederr; - int ldim = (lnx[level]+2)*(lnz[level]+2); +void MultigridAlg::solveMG(BoutReal* sol, BoutReal* rhs, int level) { +int m, MAXIT = 150; +BoutReal ini_e, perror, error, rederr; +int ldim = (lnx[level] + 2) * (lnz[level] + 2); BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i = 0;i y(ldim); - Array r(ldim); - BOUT_OMP(parallel default(shared)) +for (int i = 0; i < ldim; i++) { +sol[i] = 0.0; +} + +ini_e = vectorProd(level, rhs, rhs); +if (ini_e < 0.0) { +throw BoutException("In MG Initial Error {:10.4e} \n", ini_e); +} +ini_e = sqrt(ini_e); +if ((pcheck == 1) && (rProcI == 0)) { +printf("%d \n In MGsolve ini = %24.18f\n", numP, ini_e); +} +Array y(ldim); +Array r(ldim); +BOUT_OMP(parallel default(shared)) BOUT_OMP(for) - for(int i = 0;i dtol)) - throw BoutException("In MG Limited Error {:10.4e} \n", error); - perror = error; - } +for (int i = 0; i < ldim; i++) { +sol[i] = sol[i] + y[i]; +} +residualVec(level, sol, rhs, std::begin(r)); +error = sqrt(vectorProd(level, std::begin(r), std::begin(r))); +if ((pcheck == 1) && (rProcI == 0)) { +printf("%d \n In MGsolve error = %24.18f\n", m, error); +} +if (error < rtol * ini_e + atol) { +break; +} +if ((fabs(perror - error) / error < rtol) || (error > dtol)) { +throw BoutException("In MG Limited Error {:10.4e} \n", error); +} +perror = error; +} - if((rProcI == 0) && (pcheck == 1)) { - rederr = log(error / ini_e) / (static_cast(m) + 1.0); - rederr = exp(rederr); - if(m == MAXIT) - printf("Reached maximum iteration: %14.8f\n",error); - printf("The average error reduction of MG %d: %14.8f(%18.12f)\n",m+1,rederr,error); - fflush(stdout); - } +if ((rProcI == 0) && (pcheck == 1)) { +rederr = log(error / ini_e) / (static_cast(m) + 1.0); +rederr = exp(rederr); +if (m == MAXIT) { +printf("Reached maximum iteration: %14.8f\n", error); +} +printf("The average error reduction of MG %d: %14.8f(%18.12f)\n", m + 1, rederr, error); +fflush(stdout); +} } #endif diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx index 953c52bcbe..881063b088 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx @@ -33,8 +33,8 @@ #if not BOUT_USE_METRIC_3D #include -#include #include +#include #if BOUT_USE_OPENMP #include @@ -220,7 +220,8 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ } #if BOUT_USE_OPENMP BOUT_OMP(parallel) - BOUT_OMP(master) { output << "Num threads = " << omp_get_num_threads() << endl; } + BOUT_OMP(master) + { output << "Num threads = " << omp_get_num_threads() << endl; } #endif } } @@ -465,9 +466,7 @@ FieldPerp result{emptyFrom(b_in)}; #if CHECK > 2 // Make any unused elements NaN so that user does not try to do calculations with them -BOUT_FOR (i, result.getRegion("RGN_ALL")) { -result[i] = BoutNaN; -} +BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = BoutNaN; } #endif // Copy solution into a FieldPerp to return diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx index 236d3d139c..2567380027 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx @@ -31,8 +31,8 @@ #ifndef __MULTIGRID_LAPLACE_H__ #define __MULTIGRID_LAPLACE_H__ -#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" +#include "bout/invert_laplace.hxx" #if BOUT_USE_METRIC_3D diff --git a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx index eb7e2bdb6c..40abb663f7 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx @@ -290,7 +290,8 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { int nx = (xProcI % rMG->zNP) * lnx[0]; - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { BOUT_OMP(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; @@ -318,7 +319,8 @@ for (int ix = 1; ix < xend; ix++) { MPI_SUM, comm2D); int nz = (xProcI % rMG->zNP) * (rMG->lnz[level]); - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { int xend = rMG->lnx[level] + 1; int zend = rMG->lnz[level] + 1; BOUT_OMP(for collapse(2)) @@ -333,7 +335,8 @@ for (int ix = 1; ix < xend; ix++) { rMG->getSolution(std::begin(y), std::begin(r), 1); - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { BOUT_OMP(for) for (int i = 0; i < dimg; i++) { yl[i] = 0.0; @@ -354,7 +357,8 @@ for (int ix = 1; ix < xend; ix++) { bout::globals::mpi->MPI_Allreduce(std::begin(yl), std::begin(yg), dimg, MPI_DOUBLE, MPI_SUM, comm2D); - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { int xend = lnx[0] + 1; int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) @@ -373,7 +377,8 @@ for (int ix = 1; ix < xend; ix++) { Array y(dim); Array r(dim); int nx = xProcI * lnx[0]; - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { BOUT_OMP(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; @@ -399,7 +404,8 @@ y[i] = 0.0; } sMG->getSolution(std::begin(y), std::begin(r), 1); -BOUT_OMP(parallel default(shared)) { +BOUT_OMP(parallel default(shared)) +{ int xend = lnx[0] + 1; int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) @@ -424,7 +430,8 @@ void Multigrid1DP::convertMatrixF2D(int level) { Array yl(dim * 9); Array yg(dim * 9); int nx = (xProcI % rMG->zNP) * lnx[0]; - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { BOUT_OMP(for) for (int i = 0; i < dim * 9; i++) { yl[i] = 0.0; @@ -487,7 +494,8 @@ fclose(outf); } int nz = (xProcI % rMG->zNP) * (rMG->lnz[level]); - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { int xend = rMG->lnx[level] + 1; int zend = rMG->lnz[level] + 1; BOUT_OMP(for collapse(2)) @@ -509,7 +517,8 @@ void Multigrid1DP::convertMatrixFS(int level) { Array yl(dim * 9); BoutReal* yg = sMG->matmg[level]; int nx = xProcI * lnx[0]; - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { BOUT_OMP(for) for (int i = 0; i < dim * 9; i++) { yl[i] = 0.0; @@ -666,7 +675,8 @@ Array y(dim); Array r(dim); int nx = xProcI * lnx[0]; int nz = zProcI * lnz[0]; -BOUT_OMP(parallel default(shared)) { +BOUT_OMP(parallel default(shared)) +{ BOUT_OMP(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; @@ -692,7 +702,8 @@ for (int i = 0; i < dim; i++) { y[i] = 0.0; } sMG->getSolution(std::begin(y), std::begin(r), 1); -BOUT_OMP(parallel default(shared)) { +BOUT_OMP(parallel default(shared)) +{ int xend = lnx[0] + 1; int zend = lnz[0] + 1; BOUT_OMP(for collapse(2)) @@ -717,7 +728,8 @@ void Multigrid2DPf1D::convertMatrixFS(int level) { BoutReal* yg = sMG->matmg[level]; int nx = xProcI * lnx[0]; int nz = zProcI * lnz[0]; - BOUT_OMP(parallel default(shared)) { + BOUT_OMP(parallel default(shared)) + { BOUT_OMP(for) for (int i = 0; i < dim * 9; i++) { yl[i] = 0.0; diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx index 0811e6a6f6..af678ff7d6 100644 --- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx +++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx @@ -136,13 +136,13 @@ * * Stop: Function returns phiNext */ -#include -#include -#include #include +#include #include #include #include +#include +#include #include "naulin_laplace.hxx" diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx index 5d141cc1a4..4d446d8d60 100644 --- a/src/invert/laplace/impls/pcr/pcr.cxx +++ b/src/invert/laplace/impls/pcr/pcr.cxx @@ -39,15 +39,15 @@ #include "pcr.hxx" #include "bout/globals.hxx" +#include #include +#include +#include #include #include #include -#include -#include -#include -#include #include +#include #include "bout/boutcomm.hxx" #include @@ -162,7 +162,8 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { if (dst) { const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -209,7 +210,8 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { cr_pcr_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -232,7 +234,8 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length @@ -277,7 +280,8 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { cr_pcr_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length @@ -368,7 +372,8 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { if (dst) { const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -423,7 +428,8 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { cr_pcr_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -450,7 +456,8 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array(localmesh->LocalNz / 2 + 1); // ZFFT routine expects input of this length @@ -504,7 +511,8 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { cr_pcr_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx index 21df752f3a..15ba1f24f2 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx @@ -40,15 +40,15 @@ #include "bout/globals.hxx" #include "bout/boutcomm.hxx" +#include #include +#include +#include #include #include +#include #include #include -#include -#include -#include -#include #include #include @@ -157,7 +157,8 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { if (dst) { const BoutReal zlength = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -204,7 +205,8 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { pcr_thomas_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -227,7 +229,8 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length @@ -272,7 +275,8 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { pcr_thomas_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length @@ -363,7 +367,8 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { if (dst) { const BoutReal zlength = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -418,7 +423,8 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { pcr_thomas_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length @@ -445,7 +451,8 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array(localmesh->LocalNz / 2 + 1); // ZFFT routine expects input of this length @@ -500,7 +507,8 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { pcr_thomas_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx index b027664be1..580eb21a32 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx @@ -30,9 +30,9 @@ #include "petsc_laplace.hxx" #include +#include #include #include -#include #include #define KSP_RICHARDSON "richardson" diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx index 416db62c92..b7f8583d5e 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx @@ -29,8 +29,8 @@ #ifndef __PETSC_LAPLACE_H__ #define __PETSC_LAPLACE_H__ -#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" +#include "bout/invert_laplace.hxx" #if not BOUT_HAS_PETSC @@ -41,11 +41,11 @@ RegisterUnavailableLaplace registerlaplacepetsc(LAPLACE_PETSC, #else -#include #include #include #include #include +#include #include // PETSc creates macros for MPI calls, which interfere with the MpiWrapper class diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 646703e9a9..465dd3b532 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -31,12 +31,12 @@ #include "petsc3damg.hxx" #include +#include +#include #include #include #include #include -#include -#include #include LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mesh_in, @@ -273,19 +273,13 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { Field3D solution = guess.toField(); localmesh->communicate(solution); if (solution.hasParallelSlices()) { - BOUT_FOR (i, indexer->getRegionLowerY()) { - solution.ydown()[i] = solution[i]; - } - BOUT_FOR (i, indexer->getRegionUpperY()) { - solution.yup()[i] = solution[i]; - } + BOUT_FOR(i, indexer->getRegionLowerY()) { solution.ydown()[i] = solution[i]; } + BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup()[i] = solution[i]; } for (int b = 1; b < localmesh->ystart; b++) { - BOUT_FOR (i, indexer->getRegionLowerY()) { + BOUT_FOR(i, indexer->getRegionLowerY()) { solution.ydown(b)[i.ym(b)] = solution[i]; } - BOUT_FOR (i, indexer->getRegionUpperY()) { - solution.yup(b)[i.yp(b)] = solution[i]; - } + BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup(b)[i.yp(b)] = solution[i]; } } } @@ -293,7 +287,7 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // from single boundary cell which is set by the solver // Note: RegionInnerX is the set of points just outside the domain // (in the first boundary cell) so one boundary cell is already set - BOUT_FOR (i, indexer->getRegionInnerX()) { + BOUT_FOR(i, indexer->getRegionInnerX()) { for (int b = 1; b < localmesh->xstart; b++) { solution[i.xm(b)] = 3. * solution[i.xm(b - 1)] - 3. * solution[i.xm(b - 2)] + solution[i.xm(b - 3)]; @@ -303,7 +297,7 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Set outer boundary cells by extrapolating // Note: RegionOuterX is the set of points just outside the domain // (in the first boundary cell) so one boundary cell is already set - BOUT_FOR (i, indexer->getRegionOuterX()) { + BOUT_FOR(i, indexer->getRegionOuterX()) { for (int b = 1; b < localmesh->xstart; b++) { solution[i.xp(b)] = 3. * solution[i.xp(b - 1)] - 3. * solution[i.xp(b - 2)] + solution[i.xp(b - 3)]; diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx index 81c5893e20..818f60fbae 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx @@ -30,8 +30,8 @@ class LaplacePetsc3dAmg; #ifndef __PETSC_LAPLACE_3DAMG_H__ #define __PETSC_LAPLACE_3DAMG_H__ -#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" +#include "bout/invert_laplace.hxx" #if not BOUT_HAS_PETSC @@ -42,13 +42,13 @@ RegisterUnavailableLaplace #else -#include -#include -#include #include #include +#include #include #include +#include +#include #include class LaplacePetsc3dAmg; diff --git a/src/invert/laplace/impls/serial_band/serial_band.cxx b/src/invert/laplace/impls/serial_band/serial_band.cxx index 1eaad7359f..7ea1272ff0 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.cxx +++ b/src/invert/laplace/impls/serial_band/serial_band.cxx @@ -29,13 +29,13 @@ #if not BOUT_USE_METRIC_3D -#include -#include -#include #include +#include #include #include #include +#include +#include #include #include diff --git a/src/invert/laplace/impls/serial_band/serial_band.hxx b/src/invert/laplace/impls/serial_band/serial_band.hxx index 1eb35322ce..9dbee8632b 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.hxx +++ b/src/invert/laplace/impls/serial_band/serial_band.hxx @@ -29,8 +29,8 @@ class LaplaceSerialBand; #ifndef __SERIAL_BAND_H__ #define __SERIAL_BAND_H__ -#include "bout/invert_laplace.hxx" #include "bout/build_config.hxx" +#include "bout/invert_laplace.hxx" #if BOUT_USE_METRIC_3D diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx index f61223bb50..83c73e3309 100644 --- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx +++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx @@ -27,14 +27,14 @@ #include "serial_tri.hxx" #include "bout/globals.hxx" -#include -#include -#include #include -#include +#include #include #include +#include +#include #include +#include #include diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index 975655ca81..2abae3399d 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -31,13 +31,13 @@ * */ +#include #include +#include +#include #include #include #include -#include -#include -#include #include #include "spt.hxx" diff --git a/src/invert/laplace/impls/spt/spt.hxx b/src/invert/laplace/impls/spt/spt.hxx index c000e1991b..d92a08a460 100644 --- a/src/invert/laplace/impls/spt/spt.hxx +++ b/src/invert/laplace/impls/spt/spt.hxx @@ -41,9 +41,9 @@ class LaplaceSPT; #ifndef __SPT_H__ #define __SPT_H__ -#include #include #include +#include #include #include diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index 43d540a261..96450a0871 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -31,20 +31,20 @@ * */ -#include -#include -#include -#include -#include #include #include -#include +#include #include #include +#include #include +#include #include #include +#include +#include #include +#include // Implementations: #include "impls/cyclic/cyclic_laplace.hxx" diff --git a/src/invert/laplacexy/laplacexy.cxx b/src/invert/laplacexy/laplacexy.cxx index 3714d1b1df..df01d83767 100644 --- a/src/invert/laplacexy/laplacexy.cxx +++ b/src/invert/laplacexy/laplacexy.cxx @@ -8,10 +8,10 @@ #include -#include #include #include #include +#include #include #include diff --git a/src/invert/laplacexy2/laplacexy2.cxx b/src/invert/laplacexy2/laplacexy2.cxx index 88334982a2..3038a06803 100644 --- a/src/invert/laplacexy2/laplacexy2.cxx +++ b/src/invert/laplacexy2/laplacexy2.cxx @@ -8,9 +8,9 @@ #include -#include #include #include +#include #include #include diff --git a/src/invert/laplacexy2/laplacexy2_hypre.cxx b/src/invert/laplacexy2/laplacexy2_hypre.cxx index fc36b77aaa..b6154d1222 100644 --- a/src/invert/laplacexy2/laplacexy2_hypre.cxx +++ b/src/invert/laplacexy2/laplacexy2_hypre.cxx @@ -2,13 +2,13 @@ #if BOUT_HAS_HYPRE +#include "bout/assert.hxx" #include "bout/boutcomm.hxx" #include "bout/globals.hxx" -#include "bout/output.hxx" -#include "bout/utils.hxx" -#include "bout/assert.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" #include "bout/sys/timer.hxx" +#include "bout/utils.hxx" #include diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx index 9c32f4743e..fbe22241d8 100644 --- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx +++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx @@ -4,9 +4,9 @@ #if not BOUT_USE_METRIC_3D #include -#include #include #include +#include #include #include diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx index af46eb58c6..004b4f777a 100644 --- a/src/invert/parderiv/impls/cyclic/cyclic.cxx +++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx @@ -40,8 +40,8 @@ #if not BOUT_USE_METRIC_3D -#include #include +#include #include #include #include diff --git a/src/invert/parderiv/impls/cyclic/cyclic.hxx b/src/invert/parderiv/impls/cyclic/cyclic.hxx index 8fae47a055..0c581adc52 100644 --- a/src/invert/parderiv/impls/cyclic/cyclic.hxx +++ b/src/invert/parderiv/impls/cyclic/cyclic.hxx @@ -42,8 +42,8 @@ #ifndef __INV_PAR_CR_H__ #define __INV_PAR_CR_H__ -#include "bout/invert_parderiv.hxx" #include "bout/build_config.hxx" +#include "bout/invert_parderiv.hxx" #if BOUT_USE_METRIC_3D diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx index a0db089713..86cdb4e10d 100644 --- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx +++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx @@ -40,8 +40,8 @@ #if not BOUT_USE_METRIC_3D -#include #include +#include #include #include #include diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx index 51b6c9043f..700ef8a91f 100644 --- a/src/mesh/boundary_region.cxx +++ b/src/mesh/boundary_region.cxx @@ -1,7 +1,7 @@ -#include #include #include +#include #include #include From a014948887024d5149a20578fe34a50f7c5424ee Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 11:44:58 +0100 Subject: [PATCH 062/412] apply clang-format v15.0.7 with .clang-format@d8f14fdd --- .clang-format | 3 +- src/mesh/boundary_standard.cxx | 4 +- src/mesh/coordinates.cxx | 2 +- src/mesh/data/gridfromfile.cxx | 6 +- src/mesh/data/gridfromoptions.cxx | 4 +- src/mesh/difops.cxx | 6 +- src/mesh/fv_ops.cxx | 2 +- src/mesh/impls/bout/boutmesh.cxx | 4 +- src/mesh/index_derivs.cxx | 6 +- src/mesh/interpolation/bilinear_xz.cxx | 4 +- src/mesh/interpolation/hermite_spline_xz.cxx | 6 +- src/mesh/interpolation/hermite_spline_z.cxx | 6 +- src/mesh/interpolation/interpolation_z.cxx | 2 +- src/mesh/interpolation/lagrange_4pt_xz.cxx | 4 +- .../monotonic_hermite_spline_xz.cxx | 6 +- src/mesh/mesh.cxx | 4 +- src/mesh/parallel/fci.cxx | 4 +- src/mesh/parallel/fci.hxx | 2 +- src/mesh/parallel/shiftedmetric.cxx | 18 ++-- src/mesh/parallel/shiftedmetricinterp.cxx | 2 +- src/mesh/parallel/shiftedmetricinterp.hxx | 2 +- src/mesh/parallel_boundary_op.cxx | 4 +- src/physics/gyro_average.cxx | 4 +- src/physics/smoothing.cxx | 2 +- src/physics/snb.cxx | 2 +- src/physics/sourcex.cxx | 18 ++-- .../impls/adams_bashforth/adams_bashforth.hxx | 2 +- src/solver/impls/arkode/arkode.cxx | 2 +- src/solver/impls/cvode/cvode.cxx | 4 +- src/solver/impls/euler/euler.cxx | 2 +- src/solver/impls/euler/euler.hxx | 2 +- src/solver/impls/imex-bdf2/imex-bdf2.cxx | 2 +- src/solver/impls/imex-bdf2/imex-bdf2.hxx | 2 +- src/solver/impls/power/power.cxx | 2 +- src/solver/impls/power/power.hxx | 2 +- src/solver/impls/pvode/pvode.cxx | 4 +- src/solver/impls/pvode/pvode.hxx | 2 +- src/solver/impls/rk3-ssp/rk3-ssp.cxx | 4 +- src/solver/impls/rk3-ssp/rk3-ssp.hxx | 2 +- src/solver/impls/rk4/rk4.cxx | 2 +- src/solver/impls/rk4/rk4.hxx | 2 +- src/solver/impls/rkgeneric/rkgeneric.hxx | 2 +- src/solver/impls/rkgeneric/rkscheme.cxx | 6 +- src/solver/impls/snes/snes.hxx | 2 +- src/solver/impls/split-rk/split-rk.hxx | 2 +- src/solver/solver.cxx | 4 +- src/sys/bout_types.cxx | 2 +- src/sys/boutexception.cxx | 4 +- src/sys/expressionparser.cxx | 2 +- src/sys/hyprelib.cxx | 17 ++-- src/sys/msg_stack.cxx | 11 ++- src/sys/output.cxx | 4 +- src/sys/petsclib.cxx | 11 ++- src/sys/slepclib.cxx | 2 +- src/sys/utils.cxx | 2 +- tests/MMS/advection/advection.cxx | 2 +- tests/MMS/diffusion/diffusion.cxx | 6 +- tests/MMS/diffusion2/diffusion.cxx | 4 +- tests/MMS/elm-pb/elm_pb.cxx | 4 +- tests/MMS/fieldalign/fieldalign.cxx | 2 +- tests/MMS/hw/hw.cxx | 2 +- tests/MMS/spatial/diffusion/diffusion.cxx | 4 +- tests/MMS/tokamak/tokamak.cxx | 2 +- tests/MMS/wave-1d-y/wave.cxx | 2 +- tests/MMS/wave-1d/wave.cxx | 4 +- .../test-communications.cxx | 2 +- .../test-dataformat/test_dataformat.cxx | 2 +- .../test-drift-instability/2fluid.cxx | 2 +- .../test-globalfield/test_globalfield.cxx | 2 +- .../test-griddata/test_griddata.cxx | 2 +- .../test-interpolate-z/test_interpolate.cxx | 2 +- .../test-interpolate/test_interpolate.cxx | 2 +- .../integrated/test-laplace2/test_laplace.cxx | 2 +- .../test-laplacexy-fv/test-laplacexy.cxx | 4 +- .../test-laplacexy-short/test-laplacexy.cxx | 4 +- .../integrated/test-laplacexy/loadmetric.cxx | 2 +- .../test-laplacexy/test-laplacexy.cxx | 4 +- .../test-laplacexy2-hypre/test-laplacexy.cxx | 4 +- .../test-laplacexz/test-laplacexz.cxx | 2 +- .../test_multigrid_laplace.cxx | 4 +- .../test_naulin_laplace.cxx | 4 +- .../integrated/test-nonuniform/test_delp2.cxx | 2 +- .../test-petsc_laplace/test_petsc_laplace.cxx | 4 +- .../test_petsc_laplace_MAST_grid.cxx | 4 +- .../test_region_iterator.cxx | 6 +- tests/integrated/test-snb/test_snb.cxx | 4 +- .../test-stopCheck-file/test_stopCheck.cxx | 2 +- .../test-stopCheck/test_stopCheck.cxx | 2 +- tests/unit/bout_test_main.cxx | 4 +- tests/unit/fake_parallel_mesh.hxx | 6 +- tests/unit/field/test_field.cxx | 6 +- tests/unit/field/test_field2d.cxx | 6 +- tests/unit/field/test_field3d.cxx | 6 +- tests/unit/field/test_field_factory.cxx | 6 +- tests/unit/field/test_fieldgroup.cxx | 2 +- tests/unit/field/test_fieldperp.cxx | 8 +- tests/unit/field/test_initialprofiles.cxx | 6 +- tests/unit/field/test_vector2d.cxx | 8 +- tests/unit/field/test_vector3d.cxx | 8 +- tests/unit/field/test_where.cxx | 2 +- tests/unit/include/bout/test_array.cxx | 2 +- tests/unit/include/bout/test_deriv_store.cxx | 2 +- .../include/bout/test_hypre_interface.cxx | 19 ++-- .../unit/include/bout/test_petsc_indexer.cxx | 86 +++++++------------ tests/unit/include/bout/test_petsc_matrix.cxx | 8 +- tests/unit/include/bout/test_petsc_vector.cxx | 16 ++-- tests/unit/include/bout/test_region.cxx | 26 +++--- .../include/bout/test_single_index_ops.cxx | 38 +++----- .../bout/test_template_combinations.cxx | 2 +- tests/unit/include/test_cyclic_reduction.cxx | 4 +- tests/unit/include/test_derivs.cxx | 6 +- tests/unit/include/test_mask.cxx | 2 +- .../invert/laplace/test_laplace_cyclic.cxx | 14 +-- .../invert/laplace/test_laplace_hypre3d.cxx | 86 ++++++------------- .../laplace/test_laplace_petsc3damg.cxx | 86 ++++++------------- tests/unit/invert/test_fft.cxx | 4 +- tests/unit/mesh/data/test_gridfromoptions.cxx | 4 +- .../unit/mesh/parallel/test_shiftedmetric.cxx | 2 +- tests/unit/mesh/test_boutmesh.cxx | 2 +- tests/unit/mesh/test_coordinates.cxx | 2 +- tests/unit/mesh/test_interpolation.cxx | 8 +- tests/unit/mesh/test_mesh.cxx | 2 +- tests/unit/solver/test_solver.cxx | 4 +- tests/unit/solver/test_solverfactory.cxx | 2 +- tests/unit/src/test_bout++.cxx | 2 +- tests/unit/sys/test_boutexception.cxx | 2 +- tests/unit/sys/test_expressionparser.cxx | 4 +- tests/unit/sys/test_msg_stack.cxx | 2 +- tests/unit/sys/test_options_fields.cxx | 4 +- tests/unit/sys/test_options_netcdf.cxx | 4 +- tests/unit/sys/test_optionsreader.cxx | 2 +- tests/unit/test_extras.hxx | 4 +- 132 files changed, 379 insertions(+), 474 deletions(-) diff --git a/.clang-format b/.clang-format index b049b1a473..f51c5bde87 100644 --- a/.clang-format +++ b/.clang-format @@ -76,7 +76,8 @@ IndentCaseLabels: false # IndentPPDirectives: None IndentWidth: 2 IndentWrappedFunctionNames: false -InsertBraces: true +# requires clang-format 15+ +# InsertBraces: true KeepEmptyLinesAtTheStartOfBlocks: true MacroBlockBegin: '' MacroBlockEnd: '' diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx index 78e033b6e5..80c2053f39 100644 --- a/src/mesh/boundary_standard.cxx +++ b/src/mesh/boundary_standard.cxx @@ -1,11 +1,11 @@ -#include -#include #include #include +#include #include #include #include #include +#include #include #include #include diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx index a468054dca..c6092eab14 100644 --- a/src/mesh/coordinates.cxx +++ b/src/mesh/coordinates.cxx @@ -7,9 +7,9 @@ #include #include #include -#include #include #include +#include #include #include diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index f47d49a0b3..7e875bd109 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -2,16 +2,16 @@ #include "bout/traits.hxx" #include -#include -#include #include +#include #include #include #include #include +#include #include -#include #include +#include GridFile::GridFile(std::string gridfilename) : GridDataSource(true), data(bout::OptionsNetCDF(gridfilename).read()), diff --git a/src/mesh/data/gridfromoptions.cxx b/src/mesh/data/gridfromoptions.cxx index 311772ae2d..379e279de0 100644 --- a/src/mesh/data/gridfromoptions.cxx +++ b/src/mesh/data/gridfromoptions.cxx @@ -1,7 +1,7 @@ -#include -#include #include +#include #include +#include #include #include diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx index 3ec3b0ca97..9b7665ad30 100644 --- a/src/mesh/difops.cxx +++ b/src/mesh/difops.cxx @@ -26,12 +26,12 @@ #include "bout/build_config.hxx" #include -#include #include #include #include #include #include +#include #include #include @@ -704,7 +704,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, #if not(BOUT_USE_METRIC_3D) const int ncz = mesh->LocalNz; - BOUT_FOR (j2D, result.getRegion2D("RGN_NOBNDRY")) { + BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) { // Get constants for this iteration const BoutReal spacingFactor = 1.0 / (12 * metric->dz[j2D] * metric->dx[j2D]); const int jy = j2D.y(), jx = j2D.x(); @@ -997,7 +997,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, Field3D f_temp = f; Field3D g_temp = g; - BOUT_FOR (j2D, result.getRegion2D("RGN_NOBNDRY")) { + BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) { #if not(BOUT_USE_METRIC_3D) const BoutReal spacingFactor = 1.0 / (12 * metric->dz[j2D] * metric->dx[j2D]); #endif diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx index 28094840a2..37201b2d81 100644 --- a/src/mesh/fv_ops.cxx +++ b/src/mesh/fv_ops.cxx @@ -248,7 +248,7 @@ const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, Coordinates* coord = fin.getCoordinates(); - BOUT_FOR (i, result.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) { // Calculate flux at upper surface const auto iyp = i.yp(); diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index f2854b6b01..06ce23ead5 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -35,11 +35,10 @@ #include "boutmesh.hxx" -#include -#include #include #include #include +#include #include #include #include @@ -47,6 +46,7 @@ #include #include #include +#include #include #include diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx index c87a956749..769315ca68 100644 --- a/src/mesh/index_derivs.cxx +++ b/src/mesh/index_derivs.cxx @@ -446,7 +446,8 @@ class FFTDerivativeType { } const int kmax = ncz / 2 - kfilter; // Up to and including this wavenumber index - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { Array cv(ncz / 2 + 1); const BoutReal kwaveFac = TWOPI / ncz; @@ -504,7 +505,8 @@ class FFT2ndDerivativeType { const int ncz = theMesh->getNpoints(direction); const int kmax = ncz / 2; - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { Array cv(ncz / 2 + 1); const BoutReal kwaveFac = TWOPI / ncz; diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx index 584c8d8d29..4b071ecca0 100644 --- a/src/mesh/interpolation/bilinear_xz.cxx +++ b/src/mesh/interpolation/bilinear_xz.cxx @@ -45,7 +45,7 @@ XZBilinear::XZBilinear(int y_offset, Mesh* mesh) void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR (i, delta_x.getRegion(region)) { + BOUT_FOR(i, delta_x.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -96,7 +96,7 @@ Field3D XZBilinear::interpolate(const Field3D& f, const std::string& region) con ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR (i, f.getRegion(region)) { + BOUT_FOR(i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx index 97639c7ee8..b303ecbbea 100644 --- a/src/mesh/interpolation/hermite_spline_xz.cxx +++ b/src/mesh/interpolation/hermite_spline_xz.cxx @@ -21,8 +21,8 @@ **************************************************************************/ #include "bout/globals.hxx" -#include "bout/interpolation_xz.hxx" #include "bout/index_derivs_interface.hxx" +#include "bout/interpolation_xz.hxx" #include "bout/mesh.hxx" #include @@ -55,7 +55,7 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh) void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR (i, delta_x.getRegion(region)) { + BOUT_FOR(i, delta_x.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -176,7 +176,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region localmesh->wait(h); } - BOUT_FOR (i, f.getRegion(region)) { + BOUT_FOR(i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/interpolation/hermite_spline_z.cxx b/src/mesh/interpolation/hermite_spline_z.cxx index 5d98ff5ed5..921094af73 100644 --- a/src/mesh/interpolation/hermite_spline_z.cxx +++ b/src/mesh/interpolation/hermite_spline_z.cxx @@ -21,8 +21,8 @@ **************************************************************************/ #include "bout/globals.hxx" -#include "bout/interpolation_z.hxx" #include "bout/index_derivs_interface.hxx" +#include "bout/interpolation_z.hxx" #include "bout/mesh.hxx" #include @@ -66,7 +66,7 @@ void ZHermiteSpline::calcWeights(const Field3D& delta_z) { const auto& local_region = (y_offset == 0) ? delta_z.getRegion("RGN_ALL") : delta_z.getRegion("RGN_NOY"); - BOUT_FOR (i, local_region) { + BOUT_FOR(i, local_region) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -167,7 +167,7 @@ Field3D ZHermiteSpline::interpolate(const Field3D& f, // coordinates Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", local_fz_region); - BOUT_FOR (i, local_region) { + BOUT_FOR(i, local_region) { const auto corner = k_corner[i.ind].yp(y_offset); const auto corner_zp1 = corner.zp(); diff --git a/src/mesh/interpolation/interpolation_z.cxx b/src/mesh/interpolation/interpolation_z.cxx index 6162129965..8d39e6baa8 100644 --- a/src/mesh/interpolation/interpolation_z.cxx +++ b/src/mesh/interpolation/interpolation_z.cxx @@ -20,8 +20,8 @@ * **************************************************************************/ -#include #include +#include ZInterpolation::ZInterpolation(int y_offset, Mesh* mesh, Region region_in) : localmesh(mesh == nullptr ? bout::globals::mesh : mesh), region(region_in), diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx index 00f6752b2a..e68a7831fa 100644 --- a/src/mesh/interpolation/lagrange_4pt_xz.cxx +++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx @@ -40,7 +40,7 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh* mesh) void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z, const std::string& region) { - BOUT_FOR (i, delta_x.getRegion(region)) { + BOUT_FOR(i, delta_x.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); @@ -90,7 +90,7 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const std::string& region) ASSERT1(f.getMesh() == localmesh); Field3D f_interp{emptyFrom(f)}; - BOUT_FOR (i, f.getRegion(region)) { + BOUT_FOR(i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx index d753812da0..ffbb7b32e3 100644 --- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx +++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx @@ -21,10 +21,10 @@ **************************************************************************/ #include "bout/globals.hxx" -#include "bout/interpolation_xz.hxx" -#include "bout/output.hxx" #include "bout/index_derivs_interface.hxx" +#include "bout/interpolation_xz.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" #include @@ -58,7 +58,7 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f, localmesh->wait(h); } - BOUT_FOR (i, f.getRegion(region)) { + BOUT_FOR(i, f.getRegion(region)) { const int x = i.x(); const int y = i.y(); const int z = i.z(); diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index acfd090cdd..e754b4fe43 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -1,7 +1,7 @@ #include -#include #include #include +#include #include #include @@ -715,7 +715,7 @@ void Mesh::createDefaultRegions() { // Construct index lookup for 3D-->2D indexLookup3Dto2D = Array(LocalNx * LocalNy * LocalNz); - BOUT_FOR (ind3D, getRegion3D("RGN_ALL")) { + BOUT_FOR(ind3D, getRegion3D("RGN_ALL")) { indexLookup3Dto2D[ind3D.ind] = ind3Dto2D(ind3D).ind; } } diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index f991bde1f1..dd7171aaa6 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -39,9 +39,9 @@ #include "fci.hxx" #include "bout/parallel_boundary_op.hxx" #include "bout/parallel_boundary_region.hxx" +#include #include #include -#include #include #include @@ -118,7 +118,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, Field3D xt_prime_corner{emptyFrom(xt_prime)}; Field3D zt_prime_corner{emptyFrom(zt_prime)}; - BOUT_FOR (i, xt_prime_corner.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, xt_prime_corner.getRegion("RGN_NOBNDRY")) { // Point interpolated from (x+1/2, z+1/2) // Cache the offsets diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 4e7802b0c8..9f51b95968 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -26,10 +26,10 @@ #ifndef __FCITRANSFORM_H__ #define __FCITRANSFORM_H__ -#include #include #include #include +#include #include #include diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index 2284237701..d4b93cb274 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -7,12 +7,12 @@ */ #include "bout/paralleltransform.hxx" -#include -#include -#include #include +#include #include +#include #include +#include #include @@ -66,7 +66,7 @@ void ShiftedMetric::cachePhases() { toAlignedPhs = Tensor(mesh.LocalNx, mesh.LocalNy, nmodes); // To/From field aligned phases - BOUT_FOR (i, mesh.getRegion2D("RGN_ALL")) { + BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) { int ix = i.x(); int iy = i.y(); for (int jz = 0; jz < nmodes; jz++) { @@ -104,7 +104,7 @@ void ShiftedMetric::cachePhases() { // Parallel slice phases -- note we don't shift in the boundaries/guards for (auto& slice : parallel_slice_phases) { - BOUT_FOR (i, mesh.getRegion2D("RGN_NOY")) { + BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) { int ix = i.x(); int iy = i.y(); @@ -165,7 +165,7 @@ Field3D ShiftedMetric::shiftZ(const Field3D& f, const Tensor& phs, Field3D result{emptyFrom(f).setDirectionY(y_direction_out)}; - BOUT_FOR (i, mesh.getRegion2D(toString(region))) { + BOUT_FOR(i, mesh.getRegion2D(toString(region))) { shiftZ(&f(i, 0), &phs(i.x(), i.y(), 0), &result(i, 0)); } @@ -233,7 +233,7 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) { for (const auto& phase : parallel_slice_phases) { auto& f_slice = f.ynext(phase.y_offset); f_slice.allocate(); - BOUT_FOR (i, mesh.getRegion2D("RGN_NOY")) { + BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) { const int ix = i.x(); const int iy = i.y(); const int iy_offset = iy + phase.y_offset; @@ -256,7 +256,7 @@ ShiftedMetric::shiftZ(const Field3D& f, Matrix> f_fft(mesh.LocalNx, mesh.LocalNy); f_fft = Array(nmodes); - BOUT_FOR (i, mesh.getRegion2D("RGN_ALL")) { + BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) { int ix = i.x(); int iy = i.y(); f_fft(ix, iy).ensureUnique(); @@ -273,7 +273,7 @@ ShiftedMetric::shiftZ(const Field3D& f, current_result.allocate(); current_result.setLocation(f.getLocation()); - BOUT_FOR (i, mesh.getRegion2D("RGN_NOY")) { + BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) { // Deep copy the FFT'd field int ix = i.x(); int iy = i.y(); diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index 517d0c8bf3..fa3cbb9761 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -28,8 +28,8 @@ **************************************************************************/ #include "shiftedmetricinterp.hxx" -#include "bout/mask.hxx" #include "bout/constants.hxx" +#include "bout/mask.hxx" #include #include diff --git a/src/mesh/parallel/shiftedmetricinterp.hxx b/src/mesh/parallel/shiftedmetricinterp.hxx index 29e5a80091..56c4ffff54 100644 --- a/src/mesh/parallel/shiftedmetricinterp.hxx +++ b/src/mesh/parallel/shiftedmetricinterp.hxx @@ -27,8 +27,8 @@ #ifndef __SHIFTEDINTERP_H__ #define __SHIFTEDINTERP_H__ -#include #include +#include /*! * Shifted metric method diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx index 08fa3b9bc7..a1b2812581 100644 --- a/src/mesh/parallel_boundary_op.cxx +++ b/src/mesh/parallel_boundary_op.cxx @@ -1,9 +1,9 @@ #include "bout/parallel_boundary_op.hxx" +#include "bout/constants.hxx" #include "bout/field_factory.hxx" #include "bout/globals.hxx" -#include "bout/output.hxx" -#include "bout/constants.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" using bout::generator::Context; diff --git a/src/physics/gyro_average.cxx b/src/physics/gyro_average.cxx index 75df9e3338..10f3e02ac6 100644 --- a/src/physics/gyro_average.cxx +++ b/src/physics/gyro_average.cxx @@ -27,12 +27,12 @@ * **************************************************************/ -#include -#include #include #include #include #include +#include +#include Field3D gyroTaylor0(const Field3D& f, const Field3D& rho) { return f + SQ(rho) * Delp2(f); diff --git a/src/physics/smoothing.cxx b/src/physics/smoothing.cxx index bae428897e..78ac1814a5 100644 --- a/src/physics/smoothing.cxx +++ b/src/physics/smoothing.cxx @@ -34,9 +34,9 @@ #include "bout/build_config.hxx" -#include #include #include +#include #include #include diff --git a/src/physics/snb.cxx b/src/physics/snb.cxx index 2e495818d8..80da9e1bf8 100644 --- a/src/physics/snb.cxx +++ b/src/physics/snb.cxx @@ -2,8 +2,8 @@ /// #include "bout/snb.hxx" -#include "bout/derivs.hxx" #include "bout/constants.hxx" +#include "bout/derivs.hxx" #include "bout/fv_ops.hxx" namespace bout { diff --git a/src/physics/sourcex.cxx b/src/physics/sourcex.cxx index ccfc20750e..1cfc2fdc6e 100644 --- a/src/physics/sourcex.cxx +++ b/src/physics/sourcex.cxx @@ -2,11 +2,11 @@ * radial source and mask operators **************************************************************/ -#include #include +#include -#include #include +#include #include #include @@ -24,7 +24,7 @@ const Field2D source_tanhx(const Field2D& f, BoutReal swidth, BoutReal slength) Field2D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()) - slength; BoutReal dampl = TanH(lx / swidth); result[i] = 0.5 * (1.0 - dampl); @@ -43,7 +43,7 @@ const Field2D source_expx2(const Field2D& f, BoutReal swidth, BoutReal slength) Field2D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()) - slength; BoutReal dampl = exp(-lx * lx / swidth / swidth); result[i] = dampl; @@ -63,7 +63,7 @@ const Field3D sink_tanhx(const Field2D& UNUSED(f0), const Field3D& f, BoutReal s Field3D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal rlx = 1. - localmesh->GlobalX(i.x()) - slength; BoutReal dampr = TanH(rlx / swidth); result[i] = 0.5 * (1.0 - dampr) * f[i]; @@ -84,7 +84,7 @@ const Field3D mask_x(const Field3D& f, bool UNUSED(BoutRealspace)) { Field3D result{emptyFrom(f)}; // create a radial buffer zone to set jpar zero near radial boundary - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()); BoutReal dampl = TanH(lx / 40.0); BoutReal dampr = TanH((1. - lx) / 40.0); @@ -107,7 +107,7 @@ const Field3D sink_tanhxl(const Field2D& UNUSED(f0), const Field3D& f, BoutReal Field3D result{emptyFrom(f)}; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()) - slength; BoutReal dampl = TanH(lx / swidth); @@ -129,7 +129,7 @@ const Field3D sink_tanhxr(const Field2D& UNUSED(f0), const Field3D& f, BoutReal Field3D result{emptyFrom(f)}; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal rlx = 1. - localmesh->GlobalX(i.x()) - slength; BoutReal dampr = TanH(rlx / swidth); @@ -155,7 +155,7 @@ const Field3D buff_x(const Field3D& f, bool UNUSED(BoutRealspace)) { const BoutReal deltal = 0.05; const BoutReal deltar = 0.05; - BOUT_FOR (i, result.getRegion("RGN_ALL")) { + BOUT_FOR(i, result.getRegion("RGN_ALL")) { BoutReal lx = localmesh->GlobalX(i.x()); BoutReal rlx = 1. - lx; diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.hxx b/src/solver/impls/adams_bashforth/adams_bashforth.hxx index fa10353db5..ad8e77ed1c 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.hxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.hxx @@ -28,8 +28,8 @@ class AdamsBashforthSolver; #ifndef __ADAMSBASHFORTH_SOLVER_H__ #define __ADAMSBASHFORTH_SOLVER_H__ -#include #include +#include #include diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index acf9fa1c62..1aedd16dec 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -34,12 +34,12 @@ #include "bout/boutcomm.hxx" #include "bout/boutexception.hxx" #include "bout/field3d.hxx" +#include "bout/mesh.hxx" #include "bout/msg_stack.hxx" #include "bout/options.hxx" #include "bout/output.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/mesh.hxx" #if SUNDIALS_VERSION_MAJOR >= 4 #include diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 4da9d0c149..11190dfbc5 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -30,16 +30,16 @@ #if BOUT_HAS_CVODE +#include "bout/bout_enum_class.hxx" #include "bout/boutcomm.hxx" #include "bout/boutexception.hxx" #include "bout/field3d.hxx" +#include "bout/mesh.hxx" #include "bout/msg_stack.hxx" #include "bout/options.hxx" #include "bout/output.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/bout_enum_class.hxx" -#include "bout/mesh.hxx" #include "fmt/core.h" diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx index 6abf50e918..5b13719beb 100644 --- a/src/solver/impls/euler/euler.cxx +++ b/src/solver/impls/euler/euler.cxx @@ -1,10 +1,10 @@ #include "euler.hxx" -#include #include #include #include +#include #include #include diff --git a/src/solver/impls/euler/euler.hxx b/src/solver/impls/euler/euler.hxx index 244cef25c9..bfa0be9bb3 100644 --- a/src/solver/impls/euler/euler.hxx +++ b/src/solver/impls/euler/euler.hxx @@ -32,8 +32,8 @@ class EulerSolver; #include "mpi.h" -#include #include +#include namespace { RegisterSolver registersolvereuler("euler"); diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx index e78ba2ac0d..3e0c12f626 100644 --- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx +++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx @@ -5,9 +5,9 @@ #include "imex-bdf2.hxx" #include -#include #include #include +#include #include #include diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.hxx b/src/solver/impls/imex-bdf2/imex-bdf2.hxx index abda07606f..ac4e92870e 100644 --- a/src/solver/impls/imex-bdf2/imex-bdf2.hxx +++ b/src/solver/impls/imex-bdf2/imex-bdf2.hxx @@ -51,8 +51,8 @@ class IMEXBDF2; #include "mpi.h" -#include #include +#include #include #include diff --git a/src/solver/impls/power/power.cxx b/src/solver/impls/power/power.cxx index f8a4e27b32..888338b94c 100644 --- a/src/solver/impls/power/power.cxx +++ b/src/solver/impls/power/power.cxx @@ -2,9 +2,9 @@ #include "power.hxx" -#include #include #include +#include #include diff --git a/src/solver/impls/power/power.hxx b/src/solver/impls/power/power.hxx index a9ec754f73..757befeec5 100644 --- a/src/solver/impls/power/power.hxx +++ b/src/solver/impls/power/power.hxx @@ -29,8 +29,8 @@ class PowerSolver; #ifndef __POWER_SOLVER_H__ #define __POWER_SOLVER_H__ -#include #include +#include namespace { RegisterSolver registersolverpower("power"); diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx index 78b21c796f..da28df9d5e 100644 --- a/src/solver/impls/pvode/pvode.cxx +++ b/src/solver/impls/pvode/pvode.cxx @@ -29,12 +29,12 @@ #if BOUT_HAS_PVODE -#include -#include #include #include +#include #include #include +#include #include "bout/unused.hxx" diff --git a/src/solver/impls/pvode/pvode.hxx b/src/solver/impls/pvode/pvode.hxx index dbe1b9aa50..2ff02c22bf 100644 --- a/src/solver/impls/pvode/pvode.hxx +++ b/src/solver/impls/pvode/pvode.hxx @@ -33,8 +33,8 @@ class PvodeSolver; #ifndef __PVODE_SOLVER_H__ #define __PVODE_SOLVER_H__ -#include #include +#include #include // main CVODE header file #include diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.cxx b/src/solver/impls/rk3-ssp/rk3-ssp.cxx index e0cd7f6bc1..be3bf536b3 100644 --- a/src/solver/impls/rk3-ssp/rk3-ssp.cxx +++ b/src/solver/impls/rk3-ssp/rk3-ssp.cxx @@ -1,12 +1,12 @@ #include "rk3-ssp.hxx" -#include #include #include -#include #include +#include #include +#include #include diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.hxx b/src/solver/impls/rk3-ssp/rk3-ssp.hxx index 0e22735aa4..4080b17bb5 100644 --- a/src/solver/impls/rk3-ssp/rk3-ssp.hxx +++ b/src/solver/impls/rk3-ssp/rk3-ssp.hxx @@ -38,8 +38,8 @@ class RK3SSP; #include "mpi.h" -#include #include +#include namespace { RegisterSolver registersolverrk3ssp("rk3ssp"); diff --git a/src/solver/impls/rk4/rk4.cxx b/src/solver/impls/rk4/rk4.cxx index 1c7c6f0105..55f8e38d57 100644 --- a/src/solver/impls/rk4/rk4.cxx +++ b/src/solver/impls/rk4/rk4.cxx @@ -1,10 +1,10 @@ #include "rk4.hxx" -#include #include #include #include +#include #include #include diff --git a/src/solver/impls/rk4/rk4.hxx b/src/solver/impls/rk4/rk4.hxx index 9b710ae2f7..5838b24e8e 100644 --- a/src/solver/impls/rk4/rk4.hxx +++ b/src/solver/impls/rk4/rk4.hxx @@ -32,8 +32,8 @@ class RK4Solver; #include "mpi.h" -#include #include +#include namespace { RegisterSolver registersolverrk4("rk4"); diff --git a/src/solver/impls/rkgeneric/rkgeneric.hxx b/src/solver/impls/rkgeneric/rkgeneric.hxx index 305f27679b..a18678e724 100644 --- a/src/solver/impls/rkgeneric/rkgeneric.hxx +++ b/src/solver/impls/rkgeneric/rkgeneric.hxx @@ -30,9 +30,9 @@ class RKGenericSolver; #include "mpi.h" +#include #include #include -#include namespace { RegisterSolver registersolverrkgeneric("rkgeneric"); diff --git a/src/solver/impls/rkgeneric/rkscheme.cxx b/src/solver/impls/rkgeneric/rkscheme.cxx index 812d0d7e4a..740adec909 100644 --- a/src/solver/impls/rkgeneric/rkscheme.cxx +++ b/src/solver/impls/rkgeneric/rkscheme.cxx @@ -1,10 +1,10 @@ #include "bout/unused.hxx" -#include -#include #include -#include +#include #include #include +#include +#include // Implementations #include "impls/cashkarp/cashkarp.hxx" diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx index f6de892fd6..37ce23b16c 100644 --- a/src/solver/impls/snes/snes.hxx +++ b/src/solver/impls/snes/snes.hxx @@ -38,8 +38,8 @@ class SNESSolver; #include "mpi.h" #include -#include #include +#include #include #include diff --git a/src/solver/impls/split-rk/split-rk.hxx b/src/solver/impls/split-rk/split-rk.hxx index a35cee1156..937245941d 100644 --- a/src/solver/impls/split-rk/split-rk.hxx +++ b/src/solver/impls/split-rk/split-rk.hxx @@ -32,8 +32,8 @@ class SplitRK; #ifndef SPLITRK_HXX #define SPLITRK_HXX -#include #include +#include namespace { RegisterSolver registersolversplitrk("splitrk"); diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx index 7d039498b0..dc326a8b5e 100644 --- a/src/solver/solver.cxx +++ b/src/solver/solver.cxx @@ -22,6 +22,8 @@ #include "bout/build_config.hxx" +#include "bout/array.hxx" +#include "bout/assert.hxx" #include "bout/boutcomm.hxx" #include "bout/boutexception.hxx" #include "bout/field_factory.hxx" @@ -29,8 +31,6 @@ #include "bout/interpolation.hxx" #include "bout/msg_stack.hxx" #include "bout/output.hxx" -#include "bout/array.hxx" -#include "bout/assert.hxx" #include "bout/region.hxx" #include "bout/solver.hxx" #include "bout/sys/timer.hxx" diff --git a/src/sys/bout_types.cxx b/src/sys/bout_types.cxx index a7396fb9c6..35d37f11be 100644 --- a/src/sys/bout_types.cxx +++ b/src/sys/bout_types.cxx @@ -1,7 +1,7 @@ #include #include -#include #include +#include namespace { template diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx index b92f322b1b..9b21303cae 100644 --- a/src/sys/boutexception.cxx +++ b/src/sys/boutexception.cxx @@ -2,11 +2,11 @@ #include #include -#include -#include #include #include #include +#include +#include #if BOUT_USE_BACKTRACE #include diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx index e9e913fdc5..39f8d3bb71 100644 --- a/src/sys/expressionparser.cxx +++ b/src/sys/expressionparser.cxx @@ -26,8 +26,8 @@ #include -#include "bout/utils.hxx" #include "bout/sys/gettext.hxx" +#include "bout/utils.hxx" using std::list; using std::string; diff --git a/src/sys/hyprelib.cxx b/src/sys/hyprelib.cxx index e07e6fd27b..d6b1c95468 100644 --- a/src/sys/hyprelib.cxx +++ b/src/sys/hyprelib.cxx @@ -5,10 +5,10 @@ #include #include "bout/boutcomm.hxx" +#include "bout/openmpwrap.hxx" #include "bout/options.hxx" #include "bout/output.hxx" #include "bout/unused.hxx" -#include "bout/openmpwrap.hxx" #include #include @@ -27,7 +27,8 @@ static constexpr auto BOUT_HYPRE_MEMORY = HYPRE_MEMORY_HOST; #endif HypreLib::HypreLib() { - BOUT_OMP(critical(HypreLib)) { + BOUT_OMP(critical(HypreLib)) + { if (count == 0) { // Initialise once output_progress.write("Initialising Hypre\n"); HYPRE_Init(); @@ -39,21 +40,24 @@ HypreLib::HypreLib() { } HypreLib::HypreLib(MAYBE_UNUSED() const HypreLib& other) noexcept { - BOUT_OMP(critical(HypreLib)) { + BOUT_OMP(critical(HypreLib)) + { // No need to initialise Hypre, because it must already be initialised count++; // Copying, so increase count } } HypreLib::HypreLib(MAYBE_UNUSED() HypreLib&& other) noexcept { - BOUT_OMP(critical(HypreLib)) { + BOUT_OMP(critical(HypreLib)) + { // No need to initialise Hypre, because it must already be initialised count++; // Creating a new Hyprelib object; other will be deleted } } HypreLib::~HypreLib() { - BOUT_OMP(critical(HypreLib)) { + BOUT_OMP(critical(HypreLib)) + { count--; if (count == 0) { output_progress.write("Finalising Hypre\n"); @@ -63,7 +67,8 @@ HypreLib::~HypreLib() { } void HypreLib::cleanup() { - BOUT_OMP(critical(HypreLib)) { + BOUT_OMP(critical(HypreLib)) + { if (count > 0) { output << "Finalising Hypre. Warning: Instances of HypreLib still exist.\n"; HYPRE_Finalize(); diff --git a/src/sys/msg_stack.cxx b/src/sys/msg_stack.cxx index c2345f216b..6ea4c15a8b 100644 --- a/src/sys/msg_stack.cxx +++ b/src/sys/msg_stack.cxx @@ -25,9 +25,9 @@ **************************************************************************/ #include "bout/openmpwrap.hxx" -#include #include #include +#include #include #if BOUT_USE_OPENMP @@ -58,7 +58,8 @@ void MsgStack::pop() { if (position <= 0) { return; } - BOUT_OMP(single) { --position; } + BOUT_OMP(single) + { --position; } } void MsgStack::pop(int id) { @@ -77,14 +78,16 @@ void MsgStack::pop(int id) { } void MsgStack::clear() { - BOUT_OMP(single) { + BOUT_OMP(single) + { stack.clear(); position = 0; } } void MsgStack::dump() { - BOUT_OMP(single) { output << this->getDump(); } + BOUT_OMP(single) + { output << this->getDump(); } } std::string MsgStack::getDump() { diff --git a/src/sys/output.cxx b/src/sys/output.cxx index 0208733f16..0ab1d2e0c8 100644 --- a/src/sys/output.cxx +++ b/src/sys/output.cxx @@ -23,11 +23,11 @@ * **************************************************************************/ +#include +#include #include #include #include -#include -#include void Output::enable() { add(std::cout); diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index c772076131..91db0c44ea 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -3,8 +3,8 @@ #if BOUT_HAS_PETSC #include "bout/boutcomm.hxx" -#include "bout/options.hxx" #include "bout/openmpwrap.hxx" +#include "bout/options.hxx" #include #include @@ -18,7 +18,8 @@ char*** PetscLib::pargv = nullptr; PetscLogEvent PetscLib::USER_EVENT = 0; PetscLib::PetscLib(Options* opt) { - BOUT_OMP(critical(PetscLib)) { + BOUT_OMP(critical(PetscLib)) + { if (count == 0) { // Initialise PETSc @@ -52,7 +53,8 @@ PetscLib::PetscLib(Options* opt) { } PetscLib::~PetscLib() { - BOUT_OMP(critical(PetscLib)) { + BOUT_OMP(critical(PetscLib)) + { count--; if (count == 0) { // Finalise PETSc @@ -88,7 +90,8 @@ void PetscLib::setOptionsFromInputFile(SNES& snes) { } void PetscLib::cleanup() { - BOUT_OMP(critical(PetscLib)) { + BOUT_OMP(critical(PetscLib)) + { if (count > 0) { output << "Finalising PETSc. Warning: Instances of PetscLib still exist.\n"; PetscLogEventEnd(USER_EVENT, 0, 0, 0, 0); diff --git a/src/sys/slepclib.cxx b/src/sys/slepclib.cxx index 82614febb8..1dc89bc047 100644 --- a/src/sys/slepclib.cxx +++ b/src/sys/slepclib.cxx @@ -2,8 +2,8 @@ #if BOUT_HAS_SLEPC -#include #include +#include // Define all the static member variables int SlepcLib::count = 0; diff --git a/src/sys/utils.cxx b/src/sys/utils.cxx index b31a8d6fb4..9a15814f6d 100644 --- a/src/sys/utils.cxx +++ b/src/sys/utils.cxx @@ -23,6 +23,7 @@ * **************************************************************************/ +#include #include #include #include @@ -31,7 +32,6 @@ #include #include #include -#include #include #include "fmt/chrono.h" diff --git a/tests/MMS/advection/advection.cxx b/tests/MMS/advection/advection.cxx index 0c040a62f1..1201fbc3ac 100644 --- a/tests/MMS/advection/advection.cxx +++ b/tests/MMS/advection/advection.cxx @@ -3,9 +3,9 @@ * */ -#include #include #include +#include class AdvectMMS : public PhysicsModel { public: diff --git a/tests/MMS/diffusion/diffusion.cxx b/tests/MMS/diffusion/diffusion.cxx index 5c4f7306ba..bd969d4d86 100644 --- a/tests/MMS/diffusion/diffusion.cxx +++ b/tests/MMS/diffusion/diffusion.cxx @@ -1,10 +1,10 @@ -#include -#include #include -#include +#include #include #include +#include #include +#include class Diffusion : public PhysicsModel { protected: diff --git a/tests/MMS/diffusion2/diffusion.cxx b/tests/MMS/diffusion2/diffusion.cxx index 9df8686f0d..bd2cd72a08 100644 --- a/tests/MMS/diffusion2/diffusion.cxx +++ b/tests/MMS/diffusion2/diffusion.cxx @@ -1,8 +1,8 @@ -#include -#include #include +#include #include #include +#include #include class Diffusion : public PhysicsModel { diff --git a/tests/MMS/elm-pb/elm_pb.cxx b/tests/MMS/elm-pb/elm_pb.cxx index b138ebd01e..3ad8f70b85 100644 --- a/tests/MMS/elm-pb/elm_pb.cxx +++ b/tests/MMS/elm-pb/elm_pb.cxx @@ -9,15 +9,15 @@ * *******************************************************************************/ -#include -#include #include +#include #include #include #include #include #include #include +#include #include #include diff --git a/tests/MMS/fieldalign/fieldalign.cxx b/tests/MMS/fieldalign/fieldalign.cxx index 34af497282..75481dee9a 100644 --- a/tests/MMS/fieldalign/fieldalign.cxx +++ b/tests/MMS/fieldalign/fieldalign.cxx @@ -1,5 +1,5 @@ -#include #include +#include class FieldAlign : public PhysicsModel { protected: diff --git a/tests/MMS/hw/hw.cxx b/tests/MMS/hw/hw.cxx index 4e9bf0ddfc..c5dd25773f 100644 --- a/tests/MMS/hw/hw.cxx +++ b/tests/MMS/hw/hw.cxx @@ -1,9 +1,9 @@ #include -#include #include #include #include +#include #include class Hw : public PhysicsModel { diff --git a/tests/MMS/spatial/diffusion/diffusion.cxx b/tests/MMS/spatial/diffusion/diffusion.cxx index ec397650ed..45e516751a 100644 --- a/tests/MMS/spatial/diffusion/diffusion.cxx +++ b/tests/MMS/spatial/diffusion/diffusion.cxx @@ -1,8 +1,8 @@ -#include -#include #include +#include #include #include +#include #include class Diffusion : public PhysicsModel { diff --git a/tests/MMS/tokamak/tokamak.cxx b/tests/MMS/tokamak/tokamak.cxx index abaabef8f2..a8bf4b685e 100644 --- a/tests/MMS/tokamak/tokamak.cxx +++ b/tests/MMS/tokamak/tokamak.cxx @@ -6,9 +6,9 @@ * */ -#include #include #include +#include class TokamakMMS : public PhysicsModel { public: diff --git a/tests/MMS/wave-1d-y/wave.cxx b/tests/MMS/wave-1d-y/wave.cxx index 2b1940ea92..82db9a1bc3 100644 --- a/tests/MMS/wave-1d-y/wave.cxx +++ b/tests/MMS/wave-1d-y/wave.cxx @@ -1,6 +1,6 @@ -#include #include #include +#include #include class Wave1D : public PhysicsModel { diff --git a/tests/MMS/wave-1d/wave.cxx b/tests/MMS/wave-1d/wave.cxx index 5aad3a2646..4f53d098c6 100644 --- a/tests/MMS/wave-1d/wave.cxx +++ b/tests/MMS/wave-1d/wave.cxx @@ -1,9 +1,9 @@ #include -#include -#include #include #include +#include #include +#include BoutReal Lx, Ly, Lz; // Size of the domain diff --git a/tests/integrated/test-communications/test-communications.cxx b/tests/integrated/test-communications/test-communications.cxx index d666b55aa3..54c266ece2 100644 --- a/tests/integrated/test-communications/test-communications.cxx +++ b/tests/integrated/test-communications/test-communications.cxx @@ -10,7 +10,7 @@ int main(int argc, char** argv) { // fill non-guard cells: // interior cells - BOUT_FOR (i, f.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, f.getRegion("RGN_NOBNDRY")) { f[i] = mesh->GlobalNzNoBoundaries * (mesh->GlobalNyNoBoundaries * mesh->getGlobalXIndexNoBoundaries(i.x()) + mesh->getGlobalYIndexNoBoundaries(i.y())) diff --git a/tests/integrated/test-dataformat/test_dataformat.cxx b/tests/integrated/test-dataformat/test_dataformat.cxx index a88fc11f01..55b3ec9946 100644 --- a/tests/integrated/test-dataformat/test_dataformat.cxx +++ b/tests/integrated/test-dataformat/test_dataformat.cxx @@ -1,6 +1,6 @@ -#include #include +#include int main() { const std::string izfilename = "sample.nc"; diff --git a/tests/integrated/test-drift-instability/2fluid.cxx b/tests/integrated/test-drift-instability/2fluid.cxx index 2870e5396a..89105e970c 100644 --- a/tests/integrated/test-drift-instability/2fluid.cxx +++ b/tests/integrated/test-drift-instability/2fluid.cxx @@ -3,8 +3,8 @@ * Same as Maxim's version of BOUT - simplified 2-fluid for benchmarking *******************************************************************************/ -#include #include +#include #include #include diff --git a/tests/integrated/test-globalfield/test_globalfield.cxx b/tests/integrated/test-globalfield/test_globalfield.cxx index de714758b0..545a53b5ac 100644 --- a/tests/integrated/test-globalfield/test_globalfield.cxx +++ b/tests/integrated/test-globalfield/test_globalfield.cxx @@ -4,9 +4,9 @@ * */ +#include #include #include -#include class Test_globalfield : public PhysicsModel { protected: diff --git a/tests/integrated/test-griddata/test_griddata.cxx b/tests/integrated/test-griddata/test_griddata.cxx index abe8c1f0d6..9f12d48d9d 100644 --- a/tests/integrated/test-griddata/test_griddata.cxx +++ b/tests/integrated/test-griddata/test_griddata.cxx @@ -1,5 +1,5 @@ -#include #include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/tests/integrated/test-interpolate-z/test_interpolate.cxx b/tests/integrated/test-interpolate-z/test_interpolate.cxx index d8d4cd6258..3ef6e50425 100644 --- a/tests/integrated/test-interpolate-z/test_interpolate.cxx +++ b/tests/integrated/test-interpolate-z/test_interpolate.cxx @@ -11,9 +11,9 @@ #include #include "bout/bout.hxx" +#include "bout/constants.hxx" #include "bout/field_factory.hxx" #include "bout/interpolation_z.hxx" -#include "bout/constants.hxx" #include "bout/sys/generator_context.hxx" using bout::globals::mesh; diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx index 6da8b220c0..a090877552 100644 --- a/tests/integrated/test-interpolate/test_interpolate.cxx +++ b/tests/integrated/test-interpolate/test_interpolate.cxx @@ -11,9 +11,9 @@ #include #include "bout/bout.hxx" +#include "bout/constants.hxx" #include "bout/field_factory.hxx" #include "bout/interpolation_xz.hxx" -#include "bout/constants.hxx" #include "bout/sys/generator_context.hxx" /// Get a FieldGenerator from the options for a variable diff --git a/tests/integrated/test-laplace2/test_laplace.cxx b/tests/integrated/test-laplace2/test_laplace.cxx index 44e18c2974..75fbf1f350 100644 --- a/tests/integrated/test-laplace2/test_laplace.cxx +++ b/tests/integrated/test-laplace2/test_laplace.cxx @@ -3,10 +3,10 @@ * */ -#include #include #include #include +#include class Test_laplace : public PhysicsModel { protected: diff --git a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx index 1b34fb922b..8408f08c00 100644 --- a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx @@ -23,11 +23,11 @@ * **************************************************************************/ -#include -#include #include +#include #include #include +#include #include int main(int argc, char** argv) { diff --git a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx index 128458eaaf..3486760810 100644 --- a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx @@ -23,11 +23,11 @@ * **************************************************************************/ -#include -#include #include +#include #include #include +#include #include int main(int argc, char** argv) { diff --git a/tests/integrated/test-laplacexy/loadmetric.cxx b/tests/integrated/test-laplacexy/loadmetric.cxx index f4774b583f..6d8afad750 100644 --- a/tests/integrated/test-laplacexy/loadmetric.cxx +++ b/tests/integrated/test-laplacexy/loadmetric.cxx @@ -1,8 +1,8 @@ #include "bout/field2d.hxx" #include "bout/globals.hxx" +#include "bout/mesh.hxx" #include "bout/output.hxx" #include "bout/utils.hxx" -#include "bout/mesh.hxx" #include "loadmetric.hxx" diff --git a/tests/integrated/test-laplacexy/test-laplacexy.cxx b/tests/integrated/test-laplacexy/test-laplacexy.cxx index af14b5dfe1..62449a76ee 100644 --- a/tests/integrated/test-laplacexy/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy/test-laplacexy.cxx @@ -23,11 +23,11 @@ * **************************************************************************/ -#include -#include #include +#include #include #include +#include #include using bout::globals::dump; diff --git a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx index 93932e9792..77fbdb197c 100644 --- a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx +++ b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx @@ -23,11 +23,11 @@ * **************************************************************************/ -#include -#include #include +#include #include #include +#include #include int main(int argc, char** argv) { diff --git a/tests/integrated/test-laplacexz/test-laplacexz.cxx b/tests/integrated/test-laplacexz/test-laplacexz.cxx index 066867aa3b..6e43d2f3f7 100644 --- a/tests/integrated/test-laplacexz/test-laplacexz.cxx +++ b/tests/integrated/test-laplacexz/test-laplacexz.cxx @@ -10,9 +10,9 @@ */ #include -#include #include #include +#include int main(int argc, char** argv) { BoutInitialise(argc, argv); diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx index 8223e50da9..2b03f78049 100644 --- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx +++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx @@ -23,14 +23,14 @@ * **************************************************************************/ -#include #include #include -#include +#include #include #include #include #include +#include BoutReal max_error_at_ystart(const Field3D& error); Field3D this_Grad_perp_dot_Grad_perp(const Field3D& f, const Field3D& g); diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx index e428b9380c..07a403e2e2 100644 --- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx +++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx @@ -24,14 +24,14 @@ **************************************************************************/ #include "../../../src/invert/laplace/impls/naulin/naulin_laplace.hxx" -#include #include #include -#include +#include #include #include #include #include +#include BoutReal max_error_at_ystart(const Field3D& error); Field3D this_Grad_perp_dot_Grad_perp(const Field3D& f, const Field3D& g); diff --git a/tests/integrated/test-nonuniform/test_delp2.cxx b/tests/integrated/test-nonuniform/test_delp2.cxx index 921e86d5e6..a6465db515 100644 --- a/tests/integrated/test-nonuniform/test_delp2.cxx +++ b/tests/integrated/test-nonuniform/test_delp2.cxx @@ -7,8 +7,8 @@ * */ -#include #include +#include class Test_delp2 : public PhysicsModel { protected: diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx index 0b01241287..bfd394194f 100644 --- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx @@ -23,13 +23,13 @@ * **************************************************************************/ -#include #include +#include // #include #include -#include #include #include +#include BoutReal max_error_at_ystart(const Field3D& error); diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx index f6e94da943..7646b915a7 100644 --- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx +++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx @@ -23,13 +23,13 @@ * **************************************************************************/ -#include #include +#include // #include #include -#include #include #include +#include BoutReal max_error_at_ystart(const Field3D& error); diff --git a/tests/integrated/test-region-iterator/test_region_iterator.cxx b/tests/integrated/test-region-iterator/test_region_iterator.cxx index c89bf9ed2c..db35c288d1 100644 --- a/tests/integrated/test-region-iterator/test_region_iterator.cxx +++ b/tests/integrated/test-region-iterator/test_region_iterator.cxx @@ -1,5 +1,5 @@ -#include #include +#include #include #include @@ -20,7 +20,7 @@ int Test_region_iterator::init(bool UNUSED(restarting)) { Region reg(0, mesh->LocalNx - 1, 0, mesh->LocalNy - 1, 0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz); - BOUT_FOR (i, reg) { + BOUT_FOR(i, reg) { a[i] = 3.0; b[i] = c[i]; } @@ -46,7 +46,7 @@ int Test_region_iterator::init(bool UNUSED(restarting)) { } Field3D d = 1.0, e = 1.0, f = 2.0; - BOUT_FOR (i, d.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, d.getRegion("RGN_NOBNDRY")) { d[i] = 3.0; e[i] = f[i]; } diff --git a/tests/integrated/test-snb/test_snb.cxx b/tests/integrated/test-snb/test_snb.cxx index 8e1b55bca0..1b96bfc8b1 100644 --- a/tests/integrated/test-snb/test_snb.cxx +++ b/tests/integrated/test-snb/test_snb.cxx @@ -1,9 +1,9 @@ -#include -#include #include #include +#include #include #include +#include // Convert __LINE__ to string S__LINE__ #define S(x) #x diff --git a/tests/integrated/test-stopCheck-file/test_stopCheck.cxx b/tests/integrated/test-stopCheck-file/test_stopCheck.cxx index 46fceb446e..2d000da862 100644 --- a/tests/integrated/test-stopCheck-file/test_stopCheck.cxx +++ b/tests/integrated/test-stopCheck-file/test_stopCheck.cxx @@ -4,8 +4,8 @@ */ #include "bout/unused.hxx" -#include #include +#include class Test_stopcheck : public PhysicsModel { Field3D N; diff --git a/tests/integrated/test-stopCheck/test_stopCheck.cxx b/tests/integrated/test-stopCheck/test_stopCheck.cxx index 328805f155..bccef01a64 100644 --- a/tests/integrated/test-stopCheck/test_stopCheck.cxx +++ b/tests/integrated/test-stopCheck/test_stopCheck.cxx @@ -4,8 +4,8 @@ */ #include "bout/unused.hxx" -#include #include +#include class Test_stopcheck : public PhysicsModel { protected: diff --git a/tests/unit/bout_test_main.cxx b/tests/unit/bout_test_main.cxx index 5aaaa0e8a7..999b5b0dc3 100644 --- a/tests/unit/bout_test_main.cxx +++ b/tests/unit/bout_test_main.cxx @@ -1,9 +1,9 @@ #include -#include "bout/fft.hxx" -#include "bout/output.hxx" #include "bout/array.hxx" +#include "bout/fft.hxx" #include "bout/globalindexer.hxx" +#include "bout/output.hxx" #include "gtest/gtest.h" // Note: petsclib included after globalindexer, or MPI_Waitall // in mpi_wrapper.hxx is expanded as a macro diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx index f2ea0a7112..d276d253d7 100644 --- a/tests/unit/fake_parallel_mesh.hxx +++ b/tests/unit/fake_parallel_mesh.hxx @@ -10,14 +10,14 @@ #include "../../src/mesh/impls/bout/boutmesh.hxx" #include "bout/boundary_region.hxx" #include "bout/boutcomm.hxx" +#include "bout/coordinates.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "bout/fieldperp.hxx" -#include "bout/unused.hxx" -#include "bout/coordinates.hxx" #include "bout/fieldgroup.hxx" +#include "bout/fieldperp.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" +#include "bout/unused.hxx" class Options; diff --git a/tests/unit/field/test_field.cxx b/tests/unit/field/test_field.cxx index 16b2a0f9c9..b237ee3006 100644 --- a/tests/unit/field/test_field.cxx +++ b/tests/unit/field/test_field.cxx @@ -1,11 +1,11 @@ #include "gtest/gtest.h" -#include "bout/boutexception.hxx" -#include "bout/field.hxx" -#include "bout/output.hxx" #include "test_extras.hxx" +#include "bout/boutexception.hxx" #include "bout/constants.hxx" +#include "bout/field.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx index a13b1dd754..8608fba52e 100644 --- a/tests/unit/field/test_field2d.cxx +++ b/tests/unit/field/test_field2d.cxx @@ -4,14 +4,14 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/boutexception.hxx" +#include "bout/constants.hxx" #include "bout/field2d.hxx" +#include "bout/mesh.hxx" #include "bout/output.hxx" -#include "test_extras.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/constants.hxx" -#include "bout/mesh.hxx" #include #include diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx index 813adc212e..18ffaa3ab7 100644 --- a/tests/unit/field/test_field3d.cxx +++ b/tests/unit/field/test_field3d.cxx @@ -6,14 +6,14 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/boutexception.hxx" +#include "bout/constants.hxx" #include "bout/field3d.hxx" +#include "bout/mesh.hxx" #include "bout/output.hxx" -#include "test_extras.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/constants.hxx" -#include "bout/mesh.hxx" #include #include diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx index a65127fee4..5652f43388 100644 --- a/tests/unit/field/test_field_factory.cxx +++ b/tests/unit/field/test_field_factory.cxx @@ -1,13 +1,13 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/boutexception.hxx" +#include "bout/constants.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/field_factory.hxx" -#include "bout/output.hxx" -#include "test_extras.hxx" -#include "bout/constants.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" #include "bout/paralleltransform.hxx" #include "bout/traits.hxx" diff --git a/tests/unit/field/test_fieldgroup.cxx b/tests/unit/field/test_fieldgroup.cxx index b87d54f214..bfb001fd2f 100644 --- a/tests/unit/field/test_fieldgroup.cxx +++ b/tests/unit/field/test_fieldgroup.cxx @@ -3,9 +3,9 @@ #include "bout/field2d.hxx" #include "bout/field3d.hxx" +#include "bout/fieldgroup.hxx" #include "bout/vector2d.hxx" #include "bout/vector3d.hxx" -#include "bout/fieldgroup.hxx" #include diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx index 6c28d856cc..a765475482 100644 --- a/tests/unit/field/test_fieldperp.cxx +++ b/tests/unit/field/test_fieldperp.cxx @@ -3,15 +3,15 @@ #pragma GCC diagnostic ignored "-Wdeprecated-declarations" #include "gtest/gtest.h" +#include "test_extras.hxx" +#include "bout/array.hxx" #include "bout/boutexception.hxx" +#include "bout/constants.hxx" #include "bout/fieldperp.hxx" +#include "bout/mesh.hxx" #include "bout/output.hxx" -#include "test_extras.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/array.hxx" -#include "bout/constants.hxx" -#include "bout/mesh.hxx" #include #include diff --git a/tests/unit/field/test_initialprofiles.cxx b/tests/unit/field/test_initialprofiles.cxx index bbf0697f6e..fb340209e3 100644 --- a/tests/unit/field/test_initialprofiles.cxx +++ b/tests/unit/field/test_initialprofiles.cxx @@ -1,12 +1,12 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/boutexception.hxx" +#include "bout/constants.hxx" #include "bout/field.hxx" #include "bout/initialprofiles.hxx" -#include "bout/output.hxx" -#include "test_extras.hxx" -#include "bout/constants.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx index 4d3bf1cd3d..263c8d6d11 100644 --- a/tests/unit/field/test_vector2d.cxx +++ b/tests/unit/field/test_vector2d.cxx @@ -2,14 +2,14 @@ #include "bout/boutexception.hxx" #if not(BOUT_USE_METRIC_3D) -#include "bout/output.hxx" #include "test_extras.hxx" -#include "bout/unused.hxx" -#include "bout/vector2d.hxx" -#include "bout/vector3d.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" +#include "bout/vector2d.hxx" +#include "bout/vector3d.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/field/test_vector3d.cxx b/tests/unit/field/test_vector3d.cxx index 6b8a972b78..ece1f95fcc 100644 --- a/tests/unit/field/test_vector3d.cxx +++ b/tests/unit/field/test_vector3d.cxx @@ -1,13 +1,13 @@ #include "gtest/gtest.h" -#include "bout/boutexception.hxx" -#include "bout/output.hxx" #include "test_extras.hxx" -#include "bout/unused.hxx" -#include "bout/vector3d.hxx" +#include "bout/boutexception.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" +#include "bout/output.hxx" +#include "bout/unused.hxx" +#include "bout/vector3d.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/field/test_where.cxx b/tests/unit/field/test_where.cxx index 7f61521503..f46744d532 100644 --- a/tests/unit/field/test_where.cxx +++ b/tests/unit/field/test_where.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" -#include "bout/field.hxx" #include "test_extras.hxx" +#include "bout/field.hxx" #include "bout/where.hxx" /// Global mesh diff --git a/tests/unit/include/bout/test_array.cxx b/tests/unit/include/bout/test_array.cxx index 6b74b058fb..f8b485ba9f 100644 --- a/tests/unit/include/bout/test_array.cxx +++ b/tests/unit/include/bout/test_array.cxx @@ -1,7 +1,7 @@ #include "gtest/gtest.h" -#include "bout/boutexception.hxx" #include "bout/array.hxx" +#include "bout/boutexception.hxx" #include #include diff --git a/tests/unit/include/bout/test_deriv_store.cxx b/tests/unit/include/bout/test_deriv_store.cxx index f98765dd00..391be5432e 100644 --- a/tests/unit/include/bout/test_deriv_store.cxx +++ b/tests/unit/include/bout/test_deriv_store.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" -#include #include #include +#include #include #include diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx index 6afe69741e..554af1a7ca 100644 --- a/tests/unit/include/bout/test_hypre_interface.cxx +++ b/tests/unit/include/bout/test_hypre_interface.cxx @@ -37,7 +37,7 @@ using FieldTypes = ::testing::Types; TYPED_TEST_SUITE(HypreVectorTest, FieldTypes); TYPED_TEST(HypreVectorTest, FieldConstructor) { - BOUT_FOR (i, this->field.getRegion("RGN_ALL")) { + BOUT_FOR(i, this->field.getRegion("RGN_ALL")) { this->field[i] = static_cast(i.ind); } @@ -120,12 +120,12 @@ TYPED_TEST(HypreVectorTest, Assemble) { } TYPED_TEST(HypreVectorTest, GetElements) { - BOUT_FOR (i, this->field.getRegion("RGN_ALL")) { + BOUT_FOR(i, this->field.getRegion("RGN_ALL")) { this->field[i] = static_cast(i.ind); } HypreVector vector(this->field, this->indexer); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { EXPECT_EQ(vector(i), this->field[i]); } } @@ -133,7 +133,7 @@ TYPED_TEST(HypreVectorTest, GetElements) { TYPED_TEST(HypreVectorTest, SetElements) { HypreVector vector{this->field, this->indexer}; - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { vector(i) = static_cast(i.ind); this->field[i] = static_cast(i.ind); } @@ -295,7 +295,7 @@ TYPED_TEST(HypreMatrixTest, SetAddGetValue) { TYPED_TEST(HypreMatrixTest, SetElements) { HypreMatrix matrix(this->indexer); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { matrix.setVal(i, i, static_cast(this->indexer->getGlobal(i))); } @@ -303,15 +303,14 @@ TYPED_TEST(HypreMatrixTest, SetElements) { auto raw_matrix = matrix.get(); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { BOUT_FOR_SERIAL(j, this->field.getRegion("RGN_NOBNDRY")) { auto i_index = static_cast(this->indexer->getGlobal(i)); auto j_index = static_cast(this->indexer->getGlobal(j)); HYPRE_Int ncolumns{1}; HYPRE_Complex value; - BOUT_OMP(critical) { - HYPRE_IJMatrixGetValues(raw_matrix, 1, &ncolumns, &i_index, &j_index, &value); - } + BOUT_OMP(critical) + { HYPRE_IJMatrixGetValues(raw_matrix, 1, &ncolumns, &i_index, &j_index, &value); } if (i == j) { EXPECT_EQ(static_cast(value), static_cast(this->indexer->getGlobal(i))); @@ -338,7 +337,7 @@ TYPED_TEST(HypreMatrixTest, GetElements) { } matrix.assemble(); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { BOUT_FOR_SERIAL(j, this->field.getRegion("RGN_NOBNDRY")) { if (i == j) { EXPECT_EQ(matrix.getVal(i, j), diff --git a/tests/unit/include/bout/test_petsc_indexer.cxx b/tests/unit/include/bout/test_petsc_indexer.cxx index bd0ed6fd97..40c29ddfbd 100644 --- a/tests/unit/include/bout/test_petsc_indexer.cxx +++ b/tests/unit/include/bout/test_petsc_indexer.cxx @@ -79,7 +79,7 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { indicesGlobalDefault; // Check each of the interior global indices is unique - BOUT_FOR (i, f.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, f.getRegion("RGN_NOBNDRY")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); BOUT_OMP(critical) @@ -95,7 +95,7 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { } // Check indices of X guard cells are unique - BOUT_FOR (i, f.getRegion("RGN_XGUARDS")) { + BOUT_FOR(i, f.getRegion("RGN_XGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); BOUT_OMP(critical) @@ -109,7 +109,7 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { // Check indices of Y guard cells are unique if (!std::is_same::value) { - BOUT_FOR (i, f.getRegion("RGN_YGUARDS")) { + BOUT_FOR(i, f.getRegion("RGN_YGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); BOUT_OMP(critical) @@ -135,16 +135,16 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { } TYPED_TEST(IndexerTest, TestIsLocal) { - BOUT_FOR (i, this->globalSquareIndexer.getRegionAll()) { + BOUT_FOR(i, this->globalSquareIndexer.getRegionAll()) { EXPECT_TRUE(this->globalSquareIndexer.isLocal(i)); } - BOUT_FOR (i, this->globalStarIndexer.getRegionAll()) { + BOUT_FOR(i, this->globalStarIndexer.getRegionAll()) { EXPECT_TRUE(this->globalStarIndexer.isLocal(i)); } - BOUT_FOR (i, this->globalDefaultIndexer.getRegionAll()) { + BOUT_FOR(i, this->globalDefaultIndexer.getRegionAll()) { EXPECT_TRUE(this->globalDefaultIndexer.isLocal(i)); } - BOUT_FOR (i, this->localIndexer.getRegionAll()) { + BOUT_FOR(i, this->localIndexer.getRegionAll()) { EXPECT_TRUE(this->localIndexer.isLocal(i)); } } @@ -175,7 +175,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { Region rgn; rgn = this->globalSquareIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->ny * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalSquareIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalSquareIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -185,7 +185,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { } rgn = this->globalStarIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->ny * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalStarIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalStarIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -195,7 +195,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { } rgn = this->globalDefaultIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->ny * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalDefaultIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalDefaultIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -205,7 +205,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { } rgn = this->localIndexer.getRegionNobndry(); EXPECT_EQ(rgn.asUnique().size(), 0); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->localIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->localIndexer.getMesh()->xend); if (!std::is_same::value) { @@ -238,14 +238,10 @@ TYPED_TEST(IndexerTest, TestGetRegionLowerY) { } else { rgn = this->globalSquareIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), (this->nx + 2 * this->guardx) * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_LT(i.y(), this->globalSquareIndexer.getMesh()->ystart); - } + BOUT_FOR(i, rgn) { EXPECT_LT(i.y(), this->globalSquareIndexer.getMesh()->ystart); } rgn = this->globalStarIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_LT(i.y(), this->globalStarIndexer.getMesh()->ystart); - } + BOUT_FOR(i, rgn) { EXPECT_LT(i.y(), this->globalStarIndexer.getMesh()->ystart); } } rgn = this->globalDefaultIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), 0); @@ -263,14 +259,10 @@ TYPED_TEST(IndexerTest, TestGetRegionUpperY) { } else { rgn = this->globalSquareIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), (this->nx + 2 * this->guardx) * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_GT(i.y(), this->globalSquareIndexer.getMesh()->yend); - } + BOUT_FOR(i, rgn) { EXPECT_GT(i.y(), this->globalSquareIndexer.getMesh()->yend); } rgn = this->globalStarIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), this->nx * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_GT(i.y(), this->globalStarIndexer.getMesh()->yend); - } + BOUT_FOR(i, rgn) { EXPECT_GT(i.y(), this->globalStarIndexer.getMesh()->yend); } } rgn = this->globalDefaultIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), 0); @@ -282,14 +274,10 @@ TYPED_TEST(IndexerTest, TestGetRegionInnerX) { Region rgn; rgn = this->globalSquareIndexer.getRegionInnerX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_LT(i.x(), this->globalSquareIndexer.getMesh()->xstart); - } + BOUT_FOR(i, rgn) { EXPECT_LT(i.x(), this->globalSquareIndexer.getMesh()->xstart); } rgn = this->globalStarIndexer.getRegionInnerX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_LT(i.x(), this->globalStarIndexer.getMesh()->xstart); - } + BOUT_FOR(i, rgn) { EXPECT_LT(i.x(), this->globalStarIndexer.getMesh()->xstart); } rgn = this->globalDefaultIndexer.getRegionInnerX(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->localIndexer.getRegionInnerX(); @@ -300,14 +288,10 @@ TYPED_TEST(IndexerTest, TestGetRegionOuterX) { Region rgn; rgn = this->globalSquareIndexer.getRegionOuterX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_GT(i.x(), this->globalSquareIndexer.getMesh()->xend); - } + BOUT_FOR(i, rgn) { EXPECT_GT(i.x(), this->globalSquareIndexer.getMesh()->xend); } rgn = this->globalStarIndexer.getRegionOuterX(); EXPECT_EQ(rgn.asUnique().size(), this->ny * this->nz); - BOUT_FOR (i, rgn) { - EXPECT_GT(i.x(), this->globalStarIndexer.getMesh()->xend); - } + BOUT_FOR(i, rgn) { EXPECT_GT(i.x(), this->globalStarIndexer.getMesh()->xend); } rgn = this->globalDefaultIndexer.getRegionOuterX(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->localIndexer.getRegionOuterX(); @@ -464,7 +448,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex3D) { IndexerPtr index = this->getIndexer(indexers, this->pe_xind, this->pe_yind); // Test x boundaries - BOUT_FOR (i, this->localmesh->getRegion3D("RGN_XGUARDS")) { + BOUT_FOR(i, this->localmesh->getRegion3D("RGN_XGUARDS")) { if (i.x() < this->xstart && i.y() >= this->ystart && i.y() <= this->yend) { int global = index->getGlobal(i); if (this->pe_xind > 0) { @@ -490,7 +474,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex3D) { } // Test y boundaries - BOUT_FOR (i, this->localmesh->getRegion3D("RGN_YGUARDS")) { + BOUT_FOR(i, this->localmesh->getRegion3D("RGN_YGUARDS")) { if (i.y() < this->ystart) { if (i.x() == this->xstart) { @@ -569,7 +553,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex2D) { IndexerPtr index = this->getIndexer(indexers, this->pe_xind, this->pe_yind); // Test x boundaries - BOUT_FOR (i, this->localmesh->getRegion2D("RGN_XGUARDS")) { + BOUT_FOR(i, this->localmesh->getRegion2D("RGN_XGUARDS")) { if (i.x() < this->xstart) { int global = index->getGlobal(i); if (this->pe_xind > 0) { @@ -595,7 +579,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndex2D) { } // Test y boundaries - BOUT_FOR (i, this->localmesh->getRegion2D("RGN_YGUARDS")) { + BOUT_FOR(i, this->localmesh->getRegion2D("RGN_YGUARDS")) { if (i.y() < this->ystart && i.x() >= this->xstart && i.x() <= this->xend) { int global = index->getGlobal(i); int otherGlobal = @@ -660,7 +644,7 @@ TEST_P(ParallelIndexerTest, TestConvertIndexPerp) { IndexerPtr index = this->getIndexer(indexers, this->pe_xind, this->pe_yind); // Test x boundaries - BOUT_FOR (i, this->localmesh->getRegionPerp("RGN_XGUARDS")) { + BOUT_FOR(i, this->localmesh->getRegionPerp("RGN_XGUARDS")) { if (i.x() < this->xstart) { int global = index->getGlobal(i); if (this->pe_xind > 0) { @@ -697,7 +681,7 @@ TEST_P(ParallelIndexerTest, TestRegions3D) { rgn = index->getRegionNobndry(); EXPECT_EQ(rgn.size(), (this->nx - 2) * this->ny * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), index->getMesh()->xstart); EXPECT_LE(i.x(), index->getMesh()->xend); EXPECT_GE(i.y(), index->getMesh()->ystart); @@ -717,7 +701,7 @@ TEST_P(ParallelIndexerTest, TestRegions3D) { rgn = index->getRegionInnerX(); if (this->pe_xind == 0) { EXPECT_EQ(rgn.size(), this->ny * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -728,7 +712,7 @@ TEST_P(ParallelIndexerTest, TestRegions3D) { rgn = index->getRegionOuterX(); if (this->pe_xind == this->nxpe - 1) { EXPECT_EQ(rgn.size(), this->ny * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xend + 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -749,7 +733,7 @@ TEST_P(ParallelIndexerTest, TestRegions2D) { rgn = index->getRegionNobndry(); EXPECT_EQ(rgn.size(), (this->nx - 2) * this->ny); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), index->getMesh()->xstart); EXPECT_LE(i.x(), index->getMesh()->xend); EXPECT_GE(i.y(), index->getMesh()->ystart); @@ -769,7 +753,7 @@ TEST_P(ParallelIndexerTest, TestRegions2D) { rgn = index->getRegionInnerX(); if (this->pe_xind == 0) { EXPECT_EQ(rgn.size(), this->ny); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -780,7 +764,7 @@ TEST_P(ParallelIndexerTest, TestRegions2D) { rgn = index->getRegionOuterX(); if (this->pe_xind == this->nxpe - 1) { EXPECT_EQ(rgn.size(), this->ny); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xend + 1); EXPECT_GE(i.y(), index->getMesh()->ystart); EXPECT_LE(i.y(), index->getMesh()->yend); @@ -801,7 +785,7 @@ TEST_P(ParallelIndexerTest, TestRegionsPerp) { rgn = index->getRegionNobndry(); EXPECT_EQ(rgn.size(), (this->nx - 2) * this->nz); - BOUT_FOR (i, rgn) { + BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), index->getMesh()->xstart); EXPECT_LE(i.x(), index->getMesh()->xend); } @@ -819,18 +803,14 @@ TEST_P(ParallelIndexerTest, TestRegionsPerp) { rgn = index->getRegionInnerX(); if (this->pe_xind == 0) { EXPECT_EQ(rgn.size(), this->nz); - BOUT_FOR (i, rgn) { - EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); - } + BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xstart - 1); } } else { EXPECT_EQ(rgn.size(), 0); } rgn = index->getRegionOuterX(); if (this->pe_xind == this->nxpe - 1) { EXPECT_EQ(rgn.size(), this->nz); - BOUT_FOR (i, rgn) { - EXPECT_EQ(i.x(), index->getMesh()->xend + 1); - } + BOUT_FOR(i, rgn) { EXPECT_EQ(i.x(), index->getMesh()->xend + 1); } } else { EXPECT_EQ(rgn.size(), 0); } diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index d2720ecccd..d55f384b9c 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -170,7 +170,7 @@ TYPED_TEST(PetscMatrixTest, TestGetElements) { Mat* rawmat = matrix.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); - BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { BOUT_FOR_SERIAL(j, this->field.getRegion("RGN_NOY")) { int i_ind = this->indexer->getGlobal(i); int j_ind = this->indexer->getGlobal(j); @@ -404,7 +404,7 @@ TYPED_TEST(PetscMatrixTest, TestSwap) { TYPED_TEST(PetscMatrixTest, TestMatrixVectorMultiplyIdentity) { PetscMatrix matrix(this->indexer); this->field.allocate(); - BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { this->field[i] = static_cast(i.ind); matrix(i, i) = 1.0; } @@ -413,7 +413,7 @@ TYPED_TEST(PetscMatrixTest, TestMatrixVectorMultiplyIdentity) { matrix.assemble(); PetscVector product = matrix * vector; TypeParam prodField = product.toField(); - BOUT_FOR (i, prodField.getRegion("RGN_NOY")) { + BOUT_FOR(i, prodField.getRegion("RGN_NOY")) { EXPECT_NEAR(prodField[i], this->field[i], 1.e-10); } } @@ -434,7 +434,7 @@ TYPED_TEST(PetscMatrixTest, TestMatrixVectorMultiplyOnes) { matrix.assemble(); PetscVector product = matrix * vector; TypeParam prodField = product.toField(); - BOUT_FOR (i, prodField.getRegion("RGN_NOY")) { + BOUT_FOR(i, prodField.getRegion("RGN_NOY")) { EXPECT_NEAR(prodField[i], total, 1.e-10); } } diff --git a/tests/unit/include/bout/test_petsc_vector.cxx b/tests/unit/include/bout/test_petsc_vector.cxx index 095e212abe..101fb9480d 100644 --- a/tests/unit/include/bout/test_petsc_vector.cxx +++ b/tests/unit/include/bout/test_petsc_vector.cxx @@ -69,7 +69,7 @@ void testVectorsEqual(Vec* v1, Vec* v2) { // Test constructor from field TYPED_TEST(PetscVectorTest, FieldConstructor) { - BOUT_FOR (i, this->field.getRegion("RGN_ALL")) { + BOUT_FOR(i, this->field.getRegion("RGN_ALL")) { this->field[i] = static_cast(i.ind); } PetscVector vector(this->field, this->indexer); @@ -80,9 +80,7 @@ TYPED_TEST(PetscVectorTest, FieldConstructor) { VecGetLocalSize(*vectorPtr, &n); ASSERT_EQ(n, this->field.getNx() * this->field.getNy() * this->field.getNz()); TypeParam result = vector.toField(); - BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { - EXPECT_EQ(result[i], this->field[i]); - } + BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { EXPECT_EQ(result[i], this->field[i]); } } // Test copy constructor @@ -118,9 +116,7 @@ TYPED_TEST(PetscVectorTest, FieldAssignment) { VecGetLocalSize(*vectorPtr, &n); ASSERT_EQ(n, this->field.getNx() * this->field.getNy() * this->field.getNz()); TypeParam result = vector.toField(); - BOUT_FOR (i, this->field.getRegion("RGN_NOY")) { - EXPECT_EQ(result[i], val[i]); - } + BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { EXPECT_EQ(result[i], val[i]); } } // Test copy assignment @@ -146,7 +142,7 @@ TYPED_TEST(PetscVectorTest, MoveAssignment) { // Test getting elements TYPED_TEST(PetscVectorTest, TestGetElements) { PetscVector vector(this->field, this->indexer); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { vector(i) = (2.5 * this->field[i] - 1.0); } Vec* rawvec = vector.get(); @@ -155,7 +151,7 @@ TYPED_TEST(PetscVectorTest, TestGetElements) { VecAssemblyEnd(*rawvec); VecGetArray(*rawvec, &vecContents); TypeParam result = vector.toField(); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { EXPECT_EQ(result[i], 2.5 * this->field[i] - 1.0); } } @@ -163,7 +159,7 @@ TYPED_TEST(PetscVectorTest, TestGetElements) { // Test getting constant elements TYPED_TEST(PetscVectorTest, TestGetElementsConst) { const PetscVector vector(this->field, this->indexer); - BOUT_FOR (i, this->field.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { const BoutReal element = vector(i); EXPECT_EQ(element, this->field[i]); } diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index e6780ac059..f13fe8bd78 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -1,12 +1,12 @@ #include "gtest/gtest.h" -#include "bout/boutexception.hxx" -#include "bout/output.hxx" #include "test_extras.hxx" -#include "bout/unused.hxx" +#include "bout/boutexception.hxx" #include "bout/constants.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" #include "bout/region.hxx" +#include "bout/unused.hxx" #include #include @@ -196,9 +196,7 @@ TEST_F(RegionTest, regionLoopAll) { // Need to use a Field3D as a jig as OpenMP complicates things here Field3D a{0.}; - BOUT_FOR (i, region) { - a[i] = 1.0; - } + BOUT_FOR(i, region) { a[i] = 1.0; } for (int i = 0; i < mesh->LocalNx; ++i) { for (int j = 0; j < mesh->LocalNy; ++j) { @@ -213,9 +211,7 @@ TEST_F(RegionTest, regionLoopNoBndry) { const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); Field3D a{0.}; - BOUT_FOR (i, region) { - a[i] = 1.0; - } + BOUT_FOR(i, region) { a[i] = 1.0; } const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz; const int ninner = @@ -266,7 +262,8 @@ TEST_F(RegionTest, regionLoopAllSection) { const auto& region = mesh->getRegion3D("RGN_ALL"); int count = 0; - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { BOUT_FOR_OMP(i, region, for reduction(+:count)) { ++count; } @@ -281,7 +278,8 @@ TEST_F(RegionTest, regionLoopNoBndrySection) { const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); int count = 0; - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { BOUT_FOR_OMP(i, region, for reduction(+:count)) { ++count; } @@ -297,7 +295,8 @@ TEST_F(RegionTest, regionLoopAllInner) { const auto& region = mesh->getRegion3D("RGN_ALL"); Field3D a{0.}; - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { BOUT_FOR_INNER(i, region) { a[i] = 1.0; } } @@ -314,7 +313,8 @@ TEST_F(RegionTest, regionLoopNoBndryInner) { const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); Field3D a{0.}; - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { BOUT_FOR_INNER(i, region) { a[i] = 1.0; } } diff --git a/tests/unit/include/bout/test_single_index_ops.cxx b/tests/unit/include/bout/test_single_index_ops.cxx index 037e695214..455a857bf5 100644 --- a/tests/unit/include/bout/test_single_index_ops.cxx +++ b/tests/unit/include/bout/test_single_index_ops.cxx @@ -34,9 +34,7 @@ FieldType random_field(std::default_random_engine& re) { FieldType result; result.allocate(); // Fill with random numbers - BOUT_FOR (i, result.getRegion("RGN_ALL")) { - result[i] = unif(re); - } + BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = unif(re); } return result; } @@ -56,9 +54,7 @@ TEST_F(SingleIndexOpsTest, DDX) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = DDX(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = DDX(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -83,9 +79,7 @@ TEST_F(SingleIndexOpsTest, DDY) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = DDY(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = DDY(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -107,9 +101,7 @@ TEST_F(SingleIndexOpsTest, DDZ) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = DDZ(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = DDZ(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -137,7 +129,7 @@ TEST_F(SingleIndexOpsTest, bracket2d3d) { indexops.allocate(); auto input_acc = Field2DAccessor<>(input); auto input2_acc = FieldAccessor<>(input2); - BOUT_FOR (i, indexops.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, indexops.getRegion("RGN_NOBNDRY")) { indexops[i] = bracket(input_acc, input2_acc, i); } @@ -164,7 +156,7 @@ TEST_F(SingleIndexOpsTest, bracket3d3d) { indexops.allocate(); auto input_acc = FieldAccessor<>(input); auto input2_acc = FieldAccessor<>(input2); - BOUT_FOR (i, indexops.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, indexops.getRegion("RGN_NOBNDRY")) { indexops[i] = bracket(input_acc, input2_acc, i); } @@ -191,9 +183,7 @@ TEST_F(SingleIndexOpsTest, Delp2_3D) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = Delp2(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = Delp2(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -228,7 +218,7 @@ TEST_F(SingleIndexOpsTest, b0xGrad_dot_Grad_3D_2D) { indexops.allocate(); auto input1_acc = FieldAccessor<>(input1); auto input2_acc = Field2DAccessor<>(input2); - BOUT_FOR (i, input1.getRegion("RGN_NOBNDRY")) { + BOUT_FOR(i, input1.getRegion("RGN_NOBNDRY")) { indexops[i] = b0xGrad_dot_Grad(input1_acc, input2_acc, i); } @@ -253,9 +243,7 @@ TEST_F(SingleIndexOpsTest, D2DY2) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = D2DY2(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = D2DY2(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -278,9 +266,7 @@ TEST_F(SingleIndexOpsTest, Grad_par) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = Grad_par(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = Grad_par(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); @@ -303,9 +289,7 @@ TEST_F(SingleIndexOpsTest, Div_par) { Field3D indexops; indexops.allocate(); auto input_acc = FieldAccessor<>(input); - BOUT_FOR (i, input.getRegion("RGN_NOBNDRY")) { - indexops[i] = Div_par(input_acc, i); - } + BOUT_FOR(i, input.getRegion("RGN_NOBNDRY")) { indexops[i] = Div_par(input_acc, i); } // Check the answer is the same ASSERT_TRUE(IsFieldEqual(difops, indexops, "RGN_NOBNDRY")); diff --git a/tests/unit/include/bout/test_template_combinations.cxx b/tests/unit/include/bout/test_template_combinations.cxx index d30e69e818..594c3c6ca7 100644 --- a/tests/unit/include/bout/test_template_combinations.cxx +++ b/tests/unit/include/bout/test_template_combinations.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" -#include #include #include +#include #include diff --git a/tests/unit/include/test_cyclic_reduction.cxx b/tests/unit/include/test_cyclic_reduction.cxx index 29ecf9e4d0..e057c41bef 100644 --- a/tests/unit/include/test_cyclic_reduction.cxx +++ b/tests/unit/include/test_cyclic_reduction.cxx @@ -1,9 +1,9 @@ #include "gtest/gtest.h" -#include "bout/boutcomm.hxx" -#include "bout/cyclic_reduction.hxx" #include "test_extras.hxx" #include "bout/array.hxx" +#include "bout/boutcomm.hxx" +#include "bout/cyclic_reduction.hxx" #include #include diff --git a/tests/unit/include/test_derivs.cxx b/tests/unit/include/test_derivs.cxx index 185b4877a0..5e62ec51ce 100644 --- a/tests/unit/include/test_derivs.cxx +++ b/tests/unit/include/test_derivs.cxx @@ -1,11 +1,11 @@ #include "gtest/gtest.h" -#include "bout/bout_types.hxx" -#include "bout/fft.hxx" -#include "bout/field3d.hxx" #include "test_extras.hxx" +#include "bout/bout_types.hxx" #include "bout/constants.hxx" #include "bout/deriv_store.hxx" +#include "bout/fft.hxx" +#include "bout/field3d.hxx" #include "bout/index_derivs_interface.hxx" #include "bout/paralleltransform.hxx" diff --git a/tests/unit/include/test_mask.cxx b/tests/unit/include/test_mask.cxx index 6ba85d06cf..bce74cdab8 100644 --- a/tests/unit/include/test_mask.cxx +++ b/tests/unit/include/test_mask.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/boutexception.hxx" #include "bout/mask.hxx" -#include "test_extras.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/invert/laplace/test_laplace_cyclic.cxx b/tests/unit/invert/laplace/test_laplace_cyclic.cxx index a2f7a3a30a..252c1f21c9 100644 --- a/tests/unit/invert/laplace/test_laplace_cyclic.cxx +++ b/tests/unit/invert/laplace/test_laplace_cyclic.cxx @@ -6,18 +6,18 @@ #include #include "../../../../src/invert/laplace/impls/cyclic/cyclic_laplace.hxx" -#include "bout/invert_laplace.hxx" #include "test_extras.hxx" +#include "bout/invert_laplace.hxx" #include "gtest/gtest.h" #include "bout/derivs.hxx" #include "bout/difops.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "bout/options.hxx" -#include "bout/vecops.hxx" #include "bout/griddata.hxx" #include "bout/mesh.hxx" +#include "bout/options.hxx" +#include "bout/vecops.hxx" /// Global mesh namespace bout { @@ -51,7 +51,7 @@ class CyclicForwardOperator { bool inner_x_neumann, outer_x_neumann; // If false then use Dirichlet conditions void applyBoundaries(Field3D& newF, const Field3D& f) { - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_INNER_X")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) { if (inner_x_neumann) { newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -59,7 +59,7 @@ class CyclicForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { if (outer_x_neumann) { newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -90,12 +90,12 @@ class CyclicTest : public FakeMeshFixture, coef2.allocate(); coef3.allocate(); - BOUT_FOR (i, mesh->getRegion2D("RGN_ALL")) { + BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; coef2[i] = x + y; } - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; BoutReal z = i.z() / (BoutReal)nz - 0.5; diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx index 1509fac2bb..1a11e98506 100644 --- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx +++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx @@ -4,19 +4,19 @@ #include #include "../../../../src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx" -#include "bout/invert_laplace.hxx" #include "test_extras.hxx" +#include "bout/invert_laplace.hxx" #include "gtest/gtest.h" #include "bout/derivs.hxx" #include "bout/difops.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "bout/options.hxx" -#include "bout/vecops.hxx" #include "bout/griddata.hxx" #include "bout/hypre_interface.hxx" #include "bout/mesh.hxx" +#include "bout/options.hxx" +#include "bout/vecops.hxx" #if BOUT_HAS_HYPRE @@ -59,7 +59,7 @@ class ForwardOperator { lower_y_neumann, upper_y_neumann; void applyBoundaries(Field3D& newF, Field3D& f) { - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_INNER_X")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) { if (inner_x_neumann) { newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -67,7 +67,7 @@ class ForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { if (outer_x_neumann) { newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -75,7 +75,7 @@ class ForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { if (lower_y_neumann) { newF[i] = (f[i.yp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -83,7 +83,7 @@ class ForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { if (upper_y_neumann) { newF[i] = (f[i] - f[i.ym()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -108,12 +108,12 @@ class LaplaceHypre3dTest coef2.allocate(); coef3.allocate(); - BOUT_FOR (i, mesh->getRegion2D("RGN_ALL")) { + BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; coef2[i] = x + y; } - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; BoutReal z = i.z() / (BoutReal)nz - 0.5; @@ -167,9 +167,7 @@ TEST_P(LaplaceHypre3dTest, TestMatrixConstruction3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefA_2D) { @@ -181,9 +179,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefA_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefA_3D) { @@ -195,9 +191,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefA_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefC_2D) { @@ -210,9 +204,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefC_3D) { @@ -225,9 +217,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefC1_2D) { @@ -239,9 +229,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC1_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefC1_3D) { @@ -253,9 +241,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC1_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefC2_2D) { @@ -267,9 +253,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC2_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefC2_3D) { @@ -281,9 +265,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefC2_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefD_2D) { @@ -295,9 +277,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefD_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefD_3D) { @@ -309,9 +289,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefD_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefEx_2D) { @@ -323,9 +301,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEx_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefEx_3D) { @@ -337,9 +313,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEx_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefEz_2D) { @@ -351,9 +325,7 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEz_2D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSetCoefEz_3D) { @@ -365,25 +337,19 @@ TEST_P(LaplaceHypre3dTest, TestSetCoefEz_3D) { Field3D expected = forward(f3); matrix.computeAx(vector, result); Field3D actual = result.toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSolve3D) { Field3D expected = f3; const Field3D actual = solver.solve(forward(f3)); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSolve3DGuess) { Field3D expected = f3, guess = f3 * 1.01; const Field3D actual = solver.solve(forward(f3), guess); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(LaplaceHypre3dTest, TestSolvePerp) { diff --git a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx index 63fe78897a..832ccc8e6b 100644 --- a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx +++ b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx @@ -4,19 +4,19 @@ #include #include "../../../../src/invert/laplace/impls/petsc3damg/petsc3damg.hxx" -#include "bout/invert_laplace.hxx" #include "test_extras.hxx" +#include "bout/invert_laplace.hxx" #include "gtest/gtest.h" #include "bout/derivs.hxx" #include "bout/difops.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "bout/options.hxx" -#include "bout/vecops.hxx" #include "bout/griddata.hxx" #include "bout/mesh.hxx" +#include "bout/options.hxx" #include "bout/petsc_interface.hxx" +#include "bout/vecops.hxx" #if BOUT_HAS_PETSC @@ -59,7 +59,7 @@ class ForwardOperator { lower_y_neumann, upper_y_neumann; void applyBoundaries(Field3D& newF, Field3D& f) { - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_INNER_X")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) { if (inner_x_neumann) { newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -67,7 +67,7 @@ class ForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) { if (outer_x_neumann) { newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -75,7 +75,7 @@ class ForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) { if (lower_y_neumann) { newF[i] = (f[i.yp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -83,7 +83,7 @@ class ForwardOperator { } } - BOUT_FOR (i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { + BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) { if (upper_y_neumann) { newF[i] = (f[i] - f[i.ym()]) / coords->dx[i] / sqrt(coords->g_11[i]); } else { @@ -109,12 +109,12 @@ class Petsc3dAmgTest coef2.allocate(); coef3.allocate(); - BOUT_FOR (i, mesh->getRegion2D("RGN_ALL")) { + BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; coef2[i] = x + y; } - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { BoutReal x = i.x() / (BoutReal)nx - 0.5; BoutReal y = i.y() / (BoutReal)ny - 0.5; BoutReal z = i.z() / (BoutReal)nz - 0.5; @@ -169,9 +169,7 @@ TEST_P(Petsc3dAmgTest, TestMatrixConstruction3D) { PetscVector vector(f3, solver.getIndexer()); Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefA_2D) { @@ -181,9 +179,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefA_2D) { forward.a = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefA_3D) { @@ -193,9 +189,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefA_3D) { forward.a = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefC_2D) { @@ -206,9 +200,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefC_2D) { forward.c2 = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefC_3D) { @@ -219,9 +211,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefC_3D) { forward.c2 = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefC1_2D) { @@ -231,9 +221,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefC1_2D) { forward.c1 = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefC1_3D) { @@ -243,9 +231,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefC1_3D) { forward.c1 = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefC2_2D) { @@ -255,9 +241,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefC2_2D) { forward.c2 = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefC2_3D) { @@ -267,9 +251,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefC2_3D) { forward.c2 = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefD_2D) { @@ -279,9 +261,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefD_2D) { forward.d = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefD_3D) { @@ -291,9 +271,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefD_3D) { forward.d = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefEx_2D) { @@ -303,9 +281,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefEx_2D) { forward.ex = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefEx_3D) { @@ -315,9 +291,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefEx_3D) { forward.ex = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefEz_2D) { @@ -327,9 +301,7 @@ TEST_P(Petsc3dAmgTest, TestSetCoefEz_2D) { forward.ez = coef2; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSetCoefEz_3D) { @@ -339,25 +311,19 @@ TEST_P(Petsc3dAmgTest, TestSetCoefEz_3D) { forward.ez = coef3; Field3D expected = forward(f3); Field3D actual = (matrix * vector).toField(); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSolve3D) { Field3D expected = f3; const Field3D actual = solver.solve(forward(f3)); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSolve3DGuess) { Field3D expected = f3, guess = f3 * 1.01; const Field3D actual = solver.solve(forward(f3), guess); - BOUT_FOR (i, mesh->getRegion3D("RGN_ALL")) { - EXPECT_NEAR(expected[i], actual[i], tol); - } + BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); } } TEST_P(Petsc3dAmgTest, TestSolvePerp) { diff --git a/tests/unit/invert/test_fft.cxx b/tests/unit/invert/test_fft.cxx index f8be568095..b57cf554df 100644 --- a/tests/unit/invert/test_fft.cxx +++ b/tests/unit/invert/test_fft.cxx @@ -2,11 +2,11 @@ #include "gtest/gtest.h" -#include "bout/dcomplex.hxx" -#include "bout/fft.hxx" #include "test_extras.hxx" #include "bout/array.hxx" #include "bout/constants.hxx" +#include "bout/dcomplex.hxx" +#include "bout/fft.hxx" #include #include diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx index 49d7365e09..d2a038cb93 100644 --- a/tests/unit/mesh/data/test_gridfromoptions.cxx +++ b/tests/unit/mesh/data/test_gridfromoptions.cxx @@ -1,11 +1,11 @@ #include "gtest/gtest.h" -#include "bout/options.hxx" -#include "bout/output.hxx" #include "test_extras.hxx" #include "bout/constants.hxx" #include "bout/griddata.hxx" #include "bout/mesh.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" #include #include diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx index d60e1cc0c7..fbeaa10c3a 100644 --- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx +++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx @@ -2,8 +2,8 @@ #include "gtest/gtest.h" -#include "bout/fft.hxx" #include "test_extras.hxx" +#include "bout/fft.hxx" #if BOUT_HAS_FFTW // The unit tests use the global mesh diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx index 3b3cd70538..edf5c1f19c 100644 --- a/tests/unit/mesh/test_boutmesh.cxx +++ b/tests/unit/mesh/test_boutmesh.cxx @@ -2,9 +2,9 @@ #include "gtest/gtest.h" #include "../src/mesh/impls/bout/boutmesh.hxx" +#include "bout/griddata.hxx" #include "bout/options.hxx" #include "bout/output.hxx" -#include "bout/griddata.hxx" #include "test_extras.hxx" diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx index 83c285de5c..f862e24321 100644 --- a/tests/unit/mesh/test_coordinates.cxx +++ b/tests/unit/mesh/test_coordinates.cxx @@ -1,10 +1,10 @@ #include "gtest/gtest.h" -#include "bout/output.hxx" #include "bout/build_config.hxx" #include "bout/constants.hxx" #include "bout/coordinates.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" #include "test_extras.hxx" diff --git a/tests/unit/mesh/test_interpolation.cxx b/tests/unit/mesh/test_interpolation.cxx index 1670c50692..62a23a0db1 100644 --- a/tests/unit/mesh/test_interpolation.cxx +++ b/tests/unit/mesh/test_interpolation.cxx @@ -1,18 +1,18 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/boutexception.hxx" #include "bout/interpolation.hxx" -#include "bout/output.hxx" -#include "test_extras.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" ////// delete these #include "bout/boutexception.hxx" +#include "bout/constants.hxx" #include "bout/field3d.hxx" +#include "bout/mesh.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" -#include "bout/constants.hxx" -#include "bout/mesh.hxx" #include #include #include diff --git a/tests/unit/mesh/test_mesh.cxx b/tests/unit/mesh/test_mesh.cxx index 787831dd32..68ad738c01 100644 --- a/tests/unit/mesh/test_mesh.cxx +++ b/tests/unit/mesh/test_mesh.cxx @@ -2,8 +2,8 @@ #include "gtest/gtest.h" #include "bout/boutexception.hxx" -#include "bout/output.hxx" #include "bout/mesh.hxx" +#include "bout/output.hxx" #include "bout/region.hxx" #include "test_extras.hxx" diff --git a/tests/unit/solver/test_solver.cxx b/tests/unit/solver/test_solver.cxx index f99380e4dc..480c6c23d0 100644 --- a/tests/unit/solver/test_solver.cxx +++ b/tests/unit/solver/test_solver.cxx @@ -1,11 +1,11 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" +#include "test_extras.hxx" +#include "test_fakesolver.hxx" #include "bout/boutexception.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" -#include "test_extras.hxx" -#include "test_fakesolver.hxx" #include "bout/physicsmodel.hxx" #include "bout/solver.hxx" #include "bout/sys/uuid.h" diff --git a/tests/unit/solver/test_solverfactory.cxx b/tests/unit/solver/test_solverfactory.cxx index 694a4da3ff..ce788b0804 100644 --- a/tests/unit/solver/test_solverfactory.cxx +++ b/tests/unit/solver/test_solverfactory.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" -#include "bout/boutexception.hxx" #include "test_extras.hxx" #include "test_fakesolver.hxx" +#include "bout/boutexception.hxx" #include "bout/solver.hxx" #include diff --git a/tests/unit/src/test_bout++.cxx b/tests/unit/src/test_bout++.cxx index ec4de49e9c..7d72508e7e 100644 --- a/tests/unit/src/test_bout++.cxx +++ b/tests/unit/src/test_bout++.cxx @@ -2,9 +2,9 @@ #include "gtest/gtest.h" +#include "test_extras.hxx" #include "bout/bout.hxx" #include "bout/boutexception.hxx" -#include "test_extras.hxx" #include "bout/utils.hxx" #include "bout/version.hxx" diff --git a/tests/unit/sys/test_boutexception.cxx b/tests/unit/sys/test_boutexception.cxx index 3a36ceb740..a5b563393b 100644 --- a/tests/unit/sys/test_boutexception.cxx +++ b/tests/unit/sys/test_boutexception.cxx @@ -1,7 +1,7 @@ #include "bout/build_config.hxx" -#include "bout/boutexception.hxx" #include "test_extras.hxx" +#include "bout/boutexception.hxx" #include "gtest/gtest.h" #include diff --git a/tests/unit/sys/test_expressionparser.cxx b/tests/unit/sys/test_expressionparser.cxx index fd297d7b6a..00cb23c042 100644 --- a/tests/unit/sys/test_expressionparser.cxx +++ b/tests/unit/sys/test_expressionparser.cxx @@ -1,9 +1,9 @@ #include "gtest/gtest.h" -#include "bout/bout_types.hxx" #include "test_extras.hxx" -#include "bout/unused.hxx" +#include "bout/bout_types.hxx" #include "bout/sys/expressionparser.hxx" +#include "bout/unused.hxx" #include diff --git a/tests/unit/sys/test_msg_stack.cxx b/tests/unit/sys/test_msg_stack.cxx index 3e2c8e511b..96664c20bd 100644 --- a/tests/unit/sys/test_msg_stack.cxx +++ b/tests/unit/sys/test_msg_stack.cxx @@ -1,8 +1,8 @@ // These tests rely on MsgStack::getDump, and so won't work without it #if BOUT_USE_MSGSTACK -#include "bout/msg_stack.hxx" #include "test_extras.hxx" +#include "bout/msg_stack.hxx" #include "gtest/gtest.h" #include diff --git a/tests/unit/sys/test_options_fields.cxx b/tests/unit/sys/test_options_fields.cxx index 4858886d96..d87a0e818b 100644 --- a/tests/unit/sys/test_options_fields.cxx +++ b/tests/unit/sys/test_options_fields.cxx @@ -3,10 +3,10 @@ #include "gtest/gtest.h" -#include "bout/field3d.hxx" #include "test_extras.hxx" -#include "bout/unused.hxx" +#include "bout/field3d.hxx" #include "bout/mesh.hxx" +#include "bout/unused.hxx" /// Global mesh namespace bout { diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx index fcab2bdb9a..b086043822 100644 --- a/tests/unit/sys/test_options_netcdf.cxx +++ b/tests/unit/sys/test_options_netcdf.cxx @@ -6,10 +6,10 @@ #include "gtest/gtest.h" -#include "bout/field3d.hxx" -#include "bout/options_netcdf.hxx" #include "test_extras.hxx" +#include "bout/field3d.hxx" #include "bout/mesh.hxx" +#include "bout/options_netcdf.hxx" using bout::OptionsNetCDF; diff --git a/tests/unit/sys/test_optionsreader.cxx b/tests/unit/sys/test_optionsreader.cxx index 5d2859ea35..3bb71bb510 100644 --- a/tests/unit/sys/test_optionsreader.cxx +++ b/tests/unit/sys/test_optionsreader.cxx @@ -1,5 +1,5 @@ -#include "bout/optionsreader.hxx" #include "test_extras.hxx" +#include "bout/optionsreader.hxx" #include "gtest/gtest.h" #include "bout/boutexception.hxx" diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 8b8e3a3f4e..10ce68f9b4 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -10,12 +10,12 @@ #include "bout/boundary_region.hxx" #include "bout/boutcomm.hxx" -#include "bout/field3d.hxx" -#include "bout/unused.hxx" #include "bout/coordinates.hxx" +#include "bout/field3d.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" #include "bout/operatorstencil.hxx" +#include "bout/unused.hxx" static constexpr BoutReal BoutRealTolerance{1e-15}; // FFTs have a slightly looser tolerance than other functions From 2b00be27dc9eb8af81303bfd86ebb00a8cfd870b Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 20 Feb 2023 18:48:51 +0100 Subject: [PATCH 063/412] Fixup merge --- include/parallel_boundary_op.hxx | 1 - 1 file changed, 1 deletion(-) diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx index 7678614049..e82a88d98f 100644 --- a/include/parallel_boundary_op.hxx +++ b/include/parallel_boundary_op.hxx @@ -1,4 +1,3 @@ -<<<<<<< HEAD #pragma once // BOUT++ header shim #warning Header "parallel_boundary_op.hxx" has moved to "bout/parallel_boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix From 259e29d93fadd5ff9db76721efc4b301d38072ad Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 22 Feb 2023 19:40:02 +0100 Subject: [PATCH 064/412] Fix bad merge --- src/solver/impls/adams_bashforth/adams_bashforth.cxx | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx index 2ad60c91a7..53874f85ce 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx @@ -544,8 +544,6 @@ int AdamsBashforthSolver::run() { // avoid any additional unrequired work associated with run_rhs. run_rhs(simtime); - // Advance iteration number - iteration++; // Call the output step monitor function if (call_monitors(simtime, s, getNumberOutputSteps()) != 0) { From a5d5072e184f84648592dc13456831ecc62a005a Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 22 Feb 2023 19:02:20 +0000 Subject: [PATCH 065/412] Apply clang-format changes --- src/solver/impls/adams_bashforth/adams_bashforth.cxx | 1 - 1 file changed, 1 deletion(-) diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx index 53874f85ce..bfdea5e126 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx @@ -544,7 +544,6 @@ int AdamsBashforthSolver::run() { // avoid any additional unrequired work associated with run_rhs. run_rhs(simtime); - // Call the output step monitor function if (call_monitors(simtime, s, getNumberOutputSteps()) != 0) { break; // Stop simulation From 2c2048811e33360f8a0e4a735fcfc8e555244533 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 23 Feb 2023 09:28:47 +0100 Subject: [PATCH 066/412] Fix bad merge: always use Python3 --- cmake/FindNumpy.cmake | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/FindNumpy.cmake b/cmake/FindNumpy.cmake index 4d3ca2221a..b6de6e3e35 100644 --- a/cmake/FindNumpy.cmake +++ b/cmake/FindNumpy.cmake @@ -12,11 +12,11 @@ # Numpy_INCLUDE_DIR -find_package(Python 3.6 COMPONENTS Interpreter Development) +find_package(Python3 3.6 COMPONENTS Interpreter Development) -if (NOT Python_FOUND) +if (NOT Python3_FOUND) message(STATUS "Could not find numpy as python was not found. Maybe the developement package is missing?") - set(Numpy_FOUND ${Python_FOUND}) + set(Numpy_FOUND ${Python3_FOUND}) return() endif() From bf3152309722c4e74b4e2dfccbcb7cbd3b878f57 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 26 Apr 2023 13:59:55 +0200 Subject: [PATCH 067/412] Fix condition for inner vs outer boundary --- src/mesh/parallel/fci.cxx | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index dd7171aaa6..46396f5993 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -234,9 +234,12 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, const BoutReal dx = (dZ_dz * dR - dR_dz * dZ) / det; const BoutReal dz = (dR_dx * dZ - dZ_dx * dR) / det; - // Negative xt_prime means we've hit the inner boundary, otherwise - // the outer boundary - auto* boundary = (xt_prime[i] < 0.0) ? inner_boundary : outer_boundary; + // Negative xt_prime means we've hit the inner boundary, otherwise the + // outer boundary. However, if any of the surrounding points are negative, + // that also means inner. So to differentiate between inner and outer we + // need at least 2 points in the domain. + ASSERT2(map_mesh.xend - map_mesh.xstart >= 2); + auto* boundary = (xt_prime[i] < 1.5) ? inner_boundary : outer_boundary; boundary->add_point(x, y, z, x + dx, y + 0.5 * offset, z + dz, // Intersection point in local index space 0.5 * dy[i], // Distance to intersection From 92c193ee38d32628ecf0678d3646f4e7dfd82a04 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 3 May 2023 13:52:25 +0200 Subject: [PATCH 068/412] Remove commented out includes --- include/bout/field2d.hxx | 2 +- include/bout/field_data.hxx | 2 -- include/bout/solver.hxx | 1 - include/bout/vector2d.hxx | 2 +- include/bout/vector3d.hxx | 4 ++-- src/field/field.cxx | 2 -- src/mesh/parallel/shiftedmetric.cxx | 2 -- src/mesh/parallel/shiftedmetricinterp.cxx | 1 - src/solver/impls/petsc/petsc.cxx | 1 - tools/archiving/sdctools/sdclib/sdclib.c | 2 -- 10 files changed, 4 insertions(+), 15 deletions(-) diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index 783eb79e9e..cb63b29b9e 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -33,7 +33,7 @@ class Field2D; class Mesh; #include "bout/field.hxx" #include "bout/field_data.hxx" -class Field3D; //#include "bout/field3d.hxx" +class Field3D; #include "bout/fieldperp.hxx" #include "bout/stencils.hxx" diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx index 707c7c96f8..5c9f37ed03 100644 --- a/include/bout/field_data.hxx +++ b/include/bout/field_data.hxx @@ -38,8 +38,6 @@ class FieldData; #include #include -// Including the next line leads to compiler errors -//#include "bout/boundary_op.hxx" class BoundaryOp; class BoundaryOpPar; class Coordinates; diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index 8a3f07c27a..e830d0c2c3 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -63,7 +63,6 @@ using Jacobian = int (*)(BoutReal t); /// Solution monitor, called each timestep using TimestepMonitorFunc = int (*)(Solver* solver, BoutReal simtime, BoutReal lastdt); -//#include "bout/globals.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/generic_factory.hxx" diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx index 9ff4a69ba8..974c5f81db 100644 --- a/include/bout/vector2d.hxx +++ b/include/bout/vector2d.hxx @@ -39,7 +39,7 @@ class Vector2D; class Field2D; class Field3D; -class Vector3D; //#include "bout/vector3d.hxx" +class Vector3D; #include diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx index f3adf41ae8..6df175d199 100644 --- a/include/bout/vector3d.hxx +++ b/include/bout/vector3d.hxx @@ -33,10 +33,10 @@ class Vector3D; #ifndef __VECTOR3D_H__ #define __VECTOR3D_H__ -class Field2D; //#include "bout/field2d.hxx" +class Field2D; #include "bout/field3d.hxx" -class Vector2D; //#include "bout/vector2d.hxx" +class Vector2D; /*! * Represents a 3D vector, with x,y,z components diff --git a/src/field/field.cxx b/src/field/field.cxx index 54883c506c..e48a8f3ef7 100644 --- a/src/field/field.cxx +++ b/src/field/field.cxx @@ -23,8 +23,6 @@ * **************************************************************************/ -//#include - #include #include #include diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index 483c032d6d..3c21736cc1 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -12,8 +12,6 @@ #include #include #include -//#include -//#include #include "bout/parallel_boundary_region.hxx" #include diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index f6449531fa..b1a1b864c3 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -30,7 +30,6 @@ #include "shiftedmetricinterp.hxx" #include "bout/constants.hxx" #include "bout/parallel_boundary_region.hxx" -//#include "bout/mask.hxx" ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, Field2D zShift_in, BoutReal zlength_in, diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx index ad8e99dd38..7888cd15c1 100644 --- a/src/solver/impls/petsc/petsc.cxx +++ b/src/solver/impls/petsc/petsc.cxx @@ -29,7 +29,6 @@ #if BOUT_HAS_PETSC -//#include #include #include diff --git a/tools/archiving/sdctools/sdclib/sdclib.c b/tools/archiving/sdctools/sdclib/sdclib.c index f7db255a47..7294cc0791 100644 --- a/tools/archiving/sdctools/sdclib/sdclib.c +++ b/tools/archiving/sdctools/sdclib/sdclib.c @@ -34,8 +34,6 @@ #include "sdclib.h" -//#define DEBUG - #define DEFAULT_IFRAME 10 #define DEFAULT_ORDER 4 From 9e42f80df7f19a59bde45a1f83b44bc2588a1683 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 3 May 2023 11:58:05 +0000 Subject: [PATCH 069/412] Apply clang-format changes --- include/bout/parallel_boundary_region.hxx | 4 +++- src/mesh/impls/bout/boutmesh.cxx | 2 +- src/mesh/parallel/shiftedmetric.cxx | 2 +- tests/unit/fake_parallel_mesh.hxx | 4 ++-- tests/unit/mesh/test_boundary_factory.cxx | 2 +- tests/unit/test_extras.hxx | 2 +- 6 files changed, 9 insertions(+), 7 deletions(-) diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx index ac332c8c27..caf4f1c4bc 100644 --- a/include/bout/parallel_boundary_region.hxx +++ b/include/bout/parallel_boundary_region.hxx @@ -120,7 +120,9 @@ public: void setValid(char val) { bndry_position->valid = val; } bool contains(const BoundaryRegionPar& bndry) const { - return std::binary_search(begin(bndry_points), end(bndry_points), *bndry.bndry_position, [](const Indices& i1, const Indices& i2) { return i1.index < i2.index; }); + return std::binary_search( + begin(bndry_points), end(bndry_points), *bndry.bndry_position, + [](const Indices& i1, const Indices& i2) { return i1.index < i2.index; }); } // extrapolate a given point to the boundary diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 98670dad22..ddba7f519b 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -47,8 +47,8 @@ #include #include -#include "parallel_boundary_region.hxx" #include "boundary_region.hxx" +#include "parallel_boundary_region.hxx" #include #include diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index 3c21736cc1..b6e7a74d99 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -6,13 +6,13 @@ * */ +#include "bout/parallel_boundary_region.hxx" #include "bout/paralleltransform.hxx" #include #include #include #include #include -#include "bout/parallel_boundary_region.hxx" #include diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx index a6979e008d..805dcb2a0a 100644 --- a/tests/unit/fake_parallel_mesh.hxx +++ b/tests/unit/fake_parallel_mesh.hxx @@ -8,6 +8,8 @@ #include #include "../../src/mesh/impls/bout/boutmesh.hxx" +#include "bout/boundary_op.hxx" +#include "bout/boundary_region.hxx" #include "bout/boutcomm.hxx" #include "bout/coordinates.hxx" #include "bout/field2d.hxx" @@ -16,8 +18,6 @@ #include "bout/fieldperp.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" -#include "bout/boundary_region.hxx" -#include "bout/boundary_op.hxx" #include "bout/unused.hxx" class Options; diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx index b7a2383791..b552f7629e 100644 --- a/tests/unit/mesh/test_boundary_factory.cxx +++ b/tests/unit/mesh/test_boundary_factory.cxx @@ -1,8 +1,8 @@ #include "gtest/gtest.h" #include "bout/boundary_factory.hxx" -#include "bout/boundary_region.hxx" #include "bout/boundary_op.hxx" +#include "bout/boundary_region.hxx" #include "test_extras.hxx" diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index fc79d28c1a..b735f806f0 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -8,13 +8,13 @@ #include #include +#include "bout/boundary_region.hxx" #include "bout/boutcomm.hxx" #include "bout/coordinates.hxx" #include "bout/field3d.hxx" #include "bout/mesh.hxx" #include "bout/mpi_wrapper.hxx" #include "bout/operatorstencil.hxx" -#include "bout/boundary_region.hxx" #include "bout/unused.hxx" static constexpr BoutReal BoutRealTolerance{1e-15}; From 431f0ae68dc253c554e57c8062cd9ee98f3fba80 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 3 May 2023 14:45:48 +0200 Subject: [PATCH 070/412] Only run with one slice 2 slices are not really working ... --- tests/MMS/spatial/fci/runtest | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest index 3db54a3870..4aadcbfa49 100755 --- a/tests/MMS/spatial/fci/runtest +++ b/tests/MMS/spatial/fci/runtest @@ -27,7 +27,7 @@ nx = 3 # Not changed for these tests nlist = [8, 16, 32, 64, 128] # Number of parallel slices (in each direction) -nslices = [1, 2] +nslices = [1] directory = "data" From 39afc95dd654a192dc539832f661ce285aae11ed Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 20 Jun 2023 09:56:47 +0200 Subject: [PATCH 071/412] Get update scripts --- bin/bout-v5-header-upgrader.py | 217 +++++++++++++++++++++++++++++++++ bin/bout_4to5 | 1 - 2 files changed, 217 insertions(+), 1 deletion(-) create mode 100755 bin/bout-v5-header-upgrader.py diff --git a/bin/bout-v5-header-upgrader.py b/bin/bout-v5-header-upgrader.py new file mode 100755 index 0000000000..49a8fbcbe4 --- /dev/null +++ b/bin/bout-v5-header-upgrader.py @@ -0,0 +1,217 @@ +#!/usr/bin/env python3 + +import argparse +import copy +import difflib +import re +import textwrap +from pathlib import Path +from typing import List +from subprocess import run + + +header_shim_sentinel = "// BOUT++ header shim" + +header_warning = f"""\ +#pragma once +{header_shim_sentinel} +#warning Header "{{0}}" has moved to "bout/{{0}}". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/{{0}}" +""" + + +def header_needs_moving(header: Path) -> bool: + """Check if `header` has not yet been moved""" + with open(header, "r") as f: + return header_shim_sentinel not in f.read() + + +def deprecated_header_list(include_path: Path = Path("./include")): + """List of deprecated header paths (that is, those in bare + ``include`` directory) + + """ + return include_path.glob("*.hxx") + + +def write_header_shim(header: Path): + """Write 'shim' for header, that ``include``s new location""" + with open(header, "w") as f: + f.write(header_warning.format(header.name)) + + +def fix_library_header_locations( + include_path: Path = Path("./include"), quiet: bool = False +): + unmoved_headers = list( + filter(header_needs_moving, deprecated_header_list(include_path)) + ) + include_bout_path = include_path / "bout" + + if unmoved_headers == []: + print("No headers to move!") + return + + out = run("git diff-index --cached HEAD --quiet", shell=True) + if out.returncode: + raise RuntimeError( + "git index not clean! Please commit or discard any changes before continuing" + ) + + # First we move any existing headers and commit this change, so + # that history is preserved + for header in unmoved_headers: + new_path = include_bout_path / header.name + if not quiet: + print(f"Moving '{header}' to '{new_path}'") + run(f"git mv {header} {new_path}", shell=True, check=True) + + run(r"git commit -m 'Move headers to `include/bout`'", shell=True, check=True) + + # Now we can write the compatibility shim + for header in unmoved_headers: + write_header_shim(header) + + run(f"git add {' '.join(map(str, unmoved_headers))}", shell=True, check=True) + run( + r"git commit -m 'Add compatibility shims for old header locations'", + shell=True, + check=True, + ) + + +def make_header_regex(deprecated_headers: List[str]) -> re.Pattern: + """Create a regular expression to match deprecated header locations""" + deprecated_header_joined = "|".join((header.name for header in deprecated_headers)) + return re.compile(rf'(#include\s+<|")(?:\.\./)?({deprecated_header_joined})(>|")') + + +def apply_fixes(header_regex, source): + """Apply all fixes in this module""" + modified = copy.deepcopy(source) + + return header_regex.sub(r"\1bout/\2\3", modified) + + +def yes_or_no(question): + """Convert user input from yes/no variations to True/False""" + while True: + reply = input(question + " [y/N] ").lower().strip() + if not reply or reply[0] == "n": + return False + if reply[0] == "y": + return True + + +def create_patch(filename, original, modified): + """Create a unified diff between original and modified""" + + patch = "\n".join( + difflib.unified_diff( + original.splitlines(), + modified.splitlines(), + fromfile=filename, + tofile=filename, + lineterm="", + ) + ) + + return patch + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, + description=textwrap.dedent( + """\ + Fix deprecated header locations for BOUT++ v4 -> v5 + + All BOUT++ headers are now under ``include/bout`` and + should be included as ``#include ``. This + tool will fix such includes. + + For developers: the option ``--move-deprecated-headers`` + will move the headers from ``include`` to + ``include/bout``, and add a compatibility shim in the old + location. This option is mutually exclusive with + ``--files``, and should be used after running this tool + over the library files. + + WARNING: If any files do need moving, this will create a + git commit in order to preserve history across file moves. + If you have staged changes, this tool will not work, so to + avoid committing undesired or unrelated changes. + + """ + ), + ) + + parser.add_argument( + "--force", "-f", action="store_true", help="Make changes without asking" + ) + parser.add_argument( + "--quiet", "-q", action="store_true", help="Don't print patches" + ) + parser.add_argument( + "--patch-only", "-p", action="store_true", help="Print the patches and exit" + ) + parser.add_argument( + "--include-path", + "-i", + help="Path to `include` directory", + default="./include", + type=Path, + ) + + group = parser.add_mutually_exclusive_group(required=True) + group.add_argument("--files", nargs="*", action="store", help="Input files") + group.add_argument( + "--move-deprecated-headers", + action="store_true", + help="Move the deprecated headers", + ) + + args = parser.parse_args() + + if args.force and args.patch_only: + raise ValueError("Incompatible options: --force and --patch") + + deprecated_headers = deprecated_header_list(args.include_path) + + if args.move_deprecated_headers: + fix_library_header_locations(args.include_path, args.quiet) + exit(0) + + header_regex = make_header_regex(deprecated_headers) + + for filename in args.files: + with open(filename, "r") as f: + contents = f.read() + original = copy.deepcopy(contents) + + modified = apply_fixes(header_regex, contents) + patch = create_patch(filename, original, modified) + + if args.patch_only: + print(patch) + continue + + if not patch: + if not args.quiet: + print(f"No changes to make to {filename}") + continue + + if not args.quiet: + print("\n******************************************") + print(f"Changes to {filename}\n") + print(patch) + print("\n******************************************") + + if args.force: + make_change = True + else: + make_change = yes_or_no(f"Make changes to {filename}?") + + if make_change: + with open(filename, "w") as f: + f.write(modified) diff --git a/bin/bout_4to5 b/bin/bout_4to5 index 195bee2144..85dfbe41e9 100755 --- a/bin/bout_4to5 +++ b/bin/bout_4to5 @@ -196,7 +196,6 @@ then done fi - # # clang-format everything - disabled due to issue https://github.com/boutproject/BOUT-dev/issues/1017 # if test $# -eq 0 # then From 0e18bb7a9480d36994d86bbcc9326aaf6fcb1ac6 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 20 Jun 2023 09:56:51 +0200 Subject: [PATCH 072/412] Move headers to `include/bout` --- include/{ => bout}/boundary_factory.hxx | 0 include/{ => bout}/boundary_op.hxx | 0 include/{ => bout}/boundary_region.hxx | 0 include/{ => bout}/boundary_standard.hxx | 0 include/{ => bout}/bout.hxx | 0 include/{ => bout}/bout_types.hxx | 0 include/{ => bout}/boutcomm.hxx | 0 include/{ => bout}/boutexception.hxx | 0 include/{ => bout}/cyclic_reduction.hxx | 0 include/{ => bout}/dcomplex.hxx | 0 include/{ => bout}/derivs.hxx | 0 include/{ => bout}/difops.hxx | 0 include/{ => bout}/fft.hxx | 0 include/{ => bout}/field.hxx | 0 include/{ => bout}/field2d.hxx | 0 include/{ => bout}/field3d.hxx | 0 include/{ => bout}/field_data.hxx | 0 include/{ => bout}/field_factory.hxx | 0 include/{ => bout}/fieldperp.hxx | 0 include/{ => bout}/globals.hxx | 0 include/{ => bout}/gyro_average.hxx | 0 include/{ => bout}/initialprofiles.hxx | 0 include/{ => bout}/interpolation.hxx | 0 include/{ => bout}/interpolation_xz.hxx | 0 include/{ => bout}/interpolation_z.hxx | 0 include/{ => bout}/invert_laplace.hxx | 0 include/{ => bout}/invert_parderiv.hxx | 0 include/{ => bout}/lapack_routines.hxx | 0 include/{ => bout}/mask.hxx | 0 include/{ => bout}/msg_stack.hxx | 0 include/{ => bout}/multiostream.hxx | 0 include/{ => bout}/options.hxx | 0 include/{ => bout}/options_netcdf.hxx | 0 include/{ => bout}/optionsreader.hxx | 0 include/{ => bout}/output.hxx | 0 include/{ => bout}/parallel_boundary_op.hxx | 0 include/{ => bout}/parallel_boundary_region.hxx | 0 include/{ => bout}/smoothing.hxx | 0 include/{ => bout}/sourcex.hxx | 0 include/{ => bout}/stencils.hxx | 0 include/{ => bout}/unused.hxx | 0 include/{ => bout}/utils.hxx | 0 include/{ => bout}/vecops.hxx | 0 include/{ => bout}/vector2d.hxx | 0 include/{ => bout}/vector3d.hxx | 0 include/{ => bout}/where.hxx | 0 46 files changed, 0 insertions(+), 0 deletions(-) rename include/{ => bout}/boundary_factory.hxx (100%) rename include/{ => bout}/boundary_op.hxx (100%) rename include/{ => bout}/boundary_region.hxx (100%) rename include/{ => bout}/boundary_standard.hxx (100%) rename include/{ => bout}/bout.hxx (100%) rename include/{ => bout}/bout_types.hxx (100%) rename include/{ => bout}/boutcomm.hxx (100%) rename include/{ => bout}/boutexception.hxx (100%) rename include/{ => bout}/cyclic_reduction.hxx (100%) rename include/{ => bout}/dcomplex.hxx (100%) rename include/{ => bout}/derivs.hxx (100%) rename include/{ => bout}/difops.hxx (100%) rename include/{ => bout}/fft.hxx (100%) rename include/{ => bout}/field.hxx (100%) rename include/{ => bout}/field2d.hxx (100%) rename include/{ => bout}/field3d.hxx (100%) rename include/{ => bout}/field_data.hxx (100%) rename include/{ => bout}/field_factory.hxx (100%) rename include/{ => bout}/fieldperp.hxx (100%) rename include/{ => bout}/globals.hxx (100%) rename include/{ => bout}/gyro_average.hxx (100%) rename include/{ => bout}/initialprofiles.hxx (100%) rename include/{ => bout}/interpolation.hxx (100%) rename include/{ => bout}/interpolation_xz.hxx (100%) rename include/{ => bout}/interpolation_z.hxx (100%) rename include/{ => bout}/invert_laplace.hxx (100%) rename include/{ => bout}/invert_parderiv.hxx (100%) rename include/{ => bout}/lapack_routines.hxx (100%) rename include/{ => bout}/mask.hxx (100%) rename include/{ => bout}/msg_stack.hxx (100%) rename include/{ => bout}/multiostream.hxx (100%) rename include/{ => bout}/options.hxx (100%) rename include/{ => bout}/options_netcdf.hxx (100%) rename include/{ => bout}/optionsreader.hxx (100%) rename include/{ => bout}/output.hxx (100%) rename include/{ => bout}/parallel_boundary_op.hxx (100%) rename include/{ => bout}/parallel_boundary_region.hxx (100%) rename include/{ => bout}/smoothing.hxx (100%) rename include/{ => bout}/sourcex.hxx (100%) rename include/{ => bout}/stencils.hxx (100%) rename include/{ => bout}/unused.hxx (100%) rename include/{ => bout}/utils.hxx (100%) rename include/{ => bout}/vecops.hxx (100%) rename include/{ => bout}/vector2d.hxx (100%) rename include/{ => bout}/vector3d.hxx (100%) rename include/{ => bout}/where.hxx (100%) diff --git a/include/boundary_factory.hxx b/include/bout/boundary_factory.hxx similarity index 100% rename from include/boundary_factory.hxx rename to include/bout/boundary_factory.hxx diff --git a/include/boundary_op.hxx b/include/bout/boundary_op.hxx similarity index 100% rename from include/boundary_op.hxx rename to include/bout/boundary_op.hxx diff --git a/include/boundary_region.hxx b/include/bout/boundary_region.hxx similarity index 100% rename from include/boundary_region.hxx rename to include/bout/boundary_region.hxx diff --git a/include/boundary_standard.hxx b/include/bout/boundary_standard.hxx similarity index 100% rename from include/boundary_standard.hxx rename to include/bout/boundary_standard.hxx diff --git a/include/bout.hxx b/include/bout/bout.hxx similarity index 100% rename from include/bout.hxx rename to include/bout/bout.hxx diff --git a/include/bout_types.hxx b/include/bout/bout_types.hxx similarity index 100% rename from include/bout_types.hxx rename to include/bout/bout_types.hxx diff --git a/include/boutcomm.hxx b/include/bout/boutcomm.hxx similarity index 100% rename from include/boutcomm.hxx rename to include/bout/boutcomm.hxx diff --git a/include/boutexception.hxx b/include/bout/boutexception.hxx similarity index 100% rename from include/boutexception.hxx rename to include/bout/boutexception.hxx diff --git a/include/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx similarity index 100% rename from include/cyclic_reduction.hxx rename to include/bout/cyclic_reduction.hxx diff --git a/include/dcomplex.hxx b/include/bout/dcomplex.hxx similarity index 100% rename from include/dcomplex.hxx rename to include/bout/dcomplex.hxx diff --git a/include/derivs.hxx b/include/bout/derivs.hxx similarity index 100% rename from include/derivs.hxx rename to include/bout/derivs.hxx diff --git a/include/difops.hxx b/include/bout/difops.hxx similarity index 100% rename from include/difops.hxx rename to include/bout/difops.hxx diff --git a/include/fft.hxx b/include/bout/fft.hxx similarity index 100% rename from include/fft.hxx rename to include/bout/fft.hxx diff --git a/include/field.hxx b/include/bout/field.hxx similarity index 100% rename from include/field.hxx rename to include/bout/field.hxx diff --git a/include/field2d.hxx b/include/bout/field2d.hxx similarity index 100% rename from include/field2d.hxx rename to include/bout/field2d.hxx diff --git a/include/field3d.hxx b/include/bout/field3d.hxx similarity index 100% rename from include/field3d.hxx rename to include/bout/field3d.hxx diff --git a/include/field_data.hxx b/include/bout/field_data.hxx similarity index 100% rename from include/field_data.hxx rename to include/bout/field_data.hxx diff --git a/include/field_factory.hxx b/include/bout/field_factory.hxx similarity index 100% rename from include/field_factory.hxx rename to include/bout/field_factory.hxx diff --git a/include/fieldperp.hxx b/include/bout/fieldperp.hxx similarity index 100% rename from include/fieldperp.hxx rename to include/bout/fieldperp.hxx diff --git a/include/globals.hxx b/include/bout/globals.hxx similarity index 100% rename from include/globals.hxx rename to include/bout/globals.hxx diff --git a/include/gyro_average.hxx b/include/bout/gyro_average.hxx similarity index 100% rename from include/gyro_average.hxx rename to include/bout/gyro_average.hxx diff --git a/include/initialprofiles.hxx b/include/bout/initialprofiles.hxx similarity index 100% rename from include/initialprofiles.hxx rename to include/bout/initialprofiles.hxx diff --git a/include/interpolation.hxx b/include/bout/interpolation.hxx similarity index 100% rename from include/interpolation.hxx rename to include/bout/interpolation.hxx diff --git a/include/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx similarity index 100% rename from include/interpolation_xz.hxx rename to include/bout/interpolation_xz.hxx diff --git a/include/interpolation_z.hxx b/include/bout/interpolation_z.hxx similarity index 100% rename from include/interpolation_z.hxx rename to include/bout/interpolation_z.hxx diff --git a/include/invert_laplace.hxx b/include/bout/invert_laplace.hxx similarity index 100% rename from include/invert_laplace.hxx rename to include/bout/invert_laplace.hxx diff --git a/include/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx similarity index 100% rename from include/invert_parderiv.hxx rename to include/bout/invert_parderiv.hxx diff --git a/include/lapack_routines.hxx b/include/bout/lapack_routines.hxx similarity index 100% rename from include/lapack_routines.hxx rename to include/bout/lapack_routines.hxx diff --git a/include/mask.hxx b/include/bout/mask.hxx similarity index 100% rename from include/mask.hxx rename to include/bout/mask.hxx diff --git a/include/msg_stack.hxx b/include/bout/msg_stack.hxx similarity index 100% rename from include/msg_stack.hxx rename to include/bout/msg_stack.hxx diff --git a/include/multiostream.hxx b/include/bout/multiostream.hxx similarity index 100% rename from include/multiostream.hxx rename to include/bout/multiostream.hxx diff --git a/include/options.hxx b/include/bout/options.hxx similarity index 100% rename from include/options.hxx rename to include/bout/options.hxx diff --git a/include/options_netcdf.hxx b/include/bout/options_netcdf.hxx similarity index 100% rename from include/options_netcdf.hxx rename to include/bout/options_netcdf.hxx diff --git a/include/optionsreader.hxx b/include/bout/optionsreader.hxx similarity index 100% rename from include/optionsreader.hxx rename to include/bout/optionsreader.hxx diff --git a/include/output.hxx b/include/bout/output.hxx similarity index 100% rename from include/output.hxx rename to include/bout/output.hxx diff --git a/include/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx similarity index 100% rename from include/parallel_boundary_op.hxx rename to include/bout/parallel_boundary_op.hxx diff --git a/include/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx similarity index 100% rename from include/parallel_boundary_region.hxx rename to include/bout/parallel_boundary_region.hxx diff --git a/include/smoothing.hxx b/include/bout/smoothing.hxx similarity index 100% rename from include/smoothing.hxx rename to include/bout/smoothing.hxx diff --git a/include/sourcex.hxx b/include/bout/sourcex.hxx similarity index 100% rename from include/sourcex.hxx rename to include/bout/sourcex.hxx diff --git a/include/stencils.hxx b/include/bout/stencils.hxx similarity index 100% rename from include/stencils.hxx rename to include/bout/stencils.hxx diff --git a/include/unused.hxx b/include/bout/unused.hxx similarity index 100% rename from include/unused.hxx rename to include/bout/unused.hxx diff --git a/include/utils.hxx b/include/bout/utils.hxx similarity index 100% rename from include/utils.hxx rename to include/bout/utils.hxx diff --git a/include/vecops.hxx b/include/bout/vecops.hxx similarity index 100% rename from include/vecops.hxx rename to include/bout/vecops.hxx diff --git a/include/vector2d.hxx b/include/bout/vector2d.hxx similarity index 100% rename from include/vector2d.hxx rename to include/bout/vector2d.hxx diff --git a/include/vector3d.hxx b/include/bout/vector3d.hxx similarity index 100% rename from include/vector3d.hxx rename to include/bout/vector3d.hxx diff --git a/include/where.hxx b/include/bout/where.hxx similarity index 100% rename from include/where.hxx rename to include/bout/where.hxx From 07350db74e6a842c708bd68ea54d891339a5f57a Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 20 Jun 2023 09:56:51 +0200 Subject: [PATCH 073/412] Add compatibility shims for old header locations --- include/boundary_factory.hxx | 4 ++++ include/boundary_op.hxx | 4 ++++ include/boundary_region.hxx | 4 ++++ include/boundary_standard.hxx | 4 ++++ include/bout.hxx | 4 ++++ include/bout_types.hxx | 4 ++++ include/boutcomm.hxx | 4 ++++ include/boutexception.hxx | 4 ++++ include/cyclic_reduction.hxx | 4 ++++ include/dcomplex.hxx | 4 ++++ include/derivs.hxx | 4 ++++ include/difops.hxx | 4 ++++ include/fft.hxx | 4 ++++ include/field.hxx | 4 ++++ include/field2d.hxx | 4 ++++ include/field3d.hxx | 4 ++++ include/field_data.hxx | 4 ++++ include/field_factory.hxx | 4 ++++ include/fieldperp.hxx | 4 ++++ include/globals.hxx | 4 ++++ include/gyro_average.hxx | 4 ++++ include/initialprofiles.hxx | 4 ++++ include/interpolation.hxx | 4 ++++ include/interpolation_xz.hxx | 4 ++++ include/interpolation_z.hxx | 4 ++++ include/invert_laplace.hxx | 4 ++++ include/invert_parderiv.hxx | 4 ++++ include/lapack_routines.hxx | 4 ++++ include/mask.hxx | 4 ++++ include/msg_stack.hxx | 4 ++++ include/multiostream.hxx | 4 ++++ include/options.hxx | 4 ++++ include/options_netcdf.hxx | 4 ++++ include/optionsreader.hxx | 4 ++++ include/output.hxx | 4 ++++ include/parallel_boundary_op.hxx | 4 ++++ include/parallel_boundary_region.hxx | 4 ++++ include/smoothing.hxx | 4 ++++ include/sourcex.hxx | 4 ++++ include/stencils.hxx | 4 ++++ include/unused.hxx | 4 ++++ include/utils.hxx | 4 ++++ include/vecops.hxx | 4 ++++ include/vector2d.hxx | 4 ++++ include/vector3d.hxx | 4 ++++ include/where.hxx | 4 ++++ 46 files changed, 184 insertions(+) create mode 100644 include/boundary_factory.hxx create mode 100644 include/boundary_op.hxx create mode 100644 include/boundary_region.hxx create mode 100644 include/boundary_standard.hxx create mode 100644 include/bout.hxx create mode 100644 include/bout_types.hxx create mode 100644 include/boutcomm.hxx create mode 100644 include/boutexception.hxx create mode 100644 include/cyclic_reduction.hxx create mode 100644 include/dcomplex.hxx create mode 100644 include/derivs.hxx create mode 100644 include/difops.hxx create mode 100644 include/fft.hxx create mode 100644 include/field.hxx create mode 100644 include/field2d.hxx create mode 100644 include/field3d.hxx create mode 100644 include/field_data.hxx create mode 100644 include/field_factory.hxx create mode 100644 include/fieldperp.hxx create mode 100644 include/globals.hxx create mode 100644 include/gyro_average.hxx create mode 100644 include/initialprofiles.hxx create mode 100644 include/interpolation.hxx create mode 100644 include/interpolation_xz.hxx create mode 100644 include/interpolation_z.hxx create mode 100644 include/invert_laplace.hxx create mode 100644 include/invert_parderiv.hxx create mode 100644 include/lapack_routines.hxx create mode 100644 include/mask.hxx create mode 100644 include/msg_stack.hxx create mode 100644 include/multiostream.hxx create mode 100644 include/options.hxx create mode 100644 include/options_netcdf.hxx create mode 100644 include/optionsreader.hxx create mode 100644 include/output.hxx create mode 100644 include/parallel_boundary_op.hxx create mode 100644 include/parallel_boundary_region.hxx create mode 100644 include/smoothing.hxx create mode 100644 include/sourcex.hxx create mode 100644 include/stencils.hxx create mode 100644 include/unused.hxx create mode 100644 include/utils.hxx create mode 100644 include/vecops.hxx create mode 100644 include/vector2d.hxx create mode 100644 include/vector3d.hxx create mode 100644 include/where.hxx diff --git a/include/boundary_factory.hxx b/include/boundary_factory.hxx new file mode 100644 index 0000000000..abbead8fc4 --- /dev/null +++ b/include/boundary_factory.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_factory.hxx" has moved to "bout/boundary_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_factory.hxx" diff --git a/include/boundary_op.hxx b/include/boundary_op.hxx new file mode 100644 index 0000000000..c96310f2d4 --- /dev/null +++ b/include/boundary_op.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_op.hxx" has moved to "bout/boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_op.hxx" diff --git a/include/boundary_region.hxx b/include/boundary_region.hxx new file mode 100644 index 0000000000..f487e88aeb --- /dev/null +++ b/include/boundary_region.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_region.hxx" has moved to "bout/boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_region.hxx" diff --git a/include/boundary_standard.hxx b/include/boundary_standard.hxx new file mode 100644 index 0000000000..b7f17cf363 --- /dev/null +++ b/include/boundary_standard.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boundary_standard.hxx" has moved to "bout/boundary_standard.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boundary_standard.hxx" diff --git a/include/bout.hxx b/include/bout.hxx new file mode 100644 index 0000000000..926f035d2f --- /dev/null +++ b/include/bout.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "bout.hxx" has moved to "bout/bout.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/bout.hxx" diff --git a/include/bout_types.hxx b/include/bout_types.hxx new file mode 100644 index 0000000000..e6048eb885 --- /dev/null +++ b/include/bout_types.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "bout_types.hxx" has moved to "bout/bout_types.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/bout_types.hxx" diff --git a/include/boutcomm.hxx b/include/boutcomm.hxx new file mode 100644 index 0000000000..256df49c4f --- /dev/null +++ b/include/boutcomm.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boutcomm.hxx" has moved to "bout/boutcomm.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boutcomm.hxx" diff --git a/include/boutexception.hxx b/include/boutexception.hxx new file mode 100644 index 0000000000..9189babfb3 --- /dev/null +++ b/include/boutexception.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "boutexception.hxx" has moved to "bout/boutexception.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/boutexception.hxx" diff --git a/include/cyclic_reduction.hxx b/include/cyclic_reduction.hxx new file mode 100644 index 0000000000..3ff098b062 --- /dev/null +++ b/include/cyclic_reduction.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "cyclic_reduction.hxx" has moved to "bout/cyclic_reduction.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/cyclic_reduction.hxx" diff --git a/include/dcomplex.hxx b/include/dcomplex.hxx new file mode 100644 index 0000000000..a91c5485bf --- /dev/null +++ b/include/dcomplex.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "dcomplex.hxx" has moved to "bout/dcomplex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/dcomplex.hxx" diff --git a/include/derivs.hxx b/include/derivs.hxx new file mode 100644 index 0000000000..d0a6eb5831 --- /dev/null +++ b/include/derivs.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "derivs.hxx" has moved to "bout/derivs.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/derivs.hxx" diff --git a/include/difops.hxx b/include/difops.hxx new file mode 100644 index 0000000000..a61d9712a9 --- /dev/null +++ b/include/difops.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "difops.hxx" has moved to "bout/difops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/difops.hxx" diff --git a/include/fft.hxx b/include/fft.hxx new file mode 100644 index 0000000000..d67b257388 --- /dev/null +++ b/include/fft.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "fft.hxx" has moved to "bout/fft.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/fft.hxx" diff --git a/include/field.hxx b/include/field.hxx new file mode 100644 index 0000000000..a2fcb2464e --- /dev/null +++ b/include/field.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field.hxx" has moved to "bout/field.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field.hxx" diff --git a/include/field2d.hxx b/include/field2d.hxx new file mode 100644 index 0000000000..3b148b3a50 --- /dev/null +++ b/include/field2d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field2d.hxx" has moved to "bout/field2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field2d.hxx" diff --git a/include/field3d.hxx b/include/field3d.hxx new file mode 100644 index 0000000000..300cec057b --- /dev/null +++ b/include/field3d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field3d.hxx" has moved to "bout/field3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field3d.hxx" diff --git a/include/field_data.hxx b/include/field_data.hxx new file mode 100644 index 0000000000..90f5c96c40 --- /dev/null +++ b/include/field_data.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field_data.hxx" has moved to "bout/field_data.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field_data.hxx" diff --git a/include/field_factory.hxx b/include/field_factory.hxx new file mode 100644 index 0000000000..c6302ee298 --- /dev/null +++ b/include/field_factory.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "field_factory.hxx" has moved to "bout/field_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/field_factory.hxx" diff --git a/include/fieldperp.hxx b/include/fieldperp.hxx new file mode 100644 index 0000000000..1994e53060 --- /dev/null +++ b/include/fieldperp.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "fieldperp.hxx" has moved to "bout/fieldperp.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/fieldperp.hxx" diff --git a/include/globals.hxx b/include/globals.hxx new file mode 100644 index 0000000000..f07488c10c --- /dev/null +++ b/include/globals.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "globals.hxx" has moved to "bout/globals.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/globals.hxx" diff --git a/include/gyro_average.hxx b/include/gyro_average.hxx new file mode 100644 index 0000000000..c0d454eb50 --- /dev/null +++ b/include/gyro_average.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "gyro_average.hxx" has moved to "bout/gyro_average.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/gyro_average.hxx" diff --git a/include/initialprofiles.hxx b/include/initialprofiles.hxx new file mode 100644 index 0000000000..7bc1595261 --- /dev/null +++ b/include/initialprofiles.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "initialprofiles.hxx" has moved to "bout/initialprofiles.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/initialprofiles.hxx" diff --git a/include/interpolation.hxx b/include/interpolation.hxx new file mode 100644 index 0000000000..80ad60b4e4 --- /dev/null +++ b/include/interpolation.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "interpolation.hxx" has moved to "bout/interpolation.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/interpolation.hxx" diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx new file mode 100644 index 0000000000..8845e34b80 --- /dev/null +++ b/include/interpolation_xz.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "interpolation_xz.hxx" has moved to "bout/interpolation_xz.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/interpolation_xz.hxx" diff --git a/include/interpolation_z.hxx b/include/interpolation_z.hxx new file mode 100644 index 0000000000..a88b486026 --- /dev/null +++ b/include/interpolation_z.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "interpolation_z.hxx" has moved to "bout/interpolation_z.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/interpolation_z.hxx" diff --git a/include/invert_laplace.hxx b/include/invert_laplace.hxx new file mode 100644 index 0000000000..fbb04acaf1 --- /dev/null +++ b/include/invert_laplace.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "invert_laplace.hxx" has moved to "bout/invert_laplace.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/invert_laplace.hxx" diff --git a/include/invert_parderiv.hxx b/include/invert_parderiv.hxx new file mode 100644 index 0000000000..81a8ca4f49 --- /dev/null +++ b/include/invert_parderiv.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "invert_parderiv.hxx" has moved to "bout/invert_parderiv.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/invert_parderiv.hxx" diff --git a/include/lapack_routines.hxx b/include/lapack_routines.hxx new file mode 100644 index 0000000000..97fa2c6be9 --- /dev/null +++ b/include/lapack_routines.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "lapack_routines.hxx" has moved to "bout/lapack_routines.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/lapack_routines.hxx" diff --git a/include/mask.hxx b/include/mask.hxx new file mode 100644 index 0000000000..cbeab65d85 --- /dev/null +++ b/include/mask.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "mask.hxx" has moved to "bout/mask.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/mask.hxx" diff --git a/include/msg_stack.hxx b/include/msg_stack.hxx new file mode 100644 index 0000000000..2503961748 --- /dev/null +++ b/include/msg_stack.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "msg_stack.hxx" has moved to "bout/msg_stack.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/msg_stack.hxx" diff --git a/include/multiostream.hxx b/include/multiostream.hxx new file mode 100644 index 0000000000..7e7101aad0 --- /dev/null +++ b/include/multiostream.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "multiostream.hxx" has moved to "bout/multiostream.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/multiostream.hxx" diff --git a/include/options.hxx b/include/options.hxx new file mode 100644 index 0000000000..4693422c13 --- /dev/null +++ b/include/options.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "options.hxx" has moved to "bout/options.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/options.hxx" diff --git a/include/options_netcdf.hxx b/include/options_netcdf.hxx new file mode 100644 index 0000000000..c0d14c536a --- /dev/null +++ b/include/options_netcdf.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "options_netcdf.hxx" has moved to "bout/options_netcdf.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/options_netcdf.hxx" diff --git a/include/optionsreader.hxx b/include/optionsreader.hxx new file mode 100644 index 0000000000..2c0f8344bf --- /dev/null +++ b/include/optionsreader.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "optionsreader.hxx" has moved to "bout/optionsreader.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/optionsreader.hxx" diff --git a/include/output.hxx b/include/output.hxx new file mode 100644 index 0000000000..7eebcad478 --- /dev/null +++ b/include/output.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "output.hxx" has moved to "bout/output.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/output.hxx" diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx new file mode 100644 index 0000000000..e82a88d98f --- /dev/null +++ b/include/parallel_boundary_op.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "parallel_boundary_op.hxx" has moved to "bout/parallel_boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/parallel_boundary_op.hxx" diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx new file mode 100644 index 0000000000..dee2277007 --- /dev/null +++ b/include/parallel_boundary_region.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "parallel_boundary_region.hxx" has moved to "bout/parallel_boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/parallel_boundary_region.hxx" diff --git a/include/smoothing.hxx b/include/smoothing.hxx new file mode 100644 index 0000000000..b1a36adfb2 --- /dev/null +++ b/include/smoothing.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "smoothing.hxx" has moved to "bout/smoothing.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/smoothing.hxx" diff --git a/include/sourcex.hxx b/include/sourcex.hxx new file mode 100644 index 0000000000..e09f3e89e4 --- /dev/null +++ b/include/sourcex.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "sourcex.hxx" has moved to "bout/sourcex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/sourcex.hxx" diff --git a/include/stencils.hxx b/include/stencils.hxx new file mode 100644 index 0000000000..fc877f3e1c --- /dev/null +++ b/include/stencils.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "stencils.hxx" has moved to "bout/stencils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/stencils.hxx" diff --git a/include/unused.hxx b/include/unused.hxx new file mode 100644 index 0000000000..fa5ea7b6d1 --- /dev/null +++ b/include/unused.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "unused.hxx" has moved to "bout/unused.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/unused.hxx" diff --git a/include/utils.hxx b/include/utils.hxx new file mode 100644 index 0000000000..d1a095e491 --- /dev/null +++ b/include/utils.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "utils.hxx" has moved to "bout/utils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/utils.hxx" diff --git a/include/vecops.hxx b/include/vecops.hxx new file mode 100644 index 0000000000..1773418077 --- /dev/null +++ b/include/vecops.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "vecops.hxx" has moved to "bout/vecops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/vecops.hxx" diff --git a/include/vector2d.hxx b/include/vector2d.hxx new file mode 100644 index 0000000000..6746d3f163 --- /dev/null +++ b/include/vector2d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "vector2d.hxx" has moved to "bout/vector2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/vector2d.hxx" diff --git a/include/vector3d.hxx b/include/vector3d.hxx new file mode 100644 index 0000000000..747b6a75dd --- /dev/null +++ b/include/vector3d.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "vector3d.hxx" has moved to "bout/vector3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/vector3d.hxx" diff --git a/include/where.hxx b/include/where.hxx new file mode 100644 index 0000000000..e5b2bd9d30 --- /dev/null +++ b/include/where.hxx @@ -0,0 +1,4 @@ +#pragma once +// BOUT++ header shim +#warning Header "where.hxx" has moved to "bout/where.hxx". Run `bin/bout-v5-header-upgrader.py` to fix +#include "bout/where.hxx" From eeb57124028d980f19417c2752cecc38a4ed00ed Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 28 Jun 2023 15:09:00 +0200 Subject: [PATCH 074/412] Prefer static Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- include/bout/parallel_boundary_op.hxx | 12 ++++++------ include/bout/parallel_boundary_region.hxx | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx index f9409e0aa1..655af670f1 100644 --- a/include/bout/parallel_boundary_op.hxx +++ b/include/bout/parallel_boundary_op.hxx @@ -111,7 +111,7 @@ public: class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { bndry->dirichlet_o1(f, value); } }; @@ -119,7 +119,7 @@ public: class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { bndry->dirichlet_o2(f, value); } }; @@ -127,7 +127,7 @@ public: class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { bndry->dirichlet_o3(f, value); } }; @@ -136,7 +136,7 @@ class BoundaryOpPar_neumann_o1 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { bndry->neumann_o1(f, value); } }; @@ -145,7 +145,7 @@ class BoundaryOpPar_neumann_o2 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { bndry->neumann_o2(f, value); } }; @@ -154,7 +154,7 @@ class BoundaryOpPar_neumann_o3 : public BoundaryOpParTemp { public: using BoundaryOpParTemp::BoundaryOpParTemp; - void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { + static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) { bndry->neumann_o3(f, value); } }; diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx index caf4f1c4bc..7dfb650474 100644 --- a/include/bout/parallel_boundary_region.hxx +++ b/include/bout/parallel_boundary_region.hxx @@ -195,7 +195,7 @@ private: BoutReal& ynext(Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; } const BoutReal& yprev(const Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; } BoutReal& yprev(Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; } - Ind3D xyz2ind(int x, int y, int z, Mesh* mesh) const { + static Ind3D xyz2ind(int x, int y, int z, Mesh* mesh) { const int ny = mesh->LocalNy; const int nz = mesh->LocalNz; return Ind3D{(x * ny + y) * nz + z, ny, nz}; From f864953abdc47d61fb4331288328ab76a05faf2c Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 14 Jun 2023 17:47:50 +0100 Subject: [PATCH 075/412] Bump required C++ standard to 17 --- CMakeLists.txt | 2 +- README.md | 2 +- manual/sphinx/user_docs/installing.rst | 4 ++-- manual/sphinx/user_docs/quickstart.rst | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 26ed0f00bb..ff40d756ba 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -461,7 +461,7 @@ set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++") set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include") set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS}") -target_compile_features(bout++ PUBLIC cxx_std_14) +target_compile_features(bout++ PUBLIC cxx_std_17) set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF) # Optional compiler features diff --git a/README.md b/README.md index 35e5fba02c..5e2cd4a0d2 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,7 @@ Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/) BOUT++ needs the following: -* A C++14 compiler +* A C++17 compiler * MPI * NetCDF diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst index 28c03b6730..e7e3a1509a 100644 --- a/manual/sphinx/user_docs/installing.rst +++ b/manual/sphinx/user_docs/installing.rst @@ -124,7 +124,7 @@ Installing dependencies The bare-minimum requirements for compiling and running BOUT++ are: -#. A C++ compiler that supports C++14 +#. A C++ compiler that supports C++17 #. An MPI compiler such as OpenMPI (`www.open-mpi.org/ `__), MPICH ( `https://www.mpich.org/ `__) @@ -140,7 +140,7 @@ FFTW-3, these options will not be available. .. note:: If you use an Intel compiler, you must also make sure that you have - a version of GCC that supports C++14 (GCC 5+). + a version of GCC that supports C++17 (GCC 8+). On supercomputers, or in other environments that use a module system, you may need to load modules for both Intel and GCC. diff --git a/manual/sphinx/user_docs/quickstart.rst b/manual/sphinx/user_docs/quickstart.rst index ed736130cc..93e144daf3 100644 --- a/manual/sphinx/user_docs/quickstart.rst +++ b/manual/sphinx/user_docs/quickstart.rst @@ -17,7 +17,7 @@ the following tools and libraries: * ``git`` (>= 2.x) * `CMake `_ -* a C++-14 compiler (for example, GCC >= 5.0) +* a C++-17 compiler (for example, GCC >= 8.0) * an ``MPI`` implementation (for example OpenMPI or MPICH) * The `NetCDF C library `__ From 9f6b3f7299c08ae402b6f4fa786aee5536d25a70 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 12 Sep 2023 17:30:04 -0700 Subject: [PATCH 076/412] Build Sundials static libs if shared libs disabled. Previously if shared libs are not enabled, then neither static nor shared sundials libraries would be built. --- cmake/SetupBOUTThirdParty.cmake | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 00d796fd5d..1ee42411ca 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -231,7 +231,11 @@ if (BOUT_USE_SUNDIALS) set(EXAMPLES_INSTALL OFF CACHE BOOL "" FORCE) set(ENABLE_MPI ${BOUT_USE_MPI} CACHE BOOL "" FORCE) set(ENABLE_OPENMP OFF CACHE BOOL "" FORCE) - set(BUILD_STATIC_LIBS OFF CACHE BOOL "" FORCE) + if (BUILD_SHARED_LIBS) + set(BUILD_STATIC_LIBS OFF CACHE BOOL "" FORCE) + else() + set(BUILD_STATIC_LIBS ON CACHE BOOL "" FORCE) + endif() FetchContent_MakeAvailable(sundials) message(STATUS "SUNDIALS done configuring") else() From 1a5ce5885c2e1dd9b0412d4e93d9598630dbe1bc Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Tue, 10 Oct 2023 12:50:10 +0000 Subject: [PATCH 077/412] Apply clang-format changes --- externalpackages/PVODE/source/cvode.cpp | 2 +- include/bout/cyclic_reduction.hxx | 1 - include/bout/interpolation_xz.hxx | 2 +- include/bout/invert_laplace.hxx | 11 ++++++----- include/bout/utils.hxx | 17 ++++++++++++----- include/bout/vector2d.hxx | 17 +++++++++-------- include/bout/vector3d.hxx | 15 +++++++-------- src/mesh/mesh.cxx | 2 +- tests/unit/include/bout/test_region.cxx | 3 ++- 9 files changed, 39 insertions(+), 31 deletions(-) diff --git a/externalpackages/PVODE/source/cvode.cpp b/externalpackages/PVODE/source/cvode.cpp index 48ac3209f2..135662a40f 100644 --- a/externalpackages/PVODE/source/cvode.cpp +++ b/externalpackages/PVODE/source/cvode.cpp @@ -179,7 +179,7 @@ namespace pvode { #define MSG_Y0_NULL CVM "y0=NULL illegal.\n\n" -#define MSG_BAD_N CVM "N=%d < 1 illegal.\n\n" +#define MSG_BAD_N CVM "N=%d < 1 illegal.\n\n" #define MSG_BAD_LMM_1 CVM "lmm=%d illegal.\n" #define MSG_BAD_LMM_2 "The legal values are ADAMS=%d and BDF=%d.\n\n" diff --git a/include/bout/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx index 4c33deea72..d4ef958e93 100644 --- a/include/bout/cyclic_reduction.hxx +++ b/include/bout/cyclic_reduction.hxx @@ -540,7 +540,6 @@ private: } #endif - BOUT_OMP(parallel for) for (int j = 0; j < ns; j++) { // Calculate upper interface equation diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 234f94dea2..963033064a 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -50,7 +50,7 @@ public: XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr) : y_offset(y_offset), localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn) {} - XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr) + XZInterpolation(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr) : XZInterpolation(y_offset, mesh) { region = regionFromMask(mask, localmesh); } diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index f0ea5bdf47..c4ae5efdf8 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -132,8 +132,8 @@ constexpr int INVERT_KX_ZERO = 16; const int INVERT_DC_IN_GRADPARINV = 2097152; */ -class LaplaceFactory : public Factory { +class LaplaceFactory + : public Factory { public: static constexpr auto type_name = "Laplacian"; static constexpr auto section_name = "laplace"; @@ -261,9 +261,10 @@ public: * * @param[in] opt The options section to use. By default "laplace" will be used */ - static std::unique_ptr - create(Options* opts = nullptr, const CELL_LOC location = CELL_CENTRE, - Mesh* mesh_in = nullptr, Solver* solver = nullptr) { + static std::unique_ptr create(Options* opts = nullptr, + const CELL_LOC location = CELL_CENTRE, + Mesh* mesh_in = nullptr, + Solver* solver = nullptr) { return LaplaceFactory::getInstance().create(opts, location, mesh_in, solver); } static Laplacian* defaultInstance(); ///< Return pointer to global singleton diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index f3fd7fb14e..10147f282e 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -37,8 +37,8 @@ #include "bout/assert.hxx" #include "bout/build_config.hxx" #include "bout/msg_stack.hxx" -#include "bout/unused.hxx" #include "bout/region.hxx" +#include "bout/unused.hxx" #include #include @@ -236,7 +236,7 @@ public: data.ensureUnique(); return *this; } - + inline T& operator()(size_type i1, size_type i2) { ASSERT2(0 <= i1 && i1 < n1); ASSERT2(0 <= i2 && i2 < n2); @@ -405,7 +405,8 @@ bool operator==(const Tensor& lhs, const Tensor& rhs) { /// us to throw due to the matrix being singular (ill conditioned); /// If small is less than zero then instead of throwing we return 1. /// This is ugly but can be used to support some use cases. -template int invert3x3(Matrix &a, BoutReal small = 1.0e-15) { +template +int invert3x3(Matrix& a, BoutReal small = 1.0e-15) { TRACE("invert3x3"); // Calculate the first co-factors @@ -682,8 +683,14 @@ almost_equal(T x, T y, int ulp = 2) { /// Convert pointer or reference to pointer /// This allows consistent handling of both in macros, templates -template T *pointer(T *val) { return val; } -template T *pointer(T &val) { return &val; } +template +T* pointer(T* val) { + return val; +} +template +T* pointer(T& val) { + return &val; +} #ifndef BOUT_CONCAT /// Utility to evaluate and concatenate macro symbols diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx index 02b5cad168..9ff4a69ba8 100644 --- a/include/bout/vector2d.hxx +++ b/include/bout/vector2d.hxx @@ -162,15 +162,14 @@ private: // Non-member overloaded operators -const Vector2D operator*(BoutReal lhs, const Vector2D &rhs); -const Vector2D operator*(const Field2D &lhs, const Vector2D &rhs); -const Vector3D operator*(const Field3D &lhs, const Vector2D &rhs); - +const Vector2D operator*(BoutReal lhs, const Vector2D& rhs); +const Vector2D operator*(const Field2D& lhs, const Vector2D& rhs); +const Vector3D operator*(const Field3D& lhs, const Vector2D& rhs); /// Cross product -const Vector2D cross(const Vector2D & lhs, const Vector2D &rhs); +const Vector2D cross(const Vector2D& lhs, const Vector2D& rhs); /// Cross product -const Vector3D cross(const Vector2D & lhs, const Vector3D &rhs); +const Vector3D cross(const Vector2D& lhs, const Vector3D& rhs); /*! * Absolute value (Modulus) of given vector \p v @@ -180,12 +179,14 @@ const Vector3D cross(const Vector2D & lhs, const Vector3D &rhs); Coordinates::FieldMetric abs(const Vector2D& v, const std::string& region = "RGN_ALL"); /// Transform to and from field-aligned coordinates -inline Vector2D toFieldAligned(Vector2D v, const std::string& UNUSED(region) = "RGN_ALL") { +inline Vector2D toFieldAligned(Vector2D v, + const std::string& UNUSED(region) = "RGN_ALL") { // toFieldAligned is a null operation for the Field2D components of v, so return a copy // of the argument (hence pass-by-value instead of pass-by-reference) return v; } -inline Vector2D fromFieldAligned(Vector2D v, const std::string& UNUSED(region) = "RGN_ALL") { +inline Vector2D fromFieldAligned(Vector2D v, + const std::string& UNUSED(region) = "RGN_ALL") { // fromFieldAligned is a null operation for the Field2D components of v, so return a copy // of the argument (hence pass-by-value instead of pass-by-reference) return v; diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx index 7b9de5482b..f3adf41ae8 100644 --- a/include/bout/vector3d.hxx +++ b/include/bout/vector3d.hxx @@ -50,9 +50,9 @@ class Vector2D; //#include "bout/vector2d.hxx" * a.x; // Error! a.x not allocated * * - */ + */ class Vector3D : public FieldData { - public: +public: /*! * Copy constructor. After this the components (x,y,z) * will refer to the same data as f.(x,y,z) @@ -192,16 +192,15 @@ private: // Non-member overloaded operators -const Vector3D operator*(BoutReal lhs, const Vector3D &rhs); -const Vector3D operator*(const Field2D &lhs, const Vector3D &rhs); -const Vector3D operator*(const Field3D &lhs, const Vector3D &rhs); +const Vector3D operator*(BoutReal lhs, const Vector3D& rhs); +const Vector3D operator*(const Field2D& lhs, const Vector3D& rhs); +const Vector3D operator*(const Field3D& lhs, const Vector3D& rhs); /// Cross-product of two vectors -const Vector3D cross(const Vector3D & lhs, const Vector3D &rhs); +const Vector3D cross(const Vector3D& lhs, const Vector3D& rhs); /// Cross-product of two vectors -const Vector3D cross(const Vector3D & lhs, const Vector2D &rhs); - +const Vector3D cross(const Vector3D& lhs, const Vector2D& rhs); /*! * Absolute magnitude (modulus) of a vector |v| diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index a1fb6bf2b9..68b815823d 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -618,7 +618,7 @@ void Mesh::addRegion3D(const std::string& region_name, const Region<>& region) { regionMap3D[region_name] = id; - output_verbose.write(_("Registered region 3D {:s}"),region_name); + output_verbose.write(_("Registered region 3D {:s}"), region_name); output_verbose << "\n:\t" << region.getStats() << "\n"; } diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index 87dbf110bb..e16b7aa863 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -276,7 +276,8 @@ TEST_F(RegionTest, regionLoopAllSection) { int region_count_helper(Region region) { int count = 0; - BOUT_OMP(parallel) { + BOUT_OMP(parallel) + { BOUT_FOR_OMP(i, region, for reduction(+:count)) { ++count; } From 4f5f52c0f784b3569107710bdbd4a38e2c140121 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Wed, 23 Aug 2023 12:27:31 -0400 Subject: [PATCH 078/412] Add adios2 dependency (BOUT_HAS_ADIOS flag), and starting .hxx file --- CMakeLists.txt | 1 + bout++Config.cmake.in | 1 + cmake/SetupBOUTThirdParty.cmake | 15 + cmake_build_defines.hxx.in | 1 + include/bout/options_adios.hxx | 118 +++++ src/sys/options/options_adios.cxx | 739 ++++++++++++++++++++++++++++++ 6 files changed, 875 insertions(+) create mode 100644 include/bout/options_adios.hxx create mode 100644 src/sys/options/options_adios.cxx diff --git a/CMakeLists.txt b/CMakeLists.txt index 2db9b79528..be6976a079 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -147,6 +147,7 @@ set(BOUT_SOURCES ./include/bout/operatorstencil.hxx ./include/bout/options.hxx ./include/bout/options_netcdf.hxx + ./include/bout/options_adios.hxx ./include/bout/optionsreader.hxx ./include/bout/output.hxx ./include/bout/output_bout_types.hxx diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in index e33e950e6f..3d824e455f 100644 --- a/bout++Config.cmake.in +++ b/bout++Config.cmake.in @@ -15,6 +15,7 @@ set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@) set(BOUT_HAS_PVODE @BOUT_HAS_PVODE@) set(BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@) +set(BOUT_HAS_ADIOS @BOUT_HAS_ADIOS@) set(BOUT_HAS_FFTW @BOUT_HAS_FFTW@) set(BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@) set(BOUT_HAS_PETSC @BOUT_HAS_PETSC@) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 55f201bdad..b5470a2f46 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -185,6 +185,21 @@ endif() message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}") set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF}) +option(BOUT_USE_ADIOS "Enable support for ADIOS output" ON) +if (BOUT_USE_ADIOS) + find_package(ADIOS2) + if (ADIOS2_FOUND) + ENABLE_LANGUAGE(C) + find_package(MPI REQUIRED COMPONENTS C) + target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C) + else() + set(BOUT_USE_ADIOS OFF) + endif() +endif() +message(STATUS "ADIOS support: ${BOUT_USE_ADIOS}") +set(BOUT_HAS_ADIOS ${BOUT_USE_ADIOS}) + + option(BOUT_USE_FFTW "Enable support for FFTW" ON) if (BOUT_USE_FFTW) find_package(FFTW REQUIRED) diff --git a/cmake_build_defines.hxx.in b/cmake_build_defines.hxx.in index a637dbc46a..ed6e8685f6 100644 --- a/cmake_build_defines.hxx.in +++ b/cmake_build_defines.hxx.in @@ -13,6 +13,7 @@ #cmakedefine01 BOUT_HAS_IDA #cmakedefine01 BOUT_HAS_LAPACK #cmakedefine01 BOUT_HAS_NETCDF +#cmakedefine01 BOUT_HAS_ADIOS #cmakedefine01 BOUT_HAS_PETSC #cmakedefine01 BOUT_HAS_PRETTY_FUNCTION #cmakedefine01 BOUT_HAS_PVODE diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx new file mode 100644 index 0000000000..f781d504b5 --- /dev/null +++ b/include/bout/options_adios.hxx @@ -0,0 +1,118 @@ + +#pragma once + +#ifndef __OPTIONS_ADIOS_H__ +#define __OPTIONS_ADIOS_H__ + +#include "bout/build_config.hxx" + +#if !BOUT_HAS_ADIOS + +#include + +#include "bout/boutexception.hxx" +#include "bout/options.hxx" + +namespace bout { + +class OptionsADIOS { +public: + enum class FileMode { + replace, ///< Overwrite file when writing + append ///< Append to file when writing + }; + + OptionsADIOS(const std::string& filename, FileMode mode = FileMode::replace) {} + OptionsADIOS(const OptionsADIOS&) = default; + OptionsADIOS(OptionsADIOS&&) = default; + OptionsADIOS& operator=(const OptionsADIOS&) = default; + OptionsADIOS& operator=(OptionsADIOS&&) = default; + + /// Read options from file + Options read() { throw BoutException("OptionsADIOS not available\n"); } + + /// Write options to file + void write(const Options& options) { + throw BoutException("OptionsADIOS not available\n"); + } +}; + +} // namespace bout + +#else + +#include +#include + +#include "bout/options.hxx" + +/// Forward declare ADIOS file type so we don't need to depend +/// directly on ADIOS +namespace ADIOS { +class BPStream; +} + +namespace bout { + +class OptionsADIOS { +public: + enum class FileMode { + replace, ///< Overwrite file when writing + append ///< Append to file when writing + }; + + // Constructors need to be defined in implementation due to forward + // declaration of NcFile + OptionsADIOS(); + explicit OptionsADIOS(std::string filename, FileMode mode = FileMode::replace); + ~OptionsADIOS(); + OptionsADIOS(const OptionsADIOS&) = delete; + OptionsADIOS(OptionsADIOS&&) noexcept; + OptionsADIOS& operator=(const OptionsADIOS&) = delete; + OptionsADIOS& operator=(OptionsADIOS&&) noexcept; + + /// Read options from file + Options read(); + + /// Write options to file + void write(const Options& options) { write(options, "t"); } + void write(const Options& options, const std::string& time_dim); + + /// Check that all variables with the same time dimension have the + /// same size in that dimension. Throws BoutException if there are + /// any differences, otherwise is silent + void verifyTimesteps() const; + +private: + /// Name of the file on disk + std::string filename; + /// How to open the file for writing + FileMode file_mode{FileMode::replace}; + /// Pointer to ADIOS file so we don't introduce direct dependence + std::unique_ptr data_file; +}; + +} // namespace bout + +#endif + +namespace bout { +/// Name of the directory for restart files +std::string getRestartDirectoryName(Options& options); +/// Name of the restart file on this rank +std::string getRestartFilename(Options& options); +/// Name of the restart file on \p rank +std::string getRestartFilename(Options& options, int rank); +/// Name of the main output file on this rank +std::string getOutputFilename(Options& options); +/// Name of the main output file on \p rank +std::string getOutputFilename(Options& options, int rank); +/// Write `Options::root()` to the main output file, overwriting any +/// existing files +void writeDefaultOutputFile(); +/// Write \p options to the main output file, overwriting any existing +/// files +void writeDefaultOutputFile(Options& options); +} // namespace bout + +#endif // __OPTIONS_ADIOS_H__ diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx new file mode 100644 index 0000000000..6b7b3aea28 --- /dev/null +++ b/src/sys/options/options_adios.cxx @@ -0,0 +1,739 @@ +#include "bout/build_config.hxx" + +#if BOUT_HAS_ADIOS + +#include "bout/options_adios.hxx" + +#include "bout/bout.hxx" +#include "bout/globals.hxx" +#include "bout/mesh.hxx" +#include "bout/sys/timer.hxx" + +#include +#include +#include +#include + +using namespace ADIOS; + +namespace { +/// Name of the attribute used to track individual variable's time indices +constexpr auto current_time_index_name = "current_time_index"; + +/// ADIOS doesn't keep track of the current for each variable +/// (although the underlying HDF5 file does!), so we need to do it +/// ourselves. We'll use an attribute in the file to do so, which +/// means we don't need to keep track of it in the code +int getCurrentTimeIndex(const NcVar& var) { + const auto atts_map = var.getAtts(); + const auto time_index_attribute = atts_map.find(current_time_index_name); + if (time_index_attribute == atts_map.end()) { + // Attribute doesn't exist, so let's start at zero. There + // are various ways this might break, for example, if the + // variable was added to the file by a different + // program. But note, that if we use the size of the time + // dimension here, this will increase every time we add a + // new variable! So zero is probably the only sensible + // choice for this + return 0; + } + int current_time_index; + time_index_attribute->second.getValues(¤t_time_index); + return current_time_index; +} + +template +T readVariable(const NcVar& variable) { + T value; + variable.getVar(&value); + return value; +} + +template +T readAttribute(const NcAtt& attribute) { + T value; + attribute.getValues(&value); + return value; +} + +void readGroup(const std::string& filename, const NcGroup& group, Options& result) { + + // Iterate over all variables + for (const auto& varpair : group.getVars()) { + const auto& var_name = varpair.first; // Name of the variable + const auto& var = varpair.second; // The NcVar object + + auto var_type = var.getType(); // Variable type + auto ndims = var.getDimCount(); // Number of dimensions + auto dims = var.getDims(); // Vector of dimensions + + switch (ndims) { + case 0: { + // Scalar variables + if (var_type == ncDouble) { + result[var_name] = readVariable(var); + } else if (var_type == ncFloat) { + result[var_name] = readVariable(var); + } else if (var_type == ncInt or var_type == ncShort) { + result[var_name] = readVariable(var); + } else if (var_type == ncString) { + result[var_name] = std::string(readVariable(var)); + } + // Note: ADIOS does not support boolean atoms + // else ignore + break; + } + case 1: { + if (var_type == ncDouble or var_type == ncFloat) { + Array value(static_cast(dims[0].getSize())); + var.getVar(value.begin()); + result[var_name] = value; + } else if ((var_type == ncString) or (var_type == ncChar)) { + std::string value; + value.resize(dims[0].getSize()); + var.getVar(&(value[0])); + result[var_name] = value; + } + break; + } + case 2: { + if (var_type == ncDouble or var_type == ncFloat) { + Matrix value(static_cast(dims[0].getSize()), + static_cast(dims[1].getSize())); + var.getVar(value.begin()); + result[var_name] = value; + } + break; + } + case 3: { + if (var_type == ncDouble or var_type == ncFloat) { + Tensor value(static_cast(dims[0].getSize()), + static_cast(dims[1].getSize()), + static_cast(dims[2].getSize())); + var.getVar(value.begin()); + result[var_name] = value; + } + } + } + result[var_name].attributes["source"] = filename; + + // Get variable attributes + for (const auto& attpair : var.getAtts()) { + const auto& att_name = attpair.first; // Attribute name + const auto& att = attpair.second; // NcVarAtt object + + auto att_type = att.getType(); // Type of the attribute + + if (att_type == ncInt) { + result[var_name].attributes[att_name] = readAttribute(att); + } else if (att_type == ncFloat) { + result[var_name].attributes[att_name] = readAttribute(att); + } else if (att_type == ncDouble) { + result[var_name].attributes[att_name] = readAttribute(att); + } else if ((att_type == ncString) or (att_type == ncChar)) { + std::string value; + att.getValues(value); + result[var_name].attributes[att_name] = value; + } + // Else ignore + } + } + + // Iterate over groups + for (const auto& grouppair : group.getGroups()) { + const auto& name = grouppair.first; + const auto& subgroup = grouppair.second; + + readGroup(filename, subgroup, result[name]); + } +} +} // namespace + +namespace bout { + +Options OptionsADIOS::read() { + Timer timer("io"); + + // Open file + const NcFile read_file(filename, NcFile::read); + + if (read_file.isNull()) { + throw BoutException("Could not open ADIOS file '{:s}' for reading", filename); + } + + Options result; + readGroup(filename, read_file, result); + + return result; +} + +} // namespace bout + +namespace { + +/// Convert variant into NcType +/// If the type is not recognised then NcType null object is returned +struct NcTypeVisitor { + template + NcType operator()(const T& UNUSED(t)) { + return {}; // Null object by default + } +}; + +template <> +NcType NcTypeVisitor::operator()(const bool& UNUSED(t)) { + return ncInt; +} + +template <> +NcType NcTypeVisitor::operator()(const int& UNUSED(t)) { + return ncInt; +} + +template <> +NcType NcTypeVisitor::operator()(const double& UNUSED(t)) { + return ncDouble; +} + +template <> +MAYBE_UNUSED() +NcType NcTypeVisitor::operator()(const float& UNUSED(t)) { + return ncFloat; +} + +template <> +NcType NcTypeVisitor::operator()(const std::string& UNUSED(t)) { + return ncString; +} + +template <> +NcType NcTypeVisitor::operator()(const Field2D& UNUSED(t)) { + return operator()(0.0); +} + +template <> +NcType NcTypeVisitor::operator()(const Field3D& UNUSED(t)) { + return operator()(0.0); +} + +template <> +NcType NcTypeVisitor::operator()(const FieldPerp& UNUSED(t)) { + return operator()(0.0); +} + +/// Visit a variant type, returning dimensions +struct NcDimVisitor { + NcDimVisitor(NcGroup& group) : group(group) {} + template + std::vector operator()(const T& UNUSED(value)) { + return {}; + } + +private: + NcGroup& group; +}; + +NcDim findDimension(NcGroup& group, const std::string& name, unsigned int size) { + // Get the dimension + try { + auto dim = group.getDim(name, NcGroup::ParentsAndCurrent); + if (dim.isNull()) { + // Dimension doesn't yet exist + dim = group.addDim(name, size); + } else { + // Dimension exists, check it's the right size + if (dim.getSize() != size) { + // wrong size. Check this group + dim = group.getDim(name, NcGroup::Current); + if (!dim.isNull()) { + // Already defined in this group + return {}; // Return null object + } + // Define in this group + dim = group.addDim(name, size); + } + } + return dim; + } catch (const std::exception& e) { + throw BoutException("Error in findDimension('{:s}'): {:s}", name, e.what()); + } +} + +template <> +std::vector NcDimVisitor::operator()(const Field2D& value) { + auto xdim = findDimension(group, "x", value.getNx()); + ASSERT0(!xdim.isNull()); + + auto ydim = findDimension(group, "y", value.getNy()); + ASSERT0(!ydim.isNull()); + + return {xdim, ydim}; +} + +template <> +std::vector NcDimVisitor::operator()(const Field3D& value) { + auto xdim = findDimension(group, "x", value.getNx()); + ASSERT0(!xdim.isNull()); + + auto ydim = findDimension(group, "y", value.getNy()); + ASSERT0(!ydim.isNull()); + + auto zdim = findDimension(group, "z", value.getNz()); + ASSERT0(!zdim.isNull()); + + return {xdim, ydim, zdim}; +} + +template <> +std::vector NcDimVisitor::operator()(const FieldPerp& value) { + auto xdim = findDimension(group, "x", value.getNx()); + ASSERT0(!xdim.isNull()); + + auto zdim = findDimension(group, "z", value.getNz()); + ASSERT0(!zdim.isNull()); + + return {xdim, zdim}; +} + +/// Visit a variant type, and put the data into a NcVar +struct NcPutVarVisitor { + NcPutVarVisitor(NcVar& var) : var(var) {} + template + void operator()(const T& value) { + var.putVar(&value); + } + +private: + NcVar& var; +}; + +template <> +void NcPutVarVisitor::operator()(const bool& value) { + int int_val = value ? 1 : 0; + var.putVar(&int_val); +} + +template <> +void NcPutVarVisitor::operator()(const std::string& value) { + const char* cstr = value.c_str(); + var.putVar(&cstr); +} + +/// In addition to writing the data, set the "cell_location" attribute +template <> +void NcPutVarVisitor::operator()(const Field2D& value) { + // Pointer to data. Assumed to be contiguous array + var.putVar(&value(0, 0)); +} + +/// In addition to writing the data, set the "cell_location" attribute +template <> +void NcPutVarVisitor::operator()(const Field3D& value) { + // Pointer to data. Assumed to be contiguous array + var.putVar(&value(0, 0, 0)); +} + +template <> +void NcPutVarVisitor::operator()(const FieldPerp& value) { + // Pointer to data. Assumed to be contiguous array + var.putVar(&value(0, 0)); +} + +/// Visit a variant type, and put the data into a NcVar +struct NcPutVarCountVisitor { + NcPutVarCountVisitor(NcVar& var, const std::vector& start, + const std::vector& count) + : var(var), start(start), count(count) {} + template + void operator()(const T& value) { + var.putVar(start, &value); + } + +private: + NcVar& var; + const std::vector& start; ///< Starting (corner) index + const std::vector& count; ///< Index count in each dimension +}; + +template <> +void NcPutVarCountVisitor::operator()(const std::string& value) { + const char* cstr = value.c_str(); + var.putVar(start, &cstr); +} +template <> +void NcPutVarCountVisitor::operator()(const Field2D& value) { + // Pointer to data. Assumed to be contiguous array + var.putVar(start, count, &value(0, 0)); +} +template <> +void NcPutVarCountVisitor::operator()(const Field3D& value) { + // Pointer to data. Assumed to be contiguous array + var.putVar(start, count, &value(0, 0, 0)); +} +template <> +void NcPutVarCountVisitor::operator()(const FieldPerp& value) { + // Pointer to data. Assumed to be contiguous array + var.putVar(start, count, &value(0, 0)); +} + +/// Visit a variant type, and put the data into an attributute +struct NcPutAttVisitor { + NcPutAttVisitor(NcVar& var, std::string name) : var(var), name(std::move(name)) {} + template + void operator()(const T& UNUSED(value)) { + // Default is to ignore if unhandled + } + +private: + NcVar& var; + std::string name; +}; + +template <> +void NcPutAttVisitor::operator()(const bool& value) { + int ival = value ? 1 : 0; + var.putAtt(name, ncInt, ival); +} +template <> +void NcPutAttVisitor::operator()(const int& value) { + var.putAtt(name, ncInt, value); +} +template <> +void NcPutAttVisitor::operator()(const double& value) { + var.putAtt(name, ncDouble, value); +} +template <> +MAYBE_UNUSED() +void NcPutAttVisitor::operator()(const float& value) { + var.putAtt(name, ncFloat, value); +} +template <> +void NcPutAttVisitor::operator()(const std::string& value) { + var.putAtt(name, value); +} + +void writeGroup(const Options& options, NcGroup group, + const std::string& time_dimension) { + + for (const auto& childpair : options.getChildren()) { + const auto& name = childpair.first; + const auto& child = childpair.second; + + if (child.isValue()) { + try { + auto nctype = bout::utils::visit(NcTypeVisitor(), child.value); + + if (nctype.isNull()) { + continue; // Skip this value + } + + // Get spatial dimensions + auto spatial_dims = bout::utils::visit(NcDimVisitor(group), child.value); + + // Vector of all dimensions, including time + std::vector dims{spatial_dims}; + + // Get the time dimension + NcDim time_dim; ///< Time dimension (Null -> none) + auto time_it = child.attributes.find("time_dimension"); + if (time_it != child.attributes.end()) { + // Has a time dimension + + const auto& time_name = bout::utils::get(time_it->second); + + // Only write time-varying values that match current time + // dimension being written + if (time_name != time_dimension) { + continue; + } + + time_dim = group.getDim(time_name, NcGroup::ParentsAndCurrent); + if (time_dim.isNull()) { + time_dim = group.addDim(time_name); + } + + // prepend to vector of dimensions + dims.insert(dims.begin(), time_dim); + } + + // Check if the variable exists + auto var = group.getVar(name); + if (var.isNull()) { + // Variable doesn't exist yet + // Create variable + // Temporary NcType as a workaround for bug in ADIOS 4.4.0 and + // ADIOS-CXX4 4.2.0 + var = group.addVar(name, NcType{group, nctype.getId()}, dims); + if (!time_dim.isNull()) { + // Time evolving variable, so we'll need to keep track of its time index + var.putAtt(current_time_index_name, ncInt, 0); + } + } else { + // Variable does exist + + // Check types are the same + if (var.getType() != nctype) { + throw BoutException( + "Changed type of variable '{:s}'. Was '{:s}', now writing '{:s}'", name, + var.getType().getName(), nctype.getName()); + } + + // Check that the dimensions are correct + auto var_dims = var.getDims(); + + // Same number of dimensions? + if (var_dims.size() != dims.size()) { + throw BoutException( + "Changed dimensions for variable '{:s}'\nIn file has {:d} " + "dimensions, now writing {:d}\n", + name, var_dims.size(), dims.size()); + } + // Dimensions compatible? + for (std::vector::size_type i = 0; i < dims.size(); ++i) { + if (var_dims[i] == dims[i]) { + continue; // The same dimension -> ok + } + if (var_dims[i].isUnlimited() != dims[i].isUnlimited()) { + throw BoutException("Unlimited dimension changed for variable '{:s}'", + name); + } + if (var_dims[i].getSize() != dims[i].getSize()) { + throw BoutException("Dimension size changed for variable '{:s}'", name); + } + } + // All ok. Set dimensions to the variable's NcDims + dims = var_dims; + + if (!time_dim.isNull()) { + // A time dimension + time_dim = dims[0]; + } + } + + // Write the variable + + if (time_dim.isNull()) { + // No time index + + // Put the data into the variable + bout::utils::visit(NcPutVarVisitor(var), child.value); + + } else { + // Has a time index, so need the record index + + const int current_time_index = getCurrentTimeIndex(var); + + std::vector start_index; ///< Starting index where data will be inserted + std::vector count_index; ///< Size of each dimension + + // Dimensions, including time + for (const auto& dim : dims) { + start_index.push_back(0); + count_index.push_back(dim.getSize()); + } + // Time dimension + start_index[0] = current_time_index; + count_index[0] = 1; // Writing one record + + // Put the data into the variable + bout::utils::visit(NcPutVarCountVisitor(var, start_index, count_index), + child.value); + + // We've just written a new time slice, so we need to update + // the attribute to track it + var.putAtt(current_time_index_name, ncInt, current_time_index + 1); + } + + // Write attributes + for (const auto& attribute : child.attributes) { + const std::string& att_name = attribute.first; + const auto& att = attribute.second; + + bout::utils::visit(NcPutAttVisitor(var, att_name), att); + } + + } catch (const std::exception& e) { + throw BoutException("Error while writing value '{:s}' : {:s}", name, e.what()); + } + } + + if (child.isSection()) { + // Check if the group exists + TRACE("Writing group '{:s}'", name); + + auto subgroup = group.getGroup(name); + if (subgroup.isNull()) { + // Doesn't exist yet, so create it + subgroup = group.addGroup(name); + } + + writeGroup(child, subgroup, time_dimension); + } + } +} + +/// Helper struct for returning errors from verifyTimesteps(NcGroup) +struct TimeDimensionError { + std::string variable_name; + std::string time_name; + std::size_t expected_size; + std::size_t current_size; +}; + +std::vector verifyTimesteps(const NcGroup& group) { + + // Map of dimension -> size + std::map seen_time_dimensions; + // Variables with mismatched dimension sizes. Note that this might + // be a little odd: if the first variable we come across has the + // "wrong" dimension size, we will actually list all the others as + // being wrong! + std::vector errors; + + // For each variable, check its time dimension against what we've + // seen already. Note that this assumes a single time dimension per + // variable whose is in the attribute "time_dimension" + for (const auto& varpair : group.getVars()) { + const auto& var_name = varpair.first; // Name of the variable + const auto& var = varpair.second; // The NcVar object + + // Get the name of the time dimension from the attribute + const auto& attributes = var.getAtts(); + const auto time_it = attributes.find("time_dimension"); + if (time_it == attributes.end()) { + // No "time_dimension" attribute so presumably not a + // time-evolving variable + continue; + } + + // Use the attribute value to get the actual dimension + std::string time_name; + time_it->second.getValues(time_name); + const auto time_dim = group.getDim(time_name, NcGroup::ParentsAndCurrent); + + // Check if we've already seen this dimension + auto seen_it = seen_time_dimensions.find(time_dim); + if (seen_it == seen_time_dimensions.end()) { + // If we haven't, add it to the map with current time index + seen_time_dimensions[time_dim] = time_dim.getSize(); + continue; + } + + // If we have, check if the variable current time index matches time size + const auto current_time = static_cast(getCurrentTimeIndex(var)); + if (current_time == time_dim.getSize()) { + continue; + } + // If not, add to list of errors + errors.push_back({var_name, time_dim.getName(), time_dim.getSize(), current_time}); + } + + // Recurse down into subgroups, shoving any new errors into what + // we've already got. Don't bother reserving the new size, this + // shouldn't be big! + for (const auto& child : group.getGroups()) { + auto child_errors = verifyTimesteps(child.second); + errors.insert(errors.end(), child_errors.begin(), child_errors.end()); + } + + return errors; +} + +} // namespace + +namespace bout { + +OptionsADIOS::OptionsADIOS() : data_file(nullptr) {} + +OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) + : filename(std::move(filename)), file_mode(mode), data_file(nullptr) {} + +OptionsADIOS::~OptionsADIOS() = default; +OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; +OptionsADIOS& OptionsADIOS::operator=(OptionsADIOS&&) noexcept = default; + +void OptionsADIOS::verifyTimesteps() const { + NcFile dataFile(filename, NcFile::read); + auto errors = ::verifyTimesteps(dataFile); + + if (errors.empty()) { + // No errors + return; + } + + std::string error_string; + for (const auto& error : errors) { + error_string += fmt::format( + " variable: {}; dimension: {}; expected size: {}; actual size: {}\n", + error.variable_name, error.time_name, error.expected_size, error.current_size); + } + throw BoutException("ERROR: When checking timesteps in file '{}', some ({}) variables " + "did not have the expected size(s):\n{}", + filename, errors.size(), error_string); +} + +/// Write options to file +void OptionsADIOS::write(const Options& options, const std::string& time_dim) { + Timer timer("io"); + + // Check the file mode to use + auto ncmode = NcFile::replace; + if (file_mode == FileMode::append) { + // ADIOS doesn't have a "read-write, create if exists" mode, so + // we need to check ourselves if the file already exists; if it + // doesn't, tell ADIOS to create it + std::ifstream file(filename); + ncmode = file.good() ? NcFile::FileMode::write : NcFile::FileMode::newFile; + } + + if (not data_file) { + data_file = std::make_unique(filename, ncmode); + } + + if (data_file->isNull()) { + throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); + } + + writeGroup(options, *data_file, time_dim); + + data_file->sync(); +} + +std::string getRestartDirectoryName(Options& options) { + if (options["restartdir"].isSet()) { + // Solver-specific restart directory + return options["restartdir"].withDefault("data"); + } + // Use the root data directory + return options["datadir"].withDefault("data"); +} + +std::string getRestartFilename(Options& options) { + return getRestartFilename(options, BoutComm::rank()); +} + +std::string getRestartFilename(Options& options, int rank) { + return fmt::format("{}/BOUT.restart.{}.nc", bout::getRestartDirectoryName(options), + rank); +} + +std::string getOutputFilename(Options& options) { + return getOutputFilename(options, BoutComm::rank()); +} + +std::string getOutputFilename(Options& options, int rank) { + return fmt::format("{}/BOUT.dmp.{}.nc", + options["datadir"].withDefault("data"), rank); +} + +void writeDefaultOutputFile() { writeDefaultOutputFile(Options::root()); } + +void writeDefaultOutputFile(Options& options) { + bout::experimental::addBuildFlagsToOptions(options); + bout::globals::mesh->outputVars(options); + OptionsADIOS(getOutputFilename(Options::root())).write(options); +} + +} // namespace bout + +#endif // BOUT_HAS_ADIOS From 0fa73d6ec40deab6fcb1943582c1d170c06edf06 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Fri, 1 Sep 2023 15:33:27 -0400 Subject: [PATCH 079/412] Added adios_object.* files to initialize/finalize adios (in BoutInitialise/BoutFinalise) --- CMakeLists.txt | 3 ++ include/bout/adios_object.hxx | 53 ++++++++++++++++++++ include/bout/build_config.hxx | 1 + src/bout++.cxx | 18 ++++++- src/sys/adios_object.cxx | 92 +++++++++++++++++++++++++++++++++++ 5 files changed, 165 insertions(+), 2 deletions(-) create mode 100755 include/bout/adios_object.hxx create mode 100755 src/sys/adios_object.cxx diff --git a/CMakeLists.txt b/CMakeLists.txt index be6976a079..9d239afa0e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -83,6 +83,7 @@ function(bout_update_submodules) endfunction() set(BOUT_SOURCES + ./include/bout/adios_object.hxx ./include/bout/array.hxx ./include/bout/assert.hxx ./include/bout/boundary_factory.hxx @@ -326,6 +327,7 @@ set(BOUT_SOURCES ./src/solver/impls/split-rk/split-rk.cxx ./src/solver/impls/split-rk/split-rk.hxx ./src/solver/solver.cxx + ./src/sys/adios_object.cxx ./src/sys/bout_types.cxx ./src/sys/boutcomm.cxx ./src/sys/boutexception.cxx @@ -931,6 +933,7 @@ message(" SUNDIALS support : ${BOUT_HAS_SUNDIALS} HYPRE support : ${BOUT_HAS_HYPRE} NetCDF support : ${BOUT_HAS_NETCDF} + ADIOS support : ${BOUT_HAS_ADIOS} FFTW support : ${BOUT_HAS_FFTW} LAPACK support : ${BOUT_HAS_LAPACK} OpenMP support : ${BOUT_USE_OPENMP} diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx new file mode 100755 index 0000000000..058aa030c3 --- /dev/null +++ b/include/bout/adios_object.hxx @@ -0,0 +1,53 @@ +#ifndef ADIOS_OBJECT_HXX +#define ADIOS_OBJECT_HXX + +#include "bout/build_config.hxx" + +#if BOUT_HAS_ADIOS + +#include +#include +#include + +namespace bout { + +void ADIOSInit(MPI_Comm comm); +void ADIOSInit(const std::string configFile, MPI_Comm comm); +void ADIOSFinalize(); + +using ADIOSPtr = std::shared_ptr; +using EnginePtr = std::shared_ptr; +using IOPtr = std::shared_ptr; + +ADIOSPtr GetADIOSPtr(); +IOPtr GetIOPtr(const std::string IOName); + +struct ADIOSStruct { + adios2::IO io; + adios2::Engine engine; + adios2::Variable vCellDim, vPhysDim, vNTotalElem, vNTotalNode; + adios2::Variable vPhysTime; + adios2::Variable vStep; + adios2::Variable vElementConnectivity, vElementRange; + adios2::Variable vXco, vYco, vZco; + std::vector> vFlowVars; + std::vector> vBoundariesConnectivity; + std::vector> vBoundariesRange; + int adiosStep = 0; +}; + +extern ADIOSStruct adios_restart; +extern ADIOSStruct adios_dump; +//extern ADIOS2Param *adios2params; + +/** return one of the extern variable based on the target file name */ +ADIOSStruct& ADIOSGetStruct(const std::string& fname); + +/** Set user parameters for an IO group */ +void ADIOSSetParameters(const std::string& input, const char delimKeyValue, + const char delimItem, adios2::IO& io); + +} // namespace bout + +#endif //BOUT_HAS_ADIOS +#endif //ADIOS_OBJECT_HXX diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx index a98c615c77..c97962f7cf 100644 --- a/include/bout/build_config.hxx +++ b/include/bout/build_config.hxx @@ -17,6 +17,7 @@ constexpr auto has_gettext = static_cast(BOUT_HAS_GETTEXT); constexpr auto has_lapack = static_cast(BOUT_HAS_LAPACK); constexpr auto has_legacy_netcdf = static_cast(BOUT_HAS_LEGACY_NETCDF); constexpr auto has_netcdf = static_cast(BOUT_HAS_NETCDF); +constexpr auto has_adios = static_cast(BOUT_HAS_ADIOS); constexpr auto has_petsc = static_cast(BOUT_HAS_PETSC); constexpr auto has_hypre = static_cast(BOUT_HAS_HYPRE); constexpr auto has_umpire = static_cast(BOUT_HAS_UMPIRE); diff --git a/src/bout++.cxx b/src/bout++.cxx index 7d7b38b947..6de8798622 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -59,6 +59,10 @@ const char DEFAULT_DIR[] = "data"; #include "bout/bout.hxx" #undef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS +#if BOUT_HAS_ADIOS +#include "bout/adios_object.hxx" +#endif + #include #include @@ -161,6 +165,10 @@ int BoutInitialise(int& argc, char**& argv) { savePIDtoFile(args.data_dir, MYPE); +#if BOUT_HAS_ADIOS + bout::ADIOSInit(BoutComm::get()); +#endif + // Print the different parts of the startup info printStartupHeader(MYPE, BoutComm::size()); printCompileTimeOptions(); @@ -564,6 +572,7 @@ void printCompileTimeOptions() { constexpr auto netcdf_flavour = has_netcdf ? (has_legacy_netcdf ? " (Legacy)" : " (NetCDF4)") : ""; output_info.write(_("\tNetCDF support {}{}\n"), is_enabled(has_netcdf), netcdf_flavour); + output_info.write(_("\tADIOS support {}\n"), is_enabled(has_adios)); output_info.write(_("\tPETSc support {}\n"), is_enabled(has_petsc)); output_info.write(_("\tPretty function name support {}\n"), is_enabled(has_pretty_function)); @@ -641,7 +650,7 @@ void setupOutput(const std::string& data_dir, const std::string& log_file, int v { Output& output = *Output::getInstance(); if (MYPE == 0) { - output.enable(); // Enable writing to stdout + output.enable(); // Enable writing to stdout } else { output.disable(); // No writing to stdout } @@ -692,6 +701,7 @@ void addBuildFlagsToOptions(Options& options) { options["has_gettext"].force(bout::build::has_gettext); options["has_lapack"].force(bout::build::has_lapack); options["has_netcdf"].force(bout::build::has_netcdf); + options["has_adios"].force(bout::build::has_adios); options["has_petsc"].force(bout::build::has_petsc); options["has_hypre"].force(bout::build::has_hypre); options["has_umpire"].force(bout::build::has_umpire); @@ -787,6 +797,10 @@ int BoutFinalise(bool write_settings) { // Call HYPER_Finalize if not already called bout::HypreLib::cleanup(); +#if BOUT_HAS_ADIOS + bout::ADIOSFinalize(); +#endif + // MPI communicator, including MPI_Finalize() BoutComm::cleanup(); @@ -1042,6 +1056,6 @@ void RunMetrics::writeProgress(BoutReal simtime, bool output_split) { 100. * wtime_comms / wtime, // Communications 100. * wtime_io / wtime, // I/O 100. * (wtime - wtime_io - wtime_rhs) - / wtime); // Everything else + / wtime); // Everything else } } diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx new file mode 100755 index 0000000000..5bab7545e9 --- /dev/null +++ b/src/sys/adios_object.cxx @@ -0,0 +1,92 @@ +#include "bout/build_config.hxx" + +#if BOUT_HAS_ADIOS + +#include "bout/adios_object.hxx" + +#include +#include +#include + +namespace bout { + +static ADIOSPtr adios = nullptr; +ADIOSStruct adios_restart; +ADIOSStruct adios_dump; +//ADIOS2Param* adios2params; + +void ADIOSInit(MPI_Comm comm) { adios = std::make_shared(comm); } + +void ADIOSInit(const std::string configFile, MPI_Comm comm) { + adios = std::make_shared(configFile, comm); +} + +void ADIOSFinalize() { + if (adios == nullptr) { + throw std::runtime_error( + "ADIOS needs to be initialized first before calling ADIOSFinalize()"); + } + if (adios_dump.adiosStep > 0 && adios_dump.engine) { + adios_dump.engine.Close(); + } + adios.reset(); +} + +ADIOSPtr GetADIOSPtr() { + if (adios == nullptr) { + throw std::runtime_error( + "ADIOS needs to be initialized first before calling GetADIOSPtr()"); + } + return adios; +} + +IOPtr GetIOPtr(const std::string IOName) { + auto adios = GetADIOSPtr(); + IOPtr io = nullptr; + try { + io = std::make_shared(adios->AtIO(IOName)); + } catch (std::invalid_argument& e) { + } + return io; +} + +ADIOSStruct& ADIOSGetStruct(const std::string& fname) { + if (fname.find(".restart") != std::string::npos) + return adios_restart; + //if (fname.find(".dmp") != std::string::npos) + // return adios_dump; + return adios_dump; +} + +void ADIOSSetParameters(const std::string& input, const char delimKeyValue, + const char delimItem, adios2::IO& io) { + auto lf_Trim = [](std::string& input) { + input.erase(0, input.find_first_not_of(" \n\r\t")); // prefixing spaces + input.erase(input.find_last_not_of(" \n\r\t") + 1); // suffixing spaces + }; + + std::istringstream inputSS(input); + std::string parameter; + while (std::getline(inputSS, parameter, delimItem)) { + const size_t position = parameter.find(delimKeyValue); + if (position == parameter.npos) { + throw std::invalid_argument("ADIOSSetParameters(): wrong format for IO parameter " + + parameter + ", format must be key" + delimKeyValue + + "value for each entry"); + } + + std::string key = parameter.substr(0, position); + lf_Trim(key); + std::string value = parameter.substr(position + 1); + lf_Trim(value); + if (value.length() == 0) { + throw std::invalid_argument("ADIOS2SetParameters: empty value in IO parameter " + + parameter + ", format must be key" + delimKeyValue + + "value"); + } + io.SetParameter(key, value); + } +} + +} // namespace bout +#endif //BOUT_HAS_ADIOS From 0769805846100bd891a95bf5172cdb65f67392fc Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Tue, 5 Sep 2023 07:01:23 -0400 Subject: [PATCH 080/412] fix include of adios --- src/sys/options/options_adios.cxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 6b7b3aea28..72514bc676 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -1,6 +1,6 @@ #include "bout/build_config.hxx" -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS #include "bout/options_adios.hxx" @@ -9,9 +9,9 @@ #include "bout/mesh.hxx" #include "bout/sys/timer.hxx" +#include "adios2.h" #include #include -#include #include using namespace ADIOS; From 58aeacdb6040c404b174017552bffd3f306707bc Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Tue, 5 Sep 2023 13:54:20 -0400 Subject: [PATCH 081/412] Introduce OptionsIO as parent virtual class of OptionsNetCDF/OptionsADIOS. ADIOS code does not compile yet. --- CMakeLists.txt | 3 + include/bout/options_adios.hxx | 34 +- include/bout/options_io.hxx | 108 ++++++ include/bout/options_netcdf.hxx | 19 -- include/bout/physicsmodel.hxx | 6 +- src/physics/physicsmodel.cxx | 47 ++- src/sys/options/options_adios.cxx | 531 +++++++---------------------- src/sys/options/options_io.cxx | 99 ++++++ src/sys/options/options_netcdf.cxx | 35 -- 9 files changed, 365 insertions(+), 517 deletions(-) create mode 100644 include/bout/options_io.hxx create mode 100644 src/sys/options/options_io.cxx diff --git a/CMakeLists.txt b/CMakeLists.txt index 9d239afa0e..a580aa9f6d 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -147,6 +147,7 @@ set(BOUT_SOURCES ./include/bout/openmpwrap.hxx ./include/bout/operatorstencil.hxx ./include/bout/options.hxx + ./include/bout/options_io.hxx ./include/bout/options_netcdf.hxx ./include/bout/options_adios.hxx ./include/bout/optionsreader.hxx @@ -341,7 +342,9 @@ set(BOUT_SOURCES ./src/sys/options/optionparser.hxx ./src/sys/options/options_ini.cxx ./src/sys/options/options_ini.hxx + ./src/sys/options/options_io.cxx ./src/sys/options/options_netcdf.cxx + ./src/sys/options/options_adios.cxx ./src/sys/optionsreader.cxx ./src/sys/output.cxx ./src/sys/petsclib.cxx diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index f781d504b5..ec6c26a432 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -6,7 +6,7 @@ #include "bout/build_config.hxx" -#if !BOUT_HAS_ADIOS +#if !BOUT_HAS_ADIOS #include @@ -44,15 +44,14 @@ public: #include #include +#include "bout/adios_object.hxx" #include "bout/options.hxx" +namespace bout { + /// Forward declare ADIOS file type so we don't need to depend /// directly on ADIOS -namespace ADIOS { -class BPStream; -} - -namespace bout { +struct ADIOSStream; class OptionsADIOS { public: @@ -89,30 +88,11 @@ private: /// How to open the file for writing FileMode file_mode{FileMode::replace}; /// Pointer to ADIOS file so we don't introduce direct dependence - std::unique_ptr data_file; + std::unique_ptr data_file; }; } // namespace bout -#endif - -namespace bout { -/// Name of the directory for restart files -std::string getRestartDirectoryName(Options& options); -/// Name of the restart file on this rank -std::string getRestartFilename(Options& options); -/// Name of the restart file on \p rank -std::string getRestartFilename(Options& options, int rank); -/// Name of the main output file on this rank -std::string getOutputFilename(Options& options); -/// Name of the main output file on \p rank -std::string getOutputFilename(Options& options, int rank); -/// Write `Options::root()` to the main output file, overwriting any -/// existing files -void writeDefaultOutputFile(); -/// Write \p options to the main output file, overwriting any existing -/// files -void writeDefaultOutputFile(Options& options); -} // namespace bout +#endif // BOUT_HAS_ADIOS #endif // __OPTIONS_ADIOS_H__ diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx new file mode 100644 index 0000000000..1a51a2bebb --- /dev/null +++ b/include/bout/options_io.hxx @@ -0,0 +1,108 @@ +/* Parent class for IO/ADIOS option classes */ + +#pragma once + +#ifndef __OPTIONS_IO_H__ +#define __OPTIONS_IO_H__ + +#include "bout/build_config.hxx" + +#include +#include + +#include "bout/options.hxx" + +#if BOUT_HAS_ADIOS +#include "bout/options_adios.hxx" +#endif +#if BOUT_HAS_NETCDF +#include "bout/options_netcdf.hxx" +#endif + +namespace bout { + +class OptionsIO { +public: + enum class FileMode { + replace, ///< Overwrite file when writing + append ///< Append to file when writing + }; + + enum class Library { +#if BOUT_HAS_ADIOS + ADIOS, +#endif +#if BOUT_HAS_NETCDF + NetCDF, +#endif + Invalid + }; + + static const Library defaultIOLibrary = +#if BOUT_HAS_ADIOS + Library::ADIOS; +#elif BOUT_HAS_NETCDF + Library::NetCDF; +#else + Library::Invalid; +#endif + + OptionsIO(); + explicit OptionsIO(std::string filename, FileMode mode = FileMode::replace); + ~OptionsIO(); + OptionsIO(const OptionsIO&) = delete; + OptionsIO(OptionsIO&&) noexcept; + OptionsIO& operator=(const OptionsIO&) = delete; + OptionsIO& operator=(OptionsIO&&) noexcept; + + /// Read options from file + virtual Options read() = 0; + + /// Write options to file + void write(const Options& options) { write(options, "t"); } + virtual void write(const Options& options, const std::string& time_dim) = 0; + + /// Check that all variables with the same time dimension have the + /// same size in that dimension. Throws BoutException if there are + /// any differences, otherwise is silent + virtual void verifyTimesteps() const = 0; + +private: + /// Name of the file on disk + std::string filename; + /// How to open the file for writing + FileMode file_mode{FileMode::replace}; + Library library = Library::Invalid; +}; + +std::shared_ptr +OptionsIOFactory(std::string filename, + OptionsIO::FileMode mode = OptionsIO::FileMode::replace, + const OptionsIO::Library library = OptionsIO::defaultIOLibrary); + +OptionsIO::Library getIOLibrary(Options& options); + +/// Name of the directory for restart files +std::string getRestartDirectoryName(Options& options); +/// Name of the restart file on this rank +std::string getRestartFilename(Options& options, const OptionsIO::Library library); +/// Name of the restart file on \p rank +std::string getRestartFilename(Options& options, int rank, + const OptionsIO::Library library); +/// Name of the main output file on this rank +std::string getOutputFilename(Options& options, const OptionsIO::Library library); +/// Name of the main output file on \p rank +std::string getOutputFilename(Options& options, int rank, + const OptionsIO::Library library); +/// Write `Options::root()` to the main output file, overwriting any +/// existing files +void writeDefaultOutputFile( + const OptionsIO::Library library = OptionsIO::defaultIOLibrary); +/// Write \p options to the main output file, overwriting any existing +/// files +void writeDefaultOutputFile( + Options& options, const OptionsIO::Library library = OptionsIO::defaultIOLibrary); + +} // namespace bout + +#endif // __OPTIONS_IO_H__ diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index 2fdb71c6d4..d633596fbd 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -96,23 +96,4 @@ private: #endif -namespace bout { -/// Name of the directory for restart files -std::string getRestartDirectoryName(Options& options); -/// Name of the restart file on this rank -std::string getRestartFilename(Options& options); -/// Name of the restart file on \p rank -std::string getRestartFilename(Options& options, int rank); -/// Name of the main output file on this rank -std::string getOutputFilename(Options& options); -/// Name of the main output file on \p rank -std::string getOutputFilename(Options& options, int rank); -/// Write `Options::root()` to the main output file, overwriting any -/// existing files -void writeDefaultOutputFile(); -/// Write \p options to the main output file, overwriting any existing -/// files -void writeDefaultOutputFile(Options& options); -} // namespace bout - #endif // __OPTIONS_NETCDF_H__ diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index a9a7d7344d..eb1bae8ae1 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -42,7 +42,7 @@ class PhysicsModel; #include "bout/macro_for_each.hxx" #include "bout/msg_stack.hxx" #include "bout/options.hxx" -#include "bout/options_netcdf.hxx" +#include "bout/options_io.hxx" #include "bout/sys/variant.hxx" #include "bout/unused.hxx" #include "bout/utils.hxx" @@ -383,13 +383,13 @@ private: /// State for outputs Options output_options; /// File to write the outputs to - bout::OptionsNetCDF output_file; + std::shared_ptr output_file; /// Should we write output files bool output_enabled{true}; /// Stores the state for restarting Options restart_options; /// File to write the restart-state to - bout::OptionsNetCDF restart_file; + std::shared_ptr restart_file; /// Should we write restart files bool restart_enabled{true}; /// Split operator model? diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx index cac4bda5cc..e0658b77bb 100644 --- a/src/physics/physicsmodel.cxx +++ b/src/physics/physicsmodel.cxx @@ -73,20 +73,31 @@ bool DataFileFacade::write() { } // namespace bout PhysicsModel::PhysicsModel() - : mesh(bout::globals::mesh), - output_file(bout::getOutputFilename(Options::root()), - Options::root()["append"] - .doc("Add output data to existing (dump) files?") - .withDefault(false) - ? bout::OptionsNetCDF::FileMode::append - : bout::OptionsNetCDF::FileMode::replace), - output_enabled(Options::root()["output"]["enabled"] - .doc("Write output files") - .withDefault(true)), - restart_file(bout::getRestartFilename(Options::root())), + : mesh(bout::globals::mesh), output_enabled(Options::root()["output"]["enabled"] + .doc("Write output files") + .withDefault(true)), restart_enabled(Options::root()["restart_files"]["enabled"] .doc("Write restart files") - .withDefault(true)) {} + .withDefault(true)) + +{ + bout::OptionsIO::Library iolibrary = bout::getIOLibrary(Options::root()); + if (output_enabled) { + std::string outputFileName = bout::getOutputFilename(Options::root(), iolibrary); + auto mode = Options::root()["append"] + .doc("Add output data to existing (dump) files?") + .withDefault(false) + ? bout::OptionsIO::FileMode::append + : bout::OptionsIO::FileMode::replace; + output_file = bout::OptionsIOFactory(outputFileName, mode, iolibrary); + } + + if (restart_enabled) { + std::string restartFileName = bout::getRestartFilename(Options::root(), iolibrary); + restart_file = bout::OptionsIOFactory(restartFileName, + bout::OptionsIO::FileMode::replace, iolibrary); + } +} void PhysicsModel::initialise(Solver* s) { if (initialised) { @@ -104,7 +115,7 @@ void PhysicsModel::initialise(Solver* s) { const bool restarting = Options::root()["restart"].withDefault(false); if (restarting) { - restart_options = restart_file.read(); + restart_options = restart_file->read(); } // Call user init code to specify evolving variables @@ -187,7 +198,7 @@ int PhysicsModel::postInit(bool restarting) { restart_options["BOUT_VERSION"].force(bout::version::as_double, "PhysicsModel"); // Write _everything_ to restart file - restart_file.write(restart_options); + restart_file->write(restart_options); } // Add monitor to the solver which calls restart.write() and @@ -219,7 +230,7 @@ void PhysicsModel::restartVars(Options& options) { void PhysicsModel::writeRestartFile() { if (restart_enabled) { - restart_file.write(restart_options); + restart_file->write(restart_options); } } @@ -227,20 +238,20 @@ void PhysicsModel::writeOutputFile() { writeOutputFile(output_options); } void PhysicsModel::writeOutputFile(const Options& options) { if (output_enabled) { - output_file.write(options, "t"); + output_file->write(options, "t"); } } void PhysicsModel::writeOutputFile(const Options& options, const std::string& time_dimension) { if (output_enabled) { - output_file.write(options, time_dimension); + output_file->write(options, time_dimension); } } void PhysicsModel::finishOutputTimestep() const { if (output_enabled) { - output_file.verifyTimesteps(); + output_file->verifyTimesteps(); } } diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 72514bc676..518a8fa7ed 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -14,402 +14,139 @@ #include #include -using namespace ADIOS; +namespace bout { + +struct ADIOSStream { + adios2::IO io; + adios2::Engine engine; + adios2::Variable vStep; + adios2::Variable vTime; + int adiosStep = 0; +}; -namespace { /// Name of the attribute used to track individual variable's time indices constexpr auto current_time_index_name = "current_time_index"; -/// ADIOS doesn't keep track of the current for each variable -/// (although the underlying HDF5 file does!), so we need to do it -/// ourselves. We'll use an attribute in the file to do so, which -/// means we don't need to keep track of it in the code -int getCurrentTimeIndex(const NcVar& var) { - const auto atts_map = var.getAtts(); - const auto time_index_attribute = atts_map.find(current_time_index_name); - if (time_index_attribute == atts_map.end()) { - // Attribute doesn't exist, so let's start at zero. There - // are various ways this might break, for example, if the - // variable was added to the file by a different - // program. But note, that if we use the size of the time - // dimension here, this will increase every time we add a - // new variable! So zero is probably the only sensible - // choice for this - return 0; +template +bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, + const std::string& type, Options& result) { + bool ret = false; + std::vector data; + adios2::Variable variable = io.InquireVariable(name); + + if (variable.ShapeID() == adios2::ShapeID::GlobalValue) { + T value; + io.Get(variable, &value, adios2::Mode::Sync); + result[name] = value; + return true; } - int current_time_index; - time_index_attribute->second.getValues(¤t_time_index); - return current_time_index; -} -template -T readVariable(const NcVar& variable) { - T value; - variable.getVar(&value); - return value; -} + if (variable.ShapeID() == adios2::ShapeID::LocalArray) { + if (!rank) + std::cout << " LocalArray not supported" << std::endl; + return ret; + } -template -T readAttribute(const NcAtt& attribute) { - T value; - attribute.getValues(&value); - return value; -} + auto dims = variable.Shape(); + auto ndim = shape.size(); -void readGroup(const std::string& filename, const NcGroup& group, Options& result) { + switch (ndims) { + case 1: { + Array value(static_cast(dims[0])); + io.Get(variable, value.data(), adios2::Mode::Sync); + result[name] = value; + } + case 2: { + Matrix value(static_cast(dims[0].getSize()), + static_cast(dims[1].getSize())); + io.Get(variable, value.data(), adios2::Mode::Sync); + result[name] = value; + } + case 3: { + Tensor value(static_cast(dims[0].getSize()), + static_cast(dims[1].getSize()), + static_cast(dims[2].getSize())); + io.Get(variable, value.data(), adios2::Mode::Sync); + result[name] = value; + } + } - // Iterate over all variables - for (const auto& varpair : group.getVars()) { - const auto& var_name = varpair.first; // Name of the variable - const auto& var = varpair.second; // The NcVar object + if (!rank) + std::cout << " array has " << variable.Steps() << " steps" << std::endl; - auto var_type = var.getType(); // Variable type - auto ndims = var.getDimCount(); // Number of dimensions - auto dims = var.getDims(); // Vector of dimensions - - switch (ndims) { - case 0: { - // Scalar variables - if (var_type == ncDouble) { - result[var_name] = readVariable(var); - } else if (var_type == ncFloat) { - result[var_name] = readVariable(var); - } else if (var_type == ncInt or var_type == ncShort) { - result[var_name] = readVariable(var); - } else if (var_type == ncString) { - result[var_name] = std::string(readVariable(var)); - } - // Note: ADIOS does not support boolean atoms - // else ignore - break; - } - case 1: { - if (var_type == ncDouble or var_type == ncFloat) { - Array value(static_cast(dims[0].getSize())); - var.getVar(value.begin()); - result[var_name] = value; - } else if ((var_type == ncString) or (var_type == ncChar)) { - std::string value; - value.resize(dims[0].getSize()); - var.getVar(&(value[0])); - result[var_name] = value; - } - break; - } - case 2: { - if (var_type == ncDouble or var_type == ncFloat) { - Matrix value(static_cast(dims[0].getSize()), - static_cast(dims[1].getSize())); - var.getVar(value.begin()); - result[var_name] = value; - } - break; - } - case 3: { - if (var_type == ncDouble or var_type == ncFloat) { - Tensor value(static_cast(dims[0].getSize()), - static_cast(dims[1].getSize()), - static_cast(dims[2].getSize())); - var.getVar(value.begin()); - result[var_name] = value; - } - } - } - result[var_name].attributes["source"] = filename; - - // Get variable attributes - for (const auto& attpair : var.getAtts()) { - const auto& att_name = attpair.first; // Attribute name - const auto& att = attpair.second; // NcVarAtt object + /* Need to read the data here */ + result[name] = data.data(); + return ret; +} - auto att_type = att.getType(); // Type of the attribute - - if (att_type == ncInt) { - result[var_name].attributes[att_name] = readAttribute(att); - } else if (att_type == ncFloat) { - result[var_name].attributes[att_name] = readAttribute(att); - } else if (att_type == ncDouble) { - result[var_name].attributes[att_name] = readAttribute(att); - } else if ((att_type == ncString) or (att_type == ncChar)) { - std::string value; - att.getValues(value); - result[var_name].attributes[att_name] = value; - } - // Else ignore - } +bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, + const std::string& type, Options& result) { + bool ret; +#define declare_template_instantiation(T) \ + if (type == adios2::GetType()) { \ + ret = readVariable(reader, io, name, type, result); \ } - - // Iterate over groups - for (const auto& grouppair : group.getGroups()) { - const auto& name = grouppair.first; - const auto& subgroup = grouppair.second; - - readGroup(filename, subgroup, result[name]); + ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) +#undef declare_template_instantiation + return ret; +} + +bool readAttribute(adios2::Engine& reader, adios2::IO& io, const std::string& name, + const std::string& type, Options& result) { + bool ret; +#define declare_template_instantiation(T) \ + if (type == adios2::GetType()) { \ + adios2::Attribute a = io.InquireAtrribute(name); \ + result[name] = a.Data().data(); \ } -} -} // namespace + ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) +#undef declare_template_instantiation + return ret; +} // namespace bout -namespace bout { +void readGroup(const std::string& filename, ADIOSStruct& group, Options& result) {} Options OptionsADIOS::read() { Timer timer("io"); // Open file - const NcFile read_file(filename, NcFile::read); + ADIOSPtr adiosp = GetADIOSPtr(); + adios2::IO io; + try { + io = adiosp->AtIO(filename); + } catch (const std::invalid_argument& e) { + std::cerr << e.what() << '\n'; + io = adiosp->DeclareIO(filename); + } - if (read_file.isNull()) { + adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess); + if (!reader) { throw BoutException("Could not open ADIOS file '{:s}' for reading", filename); } Options result; - readGroup(filename, read_file, result); - - return result; -} - -} // namespace bout - -namespace { - -/// Convert variant into NcType -/// If the type is not recognised then NcType null object is returned -struct NcTypeVisitor { - template - NcType operator()(const T& UNUSED(t)) { - return {}; // Null object by default - } -}; - -template <> -NcType NcTypeVisitor::operator()(const bool& UNUSED(t)) { - return ncInt; -} - -template <> -NcType NcTypeVisitor::operator()(const int& UNUSED(t)) { - return ncInt; -} -template <> -NcType NcTypeVisitor::operator()(const double& UNUSED(t)) { - return ncDouble; -} - -template <> -MAYBE_UNUSED() -NcType NcTypeVisitor::operator()(const float& UNUSED(t)) { - return ncFloat; -} - -template <> -NcType NcTypeVisitor::operator()(const std::string& UNUSED(t)) { - return ncString; -} - -template <> -NcType NcTypeVisitor::operator()(const Field2D& UNUSED(t)) { - return operator()(0.0); -} - -template <> -NcType NcTypeVisitor::operator()(const Field3D& UNUSED(t)) { - return operator()(0.0); -} - -template <> -NcType NcTypeVisitor::operator()(const FieldPerp& UNUSED(t)) { - return operator()(0.0); -} + // Iterate over all variables + for (const auto& varpair : io.AvailableVariables()) { + const auto& var_name = varpair.first; // Name of the variable -/// Visit a variant type, returning dimensions -struct NcDimVisitor { - NcDimVisitor(NcGroup& group) : group(group) {} - template - std::vector operator()(const T& UNUSED(value)) { - return {}; - } + auto it = varpair.second.find("Type"); + const std::string& var_type = it->second; + readVariable(reader, io, var_name, var_type, result); -private: - NcGroup& group; -}; + result[var_name].attributes["source"] = filename; -NcDim findDimension(NcGroup& group, const std::string& name, unsigned int size) { - // Get the dimension - try { - auto dim = group.getDim(name, NcGroup::ParentsAndCurrent); - if (dim.isNull()) { - // Dimension doesn't yet exist - dim = group.addDim(name, size); - } else { - // Dimension exists, check it's the right size - if (dim.getSize() != size) { - // wrong size. Check this group - dim = group.getDim(name, NcGroup::Current); - if (!dim.isNull()) { - // Already defined in this group - return {}; // Return null object - } - // Define in this group - dim = group.addDim(name, size); - } + // Get variable attributes + for (const auto& attpair : io.AvailableAttributes(var_name, "/", true)) { + const auto& att_name = attpair.first; // Attribute name + const auto& att = attpair.second; // NcVarAtt object + auto it = attpair.second.find("Type"); + const std::string& att_type = it->second; + readAttribute(reader, io, att_name, att_type, result); } - return dim; - } catch (const std::exception& e) { - throw BoutException("Error in findDimension('{:s}'): {:s}", name, e.what()); - } -} - -template <> -std::vector NcDimVisitor::operator()(const Field2D& value) { - auto xdim = findDimension(group, "x", value.getNx()); - ASSERT0(!xdim.isNull()); - - auto ydim = findDimension(group, "y", value.getNy()); - ASSERT0(!ydim.isNull()); - - return {xdim, ydim}; -} - -template <> -std::vector NcDimVisitor::operator()(const Field3D& value) { - auto xdim = findDimension(group, "x", value.getNx()); - ASSERT0(!xdim.isNull()); - - auto ydim = findDimension(group, "y", value.getNy()); - ASSERT0(!ydim.isNull()); - - auto zdim = findDimension(group, "z", value.getNz()); - ASSERT0(!zdim.isNull()); - - return {xdim, ydim, zdim}; -} - -template <> -std::vector NcDimVisitor::operator()(const FieldPerp& value) { - auto xdim = findDimension(group, "x", value.getNx()); - ASSERT0(!xdim.isNull()); - - auto zdim = findDimension(group, "z", value.getNz()); - ASSERT0(!zdim.isNull()); - - return {xdim, zdim}; -} - -/// Visit a variant type, and put the data into a NcVar -struct NcPutVarVisitor { - NcPutVarVisitor(NcVar& var) : var(var) {} - template - void operator()(const T& value) { - var.putVar(&value); - } - -private: - NcVar& var; -}; - -template <> -void NcPutVarVisitor::operator()(const bool& value) { - int int_val = value ? 1 : 0; - var.putVar(&int_val); -} - -template <> -void NcPutVarVisitor::operator()(const std::string& value) { - const char* cstr = value.c_str(); - var.putVar(&cstr); -} - -/// In addition to writing the data, set the "cell_location" attribute -template <> -void NcPutVarVisitor::operator()(const Field2D& value) { - // Pointer to data. Assumed to be contiguous array - var.putVar(&value(0, 0)); -} - -/// In addition to writing the data, set the "cell_location" attribute -template <> -void NcPutVarVisitor::operator()(const Field3D& value) { - // Pointer to data. Assumed to be contiguous array - var.putVar(&value(0, 0, 0)); -} - -template <> -void NcPutVarVisitor::operator()(const FieldPerp& value) { - // Pointer to data. Assumed to be contiguous array - var.putVar(&value(0, 0)); -} - -/// Visit a variant type, and put the data into a NcVar -struct NcPutVarCountVisitor { - NcPutVarCountVisitor(NcVar& var, const std::vector& start, - const std::vector& count) - : var(var), start(start), count(count) {} - template - void operator()(const T& value) { - var.putVar(start, &value); - } - -private: - NcVar& var; - const std::vector& start; ///< Starting (corner) index - const std::vector& count; ///< Index count in each dimension -}; - -template <> -void NcPutVarCountVisitor::operator()(const std::string& value) { - const char* cstr = value.c_str(); - var.putVar(start, &cstr); -} -template <> -void NcPutVarCountVisitor::operator()(const Field2D& value) { - // Pointer to data. Assumed to be contiguous array - var.putVar(start, count, &value(0, 0)); -} -template <> -void NcPutVarCountVisitor::operator()(const Field3D& value) { - // Pointer to data. Assumed to be contiguous array - var.putVar(start, count, &value(0, 0, 0)); -} -template <> -void NcPutVarCountVisitor::operator()(const FieldPerp& value) { - // Pointer to data. Assumed to be contiguous array - var.putVar(start, count, &value(0, 0)); -} - -/// Visit a variant type, and put the data into an attributute -struct NcPutAttVisitor { - NcPutAttVisitor(NcVar& var, std::string name) : var(var), name(std::move(name)) {} - template - void operator()(const T& UNUSED(value)) { - // Default is to ignore if unhandled } -private: - NcVar& var; - std::string name; -}; - -template <> -void NcPutAttVisitor::operator()(const bool& value) { - int ival = value ? 1 : 0; - var.putAtt(name, ncInt, ival); -} -template <> -void NcPutAttVisitor::operator()(const int& value) { - var.putAtt(name, ncInt, value); -} -template <> -void NcPutAttVisitor::operator()(const double& value) { - var.putAtt(name, ncDouble, value); -} -template <> -MAYBE_UNUSED() -void NcPutAttVisitor::operator()(const float& value) { - var.putAtt(name, ncFloat, value); -} -template <> -void NcPutAttVisitor::operator()(const std::string& value) { - var.putAtt(name, value); + return result; } void writeGroup(const Options& options, NcGroup group, @@ -639,10 +376,6 @@ std::vector verifyTimesteps(const NcGroup& group) { return errors; } -} // namespace - -namespace bout { - OptionsADIOS::OptionsADIOS() : data_file(nullptr) {} OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) @@ -676,21 +409,24 @@ void OptionsADIOS::verifyTimesteps() const { void OptionsADIOS::write(const Options& options, const std::string& time_dim) { Timer timer("io"); - // Check the file mode to use - auto ncmode = NcFile::replace; - if (file_mode == FileMode::append) { - // ADIOS doesn't have a "read-write, create if exists" mode, so - // we need to check ourselves if the file already exists; if it - // doesn't, tell ADIOS to create it - std::ifstream file(filename); - ncmode = file.good() ? NcFile::FileMode::write : NcFile::FileMode::newFile; - } + adios2::Mode mode = + (file_mode == FileMode::replace) ? adios2::Mode::Write : adios2::Mode::Append; if (not data_file) { - data_file = std::make_unique(filename, ncmode); + data_file = std::make_unique(); } - if (data_file->isNull()) { + // Open file + ADIOSPtr adiosp = GetADIOSPtr(); + try { + data_file->io = adiosp->AtIO(filename); + } catch (const std::invalid_argument& e) { + std::cerr << e.what() << '\n'; + data_file->io = adiosp->DeclareIO(filename); + } + + data_file->engine = data_file->io.Open(filename, mode); + if (!data_file->engine) { throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); } @@ -699,41 +435,6 @@ void OptionsADIOS::write(const Options& options, const std::string& time_dim) { data_file->sync(); } -std::string getRestartDirectoryName(Options& options) { - if (options["restartdir"].isSet()) { - // Solver-specific restart directory - return options["restartdir"].withDefault("data"); - } - // Use the root data directory - return options["datadir"].withDefault("data"); -} - -std::string getRestartFilename(Options& options) { - return getRestartFilename(options, BoutComm::rank()); -} - -std::string getRestartFilename(Options& options, int rank) { - return fmt::format("{}/BOUT.restart.{}.nc", bout::getRestartDirectoryName(options), - rank); -} - -std::string getOutputFilename(Options& options) { - return getOutputFilename(options, BoutComm::rank()); -} - -std::string getOutputFilename(Options& options, int rank) { - return fmt::format("{}/BOUT.dmp.{}.nc", - options["datadir"].withDefault("data"), rank); -} - -void writeDefaultOutputFile() { writeDefaultOutputFile(Options::root()); } - -void writeDefaultOutputFile(Options& options) { - bout::experimental::addBuildFlagsToOptions(options); - bout::globals::mesh->outputVars(options); - OptionsADIOS(getOutputFilename(Options::root())).write(options); -} - } // namespace bout #endif // BOUT_HAS_ADIOS diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx new file mode 100644 index 0000000000..f75618827e --- /dev/null +++ b/src/sys/options/options_io.cxx @@ -0,0 +1,99 @@ +#include "bout/build_config.hxx" + +#include "bout/options_io.hxx" + +#include "bout/bout.hxx" +#include "bout/globals.hxx" +#include "bout/mesh.hxx" +#include "bout/sys/timer.hxx" + +#include +#include +#include + +namespace bout { + +OptionsIO::OptionsIO() {} + +OptionsIO::OptionsIO(std::string filename, FileMode mode) + : filename(std::move(filename)), file_mode(mode) {} + +OptionsIO::~OptionsIO() = default; +OptionsIO::OptionsIO(OptionsIO&&) noexcept = default; +OptionsIO& OptionsIO::operator=(OptionsIO&&) noexcept = default; + +OptionsIO::Library getIOLibrary(Options& options) { + if (options["iolibrary"].isSet()) { + // Solver-specific IO library + std::string iolib = options["iolibrary"]; + std::transform(iolib.begin(), iolib.end(), iolib.begin(), ::tolower); + if (iolib == "adios") + return OptionsIO::Library::ADIOS; + else if (iolib == "netcdf") + return OptionsIO::Library::NetCDF; + else + return OptionsIO::Library::Invalid; + } else { + return OptionsIO::defaultIOLibrary; + } +} + +std::string getRestartDirectoryName(Options& options) { + if (options["restartdir"].isSet()) { + // Solver-specific restart directory + return options["restartdir"].withDefault("data"); + } + // Use the root data directory + return options["datadir"].withDefault("data"); +} + +std::string getRestartFilename(Options& options, const OptionsIO::Library library) { + return getRestartFilename(options, BoutComm::rank(), library); +} + +std::string getRestartFilename(Options& options, int rank, + const OptionsIO::Library library) { + if (library == OptionsIO::Library::ADIOS) + return fmt::format("{}/BOUT.restart.bp", bout::getRestartDirectoryName(options)); + else if (library == OptionsIO::Library::NetCDF) + return fmt::format("{}/BOUT.restart.{}.nc", bout::getRestartDirectoryName(options), + rank); + else + return fmt::format("{}/BOUT.restart.{}.data", bout::getRestartDirectoryName(options), + rank); +} + +std::string getOutputFilename(Options& options, const OptionsIO::Library library) { + return getOutputFilename(options, BoutComm::rank(), library); +} + +std::string getOutputFilename(Options& options, int rank, + const OptionsIO::Library library) { + if (library == OptionsIO::Library::ADIOS) + return fmt::format("{}/BOUT.dmp.bp", + options["datadir"].withDefault("data")); + else if (library == OptionsIO::Library::NetCDF) + return fmt::format("{}/BOUT.dmp.{}.nc", + options["datadir"].withDefault("data"), rank); + else + return fmt::format("{}/BOUT.dmp.{}.data", + options["datadir"].withDefault("data"), rank); +} + +void writeDefaultOutputFile(const OptionsIO::Library library) { + writeDefaultOutputFile(Options::root(), library); +} + +void writeDefaultOutputFile(Options& options, const OptionsIO::Library library) { + bout::experimental::addBuildFlagsToOptions(options); + bout::globals::mesh->outputVars(options); + auto mode = options["append"] + .doc("Add output data to existing (dump) files?") + .withDefault(false) + ? bout::OptionsIO::FileMode::append + : bout::OptionsIO::FileMode::replace; + auto io = OptionsIOFactory(getOutputFilename(options, library), mode, library); + io->write(options); +} + +} // namespace bout diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx index d7ceeaea60..dba056425e 100644 --- a/src/sys/options/options_netcdf.cxx +++ b/src/sys/options/options_netcdf.cxx @@ -699,41 +699,6 @@ void OptionsNetCDF::write(const Options& options, const std::string& time_dim) { data_file->sync(); } -std::string getRestartDirectoryName(Options& options) { - if (options["restartdir"].isSet()) { - // Solver-specific restart directory - return options["restartdir"].withDefault("data"); - } - // Use the root data directory - return options["datadir"].withDefault("data"); -} - -std::string getRestartFilename(Options& options) { - return getRestartFilename(options, BoutComm::rank()); -} - -std::string getRestartFilename(Options& options, int rank) { - return fmt::format("{}/BOUT.restart.{}.nc", bout::getRestartDirectoryName(options), - rank); -} - -std::string getOutputFilename(Options& options) { - return getOutputFilename(options, BoutComm::rank()); -} - -std::string getOutputFilename(Options& options, int rank) { - return fmt::format("{}/BOUT.dmp.{}.nc", - options["datadir"].withDefault("data"), rank); -} - -void writeDefaultOutputFile() { writeDefaultOutputFile(Options::root()); } - -void writeDefaultOutputFile(Options& options) { - bout::experimental::addBuildFlagsToOptions(options); - bout::globals::mesh->outputVars(options); - OptionsNetCDF(getOutputFilename(Options::root())).write(options); -} - } // namespace bout #endif // BOUT_HAS_NETCDF From 3fd53b9ce4312f16118ffab9983e7c81bfa4e54a Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Wed, 6 Sep 2023 16:42:12 -0400 Subject: [PATCH 082/412] save daily work --- include/bout/adios_object.hxx | 17 +- include/bout/options_adios.hxx | 22 +- include/bout/options_io.hxx | 9 +- include/bout/options_netcdf.hxx | 12 +- src/sys/adios_object.cxx | 6 +- src/sys/options/options_adios.cxx | 417 +++++++++++------------------- src/sys/options/options_io.cxx | 23 ++ 7 files changed, 194 insertions(+), 312 deletions(-) diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx index 058aa030c3..47232d685e 100755 --- a/include/bout/adios_object.hxx +++ b/include/bout/adios_object.hxx @@ -22,26 +22,21 @@ using IOPtr = std::shared_ptr; ADIOSPtr GetADIOSPtr(); IOPtr GetIOPtr(const std::string IOName); -struct ADIOSStruct { +class ADIOSStream { +public: adios2::IO io; adios2::Engine engine; - adios2::Variable vCellDim, vPhysDim, vNTotalElem, vNTotalNode; - adios2::Variable vPhysTime; + adios2::Variable vTime; adios2::Variable vStep; - adios2::Variable vElementConnectivity, vElementRange; - adios2::Variable vXco, vYco, vZco; - std::vector> vFlowVars; - std::vector> vBoundariesConnectivity; - std::vector> vBoundariesRange; int adiosStep = 0; }; -extern ADIOSStruct adios_restart; -extern ADIOSStruct adios_dump; +extern ADIOSStream adios_restart; +extern ADIOSStream adios_dump; //extern ADIOS2Param *adios2params; /** return one of the extern variable based on the target file name */ -ADIOSStruct& ADIOSGetStruct(const std::string& fname); +ADIOSStream& ADIOSGetStream(const std::string& fname); /** Set user parameters for an IO group */ void ADIOSSetParameters(const std::string& input, const char delimKeyValue, diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index ec6c26a432..9457293780 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -44,10 +44,12 @@ public: #include #include -#include "bout/adios_object.hxx" #include "bout/options.hxx" +#include "bout/options_io.hxx" namespace bout { +const Options& x = Options::root(); +const bout::OptionsIO::FileMode m = OptionsIO::FileMode::replace; /// Forward declare ADIOS file type so we don't need to depend /// directly on ADIOS @@ -55,15 +57,11 @@ struct ADIOSStream; class OptionsADIOS { public: - enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing - }; - // Constructors need to be defined in implementation due to forward - // declaration of NcFile + // declaration of ADIOSStream OptionsADIOS(); - explicit OptionsADIOS(std::string filename, FileMode mode = FileMode::replace); + explicit OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode = + bout::OptionsIO::FileMode::replace); ~OptionsADIOS(); OptionsADIOS(const OptionsADIOS&) = delete; OptionsADIOS(OptionsADIOS&&) noexcept; @@ -83,12 +81,8 @@ public: void verifyTimesteps() const; private: - /// Name of the file on disk - std::string filename; - /// How to open the file for writing - FileMode file_mode{FileMode::replace}; - /// Pointer to ADIOS file so we don't introduce direct dependence - std::unique_ptr data_file; + /// Pointer to ADIOS stream so we don't introduce direct dependence + std::unique_ptr stream; }; } // namespace bout diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 1a51a2bebb..49d5d51c04 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -12,13 +12,6 @@ #include "bout/options.hxx" -#if BOUT_HAS_ADIOS -#include "bout/options_adios.hxx" -#endif -#if BOUT_HAS_NETCDF -#include "bout/options_netcdf.hxx" -#endif - namespace bout { class OptionsIO { @@ -67,7 +60,7 @@ public: /// any differences, otherwise is silent virtual void verifyTimesteps() const = 0; -private: +protected: /// Name of the file on disk std::string filename; /// How to open the file for writing diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index d633596fbd..2096beeba0 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -45,6 +45,7 @@ public: #include #include "bout/options.hxx" +#include "bout/options_io.hxx" /// Forward declare netCDF file type so we don't need to depend /// directly on netCDF @@ -54,13 +55,8 @@ class NcFile; namespace bout { -class OptionsNetCDF { +class OptionsNetCDF : public OptionsIO { public: - enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing - }; - // Constructors need to be defined in implementation due to forward // declaration of NcFile OptionsNetCDF(); @@ -84,10 +80,6 @@ public: void verifyTimesteps() const; private: - /// Name of the file on disk - std::string filename; - /// How to open the file for writing - FileMode file_mode{FileMode::replace}; /// Pointer to netCDF file so we don't introduce direct dependence std::unique_ptr data_file; }; diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx index 5bab7545e9..e694e483e0 100755 --- a/src/sys/adios_object.cxx +++ b/src/sys/adios_object.cxx @@ -11,8 +11,8 @@ namespace bout { static ADIOSPtr adios = nullptr; -ADIOSStruct adios_restart; -ADIOSStruct adios_dump; +ADIOSStream adios_restart; +ADIOSStream adios_dump; //ADIOS2Param* adios2params; void ADIOSInit(MPI_Comm comm) { adios = std::make_shared(comm); } @@ -50,7 +50,7 @@ IOPtr GetIOPtr(const std::string IOName) { return io; } -ADIOSStruct& ADIOSGetStruct(const std::string& fname) { +ADIOSStream& ADIOSGetStream(const std::string& fname) { if (fname.find(".restart") != std::string::npos) return adios_restart; //if (fname.find(".dmp") != std::string::npos) diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 518a8fa7ed..1d42e30cb9 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -2,6 +2,7 @@ #if BOUT_HAS_ADIOS +#include "bout/adios_object.hxx" #include "bout/options_adios.hxx" #include "bout/bout.hxx" @@ -16,95 +17,94 @@ namespace bout { -struct ADIOSStream { - adios2::IO io; - adios2::Engine engine; - adios2::Variable vStep; - adios2::Variable vTime; - int adiosStep = 0; -}; +OptionsADIOS::OptionsADIOS() : stream(nullptr) {} + +OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) + : filename(std::move(filename)), file_mode(mode), stream(nullptr) {} + +OptionsADIOS::~OptionsADIOS() = default; +OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; +OptionsADIOS& OptionsADIOS::operator=(OptionsADIOS&&) noexcept = default; /// Name of the attribute used to track individual variable's time indices constexpr auto current_time_index_name = "current_time_index"; template bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, - const std::string& type, Options& result) { - bool ret = false; + Options& result) { std::vector data; adios2::Variable variable = io.InquireVariable(name); if (variable.ShapeID() == adios2::ShapeID::GlobalValue) { T value; - io.Get(variable, &value, adios2::Mode::Sync); + reader.Get(variable, &value, adios2::Mode::Sync); result[name] = value; return true; } if (variable.ShapeID() == adios2::ShapeID::LocalArray) { - if (!rank) + if (!BoutComm::rank()) { std::cout << " LocalArray not supported" << std::endl; - return ret; + } + return false; } auto dims = variable.Shape(); - auto ndim = shape.size(); + auto ndims = dims.size(); switch (ndims) { case 1: { Array value(static_cast(dims[0])); - io.Get(variable, value.data(), adios2::Mode::Sync); - result[name] = value; + reader.Get(variable, value.begin(), adios2::Mode::Sync); + //result[name] = value; + break; } case 2: { - Matrix value(static_cast(dims[0].getSize()), - static_cast(dims[1].getSize())); - io.Get(variable, value.data(), adios2::Mode::Sync); - result[name] = value; + Matrix value(static_cast(dims[0]), static_cast(dims[1])); + reader.Get(variable, value.begin(), adios2::Mode::Sync); + //[name] = value; + break; } case 3: { - Tensor value(static_cast(dims[0].getSize()), - static_cast(dims[1].getSize()), - static_cast(dims[2].getSize())); - io.Get(variable, value.data(), adios2::Mode::Sync); - result[name] = value; + Tensor value(static_cast(dims[0]), static_cast(dims[1]), + static_cast(dims[2])); + reader.Get(variable, value.begin(), adios2::Mode::Sync); + //result[name] = value; + break; } } - if (!rank) + if (!BoutComm::rank()) std::cout << " array has " << variable.Steps() << " steps" << std::endl; /* Need to read the data here */ result[name] = data.data(); - return ret; + return true; } bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, const std::string& type, Options& result) { bool ret; -#define declare_template_instantiation(T) \ - if (type == adios2::GetType()) { \ - ret = readVariable(reader, io, name, type, result); \ +#define declare_template_instantiation(T) \ + if (type == adios2::GetType()) { \ + ret = readVariable(reader, io, name, result); \ } ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) #undef declare_template_instantiation return ret; } -bool readAttribute(adios2::Engine& reader, adios2::IO& io, const std::string& name, - const std::string& type, Options& result) { - bool ret; +bool readAttribute(adios2::IO& io, const std::string& name, const std::string& type, + Options& result) { #define declare_template_instantiation(T) \ if (type == adios2::GetType()) { \ - adios2::Attribute a = io.InquireAtrribute(name); \ + adios2::Attribute a = io.InquireAttribute(name); \ result[name] = a.Data().data(); \ } ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) #undef declare_template_instantiation - return ret; -} // namespace bout - -void readGroup(const std::string& filename, ADIOSStruct& group, Options& result) {} + return true; +} Options OptionsADIOS::read() { Timer timer("io"); @@ -139,174 +139,16 @@ Options OptionsADIOS::read() { // Get variable attributes for (const auto& attpair : io.AvailableAttributes(var_name, "/", true)) { const auto& att_name = attpair.first; // Attribute name - const auto& att = attpair.second; // NcVarAtt object - auto it = attpair.second.find("Type"); + const auto& att = attpair.second; // attribute params + auto it = att.find("Type"); const std::string& att_type = it->second; - readAttribute(reader, io, att_name, att_type, result); + readAttribute(io, att_name, att_type, result); } } - return result; -} - -void writeGroup(const Options& options, NcGroup group, - const std::string& time_dimension) { - - for (const auto& childpair : options.getChildren()) { - const auto& name = childpair.first; - const auto& child = childpair.second; - - if (child.isValue()) { - try { - auto nctype = bout::utils::visit(NcTypeVisitor(), child.value); - - if (nctype.isNull()) { - continue; // Skip this value - } - - // Get spatial dimensions - auto spatial_dims = bout::utils::visit(NcDimVisitor(group), child.value); - - // Vector of all dimensions, including time - std::vector dims{spatial_dims}; - - // Get the time dimension - NcDim time_dim; ///< Time dimension (Null -> none) - auto time_it = child.attributes.find("time_dimension"); - if (time_it != child.attributes.end()) { - // Has a time dimension - - const auto& time_name = bout::utils::get(time_it->second); - - // Only write time-varying values that match current time - // dimension being written - if (time_name != time_dimension) { - continue; - } - - time_dim = group.getDim(time_name, NcGroup::ParentsAndCurrent); - if (time_dim.isNull()) { - time_dim = group.addDim(time_name); - } - - // prepend to vector of dimensions - dims.insert(dims.begin(), time_dim); - } - - // Check if the variable exists - auto var = group.getVar(name); - if (var.isNull()) { - // Variable doesn't exist yet - // Create variable - // Temporary NcType as a workaround for bug in ADIOS 4.4.0 and - // ADIOS-CXX4 4.2.0 - var = group.addVar(name, NcType{group, nctype.getId()}, dims); - if (!time_dim.isNull()) { - // Time evolving variable, so we'll need to keep track of its time index - var.putAtt(current_time_index_name, ncInt, 0); - } - } else { - // Variable does exist - - // Check types are the same - if (var.getType() != nctype) { - throw BoutException( - "Changed type of variable '{:s}'. Was '{:s}', now writing '{:s}'", name, - var.getType().getName(), nctype.getName()); - } - - // Check that the dimensions are correct - auto var_dims = var.getDims(); - - // Same number of dimensions? - if (var_dims.size() != dims.size()) { - throw BoutException( - "Changed dimensions for variable '{:s}'\nIn file has {:d} " - "dimensions, now writing {:d}\n", - name, var_dims.size(), dims.size()); - } - // Dimensions compatible? - for (std::vector::size_type i = 0; i < dims.size(); ++i) { - if (var_dims[i] == dims[i]) { - continue; // The same dimension -> ok - } - if (var_dims[i].isUnlimited() != dims[i].isUnlimited()) { - throw BoutException("Unlimited dimension changed for variable '{:s}'", - name); - } - if (var_dims[i].getSize() != dims[i].getSize()) { - throw BoutException("Dimension size changed for variable '{:s}'", name); - } - } - // All ok. Set dimensions to the variable's NcDims - dims = var_dims; - - if (!time_dim.isNull()) { - // A time dimension - time_dim = dims[0]; - } - } - - // Write the variable - - if (time_dim.isNull()) { - // No time index - - // Put the data into the variable - bout::utils::visit(NcPutVarVisitor(var), child.value); - - } else { - // Has a time index, so need the record index - - const int current_time_index = getCurrentTimeIndex(var); - - std::vector start_index; ///< Starting index where data will be inserted - std::vector count_index; ///< Size of each dimension - - // Dimensions, including time - for (const auto& dim : dims) { - start_index.push_back(0); - count_index.push_back(dim.getSize()); - } - // Time dimension - start_index[0] = current_time_index; - count_index[0] = 1; // Writing one record - - // Put the data into the variable - bout::utils::visit(NcPutVarCountVisitor(var, start_index, count_index), - child.value); - - // We've just written a new time slice, so we need to update - // the attribute to track it - var.putAtt(current_time_index_name, ncInt, current_time_index + 1); - } - - // Write attributes - for (const auto& attribute : child.attributes) { - const std::string& att_name = attribute.first; - const auto& att = attribute.second; - - bout::utils::visit(NcPutAttVisitor(var, att_name), att); - } - - } catch (const std::exception& e) { - throw BoutException("Error while writing value '{:s}' : {:s}", name, e.what()); - } - } - - if (child.isSection()) { - // Check if the group exists - TRACE("Writing group '{:s}'", name); + reader.Close(); - auto subgroup = group.getGroup(name); - if (subgroup.isNull()) { - // Doesn't exist yet, so create it - subgroup = group.addGroup(name); - } - - writeGroup(child, subgroup, time_dimension); - } - } + return result; } /// Helper struct for returning errors from verifyTimesteps(NcGroup) @@ -317,77 +159,36 @@ struct TimeDimensionError { std::size_t current_size; }; -std::vector verifyTimesteps(const NcGroup& group) { +std::vector verifyTimesteps(adios2::Engine& reader) { + reader.CurrentStep(); // just to avoid warning on unused variable - // Map of dimension -> size - std::map seen_time_dimensions; // Variables with mismatched dimension sizes. Note that this might // be a little odd: if the first variable we come across has the // "wrong" dimension size, we will actually list all the others as // being wrong! std::vector errors; - // For each variable, check its time dimension against what we've - // seen already. Note that this assumes a single time dimension per - // variable whose is in the attribute "time_dimension" - for (const auto& varpair : group.getVars()) { - const auto& var_name = varpair.first; // Name of the variable - const auto& var = varpair.second; // The NcVar object - - // Get the name of the time dimension from the attribute - const auto& attributes = var.getAtts(); - const auto time_it = attributes.find("time_dimension"); - if (time_it == attributes.end()) { - // No "time_dimension" attribute so presumably not a - // time-evolving variable - continue; - } - - // Use the attribute value to get the actual dimension - std::string time_name; - time_it->second.getValues(time_name); - const auto time_dim = group.getDim(time_name, NcGroup::ParentsAndCurrent); - - // Check if we've already seen this dimension - auto seen_it = seen_time_dimensions.find(time_dim); - if (seen_it == seen_time_dimensions.end()) { - // If we haven't, add it to the map with current time index - seen_time_dimensions[time_dim] = time_dim.getSize(); - continue; - } - - // If we have, check if the variable current time index matches time size - const auto current_time = static_cast(getCurrentTimeIndex(var)); - if (current_time == time_dim.getSize()) { - continue; - } - // If not, add to list of errors - errors.push_back({var_name, time_dim.getName(), time_dim.getSize(), current_time}); - } - - // Recurse down into subgroups, shoving any new errors into what - // we've already got. Don't bother reserving the new size, this - // shouldn't be big! - for (const auto& child : group.getGroups()) { - auto child_errors = verifyTimesteps(child.second); - errors.insert(errors.end(), child_errors.begin(), child_errors.end()); - } - return errors; } -OptionsADIOS::OptionsADIOS() : data_file(nullptr) {} +void OptionsADIOS::verifyTimesteps() const { -OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) - : filename(std::move(filename)), file_mode(mode), data_file(nullptr) {} + // Open file + ADIOSPtr adiosp = GetADIOSPtr(); + adios2::IO io; + try { + io = adiosp->AtIO(filename); + } catch (const std::invalid_argument& e) { + std::cerr << e.what() << '\n'; + io = adiosp->DeclareIO(filename); + } -OptionsADIOS::~OptionsADIOS() = default; -OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; -OptionsADIOS& OptionsADIOS::operator=(OptionsADIOS&&) noexcept = default; + adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess); + if (!reader) { + throw BoutException("Could not open ADIOS file '{:s}' for reading", filename); + } -void OptionsADIOS::verifyTimesteps() const { - NcFile dataFile(filename, NcFile::read); - auto errors = ::verifyTimesteps(dataFile); + auto errors = bout::verifyTimesteps(reader); if (errors.empty()) { // No errors @@ -405,6 +206,89 @@ void OptionsADIOS::verifyTimesteps() const { filename, errors.size(), error_string); } +/// Visit a variant type, and put the data into a NcVar +struct ADIOSPutVarVisitor { + ADIOSPutVarVisitor(const std::string& name, ADIOSStream& stream) + : varname(name), stream(stream) {} + template + void operator()(const T& value) { + adios2::Variable var = stream.io.DefineVariable(varname); + stream.engine.Put(var, value); + } + +private: + const std::string& varname; + ADIOSStream& stream; +}; + +//template <> +//void ADIOSPutVarVisitor::operator()(const bool& value) { +// int int_val = value ? 1 : 0; +//} + +/// Visit a variant type, and put the data into a NcVar +struct ADIOSPutAttVisitor { + ADIOSPutAttVisitor(const std::string& varname, const std::string& attrname, + ADIOSStream& stream) + : varname(varname), attrname(attrname), stream(stream) {} + template + void operator()(const T& value) { + stream.io.DefineAttribute(attrname, value, varname, "/", false); + } + +private: + const std::string& varname; + const std::string& attrname; + ADIOSStream& stream; +}; + +void writeGroup(const Options& options, ADIOSStream& stream, const std::string& groupname, + const std::string& time_dimension) { + + for (const auto& childpair : options.getChildren()) { + const auto& name = childpair.first; + const auto& child = childpair.second; + + if (child.isSection()) { + TRACE("Writing group '{:s}'", name); + writeGroup(child, stream, name, time_dimension); + continue; + } + + if (child.isValue()) { + try { + auto time_it = child.attributes.find("time_dimension"); + if (time_it != child.attributes.end()) { + // Has a time dimension + + const auto& time_name = bout::utils::get(time_it->second); + + // Only write time-varying values that match current time + // dimension being written + if (time_name != time_dimension) { + continue; + } + } + + // Write the variable + std::string varname = groupname.empty() ? name : groupname + "/" + name; + bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value); + + // Write attributes + for (const auto& attribute : child.attributes) { + const std::string& att_name = attribute.first; + const auto& att = attribute.second; + + bout::utils::visit(ADIOSPutAttVisitor(varname, att_name, stream), att); + } + + } catch (const std::exception& e) { + throw BoutException("Error while writing value '{:s}' : {:s}", name, e.what()); + } + } + } +} + /// Write options to file void OptionsADIOS::write(const Options& options, const std::string& time_dim) { Timer timer("io"); @@ -412,27 +296,28 @@ void OptionsADIOS::write(const Options& options, const std::string& time_dim) { adios2::Mode mode = (file_mode == FileMode::replace) ? adios2::Mode::Write : adios2::Mode::Append; - if (not data_file) { - data_file = std::make_unique(); + if (not stream) { + stream = std::make_unique(); } // Open file ADIOSPtr adiosp = GetADIOSPtr(); try { - data_file->io = adiosp->AtIO(filename); + stream->io = adiosp->AtIO(filename); } catch (const std::invalid_argument& e) { std::cerr << e.what() << '\n'; - data_file->io = adiosp->DeclareIO(filename); + stream->io = adiosp->DeclareIO(filename); } - data_file->engine = data_file->io.Open(filename, mode); - if (!data_file->engine) { + stream->engine = stream->io.Open(filename, mode); + if (!stream->engine) { throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); } - writeGroup(options, *data_file, time_dim); + stream->engine.BeginStep(); + writeGroup(options, *stream, "", time_dim); - data_file->sync(); + stream->engine.EndStep(); } } // namespace bout diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index f75618827e..32187981ba 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -11,6 +11,13 @@ #include #include +#if BOUT_HAS_ADIOS +#include "bout/options_adios.hxx" +#endif +#if BOUT_HAS_NETCDF +#include "bout/options_netcdf.hxx" +#endif + namespace bout { OptionsIO::OptionsIO() {} @@ -38,6 +45,22 @@ OptionsIO::Library getIOLibrary(Options& options) { } } +std::shared_ptr OptionsIOFactory(std::string filename, + OptionsIO::FileMode mode, + const OptionsIO::Library library) { + if (library == OptionsIO::Library::ADIOS) { + std::shared_ptr ptr(OptionsADIOS); + //std::shared_ptr ptr = + // std::make_shared(OptionsADIOS(filename, mode)); + //std::shared_ptr p2 = std::shared_ptr(ptr); + return ptr; + } else if (library == OptionsIO::Library::NetCDF) { + return std::make_shared(OptionsNetCDF(filename, mode)); + } else { + return nullptr; + } +} + std::string getRestartDirectoryName(Options& options) { if (options["restartdir"].isSet()) { // Solver-specific restart directory From db995f211cc6ffd937339ad446e36866e26e000f Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Mon, 11 Sep 2023 07:33:51 -0400 Subject: [PATCH 083/412] Finally compiles, but invalid type use for adios: adios2::Engine::Put --- include/bout/options_adios.hxx | 4 +--- src/sys/options/options_adios.cxx | 2 +- src/sys/options/options_io.cxx | 8 ++------ src/sys/options/options_netcdf.cxx | 2 +- 4 files changed, 5 insertions(+), 11 deletions(-) diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index 9457293780..a4d5e1b6b2 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -48,14 +48,12 @@ public: #include "bout/options_io.hxx" namespace bout { -const Options& x = Options::root(); -const bout::OptionsIO::FileMode m = OptionsIO::FileMode::replace; /// Forward declare ADIOS file type so we don't need to depend /// directly on ADIOS struct ADIOSStream; -class OptionsADIOS { +class OptionsADIOS : public OptionsIO { public: // Constructors need to be defined in implementation due to forward // declaration of ADIOSStream diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 1d42e30cb9..bbba120aae 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -20,7 +20,7 @@ namespace bout { OptionsADIOS::OptionsADIOS() : stream(nullptr) {} OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) - : filename(std::move(filename)), file_mode(mode), stream(nullptr) {} + : OptionsIO(filename, mode), stream(nullptr) {} OptionsADIOS::~OptionsADIOS() = default; OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 32187981ba..8183273e7f 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -49,13 +49,9 @@ std::shared_ptr OptionsIOFactory(std::string filename, OptionsIO::FileMode mode, const OptionsIO::Library library) { if (library == OptionsIO::Library::ADIOS) { - std::shared_ptr ptr(OptionsADIOS); - //std::shared_ptr ptr = - // std::make_shared(OptionsADIOS(filename, mode)); - //std::shared_ptr p2 = std::shared_ptr(ptr); - return ptr; + return std::make_shared(OptionsADIOS(filename, mode)); } else if (library == OptionsIO::Library::NetCDF) { - return std::make_shared(OptionsNetCDF(filename, mode)); + return std::make_shared(OptionsNetCDF(filename, mode)); } else { return nullptr; } diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx index dba056425e..8aadcd5363 100644 --- a/src/sys/options/options_netcdf.cxx +++ b/src/sys/options/options_netcdf.cxx @@ -646,7 +646,7 @@ namespace bout { OptionsNetCDF::OptionsNetCDF() : data_file(nullptr) {} OptionsNetCDF::OptionsNetCDF(std::string filename, FileMode mode) - : filename(std::move(filename)), file_mode(mode), data_file(nullptr) {} + : OptionsIO(filename, mode), data_file(nullptr) {} OptionsNetCDF::~OptionsNetCDF() = default; OptionsNetCDF::OptionsNetCDF(OptionsNetCDF&&) noexcept = default; From 93933a243d2a50c582670943d2b9c78da20780f3 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Mon, 11 Sep 2023 08:26:32 -0400 Subject: [PATCH 084/412] conduction example compiles --- src/sys/options/options_adios.cxx | 67 ++++++++++++++++++++++++++++--- 1 file changed, 62 insertions(+), 5 deletions(-) diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index bbba120aae..26f9b9938e 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -221,10 +221,62 @@ struct ADIOSPutVarVisitor { ADIOSStream& stream; }; -//template <> -//void ADIOSPutVarVisitor::operator()(const bool& value) { -// int int_val = value ? 1 : 0; -//} +template <> +void ADIOSPutVarVisitor::operator()(const bool& value) { + adios2::Variable var = stream.io.DefineVariable(varname); + stream.engine.Put(var, (int)value); +} + +template <> +void ADIOSPutVarVisitor::operator()(const Field2D& value) { + // Pointer to data. Assumed to be contiguous array + adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNy()}; + adios2::Variable var = stream.io.DefineVariable(varname, shape); + stream.engine.Put(var, &value(0, 0)); +} + +template <> +void ADIOSPutVarVisitor::operator()(const Field3D& value) { + // Pointer to data. Assumed to be contiguous array + adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNz()}; + adios2::Variable var = stream.io.DefineVariable(varname, shape); + stream.engine.Put(var, &value(0, 0, 0)); +} + +template <> +void ADIOSPutVarVisitor::operator()(const FieldPerp& value) { + // Pointer to data. Assumed to be contiguous array + adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNz()}; + adios2::Variable var = stream.io.DefineVariable(varname, shape); + stream.engine.Put(var, &value(0, 0)); +} + +template <> +void ADIOSPutVarVisitor::operator()>(const Array& value) { + // Pointer to data. Assumed to be contiguous array + adios2::Dims shape = {(size_t)value.size()}; + adios2::Variable var = stream.io.DefineVariable(varname, shape); + stream.engine.Put(var, value.begin()); +} + +template <> +void ADIOSPutVarVisitor::operator()>(const Matrix& value) { + // Pointer to data. Assumed to be contiguous array + auto s = value.shape(); + adios2::Dims shape = {(size_t)std::get<0>(s), (size_t)std::get<1>(s)}; + adios2::Variable var = stream.io.DefineVariable(varname, shape); + stream.engine.Put(var, value.begin()); +} + +template <> +void ADIOSPutVarVisitor::operator()>(const Tensor& value) { + // Pointer to data. Assumed to be contiguous array + auto s = value.shape(); + adios2::Dims shape = {(size_t)std::get<0>(s), (size_t)std::get<1>(s), + (size_t)std::get<2>(s)}; + adios2::Variable var = stream.io.DefineVariable(varname, shape); + stream.engine.Put(var, value.begin()); +} /// Visit a variant type, and put the data into a NcVar struct ADIOSPutAttVisitor { @@ -233,7 +285,7 @@ struct ADIOSPutAttVisitor { : varname(varname), attrname(attrname), stream(stream) {} template void operator()(const T& value) { - stream.io.DefineAttribute(attrname, value, varname, "/", false); + stream.io.DefineAttribute(attrname, value, varname, "/", false); } private: @@ -242,6 +294,11 @@ struct ADIOSPutAttVisitor { ADIOSStream& stream; }; +template <> +void ADIOSPutAttVisitor::operator()(const bool& value) { + stream.io.DefineAttribute(attrname, (int)value, varname, "/", false); +} + void writeGroup(const Options& options, ADIOSStream& stream, const std::string& groupname, const std::string& time_dimension) { From 686f9e06411db3fb93006bbe159a2929b6fd48cb Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Mon, 11 Sep 2023 12:27:59 -0400 Subject: [PATCH 085/412] test-options-adios: writes correctly settings.bp and test-out.bp --- include/bout/options_adios.hxx | 15 +--- include/bout/options_netcdf.hxx | 15 ++-- src/sys/options/options_adios.cxx | 30 ++++--- tests/integrated/CMakeLists.txt | 1 + .../test-options-adios/CMakeLists.txt | 6 ++ .../test-options-adios/data/BOUT.inp | 6 ++ tests/integrated/test-options-adios/makefile | 6 ++ tests/integrated/test-options-adios/runtest | 73 ++++++++++++++++ .../test-options-adios/test-options-adios.cxx | 85 +++++++++++++++++++ .../test-options-netcdf.cxx | 3 +- 10 files changed, 208 insertions(+), 32 deletions(-) create mode 100644 tests/integrated/test-options-adios/CMakeLists.txt create mode 100644 tests/integrated/test-options-adios/data/BOUT.inp create mode 100644 tests/integrated/test-options-adios/makefile create mode 100755 tests/integrated/test-options-adios/runtest create mode 100644 tests/integrated/test-options-adios/test-options-adios.cxx diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index a4d5e1b6b2..81c9e85d3e 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -5,24 +5,20 @@ #define __OPTIONS_ADIOS_H__ #include "bout/build_config.hxx" +#include "bout/options.hxx" +#include "bout/options_io.hxx" #if !BOUT_HAS_ADIOS #include #include "bout/boutexception.hxx" -#include "bout/options.hxx" namespace bout { -class OptionsADIOS { +class OptionsADIOS : public OptionsIO { public: - enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing - }; - - OptionsADIOS(const std::string& filename, FileMode mode = FileMode::replace) {} + OptionsADIOS(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} OptionsADIOS(const OptionsADIOS&) = default; OptionsADIOS(OptionsADIOS&&) = default; OptionsADIOS& operator=(const OptionsADIOS&) = default; @@ -44,9 +40,6 @@ public: #include #include -#include "bout/options.hxx" -#include "bout/options_io.hxx" - namespace bout { /// Forward declare ADIOS file type so we don't need to depend diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index 2096beeba0..0d94594d9d 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -6,6 +6,9 @@ #include "bout/build_config.hxx" +#include "bout/options.hxx" +#include "bout/options_io.hxx" + #if !BOUT_HAS_NETCDF || BOUT_HAS_LEGACY_NETCDF #include @@ -15,14 +18,9 @@ namespace bout { -class OptionsNetCDF { +class OptionsNetCDF : public OptionsIO{ public: - enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing - }; - - OptionsNetCDF(const std::string& filename, FileMode mode = FileMode::replace) {} + OptionsNetCDF(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} OptionsNetCDF(const OptionsNetCDF&) = default; OptionsNetCDF(OptionsNetCDF&&) = default; OptionsNetCDF& operator=(const OptionsNetCDF&) = default; @@ -44,9 +42,6 @@ public: #include #include -#include "bout/options.hxx" -#include "bout/options_io.hxx" - /// Forward declare netCDF file type so we don't need to depend /// directly on netCDF namespace netCDF { diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 26f9b9938e..61ba360439 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -112,11 +112,11 @@ Options OptionsADIOS::read() { // Open file ADIOSPtr adiosp = GetADIOSPtr(); adios2::IO io; + std::string ioname = "read_"+filename; try { - io = adiosp->AtIO(filename); + io = adiosp->AtIO(ioname); } catch (const std::invalid_argument& e) { - std::cerr << e.what() << '\n'; - io = adiosp->DeclareIO(filename); + io = adiosp->DeclareIO(ioname); } adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess); @@ -227,6 +227,13 @@ void ADIOSPutVarVisitor::operator()(const bool& value) { stream.engine.Put(var, (int)value); } +template <> +void ADIOSPutVarVisitor::operator()(const std::string& value) { + adios2::Variable var = stream.io.DefineVariable(varname); + std::cout << "-- Write string variable " << var.Name() << " value = " << value << std::endl; + stream.engine.Put(var, (std::string)value, adios2::Mode::Sync); +} + template <> void ADIOSPutVarVisitor::operator()(const Field2D& value) { // Pointer to data. Assumed to be contiguous array @@ -332,11 +339,14 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string& bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value); // Write attributes - for (const auto& attribute : child.attributes) { - const std::string& att_name = attribute.first; - const auto& att = attribute.second; + if (!BoutComm::rank()) + { + for (const auto& attribute : child.attributes) { + const std::string& att_name = attribute.first; + const auto& att = attribute.second; - bout::utils::visit(ADIOSPutAttVisitor(varname, att_name, stream), att); + bout::utils::visit(ADIOSPutAttVisitor(varname, att_name, stream), att); + } } } catch (const std::exception& e) { @@ -359,11 +369,11 @@ void OptionsADIOS::write(const Options& options, const std::string& time_dim) { // Open file ADIOSPtr adiosp = GetADIOSPtr(); + std::string ioname = "write_"+filename; try { - stream->io = adiosp->AtIO(filename); + stream->io = adiosp->AtIO(ioname); } catch (const std::invalid_argument& e) { - std::cerr << e.what() << '\n'; - stream->io = adiosp->DeclareIO(filename); + stream->io = adiosp->DeclareIO(ioname); } stream->engine = stream->io.Open(filename, mode); diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt index 8dd892ebad..7d3e8e81ce 100644 --- a/tests/integrated/CMakeLists.txt +++ b/tests/integrated/CMakeLists.txt @@ -30,6 +30,7 @@ add_subdirectory(test-laplacexz) add_subdirectory(test-multigrid_laplace) add_subdirectory(test-naulin-laplace) add_subdirectory(test-options-netcdf) +add_subdirectory(test-options-adios) add_subdirectory(test-petsc_laplace) add_subdirectory(test-petsc_laplace_MAST-grid) add_subdirectory(test-restart-io) diff --git a/tests/integrated/test-options-adios/CMakeLists.txt b/tests/integrated/test-options-adios/CMakeLists.txt new file mode 100644 index 0000000000..110773d6fd --- /dev/null +++ b/tests/integrated/test-options-adios/CMakeLists.txt @@ -0,0 +1,6 @@ +bout_add_integrated_test(test-options-adios + SOURCES test-options-adios.cxx + USE_RUNTEST + USE_DATA_BOUT_INP + REQUIRES BOUT_HAS_ADIOS + ) diff --git a/tests/integrated/test-options-adios/data/BOUT.inp b/tests/integrated/test-options-adios/data/BOUT.inp new file mode 100644 index 0000000000..fa0f6d3681 --- /dev/null +++ b/tests/integrated/test-options-adios/data/BOUT.inp @@ -0,0 +1,6 @@ + + +[mesh] +nx = 5 +ny = 2 +nz = 2 diff --git a/tests/integrated/test-options-adios/makefile b/tests/integrated/test-options-adios/makefile new file mode 100644 index 0000000000..7dbbce8736 --- /dev/null +++ b/tests/integrated/test-options-adios/makefile @@ -0,0 +1,6 @@ + +BOUT_TOP = ../../.. + +SOURCEC = test-options-adios.cxx + +include $(BOUT_TOP)/make.config diff --git a/tests/integrated/test-options-adios/runtest b/tests/integrated/test-options-adios/runtest new file mode 100755 index 0000000000..7a3541df2d --- /dev/null +++ b/tests/integrated/test-options-adios/runtest @@ -0,0 +1,73 @@ +#!/usr/bin/env python3 + +# Note: This test requires NCDF4, whereas on Travis NCDF is used +# requires: netcdf +# requires: not legacy_netcdf + +from boututils.datafile import DataFile +from boututils.run_wrapper import build_and_log, shell, launch +from boutdata.data import BoutOptionsFile + +import math +import numpy as np + +build_and_log("options-netcdf test") +shell("rm -f test-out.ini") +shell("rm -f test-out.nc") + +# Create a NetCDF input file +with DataFile("test.nc", create=True, format="NETCDF4") as f: + f.write("int", 42) + f.write("real", 3.1415) + f.write("string", "hello") + +# run BOUT++ +launch("./test-options-adios", nproc=1, mthread=1) + +# Check the output INI file +result = BoutOptionsFile("test-out.ini") + +print(result) + +assert result["int"] == 42 +assert math.isclose(result["real"], 3.1415) +assert result["string"] == "hello" + +print("Checking saved ADIOS test-out file -- Not implemented") + +# Check the output NetCDF file +# with DataFile("test-out.nc") as f: +# assert f["int"] == 42 +# assert math.isclose(f["real"], 3.1415) +# assert result["string"] == "hello" + +print("Checking saved settings.ini") + +# Check the settings.ini file, coming from BOUT.inp +# which is converted to NetCDF, read in, then written again +settings = BoutOptionsFile("settings.ini") + +assert settings["mesh"]["nx"] == 5 +assert settings["mesh"]["ny"] == 2 + +print("Checking saved fields.bp -- Not implemented") + +# with DataFile("fields.nc") as f: +# assert f["f2d"].shape == (5, 6) # Field2D +# assert f["f3d"].shape == (5, 6, 2) # Field3D +# assert f["fperp"].shape == (5, 2) # FieldPerp +# assert np.allclose(f["f2d"], 1.0) +# assert np.allclose(f["f3d"], 2.0) +# assert np.allclose(f["fperp"], 3.0) + +print("Checking saved fields2.bp -- Not implemented") + +# with DataFile("fields2.nc") as f: +# assert f["f2d"].shape == (5, 6) # Field2D +# assert f["f3d"].shape == (5, 6, 2) # Field3D +# assert f["fperp"].shape == (5, 2) # FieldPerp +# assert np.allclose(f["f2d"], 1.0) +# assert np.allclose(f["f3d"], 2.0) +# assert np.allclose(f["fperp"], 3.0) + +print(" => Passed") diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx new file mode 100644 index 0000000000..17eeb17128 --- /dev/null +++ b/tests/integrated/test-options-adios/test-options-adios.cxx @@ -0,0 +1,85 @@ + +#include "bout/bout.hxx" + +#include "bout/options_io.hxx" +#include "bout/options_netcdf.hxx" +#include "bout/options_adios.hxx" +#include "bout/optionsreader.hxx" + +using bout::OptionsADIOS; + +int main(int argc, char** argv) { + BoutInitialise(argc, argv); + + // Read values from a NetCDF file + bout::OptionsNetCDF file("test.nc"); + + auto values = file.read(); + + values.printUnused(); + + // Write to an INI text file + OptionsReader* reader = OptionsReader::getInstance(); + reader->write(&values, "test-out.ini"); + + // Write to a NetCDF file + OptionsADIOS("test-out.bp").write(values); + + /////////////////////////// + + // Write the BOUT.inp settings to NetCDF file + OptionsADIOS("settings.bp").write(Options::root()); + + // Read back in + auto settings = OptionsADIOS("settings.bp").read(); + + // Write to INI file + reader->write(&settings, "settings.ini"); + + /////////////////////////// + // Write fields + + Options fields; + fields["f2d"] = Field2D(1.0); + fields["f3d"] = Field3D(2.0); + fields["fperp"] = FieldPerp(3.0); + OptionsADIOS("fields.bp").write(fields); + + /////////////////////////// + // Read fields + + Options fields_in = OptionsADIOS("fields.bp").read(); + + auto f2d = fields_in["f2d"].as(bout::globals::mesh); + auto f3d = fields_in["f3d"].as(bout::globals::mesh); + auto fperp = fields_in["fperp"].as(bout::globals::mesh); + + Options fields2; + fields2["f2d"] = f2d; + fields2["f3d"] = f3d; + fields2["fperp"] = fperp; + + // Write out again + OptionsADIOS("fields2.bp").write(fields2); + + /////////////////////////// + // Time dependent values + + Options data; + data["scalar"] = 1.0; + data["scalar"].attributes["time_dimension"] = "t"; + + data["field"] = Field3D(2.0); + data["field"].attributes["time_dimension"] = "t"; + + OptionsADIOS("time.bp").write(data); + + // Update time-dependent values + data["scalar"] = 2.0; + data["field"] = Field3D(3.0); + + // Append data to file + OptionsADIOS("time.nc", bout::OptionsIO::FileMode::append).write(data); + + BoutFinalise(); +}; diff --git a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx index 01c5749972..7da6199535 100644 --- a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx +++ b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx @@ -1,6 +1,7 @@ #include "bout/bout.hxx" +#include "bout/options_io.hxx" #include "bout/options_netcdf.hxx" #include "bout/optionsreader.hxx" @@ -77,7 +78,7 @@ int main(int argc, char** argv) { data["field"] = Field3D(3.0); // Append data to file - OptionsNetCDF("time.nc", OptionsNetCDF::FileMode::append).write(data); + OptionsNetCDF("time.nc", bout::OptionsIO::FileMode::append).write(data); BoutFinalise(); }; From 2d7078e9f09fc10a89cb6d4caa32c79304d42caa Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Mon, 11 Sep 2023 15:26:12 -0400 Subject: [PATCH 086/412] fix build errors with cmake --- include/bout/options_adios.hxx | 12 ++++-- include/bout/options_io.hxx | 6 +-- include/bout/options_netcdf.hxx | 8 +++- src/sys/options/options_adios.cxx | 37 +++++++++++++------ src/sys/options/options_io.cxx | 4 -- .../test-options-adios/test-options-adios.cxx | 2 +- 6 files changed, 42 insertions(+), 27 deletions(-) diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index 81c9e85d3e..fe9f0f5316 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -18,7 +18,7 @@ namespace bout { class OptionsADIOS : public OptionsIO { public: - OptionsADIOS(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} + explicit OptionsADIOS(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} OptionsADIOS(const OptionsADIOS&) = default; OptionsADIOS(OptionsADIOS&&) = default; OptionsADIOS& operator=(const OptionsADIOS&) = default; @@ -28,9 +28,15 @@ public: Options read() { throw BoutException("OptionsADIOS not available\n"); } /// Write options to file - void write(const Options& options) { + void write(const Options& options, const std::string& time_dim) { throw BoutException("OptionsADIOS not available\n"); } + + void verifyTimesteps() const{ + throw BoutException("OptionsADIOS not available\n"); + } + + }; } // namespace bout @@ -51,7 +57,7 @@ public: // Constructors need to be defined in implementation due to forward // declaration of ADIOSStream OptionsADIOS(); - explicit OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode = + OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace); ~OptionsADIOS(); OptionsADIOS(const OptionsADIOS&) = delete; diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 49d5d51c04..553f278a01 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -22,12 +22,8 @@ public: }; enum class Library { -#if BOUT_HAS_ADIOS ADIOS, -#endif -#if BOUT_HAS_NETCDF NetCDF, -#endif Invalid }; @@ -41,7 +37,7 @@ public: #endif OptionsIO(); - explicit OptionsIO(std::string filename, FileMode mode = FileMode::replace); + OptionsIO(std::string filename, FileMode mode = FileMode::replace); ~OptionsIO(); OptionsIO(const OptionsIO&) = delete; OptionsIO(OptionsIO&&) noexcept; diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index 0d94594d9d..5229e8fddc 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -30,9 +30,13 @@ public: Options read() { throw BoutException("OptionsNetCDF not available\n"); } /// Write options to file - void write(const Options& options) { + void write(const Options& options, const std::string& time_dim) { throw BoutException("OptionsNetCDF not available\n"); } + + void verifyTimesteps() const{ + throw BoutException("OptionsADIOS not available\n"); + } }; } // namespace bout @@ -55,7 +59,7 @@ public: // Constructors need to be defined in implementation due to forward // declaration of NcFile OptionsNetCDF(); - explicit OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace); + OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace); ~OptionsNetCDF(); OptionsNetCDF(const OptionsNetCDF&) = delete; OptionsNetCDF(OptionsNetCDF&&) noexcept; diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 61ba360439..fde7a3ad56 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -237,32 +237,41 @@ void ADIOSPutVarVisitor::operator()(const std::string& value) { template <> void ADIOSPutVarVisitor::operator()(const Field2D& value) { // Pointer to data. Assumed to be contiguous array - adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNy()}; - adios2::Variable var = stream.io.DefineVariable(varname, shape); + auto mesh = value.getMesh(); + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNy()}; + adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0}; + adios2::Dims count = {1, shape[1], shape[2]}; + adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); stream.engine.Put(var, &value(0, 0)); } template <> void ADIOSPutVarVisitor::operator()(const Field3D& value) { // Pointer to data. Assumed to be contiguous array - adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNz()}; - adios2::Variable var = stream.io.DefineVariable(varname, shape); + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNy(), (size_t)value.getNz()}; + adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0}; + adios2::Dims count = {1, shape[1], shape[2], shape[3]}; + adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); stream.engine.Put(var, &value(0, 0, 0)); } template <> void ADIOSPutVarVisitor::operator()(const FieldPerp& value) { // Pointer to data. Assumed to be contiguous array - adios2::Dims shape = {(size_t)value.getNx(), (size_t)value.getNz()}; - adios2::Variable var = stream.io.DefineVariable(varname, shape); + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNz()}; + adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0}; + adios2::Dims count = {1, shape[1], shape[2]}; + adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); stream.engine.Put(var, &value(0, 0)); } template <> void ADIOSPutVarVisitor::operator()>(const Array& value) { // Pointer to data. Assumed to be contiguous array - adios2::Dims shape = {(size_t)value.size()}; - adios2::Variable var = stream.io.DefineVariable(varname, shape); + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()}; + adios2::Dims start = {(size_t)BoutComm::rank(), 0}; + adios2::Dims count = {1, shape[1]}; + adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); stream.engine.Put(var, value.begin()); } @@ -270,8 +279,10 @@ template <> void ADIOSPutVarVisitor::operator()>(const Matrix& value) { // Pointer to data. Assumed to be contiguous array auto s = value.shape(); - adios2::Dims shape = {(size_t)std::get<0>(s), (size_t)std::get<1>(s)}; - adios2::Variable var = stream.io.DefineVariable(varname, shape); + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), (size_t)std::get<1>(s)}; + adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0}; + adios2::Dims count = {1, shape[1], shape[2]}; + adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); stream.engine.Put(var, value.begin()); } @@ -279,9 +290,11 @@ template <> void ADIOSPutVarVisitor::operator()>(const Tensor& value) { // Pointer to data. Assumed to be contiguous array auto s = value.shape(); - adios2::Dims shape = {(size_t)std::get<0>(s), (size_t)std::get<1>(s), + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), (size_t)std::get<1>(s), (size_t)std::get<2>(s)}; - adios2::Variable var = stream.io.DefineVariable(varname, shape); + adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0}; + adios2::Dims count = {1, shape[1], shape[2], shape[3]}; + adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); stream.engine.Put(var, value.begin()); } diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 8183273e7f..c5bdde50ea 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -11,12 +11,8 @@ #include #include -#if BOUT_HAS_ADIOS #include "bout/options_adios.hxx" -#endif -#if BOUT_HAS_NETCDF #include "bout/options_netcdf.hxx" -#endif namespace bout { diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx index 17eeb17128..12b5bf034d 100644 --- a/tests/integrated/test-options-adios/test-options-adios.cxx +++ b/tests/integrated/test-options-adios/test-options-adios.cxx @@ -79,7 +79,7 @@ int main(int argc, char** argv) { data["field"] = Field3D(3.0); // Append data to file - OptionsADIOS("time.nc", bout::OptionsIO::FileMode::append).write(data); + OptionsADIOS("time.bp", bout::OptionsIO::FileMode::append).write(data); BoutFinalise(); }; From 4aba3e183595e1f88164646ea51e54f1bab15ced Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 11 Sep 2023 17:55:16 -0700 Subject: [PATCH 087/412] ADIOS2 and array index mapping In general file I/O maps a logically rectangular subset of the local (nx, ny, nz) array onto a part of a global array. That global array may be sparse i.e. there might be holes in it. The mapping does not cover the entire local array because we insert communication guard cells around the outside. To perform this mapping we use ADIOS Put() function to get a span of a buffer, and then iterate over fields to copy data into those buffers. --- include/bout/mesh.hxx | 11 +++ src/mesh/impls/bout/boutmesh.cxx | 45 +++++++++- src/sys/options/options_adios.cxx | 137 ++++++++++++++++++++++++++---- 3 files changed, 175 insertions(+), 18 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 45ea392482..2a336383f4 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -503,9 +503,20 @@ public: int GlobalNx, GlobalNy, GlobalNz; ///< Size of the global arrays. Note: can have holes /// Size of the global arrays excluding boundary points. int GlobalNxNoBoundaries, GlobalNyNoBoundaries, GlobalNzNoBoundaries; + + /// Note: These offsets only correct if Y guards are not included in the global array + /// and are corrected in gridfromfile.cxx int OffsetX, OffsetY, OffsetZ; ///< Offset of this mesh within the global array ///< so startx on this processor is OffsetX in global + /// Map between local and global indices + /// (MapGlobalX, MapGlobalY, MapGlobalZ) in the global index space maps to (MapLocalX, MapLocalY, MapLocalZ) locally. + /// Note that boundary cells are included in the global index space, but communication + /// guard cells are not. + int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices + int MapLocalX, MapLocalY, MapLocalZ; ///< Start local indices + int MapCountX, MapCountY, MapCountZ; ///< Size of the mapped region + /// Returns the number of unique cells (i.e., ones not used for /// communication) on this processor for 3D fields. Boundaries /// are only included to a depth of 1. diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index a802d3f5b3..4b5164d488 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -333,7 +333,7 @@ void BoutMesh::setDerivedGridSizes() { } GlobalNx = nx; - GlobalNy = ny + 2 * MYG; + GlobalNy = ny + 2 * MYG; // Note: For double null this should be be 4 * MYG if boundary cells are stored GlobalNz = nz; // If we've got a second pair of diverator legs, we need an extra @@ -374,6 +374,7 @@ void BoutMesh::setDerivedGridSizes() { } // Set global offsets + // Note: These don't properly include guard/boundary cells OffsetX = PE_XIND * MXSUB; OffsetY = PE_YIND * MYSUB; OffsetZ = 0; @@ -392,6 +393,48 @@ void BoutMesh::setDerivedGridSizes() { zstart = MZG; zend = MZG + MZSUB - 1; + + // Mapping local to global indices + if (periodicX) { + // No boundary cells in X + MapGlobalX = PE_XIND * MXSUB; + MapLocalX = MXG; + MapCountX = MXSUB; + } else { + // X boundaries stored for firstX and lastX processors + if (firstX()) { + MapGlobalX = 0; + MapLocalX = 0; + MapCountX = MXG + MXSUB; + } else { + MapGlobalX = MXG + PE_XIND * MXSUB; + MapLocalX = MXG; // Guard cells not included + MapCountX = MXSUB; + } + if (lastX()) { + // Doesn't change the origin, but adds outer X boundary cells + MapCountX += MXG; + } + } + + if (PE_YIND == 0) { + // Include Y boundary cells + MapGlobalY = 0; + MapLocalY = 0; + MapCountY = MYG + MYSUB; + } else { + MapGlobalY = MYG + PE_YIND * MYSUB; + MapLocalY = MYG; + MapCountY = MYSUB; + } + if (PE_YIND == NYPE - 1) { + // Include Y upper boundary region. + MapCountY += MYG; + } + + MapGlobalZ = 0; + MapLocalZ = MZG; // Omit boundary cells + MapCountZ = MZSUB; } int BoutMesh::load() { diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index fde7a3ad56..1e44fff91a 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -223,46 +223,149 @@ struct ADIOSPutVarVisitor { template <> void ADIOSPutVarVisitor::operator()(const bool& value) { + // Scalars are only written from processor 0 + if (BoutComm::rank() != 0) { + return; + } + adios2::Variable var = stream.io.DefineVariable(varname); + stream.engine.Put(var, static_cast(value)); +} + +template <> +void ADIOSPutVarVisitor::operator()(const int& value) { + // Scalars are only written from processor 0 + if (BoutComm::rank() != 0) { + return; + } adios2::Variable var = stream.io.DefineVariable(varname); - stream.engine.Put(var, (int)value); + stream.engine.Put(var, value); +} + +template <> +void ADIOSPutVarVisitor::operator()(const BoutReal& value) { + // Scalars are only written from processor 0 + if (BoutComm::rank() != 0) { + return; + } + adios2::Variable var = stream.io.DefineVariable(varname); + stream.engine.Put(var, value); } template <> void ADIOSPutVarVisitor::operator()(const std::string& value) { + // Scalars are only written from processor 0 + if (BoutComm::rank() != 0) { + return; + } + adios2::Variable var = stream.io.DefineVariable(varname); std::cout << "-- Write string variable " << var.Name() << " value = " << value << std::endl; - stream.engine.Put(var, (std::string)value, adios2::Mode::Sync); + stream.engine.Put(var, value, adios2::Mode::Sync); } template <> void ADIOSPutVarVisitor::operator()(const Field2D& value) { - // Pointer to data. Assumed to be contiguous array + // Get the mesh that describes how local data relates to global arrays auto mesh = value.getMesh(); - adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNy()}; - adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0}; - adios2::Dims count = {1, shape[1], shape[2]}; + + // The global size of this array includes boundary cells but not communication guard cells. + // In general this array will be sparse because it may have gaps. + adios2::Dims shape = {static_cast(mesh->GlobalNx), + static_cast(mesh->GlobalNy)}; + + // Offset of this processor's data into the global array + adios2::Dims start = {static_cast(mesh->MapGlobalX), static_cast(mesh->MapGlobalY)}; + + // The size of the mapped region + adios2::Dims count = {static_cast(mesh->MapCountX), static_cast(mesh->MapCountY)}; adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); - stream.engine.Put(var, &value(0, 0)); + + // Get a Span of an internal engine buffer that we can fill with data + auto span = stream.engine.Put(var); + + // Iterate over the span and the Field2D array + // Note: The Field2D includes communication guard cells that are not written + auto it = span.begin(); + for (int x = mesh->MapLocalX; x < (mesh->MapLocalX + mesh->MapCountX); ++x) { + for (int y = mesh->MapLocalY; y < (mesh->MapLocalY + mesh->MapCountY); ++y) { + *it = value(x, y); + ++it; + } + } + ASSERT1(it == span.end()); } template <> void ADIOSPutVarVisitor::operator()(const Field3D& value) { - // Pointer to data. Assumed to be contiguous array - adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNy(), (size_t)value.getNz()}; - adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0}; - adios2::Dims count = {1, shape[1], shape[2], shape[3]}; + // Get the mesh that describes how local data relates to global arrays + auto mesh = value.getMesh(); + + // The global size of this array includes boundary cells but not communication guard cells. + // In general this array will be sparse because it may have gaps. + adios2::Dims shape = {static_cast(mesh->GlobalNx), + static_cast(mesh->GlobalNy), + static_cast(mesh->GlobalNz)}; + + // Offset of this processor's data into the global array + adios2::Dims start = {static_cast(mesh->MapGlobalX), + static_cast(mesh->MapGlobalY), + static_cast(mesh->MapGlobalZ)}; + + // The size of the mapped region + adios2::Dims count = {static_cast(mesh->MapCountX), + static_cast(mesh->MapCountY), + static_cast(mesh->MapCountZ)}; adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); - stream.engine.Put(var, &value(0, 0, 0)); + + // Get a Span of an internal engine buffer. + auto span = stream.engine.Put(var); + + // Iterate over the span and the Field3D array + // Note: The Field3D includes communication guard cells that are not written + auto it = span.begin(); + for (int x = mesh->MapLocalX; x < (mesh->MapLocalX + mesh->MapCountX); ++x) { + for (int y = mesh->MapLocalY; y < (mesh->MapLocalY + mesh->MapCountY); ++y) { + for (int z = mesh->MapLocalZ; z < (mesh->MapLocalZ + mesh->MapCountZ); ++z) { + *it = value(x, y, z); + ++it; + } + } + } + ASSERT1(it == span.end()); } template <> void ADIOSPutVarVisitor::operator()(const FieldPerp& value) { - // Pointer to data. Assumed to be contiguous array - adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.getNx(), (size_t)value.getNz()}; - adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0}; - adios2::Dims count = {1, shape[1], shape[2]}; + // Get the mesh that describes how local data relates to global arrays + auto mesh = value.getMesh(); + + // The global size of this array includes boundary cells but not communication guard cells. + // In general this array will be sparse because it may have gaps. + adios2::Dims shape = {static_cast(mesh->GlobalNx), + static_cast(mesh->GlobalNz)}; + + // Offset of this processor's data into the global array + adios2::Dims start = {static_cast(mesh->MapGlobalX), + static_cast(mesh->MapGlobalZ)}; + + // The size of the mapped region + adios2::Dims count = {static_cast(mesh->MapCountX), + static_cast(mesh->MapCountZ)}; adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); - stream.engine.Put(var, &value(0, 0)); + + // Get a Span of an internal engine buffer. + auto span = stream.engine.Put(var); + + // Iterate over the span and the Field3D array + // Note: The Field3D includes communication guard cells that are not written + auto it = span.begin(); + for (int x = mesh->MapLocalX; x < (mesh->MapLocalX + mesh->MapCountX); ++x) { + for (int z = mesh->MapLocalZ; z < (mesh->MapLocalZ + mesh->MapCountZ); ++z) { + *it = value(x, z); + ++it; + } + } + ASSERT1(it == span.end()); } template <> From eb309dc13539518e031cfa03679d9698a323c686 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Tue, 12 Sep 2023 17:42:47 -0400 Subject: [PATCH 088/412] Handle ADIOS steps boundary controlled by OptionsIO::verifyTimesteps(). Add helper functions to avoid redefining variables in an adios2::IO object. --- include/bout/adios_object.hxx | 36 +++++-- include/bout/options_adios.hxx | 16 ++- include/bout/options_io.hxx | 6 +- src/sys/adios_object.cxx | 32 +++--- src/sys/options/options_adios.cxx | 172 ++++++++++++++++-------------- 5 files changed, 150 insertions(+), 112 deletions(-) diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx index 47232d685e..7568810cfd 100755 --- a/include/bout/adios_object.hxx +++ b/include/bout/adios_object.hxx @@ -29,14 +29,38 @@ public: adios2::Variable vTime; adios2::Variable vStep; int adiosStep = 0; -}; + bool isInStep = false; // true if BeginStep was called and EndStep was not yet called + + /** create or return the ADIOSStream based on the target file name */ + static ADIOSStream& ADIOSGetStream(const std::string& fname); + + ~ADIOSStream(); -extern ADIOSStream adios_restart; -extern ADIOSStream adios_dump; -//extern ADIOS2Param *adios2params; + template + adios2::Variable GetValueVariable(const std::string& varname) { + auto v = io.InquireVariable(varname); + if (!v) { + v = io.DefineVariable(varname); + } + return v; + } -/** return one of the extern variable based on the target file name */ -ADIOSStream& ADIOSGetStream(const std::string& fname); + template + adios2::Variable GetArrayVariable(const std::string& varname, adios2::Dims& shape) { + adios2::Variable v = io.InquireVariable(varname); + if (!v) { + adios2::Dims start(shape.size()); + v = io.DefineVariable(varname, shape, start, shape); + } else { + v.SetShape(shape); + } + return v; + } + +private: + ADIOSStream(const std::string fname) : fname(fname){}; + std::string fname; +}; /** Set user parameters for an IO group */ void ADIOSSetParameters(const std::string& input, const char delimKeyValue, diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index fe9f0f5316..0b6ae3ab68 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -18,7 +18,9 @@ namespace bout { class OptionsADIOS : public OptionsIO { public: - explicit OptionsADIOS(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} + explicit OptionsADIOS( + const std::string& filename, + bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} OptionsADIOS(const OptionsADIOS&) = default; OptionsADIOS(OptionsADIOS&&) = default; OptionsADIOS& operator=(const OptionsADIOS&) = default; @@ -32,11 +34,7 @@ public: throw BoutException("OptionsADIOS not available\n"); } - void verifyTimesteps() const{ - throw BoutException("OptionsADIOS not available\n"); - } - - + void verifyTimesteps() const { throw BoutException("OptionsADIOS not available\n"); } }; } // namespace bout @@ -57,8 +55,8 @@ public: // Constructors need to be defined in implementation due to forward // declaration of ADIOSStream OptionsADIOS(); - OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode = - bout::OptionsIO::FileMode::replace); + OptionsADIOS(std::string filename, + bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace); ~OptionsADIOS(); OptionsADIOS(const OptionsADIOS&) = delete; OptionsADIOS(OptionsADIOS&&) noexcept; @@ -78,8 +76,6 @@ public: void verifyTimesteps() const; private: - /// Pointer to ADIOS stream so we don't introduce direct dependence - std::unique_ptr stream; }; } // namespace bout diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 553f278a01..5d71382c06 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -21,11 +21,7 @@ public: append ///< Append to file when writing }; - enum class Library { - ADIOS, - NetCDF, - Invalid - }; + enum class Library { ADIOS, NetCDF, Invalid }; static const Library defaultIOLibrary = #if BOUT_HAS_ADIOS diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx index e694e483e0..21bbd8b855 100755 --- a/src/sys/adios_object.cxx +++ b/src/sys/adios_object.cxx @@ -11,9 +11,7 @@ namespace bout { static ADIOSPtr adios = nullptr; -ADIOSStream adios_restart; -ADIOSStream adios_dump; -//ADIOS2Param* adios2params; +static std::unordered_map adiosStreams; void ADIOSInit(MPI_Comm comm) { adios = std::make_shared(comm); } @@ -26,9 +24,7 @@ void ADIOSFinalize() { throw std::runtime_error( "ADIOS needs to be initialized first before calling ADIOSFinalize()"); } - if (adios_dump.adiosStep > 0 && adios_dump.engine) { - adios_dump.engine.Close(); - } + adiosStreams.clear(); adios.reset(); } @@ -50,12 +46,24 @@ IOPtr GetIOPtr(const std::string IOName) { return io; } -ADIOSStream& ADIOSGetStream(const std::string& fname) { - if (fname.find(".restart") != std::string::npos) - return adios_restart; - //if (fname.find(".dmp") != std::string::npos) - // return adios_dump; - return adios_dump; +ADIOSStream::~ADIOSStream() { + if (engine) { + if (isInStep) { + engine.EndStep(); + isInStep = false; + std::cout << "ADIOSStream::~ADIOSStream: END adios file = " << engine.Name() + << " step = " << engine.CurrentStep() << std::endl; + } + engine.Close(); + } +} + +ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname) { + auto it = adiosStreams.find(fname); + if (it == adiosStreams.end()) { + it = adiosStreams.emplace(fname, ADIOSStream(fname)).first; + } + return it->second; } void ADIOSSetParameters(const std::string& input, const char delimKeyValue, diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 1e44fff91a..becd0f51ae 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -17,10 +17,10 @@ namespace bout { -OptionsADIOS::OptionsADIOS() : stream(nullptr) {} +OptionsADIOS::OptionsADIOS() {} OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) - : OptionsIO(filename, mode), stream(nullptr) {} + : OptionsIO(filename, mode) {} OptionsADIOS::~OptionsADIOS() = default; OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; @@ -84,7 +84,7 @@ bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& nam bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, const std::string& type, Options& result) { - bool ret; + bool ret = false; #define declare_template_instantiation(T) \ if (type == adios2::GetType()) { \ ret = readVariable(reader, io, name, result); \ @@ -112,13 +112,14 @@ Options OptionsADIOS::read() { // Open file ADIOSPtr adiosp = GetADIOSPtr(); adios2::IO io; - std::string ioname = "read_"+filename; + std::string ioname = "read_" + filename; try { io = adiosp->AtIO(ioname); } catch (const std::invalid_argument& e) { io = adiosp->DeclareIO(ioname); } + std::cout << "OptionsADIOS::read: open " << filename << std::endl; adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess); if (!reader) { throw BoutException("Could not open ADIOS file '{:s}' for reading", filename); @@ -172,38 +173,12 @@ std::vector verifyTimesteps(adios2::Engine& reader) { } void OptionsADIOS::verifyTimesteps() const { - - // Open file - ADIOSPtr adiosp = GetADIOSPtr(); - adios2::IO io; - try { - io = adiosp->AtIO(filename); - } catch (const std::invalid_argument& e) { - std::cerr << e.what() << '\n'; - io = adiosp->DeclareIO(filename); - } - - adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess); - if (!reader) { - throw BoutException("Could not open ADIOS file '{:s}' for reading", filename); - } - - auto errors = bout::verifyTimesteps(reader); - - if (errors.empty()) { - // No errors - return; - } - - std::string error_string; - for (const auto& error : errors) { - error_string += fmt::format( - " variable: {}; dimension: {}; expected size: {}; actual size: {}\n", - error.variable_name, error.time_name, error.expected_size, error.current_size); - } - throw BoutException("ERROR: When checking timesteps in file '{}', some ({}) variables " - "did not have the expected size(s):\n{}", - filename, errors.size(), error_string); + ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename); + std::cout << "OptionsADIOS::write: END adios step = " << stream.engine.CurrentStep() + << std::endl; + stream.engine.EndStep(); + stream.isInStep = false; + return; } /// Visit a variant type, and put the data into a NcVar @@ -212,7 +187,7 @@ struct ADIOSPutVarVisitor { : varname(name), stream(stream) {} template void operator()(const T& value) { - adios2::Variable var = stream.io.DefineVariable(varname); + adios2::Variable var = stream.GetValueVariable(varname); stream.engine.Put(var, value); } @@ -227,7 +202,7 @@ void ADIOSPutVarVisitor::operator()(const bool& value) { if (BoutComm::rank() != 0) { return; } - adios2::Variable var = stream.io.DefineVariable(varname); + adios2::Variable var = stream.GetValueVariable(varname); stream.engine.Put(var, static_cast(value)); } @@ -237,7 +212,7 @@ void ADIOSPutVarVisitor::operator()(const int& value) { if (BoutComm::rank() != 0) { return; } - adios2::Variable var = stream.io.DefineVariable(varname); + adios2::Variable var = stream.GetValueVariable(varname); stream.engine.Put(var, value); } @@ -247,7 +222,7 @@ void ADIOSPutVarVisitor::operator()(const BoutReal& value) { if (BoutComm::rank() != 0) { return; } - adios2::Variable var = stream.io.DefineVariable(varname); + adios2::Variable var = stream.GetValueVariable(varname); stream.engine.Put(var, value); } @@ -257,9 +232,7 @@ void ADIOSPutVarVisitor::operator()(const std::string& value) { if (BoutComm::rank() != 0) { return; } - - adios2::Variable var = stream.io.DefineVariable(varname); - std::cout << "-- Write string variable " << var.Name() << " value = " << value << std::endl; + adios2::Variable var = stream.GetValueVariable(varname); stream.engine.Put(var, value, adios2::Mode::Sync); } @@ -274,11 +247,14 @@ void ADIOSPutVarVisitor::operator()(const Field2D& value) { static_cast(mesh->GlobalNy)}; // Offset of this processor's data into the global array - adios2::Dims start = {static_cast(mesh->MapGlobalX), static_cast(mesh->MapGlobalY)}; + adios2::Dims start = {static_cast(mesh->MapGlobalX), + static_cast(mesh->MapGlobalY)}; // The size of the mapped region - adios2::Dims count = {static_cast(mesh->MapCountX), static_cast(mesh->MapCountY)}; - adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); + adios2::Dims count = {static_cast(mesh->MapCountX), + static_cast(mesh->MapCountY)}; + adios2::Variable var = stream.GetArrayVariable(varname, shape); + var.SetSelection({start, count}); // Get a Span of an internal engine buffer that we can fill with data auto span = stream.engine.Put(var); @@ -315,8 +291,9 @@ void ADIOSPutVarVisitor::operator()(const Field3D& value) { adios2::Dims count = {static_cast(mesh->MapCountX), static_cast(mesh->MapCountY), static_cast(mesh->MapCountZ)}; - adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); + adios2::Variable var = stream.GetArrayVariable(varname, shape); + var.SetSelection({start, count}); // Get a Span of an internal engine buffer. auto span = stream.engine.Put(var); @@ -351,7 +328,9 @@ void ADIOSPutVarVisitor::operator()(const FieldPerp& value) { // The size of the mapped region adios2::Dims count = {static_cast(mesh->MapCountX), static_cast(mesh->MapCountZ)}; - adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); + + adios2::Variable var = stream.GetArrayVariable(varname, shape); + var.SetSelection({start, count}); // Get a Span of an internal engine buffer. auto span = stream.engine.Put(var); @@ -374,7 +353,8 @@ void ADIOSPutVarVisitor::operator()>(const Array& valu adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()}; adios2::Dims start = {(size_t)BoutComm::rank(), 0}; adios2::Dims count = {1, shape[1]}; - adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); + adios2::Variable var = stream.GetArrayVariable(varname, shape); + var.SetSelection({start, count}); stream.engine.Put(var, value.begin()); } @@ -382,10 +362,12 @@ template <> void ADIOSPutVarVisitor::operator()>(const Matrix& value) { // Pointer to data. Assumed to be contiguous array auto s = value.shape(); - adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), (size_t)std::get<1>(s)}; + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), + (size_t)std::get<1>(s)}; adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0}; adios2::Dims count = {1, shape[1], shape[2]}; - adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); + adios2::Variable var = stream.GetArrayVariable(varname, shape); + var.SetSelection({start, count}); stream.engine.Put(var, value.begin()); } @@ -393,11 +375,12 @@ template <> void ADIOSPutVarVisitor::operator()>(const Tensor& value) { // Pointer to data. Assumed to be contiguous array auto s = value.shape(); - adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), (size_t)std::get<1>(s), - (size_t)std::get<2>(s)}; + adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s), + (size_t)std::get<1>(s), (size_t)std::get<2>(s)}; adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0}; adios2::Dims count = {1, shape[1], shape[2], shape[3]}; - adios2::Variable var = stream.io.DefineVariable(varname, shape, start, count); + adios2::Variable var = stream.GetArrayVariable(varname, shape); + var.SetSelection({start, count}); stream.engine.Put(var, value.begin()); } @@ -438,7 +421,12 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string& if (child.isValue()) { try { auto time_it = child.attributes.find("time_dimension"); - if (time_it != child.attributes.end()) { + if (time_it == child.attributes.end()) { + if (stream.adiosStep > 0) { + // we should only write the non-varying values in the first step + continue; + } + } else { // Has a time dimension const auto& time_name = bout::utils::get(time_it->second); @@ -455,11 +443,10 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string& bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value); // Write attributes - if (!BoutComm::rank()) - { + if (!BoutComm::rank()) { for (const auto& attribute : child.attributes) { - const std::string& att_name = attribute.first; - const auto& att = attribute.second; + const std::string& att_name = attribute.first; + const auto& att = attribute.second; bout::utils::visit(ADIOSPutAttVisitor(varname, att_name, stream), att); } @@ -476,31 +463,58 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string& void OptionsADIOS::write(const Options& options, const std::string& time_dim) { Timer timer("io"); - adios2::Mode mode = - (file_mode == FileMode::replace) ? adios2::Mode::Write : adios2::Mode::Append; - - if (not stream) { - stream = std::make_unique(); + // ADIOSStream is just a BOUT++ object, it does not create anything inside ADIOS + ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename); + + // Need to have an adios2::IO object first, which can only be created once. + if (!stream.io) { + ADIOSPtr adiosp = GetADIOSPtr(); + std::string ioname = "write_" + filename; + try { + stream.io = adiosp->AtIO(ioname); + } catch (const std::invalid_argument& e) { + stream.io = adiosp->DeclareIO(ioname); + stream.io.SetEngine("BP4"); + } } - // Open file - ADIOSPtr adiosp = GetADIOSPtr(); - std::string ioname = "write_"+filename; - try { - stream->io = adiosp->AtIO(ioname); - } catch (const std::invalid_argument& e) { - stream->io = adiosp->DeclareIO(ioname); + if (file_mode == FileMode::append) { + // Open file once and keep it open, close in stream desctructor + if (!stream.engine) { + std::cout << "OptionsADIOS::write: open for append " << filename + << " timedim = " << time_dim << std::endl; + stream.engine = stream.io.Open(filename, adios2::Mode::Append); + if (!stream.engine) { + throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); + } + } else { + std::cout << "OptionsADIOS::write: revisiting append " << filename + << " timedim = " << time_dim << std::endl; + } + } else { + if (!stream.engine) { + std::cout << "OptionsADIOS::write: create " << filename << " timedim = " << time_dim + << std::endl; + stream.engine = stream.io.Open(filename, adios2::Mode::Write); + } else { + std::cout << "OptionsADIOS::write: revisiting write " << filename + << " timedim = " << time_dim << std::endl; + } } - stream->engine = stream->io.Open(filename, mode); - if (!stream->engine) { - throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); + std::cout << " BetweenStepPairs = " << stream.isInStep << std::endl; + + if (!stream.isInStep) { + stream.engine.BeginStep(); + stream.isInStep = true; + stream.adiosStep = stream.engine.CurrentStep(); + std::cout << "OptionsADIOS::write: BEGIN adios step = " << stream.adiosStep + << " BetweenStepPairs = " << stream.isInStep << std::endl; + } else { + std::cout << "OptionsADIOS::write: continue writing adios step = " << stream.adiosStep + << std::endl; } - - stream->engine.BeginStep(); - writeGroup(options, *stream, "", time_dim); - - stream->engine.EndStep(); + writeGroup(options, stream, "", time_dim); } } // namespace bout From 4f55840bc93053ab43a204238386b093cdf4ee90 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Wed, 13 Sep 2023 07:20:37 -0400 Subject: [PATCH 089/412] Added singleWriteFile argument to OptionsIO() which must be set true for restart files when using ADIOS. Replaced the use of Span and manual copy for memory selections to write data without ghost cells. --- include/bout/options_adios.hxx | 3 +- include/bout/options_io.hxx | 17 +- include/bout/options_netcdf.hxx | 12 +- src/physics/physicsmodel.cxx | 4 +- src/sys/options/options_adios.cxx | 171 ++++++++---------- src/sys/options/options_io.cxx | 12 +- src/sys/options/options_netcdf.cxx | 4 +- .../test-options-adios/test-options-adios.cxx | 24 ++- 8 files changed, 120 insertions(+), 127 deletions(-) diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index 0b6ae3ab68..11e18f3a1a 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -56,7 +56,8 @@ public: // declaration of ADIOSStream OptionsADIOS(); OptionsADIOS(std::string filename, - bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace); + bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, + bool singleWriteFile = false); ~OptionsADIOS(); OptionsADIOS(const OptionsADIOS&) = delete; OptionsADIOS(OptionsADIOS&&) noexcept; diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 5d71382c06..7bb689c0b0 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -33,7 +33,8 @@ public: #endif OptionsIO(); - OptionsIO(std::string filename, FileMode mode = FileMode::replace); + OptionsIO(std::string filename, FileMode mode = FileMode::replace, + bool singleWriteFile = false); ~OptionsIO(); OptionsIO(const OptionsIO&) = delete; OptionsIO(OptionsIO&&) noexcept; @@ -47,23 +48,29 @@ public: void write(const Options& options) { write(options, "t"); } virtual void write(const Options& options, const std::string& time_dim) = 0; - /// Check that all variables with the same time dimension have the + /// NetCDF: Check that all variables with the same time dimension have the /// same size in that dimension. Throws BoutException if there are - /// any differences, otherwise is silent + /// any differences, otherwise is silent. + /// ADIOS: Indicate completion of an output step. virtual void verifyTimesteps() const = 0; + /// ADIOS: close file at the end of write(). NetCDF: no effect. + /// restart file must have this true if using ADIOS + //void setSingleWriteFile(const bool flag) { singleWriteFile = flag; }; + protected: /// Name of the file on disk std::string filename; /// How to open the file for writing FileMode file_mode{FileMode::replace}; - Library library = Library::Invalid; + bool singleWriteFile = false; }; std::shared_ptr OptionsIOFactory(std::string filename, OptionsIO::FileMode mode = OptionsIO::FileMode::replace, - const OptionsIO::Library library = OptionsIO::defaultIOLibrary); + const OptionsIO::Library library = OptionsIO::defaultIOLibrary, + const bool singleWriteFile = false); OptionsIO::Library getIOLibrary(Options& options); diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index 5229e8fddc..910c2423fe 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -18,9 +18,10 @@ namespace bout { -class OptionsNetCDF : public OptionsIO{ +class OptionsNetCDF : public OptionsIO { public: - OptionsNetCDF(const std::string& filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} + OptionsNetCDF(const std::string& filename, + bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} OptionsNetCDF(const OptionsNetCDF&) = default; OptionsNetCDF(OptionsNetCDF&&) = default; OptionsNetCDF& operator=(const OptionsNetCDF&) = default; @@ -34,9 +35,7 @@ public: throw BoutException("OptionsNetCDF not available\n"); } - void verifyTimesteps() const{ - throw BoutException("OptionsADIOS not available\n"); - } + void verifyTimesteps() const { throw BoutException("OptionsADIOS not available\n"); } }; } // namespace bout @@ -59,7 +58,8 @@ public: // Constructors need to be defined in implementation due to forward // declaration of NcFile OptionsNetCDF(); - OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace); + OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace, + bool singleWriteFile = false); ~OptionsNetCDF(); OptionsNetCDF(const OptionsNetCDF&) = delete; OptionsNetCDF(OptionsNetCDF&&) noexcept; diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx index e0658b77bb..538851f4cb 100644 --- a/src/physics/physicsmodel.cxx +++ b/src/physics/physicsmodel.cxx @@ -94,8 +94,8 @@ PhysicsModel::PhysicsModel() if (restart_enabled) { std::string restartFileName = bout::getRestartFilename(Options::root(), iolibrary); - restart_file = bout::OptionsIOFactory(restartFileName, - bout::OptionsIO::FileMode::replace, iolibrary); + restart_file = bout::OptionsIOFactory( + restartFileName, bout::OptionsIO::FileMode::replace, iolibrary, true); } } diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index becd0f51ae..10c74b119c 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -19,8 +19,8 @@ namespace bout { OptionsADIOS::OptionsADIOS() {} -OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode) - : OptionsIO(filename, mode) {} +OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode, bool singleWriteFile) + : OptionsIO(filename, mode, singleWriteFile) {} OptionsADIOS::~OptionsADIOS() = default; OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; @@ -74,9 +74,6 @@ bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& nam } } - if (!BoutComm::rank()) - std::cout << " array has " << variable.Steps() << " steps" << std::endl; - /* Need to read the data here */ result[name] = data.data(); return true; @@ -119,7 +116,6 @@ Options OptionsADIOS::read() { io = adiosp->DeclareIO(ioname); } - std::cout << "OptionsADIOS::read: open " << filename << std::endl; adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess); if (!reader) { throw BoutException("Could not open ADIOS file '{:s}' for reading", filename); @@ -152,30 +148,8 @@ Options OptionsADIOS::read() { return result; } -/// Helper struct for returning errors from verifyTimesteps(NcGroup) -struct TimeDimensionError { - std::string variable_name; - std::string time_name; - std::size_t expected_size; - std::size_t current_size; -}; - -std::vector verifyTimesteps(adios2::Engine& reader) { - reader.CurrentStep(); // just to avoid warning on unused variable - - // Variables with mismatched dimension sizes. Note that this might - // be a little odd: if the first variable we come across has the - // "wrong" dimension size, we will actually list all the others as - // being wrong! - std::vector errors; - - return errors; -} - void OptionsADIOS::verifyTimesteps() const { ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename); - std::cout << "OptionsADIOS::write: END adios step = " << stream.engine.CurrentStep() - << std::endl; stream.engine.EndStep(); stream.isInStep = false; return; @@ -253,22 +227,24 @@ void ADIOSPutVarVisitor::operator()(const Field2D& value) { // The size of the mapped region adios2::Dims count = {static_cast(mesh->MapCountX), static_cast(mesh->MapCountY)}; - adios2::Variable var = stream.GetArrayVariable(varname, shape); - var.SetSelection({start, count}); - // Get a Span of an internal engine buffer that we can fill with data - auto span = stream.engine.Put(var); + // Where the actual data starts in data pointer (to exclude ghost cells) + adios2::Dims memStart = {static_cast(mesh->MapLocalX), + static_cast(mesh->MapLocalY)}; - // Iterate over the span and the Field2D array - // Note: The Field2D includes communication guard cells that are not written - auto it = span.begin(); - for (int x = mesh->MapLocalX; x < (mesh->MapLocalX + mesh->MapCountX); ++x) { - for (int y = mesh->MapLocalY; y < (mesh->MapLocalY + mesh->MapCountY); ++y) { - *it = value(x, y); - ++it; - } - } - ASSERT1(it == span.end()); + // The actual size of data pointer in memory (including ghost cells) + adios2::Dims memCount = {static_cast(value.getNx()), + static_cast(value.getNy())}; + + adios2::Variable var = stream.GetArrayVariable(varname, shape); + /* std::cout << "PutVar Field2D rank " << BoutComm::rank() << " var = " << varname + << " shape = " << shape[0] << "x" << shape[1] << " count = " << count[0] + << "x" << count[1] << " Nx*Ny = " << value.getNx() << "x" << value.getNy() + << " memStart = " << memStart[0] << "x" << memStart[1] + << " memCount = " << memCount[0] << "x" << memCount[1] << std::endl;*/ + var.SetSelection({start, count}); + var.SetMemorySelection({memStart, memCount}); + stream.engine.Put(var, &value(0, 0)); } template <> @@ -292,23 +268,27 @@ void ADIOSPutVarVisitor::operator()(const Field3D& value) { static_cast(mesh->MapCountY), static_cast(mesh->MapCountZ)}; + // Where the actual data starts in data pointer (to exclude ghost cells) + adios2::Dims memStart = {static_cast(mesh->MapLocalX), + static_cast(mesh->MapLocalY), + static_cast(mesh->MapLocalZ)}; + + // The actual size of data pointer in memory (including ghost cells) + adios2::Dims memCount = {static_cast(value.getNx()), + static_cast(value.getNy()), + static_cast(value.getNz())}; + adios2::Variable var = stream.GetArrayVariable(varname, shape); + /*std::cout << "PutVar Field3D rank " << BoutComm::rank() << " var = " << varname + << " shape = " << shape[0] << "x" << shape[1] << "x" << shape[2] + << " count = " << count[0] << "x" << count[1] << "x" << count[2] + << " Nx*Ny = " << value.getNx() << "x" << value.getNy() << "x" + << value.getNz() << " memStart = " << memStart[0] << "x" << memStart[1] << "x" + << memStart[2] << " memCount = " << memCount[0] << "x" << memCount[1] << "x" + << memCount[2] << std::endl;*/ var.SetSelection({start, count}); - // Get a Span of an internal engine buffer. - auto span = stream.engine.Put(var); - - // Iterate over the span and the Field3D array - // Note: The Field3D includes communication guard cells that are not written - auto it = span.begin(); - for (int x = mesh->MapLocalX; x < (mesh->MapLocalX + mesh->MapCountX); ++x) { - for (int y = mesh->MapLocalY; y < (mesh->MapLocalY + mesh->MapCountY); ++y) { - for (int z = mesh->MapLocalZ; z < (mesh->MapLocalZ + mesh->MapCountZ); ++z) { - *it = value(x, y, z); - ++it; - } - } - } - ASSERT1(it == span.end()); + var.SetMemorySelection({memStart, memCount}); + stream.engine.Put(var, &value(0, 0, 0)); } template <> @@ -329,22 +309,23 @@ void ADIOSPutVarVisitor::operator()(const FieldPerp& value) { adios2::Dims count = {static_cast(mesh->MapCountX), static_cast(mesh->MapCountZ)}; - adios2::Variable var = stream.GetArrayVariable(varname, shape); - var.SetSelection({start, count}); + // Where the actual data starts in data pointer (to exclude ghost cells) + adios2::Dims memStart = {static_cast(mesh->MapLocalX), + static_cast(mesh->MapLocalZ)}; - // Get a Span of an internal engine buffer. - auto span = stream.engine.Put(var); + // The actual size of data pointer in memory (including ghost cells) + adios2::Dims memCount = {static_cast(value.getNx()), + static_cast(value.getNz())}; - // Iterate over the span and the Field3D array - // Note: The Field3D includes communication guard cells that are not written - auto it = span.begin(); - for (int x = mesh->MapLocalX; x < (mesh->MapLocalX + mesh->MapCountX); ++x) { - for (int z = mesh->MapLocalZ; z < (mesh->MapLocalZ + mesh->MapCountZ); ++z) { - *it = value(x, z); - ++it; - } - } - ASSERT1(it == span.end()); + adios2::Variable var = stream.GetArrayVariable(varname, shape); + /* std::cout << "PutVar FieldPerp rank " << BoutComm::rank() << " var = " << varname + << " shape = " << shape[0] << "x" << shape[1] << " count = " << count[0] + << "x" << count[1] << " Nx*Ny = " << value.getNx() << "x" << value.getNy() + << " memStart = " << memStart[0] << "x" << memStart[1] + << " memCount = " << memCount[0] << "x" << memCount[1] << std::endl; */ + var.SetSelection({start, count}); + var.SetMemorySelection({memStart, memCount}); + stream.engine.Put(var, &value(0, 0)); } template <> @@ -474,47 +455,39 @@ void OptionsADIOS::write(const Options& options, const std::string& time_dim) { stream.io = adiosp->AtIO(ioname); } catch (const std::invalid_argument& e) { stream.io = adiosp->DeclareIO(ioname); - stream.io.SetEngine("BP4"); + stream.io.SetEngine("BP5"); } } - if (file_mode == FileMode::append) { - // Open file once and keep it open, close in stream desctructor - if (!stream.engine) { - std::cout << "OptionsADIOS::write: open for append " << filename - << " timedim = " << time_dim << std::endl; - stream.engine = stream.io.Open(filename, adios2::Mode::Append); - if (!stream.engine) { - throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); - } - } else { - std::cout << "OptionsADIOS::write: revisiting append " << filename - << " timedim = " << time_dim << std::endl; - } - } else { + /* Open file once and keep it open, close in stream desctructor + or close after writing if singleWriteFile == true + */ + if (!stream.engine) { + adios2::Mode amode = + (file_mode == FileMode::append ? adios2::Mode::Append : adios2::Mode::Write); + stream.engine = stream.io.Open(filename, amode); if (!stream.engine) { - std::cout << "OptionsADIOS::write: create " << filename << " timedim = " << time_dim - << std::endl; - stream.engine = stream.io.Open(filename, adios2::Mode::Write); - } else { - std::cout << "OptionsADIOS::write: revisiting write " << filename - << " timedim = " << time_dim << std::endl; + throw BoutException("Could not open ADIOS file '{:s}' for writing", filename); } } - std::cout << " BetweenStepPairs = " << stream.isInStep << std::endl; - + /* Multiple write() calls allowed in a single adios step to output multiple + Options objects in the same step. verifyTimesteps() will indicate the + completion of the step (and adios will publish the step). + */ if (!stream.isInStep) { stream.engine.BeginStep(); stream.isInStep = true; stream.adiosStep = stream.engine.CurrentStep(); - std::cout << "OptionsADIOS::write: BEGIN adios step = " << stream.adiosStep - << " BetweenStepPairs = " << stream.isInStep << std::endl; - } else { - std::cout << "OptionsADIOS::write: continue writing adios step = " << stream.adiosStep - << std::endl; } + writeGroup(options, stream, "", time_dim); + + /* In singleWriteFile mode, we complete the step and close the file */ + if (singleWriteFile) { + stream.engine.EndStep(); + stream.engine.Close(); + } } } // namespace bout diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index c5bdde50ea..6bae83c4c8 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -18,8 +18,8 @@ namespace bout { OptionsIO::OptionsIO() {} -OptionsIO::OptionsIO(std::string filename, FileMode mode) - : filename(std::move(filename)), file_mode(mode) {} +OptionsIO::OptionsIO(std::string filename, FileMode mode, bool singleWriteFile) + : filename(std::move(filename)), file_mode(mode), singleWriteFile(singleWriteFile) {} OptionsIO::~OptionsIO() = default; OptionsIO::OptionsIO(OptionsIO&&) noexcept = default; @@ -43,11 +43,13 @@ OptionsIO::Library getIOLibrary(Options& options) { std::shared_ptr OptionsIOFactory(std::string filename, OptionsIO::FileMode mode, - const OptionsIO::Library library) { + const OptionsIO::Library library, + const bool singleWriteFile) { if (library == OptionsIO::Library::ADIOS) { - return std::make_shared(OptionsADIOS(filename, mode)); + return std::make_shared(OptionsADIOS(filename, mode, singleWriteFile)); } else if (library == OptionsIO::Library::NetCDF) { - return std::make_shared(OptionsNetCDF(filename, mode)); + return std::make_shared( + OptionsNetCDF(filename, mode, singleWriteFile)); } else { return nullptr; } diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx index 8aadcd5363..0262e0cbbd 100644 --- a/src/sys/options/options_netcdf.cxx +++ b/src/sys/options/options_netcdf.cxx @@ -645,8 +645,8 @@ namespace bout { OptionsNetCDF::OptionsNetCDF() : data_file(nullptr) {} -OptionsNetCDF::OptionsNetCDF(std::string filename, FileMode mode) - : OptionsIO(filename, mode), data_file(nullptr) {} +OptionsNetCDF::OptionsNetCDF(std::string filename, FileMode mode, bool singleWriteFile) + : OptionsIO(filename, mode, singleWriteFile), data_file(nullptr) {} OptionsNetCDF::~OptionsNetCDF() = default; OptionsNetCDF::OptionsNetCDF(OptionsNetCDF&&) noexcept = default; diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx index 12b5bf034d..a293aeafc0 100644 --- a/tests/integrated/test-options-adios/test-options-adios.cxx +++ b/tests/integrated/test-options-adios/test-options-adios.cxx @@ -1,9 +1,9 @@ #include "bout/bout.hxx" +#include "bout/options_adios.hxx" #include "bout/options_io.hxx" #include "bout/options_netcdf.hxx" -#include "bout/options_adios.hxx" #include "bout/optionsreader.hxx" using bout::OptionsADIOS; @@ -23,12 +23,13 @@ int main(int argc, char** argv) { reader->write(&values, "test-out.ini"); // Write to a NetCDF file - OptionsADIOS("test-out.bp").write(values); + OptionsADIOS("test-out.bp", bout::OptionsIO::FileMode::replace, true).write(values); /////////////////////////// // Write the BOUT.inp settings to NetCDF file - OptionsADIOS("settings.bp").write(Options::root()); + OptionsADIOS("settings.bp", bout::OptionsIO::FileMode::replace, true) + .write(Options::root()); // Read back in auto settings = OptionsADIOS("settings.bp").read(); @@ -43,7 +44,14 @@ int main(int argc, char** argv) { fields["f2d"] = Field2D(1.0); fields["f3d"] = Field3D(2.0); fields["fperp"] = FieldPerp(3.0); - OptionsADIOS("fields.bp").write(fields); + auto f = OptionsADIOS("fields.bp"); + /* + write() for adios only buffers data but does not guarantee writing to disk + unless singleWriteFile is set to true + */ + f.write(fields); + // indicate completion of step, required to get data on disk + f.verifyTimesteps(); /////////////////////////// // Read fields @@ -60,7 +68,9 @@ int main(int argc, char** argv) { fields2["fperp"] = fperp; // Write out again - OptionsADIOS("fields2.bp").write(fields2); + auto f2 = bout::OptionsIOFactory("fields2.bp", bout::OptionsIO::FileMode::replace, + bout::OptionsIO::Library::ADIOS, true); + f2->write(fields2); /////////////////////////// // Time dependent values @@ -72,14 +82,14 @@ int main(int argc, char** argv) { data["field"] = Field3D(2.0); data["field"].attributes["time_dimension"] = "t"; - OptionsADIOS("time.bp").write(data); + OptionsADIOS("time.bp", bout::OptionsIO::FileMode::replace, true).write(data); // Update time-dependent values data["scalar"] = 2.0; data["field"] = Field3D(3.0); // Append data to file - OptionsADIOS("time.bp", bout::OptionsIO::FileMode::append).write(data); + OptionsADIOS("time.bp", bout::OptionsIO::FileMode::append, true).write(data); BoutFinalise(); }; From 958b7d4feb2e6ca7358c364c74538b8f7db65d7f Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Wed, 13 Sep 2023 08:44:45 -0400 Subject: [PATCH 090/412] Implement reading arrays (BoutReal type only). --- src/sys/options/options_adios.cxx | 62 +++++++++++++++++++++---------- 1 file changed, 42 insertions(+), 20 deletions(-) diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 10c74b119c..04bf242d1a 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -31,7 +31,7 @@ constexpr auto current_time_index_name = "current_time_index"; template bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, - Options& result) { + const std::string& type, Options& result) { std::vector data; adios2::Variable variable = io.InquireVariable(name); @@ -43,48 +43,70 @@ bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& nam } if (variable.ShapeID() == adios2::ShapeID::LocalArray) { - if (!BoutComm::rank()) { - std::cout << " LocalArray not supported" << std::endl; - } - return false; + throw std::invalid_argument( + "ADIOS reader did not implement reading local arrays like " + type + " " + name + + " in file " + reader.Name()); + } + + if (type != "double" && type != "float") { + throw std::invalid_argument( + "ADIOS reader did not implement reading arrays that are not double/float type. " + "Found " + + type + " " + name + " in file " + reader.Name()); + } + + if (type == "double" && sizeof(BoutReal) != sizeof(double)) { + throw std::invalid_argument( + "ADIOS does not allow for implicit type conversions. BoutReal type is " + "float but found " + + type + " " + name + " in file " + reader.Name()); + } + + if (type == "float" && sizeof(BoutReal) != sizeof(float)) { + throw std::invalid_argument( + "ADIOS reader does not allow for implicit type conversions. BoutReal type is " + "double but found " + + type + " " + name + " in file " + reader.Name()); } auto dims = variable.Shape(); auto ndims = dims.size(); + adios2::Variable variableD = io.InquireVariable(name); switch (ndims) { case 1: { - Array value(static_cast(dims[0])); - reader.Get(variable, value.begin(), adios2::Mode::Sync); - //result[name] = value; + Array value(static_cast(dims[0])); + BoutReal* data = value.begin(); + reader.Get(variableD, data, adios2::Mode::Sync); + result[name] = value; break; } case 2: { - Matrix value(static_cast(dims[0]), static_cast(dims[1])); - reader.Get(variable, value.begin(), adios2::Mode::Sync); - //[name] = value; + Matrix value(static_cast(dims[0]), static_cast(dims[1])); + BoutReal* data = value.begin(); + reader.Get(variableD, data, adios2::Mode::Sync); + result[name] = value; break; } case 3: { - Tensor value(static_cast(dims[0]), static_cast(dims[1]), - static_cast(dims[2])); - reader.Get(variable, value.begin(), adios2::Mode::Sync); - //result[name] = value; + Tensor value(static_cast(dims[0]), static_cast(dims[1]), + static_cast(dims[2])); + BoutReal* data = value.begin(); + reader.Get(variableD, data, adios2::Mode::Sync); + result[name] = value; break; } } - /* Need to read the data here */ - result[name] = data.data(); return true; } bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, const std::string& type, Options& result) { bool ret = false; -#define declare_template_instantiation(T) \ - if (type == adios2::GetType()) { \ - ret = readVariable(reader, io, name, result); \ +#define declare_template_instantiation(T) \ + if (type == adios2::GetType()) { \ + ret = readVariable(reader, io, name, type, result); \ } ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) #undef declare_template_instantiation From 54d4d139eadc6ce0baf758a7181194e567cea664 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Wed, 13 Sep 2023 09:27:15 -0400 Subject: [PATCH 091/412] Fix function signature for when ADIOS/NetCDF is not used --- include/bout/options_adios.hxx | 3 ++- include/bout/options_io.hxx | 2 +- include/bout/options_netcdf.hxx | 3 ++- src/sys/adios_object.cxx | 2 -- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index 11e18f3a1a..0c4853bc38 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -20,7 +20,8 @@ class OptionsADIOS : public OptionsIO { public: explicit OptionsADIOS( const std::string& filename, - bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} + bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, + bool singleWriteFile = false) {} OptionsADIOS(const OptionsADIOS&) = default; OptionsADIOS(OptionsADIOS&&) = default; OptionsADIOS& operator=(const OptionsADIOS&) = default; diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 7bb689c0b0..b0ffdb5bb1 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -25,7 +25,7 @@ public: static const Library defaultIOLibrary = #if BOUT_HAS_ADIOS - Library::ADIOS; + Library::NetCDF; #elif BOUT_HAS_NETCDF Library::NetCDF; #else diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx index 910c2423fe..5cbbf7e5fc 100644 --- a/include/bout/options_netcdf.hxx +++ b/include/bout/options_netcdf.hxx @@ -21,7 +21,8 @@ namespace bout { class OptionsNetCDF : public OptionsIO { public: OptionsNetCDF(const std::string& filename, - bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace) {} + bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, + bool singleWriteFile = false) {} OptionsNetCDF(const OptionsNetCDF&) = default; OptionsNetCDF(OptionsNetCDF&&) = default; OptionsNetCDF& operator=(const OptionsNetCDF&) = default; diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx index 21bbd8b855..35126090f8 100755 --- a/src/sys/adios_object.cxx +++ b/src/sys/adios_object.cxx @@ -51,8 +51,6 @@ ADIOSStream::~ADIOSStream() { if (isInStep) { engine.EndStep(); isInStep = false; - std::cout << "ADIOSStream::~ADIOSStream: END adios file = " << engine.Name() - << " step = " << engine.CurrentStep() << std::endl; } engine.Close(); } From c0759ed8d421a9e9eff8b46d82da3a30c9710ced Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 2 Oct 2023 16:40:37 -0700 Subject: [PATCH 092/412] fix writeDefaultOutputFile The Options tree passed to this function contains the data to be written to file, not necessarily the input settings. The output file name should be set from the Options::root() input options, not the input options tree. --- src/sys/options/options_io.cxx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 6bae83c4c8..514307ec59 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -109,7 +109,9 @@ void writeDefaultOutputFile(Options& options, const OptionsIO::Library library) .withDefault(false) ? bout::OptionsIO::FileMode::append : bout::OptionsIO::FileMode::replace; - auto io = OptionsIOFactory(getOutputFilename(options, library), mode, library); + // Note: `options` contains the data to write. + // Get the output file from the `Options::root()` input settings. + auto io = OptionsIOFactory(getOutputFilename(Options::root(), library), mode, library); io->write(options); } From 85aea5a31a88837b80cb7e068513965997a3b4af Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 2 Oct 2023 17:07:55 -0700 Subject: [PATCH 093/412] configure.ac: Add BOUT_HAS_ADIOS Using autoconf this should be defined, but is always "no" Haven't yet regenerated configure script --- configure.ac | 2 ++ 1 file changed, 2 insertions(+) diff --git a/configure.ac b/configure.ac index 0bacd1097a..9fd1a6a945 100644 --- a/configure.ac +++ b/configure.ac @@ -1350,11 +1350,13 @@ BOUT_HAS_CUDA="no" BOUT_HAS_RAJA="no" BOUT_HAS_UMPIRE="no" BOUT_HAS_CALIPER="no" +BOUT_HAS_ADIOS="no" BOUT_DEFINE_SUBST(BOUT_HAS_CUDA, [Enable CUDA]) BOUT_DEFINE_SUBST(BOUT_HAS_RAJA, [RAJA support]) BOUT_DEFINE_SUBST(BOUT_HAS_UMPIRE, [Umpire support]) BOUT_DEFINE_SUBST(BOUT_HAS_CALIPER, [Caliper support]) +BOUT_DEFINE_SUBST(BOUT_HAS_ADIOS, [ADIOS support]) ############################################################# # Write configuration to bout-config From 115ed0ac58afeb44acacb8e70516f607834c246a Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 2 Oct 2023 17:42:21 -0700 Subject: [PATCH 094/412] Update configure script --- autoconf_build_defines.hxx.in | 123 ++++++++++++++++++++++++++++++++-- configure | 40 +++++++---- 2 files changed, 147 insertions(+), 16 deletions(-) diff --git a/autoconf_build_defines.hxx.in b/autoconf_build_defines.hxx.in index a1f23082a1..7dc2daf5d2 100644 --- a/autoconf_build_defines.hxx.in +++ b/autoconf_build_defines.hxx.in @@ -3,12 +3,18 @@ /* Runtime error checking level */ #undef BOUT_CHECK_LEVEL +/* ADIOS support */ +#undef BOUT_HAS_ADIOS + /* ARKODE support */ #undef BOUT_HAS_ARKODE /* Caliper support */ #undef BOUT_HAS_CALIPER +/* Enable CUDA */ +#undef BOUT_HAS_CUDA + /* CVODE support */ #undef BOUT_HAS_CVODE @@ -75,9 +81,6 @@ /* Enable color logs option */ #undef BOUT_USE_COLOR -/* Enable CUDA */ -#undef BOUT_HAS_CUDA - /* Is the metric field 3D */ #undef BOUT_USE_METRIC_3D @@ -99,4 +102,116 @@ /* Enable field name tracking */ #undef BOUT_USE_TRACK -// NOTE TO DEVELOPERS: PLEASE KEEP THIS LINE AND DELETE AUTOGENERATED CONTENT BELOW! +/* Define to 1 if translation of program messages to the user's native + language is requested. */ +#undef ENABLE_NLS + +/* Define to 1 if you have the `backtrace' function. */ +#undef HAVE_BACKTRACE + +/* Define to 1 if you have the Mac OS X function CFLocaleCopyCurrent in the + CoreFoundation framework. */ +#undef HAVE_CFLOCALECOPYCURRENT + +/* Define to 1 if you have the Mac OS X function CFPreferencesCopyAppValue in + the CoreFoundation framework. */ +#undef HAVE_CFPREFERENCESCOPYAPPVALUE + +/* define if the compiler supports basic C++14 syntax */ +#undef HAVE_CXX14 + +/* Define if the GNU dcgettext() function is already present or preinstalled. + */ +#undef HAVE_DCGETTEXT + +/* Define to 1 if you have the header file. */ +#undef HAVE_DLFCN_H + +/* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */ +#undef HAVE_DOPRNT + +/* Define to 1 if you have the header file. */ +#undef HAVE_EXECINFO_H + +/* Define if the GNU gettext() function is already present or preinstalled. */ +#undef HAVE_GETTEXT + +/* Define if you have the iconv() function and it works. */ +#undef HAVE_ICONV + +/* Define to 1 if you have the header file. */ +#undef HAVE_INTTYPES_H + +/* Define to 1 if you have the `m' library (-lm). */ +#undef HAVE_LIBM + +/* Define to 1 if your system has a GNU libc compatible `malloc' function, and + to 0 otherwise. */ +#undef HAVE_MALLOC + +/* Define to 1 if you have the header file. */ +#undef HAVE_MALLOC_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_MEMORY_H + +/* Define if you have the MPI library. */ +#undef HAVE_MPI + +/* Define to 1 if you have the `popen' function. */ +#undef HAVE_POPEN + +/* Define to 1 if your system has a GNU libc compatible `realloc' function, + and to 0 otherwise. */ +#undef HAVE_REALLOC + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDINT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDLIB_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRINGS_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRING_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_STAT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TYPES_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_UNISTD_H + +/* Define to 1 if you have the `vprintf' function. */ +#undef HAVE_VPRINTF + +/* Define to the address where bug reports for this package should be sent. */ +#undef PACKAGE_BUGREPORT + +/* Define to the full name of this package. */ +#undef PACKAGE_NAME + +/* Define to the full name and version of this package. */ +#undef PACKAGE_STRING + +/* Define to the one symbol short name of this package. */ +#undef PACKAGE_TARNAME + +/* Define to the home page for this package. */ +#undef PACKAGE_URL + +/* Define to the version of this package. */ +#undef PACKAGE_VERSION + +/* Define to 1 if you have the ANSI C header files. */ +#undef STDC_HEADERS + +/* Define to rpl_malloc if the replacement function should be used. */ +#undef malloc + +/* Define to rpl_realloc if the replacement function should be used. */ +#undef realloc diff --git a/configure b/configure index 359fd6d7a9..e2af9bd42f 100755 --- a/configure +++ b/configure @@ -677,6 +677,7 @@ BOUT_INCLUDE_PATH BOUT_LIB_PATH CONFIG_LDFLAGS CONFIG_CFLAGS +BOUT_HAS_ADIOS BOUT_HAS_CALIPER BOUT_HAS_UMPIRE BOUT_HAS_RAJA @@ -2402,6 +2403,8 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var. ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. + + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: ./configure is deprecated and will be removed in a future version, please use CMake instead" >&5 $as_echo "$as_me: WARNING: ./configure is deprecated and will be removed in a future version, please use CMake instead" >&2;} @@ -7909,8 +7912,8 @@ else pkg_failed=no -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for PETSc >= 3.4.0 " >&5 -$as_echo_n "checking for PETSc >= 3.4.0 ... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for PETSC" >&5 +$as_echo_n "checking for PETSC... " >&6; } if test -n "$PETSC_CFLAGS"; then pkg_cv_PETSC_CFLAGS="$PETSC_CFLAGS" @@ -7950,7 +7953,7 @@ fi if test $pkg_failed = yes; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then @@ -7969,8 +7972,8 @@ fi pkg_failed=no -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for petsc >= 3.4.0 " >&5 -$as_echo_n "checking for petsc >= 3.4.0 ... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for PETSC" >&5 +$as_echo_n "checking for PETSC... " >&6; } if test -n "$PETSC_CFLAGS"; then pkg_cv_PETSC_CFLAGS="$PETSC_CFLAGS" @@ -8010,7 +8013,7 @@ fi if test $pkg_failed = yes; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then @@ -8035,7 +8038,7 @@ fi " "$LINENO" 5 elif test $pkg_failed = untried; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } as_fn_error $? "--with-petsc was specified but could not find PETSc distribution. @@ -8054,13 +8057,13 @@ $as_echo "yes" >&6; } fi elif test $pkg_failed = untried; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } pkg_failed=no -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for petsc >= 3.4.0 " >&5 -$as_echo_n "checking for petsc >= 3.4.0 ... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for PETSC" >&5 +$as_echo_n "checking for PETSC... " >&6; } if test -n "$PETSC_CFLAGS"; then pkg_cv_PETSC_CFLAGS="$PETSC_CFLAGS" @@ -8100,7 +8103,7 @@ fi if test $pkg_failed = yes; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then @@ -8125,7 +8128,7 @@ fi " "$LINENO" 5 elif test $pkg_failed = untried; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } as_fn_error $? "--with-petsc was specified but could not find PETSc distribution. @@ -15268,6 +15271,7 @@ BOUT_HAS_CUDA="no" BOUT_HAS_RAJA="no" BOUT_HAS_UMPIRE="no" BOUT_HAS_CALIPER="no" +BOUT_HAS_ADIOS="no" if test "x$BOUT_HAS_CUDA" = "xyes"; then : @@ -15318,6 +15322,18 @@ fi +if test "x$BOUT_HAS_ADIOS" = "xyes"; then : + +$as_echo "#define BOUT_HAS_ADIOS 1" >>confdefs.h + +else + +$as_echo "#define BOUT_HAS_ADIOS 0" >>confdefs.h + +fi + + + ############################################################# # Write configuration to bout-config ############################################################# From 0db37d650ac4706583e53f57a2cb1ff6feda3fbf Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 2 Oct 2023 17:54:28 -0700 Subject: [PATCH 095/412] Trying again with autoreconf Generated new configure script, updated autoconf_build_defines.hxx.in --- configure | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/configure b/configure index e2af9bd42f..7944667781 100755 --- a/configure +++ b/configure @@ -1,6 +1,10 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. +<<<<<<< HEAD # Generated by GNU Autoconf 2.69 for BOUT++ 5.1.0. +======= +# Generated by GNU Autoconf 2.69 for BOUT++ 5.0.0. +>>>>>>> a889598fd (Trying again with autoreconf) # # Report bugs to . # @@ -681,7 +685,11 @@ BOUT_HAS_ADIOS BOUT_HAS_CALIPER BOUT_HAS_UMPIRE BOUT_HAS_RAJA +<<<<<<< HEAD BOUT_HAS_CUDA +======= +BOUT_USE_CUDA +>>>>>>> a889598fd (Trying again with autoreconf) LTLIBOBJS POSUB LTLIBINTL @@ -1618,7 +1626,11 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF +<<<<<<< HEAD BOUT++ configure 5.1.0 +======= +BOUT++ configure 5.0.0 +>>>>>>> a889598fd (Trying again with autoreconf) generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -2025,7 +2037,11 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. +<<<<<<< HEAD It was created by BOUT++ $as_me 5.1.0, which was +======= +It was created by BOUT++ $as_me 5.0.0, which was +>>>>>>> a889598fd (Trying again with autoreconf) generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -14453,7 +14469,11 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" +<<<<<<< HEAD This file was extended by BOUT++ $as_me 5.1.0, which was +======= +This file was extended by BOUT++ $as_me 5.0.0, which was +>>>>>>> a889598fd (Trying again with autoreconf) generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -14514,7 +14534,11 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ +<<<<<<< HEAD BOUT++ config.status 5.1.0 +======= +BOUT++ config.status 5.0.0 +>>>>>>> a889598fd (Trying again with autoreconf) configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" @@ -15274,6 +15298,7 @@ BOUT_HAS_CALIPER="no" BOUT_HAS_ADIOS="no" +<<<<<<< HEAD if test "x$BOUT_HAS_CUDA" = "xyes"; then : $as_echo "#define BOUT_HAS_CUDA 1" >>confdefs.h @@ -15281,6 +15306,15 @@ $as_echo "#define BOUT_HAS_CUDA 1" >>confdefs.h else $as_echo "#define BOUT_HAS_CUDA 0" >>confdefs.h +======= +if test "x$BOUT_USE_CUDA" = "xyes"; then : + +$as_echo "#define BOUT_USE_CUDA 1" >>confdefs.h + +else + +$as_echo "#define BOUT_USE_CUDA 0" >>confdefs.h +>>>>>>> a889598fd (Trying again with autoreconf) fi @@ -16225,7 +16259,11 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" +<<<<<<< HEAD This file was extended by BOUT++ $as_me 5.1.0, which was +======= +This file was extended by BOUT++ $as_me 5.0.0, which was +>>>>>>> a889598fd (Trying again with autoreconf) generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -16295,7 +16333,11 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ +<<<<<<< HEAD BOUT++ config.status 5.1.0 +======= +BOUT++ config.status 5.0.0 +>>>>>>> a889598fd (Trying again with autoreconf) configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" From 88eb401a825d54ab868c03acf2fb901876eb8865 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 3 Oct 2023 15:38:04 -0700 Subject: [PATCH 096/412] Autoconf build: Add options_io.cxx Needs to be added to the makefile to be built. --- src/sys/options/makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sys/options/makefile b/src/sys/options/makefile index e38608b68c..f8f0c76f69 100644 --- a/src/sys/options/makefile +++ b/src/sys/options/makefile @@ -1,5 +1,5 @@ BOUT_TOP = ../../.. -SOURCEC = options_ini.cxx options_netcdf.cxx +SOURCEC = options_ini.cxx options_netcdf.cxx options_io.cxx SOURCEH = $(SOURCEC:%.cxx=%.hxx) globals.hxx bout_types.hxx multiostream.hxx TARGET = lib From 37fbcd4881cbd9970b9a6cc02f3bc2e6b3f2d2e6 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 3 Oct 2023 18:27:37 -0700 Subject: [PATCH 097/412] test-options-adios requires ADIOS Add --has-adios option to bout-config, and require in test-options-adios integrated test. --- bin/bout-config.in | 7 +++++++ tests/integrated/test-options-adios/runtest | 1 + tests/integrated/test-options-adios/test-options-adios.cxx | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/bin/bout-config.in b/bin/bout-config.in index 697d3ddc71..a9045fff39 100755 --- a/bin/bout-config.in +++ b/bin/bout-config.in @@ -29,6 +29,7 @@ idlpath="@IDLCONFIGPATH@" pythonpath="@PYTHONCONFIGPATH@" has_netcdf="@BOUT_HAS_NETCDF@" +has_adios="@BOUT_HAS_ADIOS@" has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@" has_pnetcdf="@BOUT_HAS_PNETCDF@" has_pvode="@BOUT_HAS_PVODE@" @@ -71,6 +72,7 @@ Available values for OPTION include: --python Python path --has-netcdf NetCDF file support + --has-adios ADIOS file support --has-legacy-netcdf Legacy NetCDF file support --has-pnetcdf Parallel NetCDF file support --has-pvode PVODE solver support @@ -109,6 +111,7 @@ all() echo " --python -> $pythonpath" echo echo " --has-netcdf -> $has_netcdf" + echo " --has-adios -> $has_adios" echo " --has-legacy-netcdf -> $has_legacy_netcdf" echo " --has-pnetcdf -> $has_pnetcdf" echo " --has-pvode -> $has_pvode" @@ -197,6 +200,10 @@ while test $# -gt 0; do echo $has_netcdf ;; + --has-adios) + echo $has_adios + ;; + --has-legacy-netcdf) echo $has_legacy_netcdf ;; diff --git a/tests/integrated/test-options-adios/runtest b/tests/integrated/test-options-adios/runtest index 7a3541df2d..1621c686a3 100755 --- a/tests/integrated/test-options-adios/runtest +++ b/tests/integrated/test-options-adios/runtest @@ -2,6 +2,7 @@ # Note: This test requires NCDF4, whereas on Travis NCDF is used # requires: netcdf +# requires: adios # requires: not legacy_netcdf from boututils.datafile import DataFile diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx index a293aeafc0..efd74344c0 100644 --- a/tests/integrated/test-options-adios/test-options-adios.cxx +++ b/tests/integrated/test-options-adios/test-options-adios.cxx @@ -22,7 +22,7 @@ int main(int argc, char** argv) { OptionsReader* reader = OptionsReader::getInstance(); reader->write(&values, "test-out.ini"); - // Write to a NetCDF file + // Write to ADIOS file OptionsADIOS("test-out.bp", bout::OptionsIO::FileMode::replace, true).write(values); /////////////////////////// From 59492bea2ca36214e6cb0256954fa811a5004fcd Mon Sep 17 00:00:00 2001 From: bendudson Date: Thu, 12 Oct 2023 14:41:14 +0000 Subject: [PATCH 098/412] Apply clang-format changes --- src/bout++.cxx | 6 +++--- src/mesh/impls/bout/boutmesh.cxx | 4 +++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/bout++.cxx b/src/bout++.cxx index 6de8798622..369497a154 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -650,7 +650,7 @@ void setupOutput(const std::string& data_dir, const std::string& log_file, int v { Output& output = *Output::getInstance(); if (MYPE == 0) { - output.enable(); // Enable writing to stdout + output.enable(); // Enable writing to stdout } else { output.disable(); // No writing to stdout } @@ -798,7 +798,7 @@ int BoutFinalise(bool write_settings) { bout::HypreLib::cleanup(); #if BOUT_HAS_ADIOS - bout::ADIOSFinalize(); + bout::ADIOSFinalize(); #endif // MPI communicator, including MPI_Finalize() @@ -1056,6 +1056,6 @@ void RunMetrics::writeProgress(BoutReal simtime, bool output_split) { 100. * wtime_comms / wtime, // Communications 100. * wtime_io / wtime, // I/O 100. * (wtime - wtime_io - wtime_rhs) - / wtime); // Everything else + / wtime); // Everything else } } diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 4b5164d488..956aba0f79 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -333,7 +333,9 @@ void BoutMesh::setDerivedGridSizes() { } GlobalNx = nx; - GlobalNy = ny + 2 * MYG; // Note: For double null this should be be 4 * MYG if boundary cells are stored + GlobalNy = + ny + + 2 * MYG; // Note: For double null this should be be 4 * MYG if boundary cells are stored GlobalNz = nz; // If we've got a second pair of diverator legs, we need an extra From c41e7dfb07537c63079f266b8150b964e5cd50dd Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 12 Oct 2023 17:32:42 +0100 Subject: [PATCH 099/412] Docs: Remove remaining references to `./configure` from docs --- manual/sphinx/user_docs/advanced_install.rst | 144 ++----------------- manual/sphinx/user_docs/installing.rst | 57 +------- 2 files changed, 12 insertions(+), 189 deletions(-) diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst index b2b6b49c80..957173b820 100644 --- a/manual/sphinx/user_docs/advanced_install.rst +++ b/manual/sphinx/user_docs/advanced_install.rst @@ -47,7 +47,7 @@ source directory: CHECK=no bin/bout-build-deps.sh # or with openmp - not tested, maybe not good to add it to FFTW PETSCFLAGS=--with-openmp=1 FFTWFLAGS="--enable-avx512 --enable-avx-128-fma --with-openmp --enable-threads" bin/bout-build-deps.sh - # and add "--enable-openmp" to ./configure + # and add "-DBOUT_ENABLE_OPENMP=ON" to cmake configure line Infos about options and further info can be obtained by running: @@ -84,29 +84,6 @@ When using CMake on Cray systems like Archer, you need to pass ``-DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment`` so that the Cray compiler wrappers are detected properly. -KNL @ Archer -~~~~~~~~~~~~ - -To use the KNL system, configure BOUT++ as follows: - -.. code-block:: bash - - ./configure MPICXX=CC --host=knl --with-netcdf --with-pnetcdf=no --with-hypre=no CXXFLAGS="-xMIC-AVX512 -D_GLIBCXX_USE_CXX11_ABI=0" - -Atlas -~~~~~ - -.. code-block:: bash - - ./configure --with-netcdf=/usr/local/tools/hdf5-gnu-serial-1.8.1/lib --with-fftw=/usr/local --with-pdb=/usr/gapps/pact/new/lnx-2.5-ib/gnu - -Cab -~~~ - -.. code-block:: bash - - ./configure --with-netcdf=/usr/local/tools/hdf5-gnu-serial-1.8.1/lib --with-fftw=/usr/local/tools/fftw3-3.2 --with-pdb=/usr/gapps/pact/new/lnx-2.5-ib/gnu - Cori ~~~~ @@ -152,52 +129,6 @@ on GPU machines, including Cori. Note that in order to access GPU nodes a request must be made through `NERSC services `_. -Edison -~~~~~~ - -.. code-block:: bash - - module swap PrgEnv-intel PrgEnv-gnu - module load fftw - ./configure MPICC=cc MPICXX=CC --with-netcdf=/global/u2/c/chma/PUBLIC/netcdf_edison/netcdf --with-fftw=/opt/fftw/3.3.0.1/x86_64 - -Hoffman2 -~~~~~~~~ - -.. code-block:: bash - - ./configure --with-netcdf=/u/local/apps/netcdf/current --with-fftw=/u/local/apps/fftw3/current --with-cvode=/u/local/apps/sundials/2.4.0 --with-lapack=/u/local/apps/lapack/current - -Hopper -~~~~~~ - -.. code-block:: bash - - module swap PrgEnv-pgi PrgEnv-gnu - module load netcdf - module swap netcdf netcdf/4.1.3 - module swap gcc gcc/4.6.3 - ./configure MPICC=cc MPICXX=CC --with-fftw=/opt/fftw/3.2.2.1 --with-pdb=/global/homes/u/umansky/PUBLIC/PACT_HOPP2/pact - -Hyperion -~~~~~~~~ - -With the bash shell use - -.. code-block:: bash - - export PETSC_DIR=~farley9/projects/petsc/petsc-3.2-p1 - export PETSC_ARCH=arch-c - ./configure --with-netcdf=/usr/local/tools/netcdf-gnu-4.1 --with-fftw=/usr/local MPICXX=mpiCC EXTRA_LIBS=-lcurl --with-petsc --with-cvode=~farley9/local --with-ida=~farley9/local - -With the tcsh shell use - -.. code-block:: tcsh - - setenv PETSC_DIR ~farley9/projects/petsc/petsc-3.2-p1 - setenv PETSC_ARCH arch-c - ./configure --with-netcdf=/usr/local/tools/netcdf-gnu-4.1 --with-fftw=/usr/local MPICXX=mpiCC EXTRA_LIBS=-lcurl --with-petsc --with-cvode=~farley9/local --with-ida=~farley9/local - MacOS / Apple Darwin ~~~~~~~~~~~~~~~~~~~~ @@ -211,71 +142,9 @@ Compiling with Apple Clang 12, the following configuration has been known to wor where ```` is the path to the build directory -Marconi -~~~~~~~ - -.. code-block:: bash - - module load intel intelmpi fftw lapack - module load szip zlib/1.2.8--gnu--6.1.0 - module load hdf5/1.8.17--intel--pe-xe-2017--binary - module load netcdf-cxx4 - module load python - -To compile for the SKL partition, configure with - -.. code-block:: bash - - ./configure --enable-checks=0 CPPFLAGS="-Ofast -funroll-loops -xCORE-AVX512 -mtune=skylake" --host skl - -to enable AVX512 vectorization. - -.. note:: As of 20/04/2018, an issue with the netcdf and netcdf-cxx4 - modules means that you will need to remove ``-lnetcdf`` from - ``EXTRA_LIBS`` in ``make.config`` after running - ``./configure`` and before running ``make``. ``-lnetcdf`` - needs also to be removed from ``bin/bout-config`` to allow a - successful build of the python interface. Recreation of - ``boutpp.pyx`` needs to be manually triggered, if - ``boutpp.pyx`` has already been created. - -Marconi with gnu compilers -************************** - -It is also possible to configure on Marconi using gnu compilers, which may give better performance. A set of modules which work as of 4/5/2021 is - -.. code-block:: bash - - module load env-skl - module load profile/advanced - module load intel/pe-xe-2018--binary # note need to keep the 'intel' module loaded in order for shared libraries needed by numpy/scipy to be available - module load gnu/7.3.0 - module load openmpi/4.0.1--gnu--7.3.0 - module load mkl/2017--binary - module load python/3.6.4 - module load szip/2.1--gnu--6.1.0 zlib/1.2.8--gnu--6.1.0 - - bin/bout-build-deps.sh - -And follow the instructions. The result could look something like this with <...> the appropriate path. - -* for an optimized build (some experimentation with optimisation flags would be welcome, please share the results if you do!):: - - ./configure --enable-optimize=3 --enable-checks=no --enable-static --with-netcdf=<...> --with-sundials=<...> --with-fftw=<...> --with-petsc=<...> - -* for a debugging build:: - - ./configure --enable-debug --enable-static --with-netcdf=<...> --with-sundials=<...> --with-fftw=<...> --with-petsc=<...> - -Ubgl -~~~~ - -.. code-block:: bash - - ./configure --with-netcdf CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK CFLAGS=-DMPICH_IGNORE_CXX_SEEK --with-pdb=/usr/gapps/pact/new_s/lnx-2.5-ib --with-netcdf=/usr/local/tools/netcdf/netcdf-4.1_c++ -Raven / Cobra / Draco -~~~~~~~~~~~~~~~~~~~~~ +MPCDF HPC Systems +~~~~~~~~~~~~~~~~~ .. code-block:: bash module purge # or at least onload intel and impi and mkl @@ -290,7 +159,12 @@ for a production run use: .. code-block:: bash module load bout-dep - ./configure --with-netcdf=$BOUT_DEP --with-sundials=$BOUT_DEP --with-fftw=$BOUT_DEP --with-petsc=$BOUT_DEP --enable-optimize --enable-openmp + cmake .. -DBOUT_USE_NETCDF=ON -DnetCDF_ROOT=$BOUT_DEP -DnetCDFCxx_ROOT=$BOUT_DEP \ + -DBOUT_USE_PETSC=ON -DPETSC_DIR=$BOUT_DEP \ + -DBOUT_USE_FFTW=ON -DFFTW_ROOT=$BOUT_DEP \ + -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=$BOUT_DEP \ + -DBOUT_ENABLE_OPENMP=ON \ + -DCMAKE_BUILD_TYPE=Release File formats diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst index 7f8c26ffbe..8e3daaa57a 100644 --- a/manual/sphinx/user_docs/installing.rst +++ b/manual/sphinx/user_docs/installing.rst @@ -218,10 +218,10 @@ To get precompiled BOUT++ run:: $ # get the python3 modules - python2 is available as well $ sudo dnf install python3-bout++ -.. _sec-cmake: +.. _sec-config-bout: -CMake ------ +Configuring BOUT++ +------------------ BOUT++ uses the `CMake `_ build system generator. You will need CMake >= 3.17. @@ -391,57 +391,6 @@ The recommended way to use ``googletest`` is to compile it at the same time as your project, therefore there is no option to use an external installation for that. -.. _sec-config-bout: - -./configure ------------ - -.. warning:: - As of BOUT++ 5.0, ``./configure`` is no longer supported and will - be removed in 6.0. Please switch to using CMake to build BOUT++. - -To compile BOUT++, you first need to configure it. -Go into the ``BOUT-dev`` directory and run:: - - $ ./configure - -If this finishes by printing a summary, and paths for IDL, Python, and -Octave, then the libraries are set up and you can skip to the next -section. If you see a message -“``ERROR: FFTW not found. Required by BOUT++``” then make sure -FFTW-3 is installed (See the previous section on :ref:`installing dependencies ` ). - -If FFTW-3 is installed in a non-standard location, you can specify the -directory with the ``–with-fftw=`` option e.g:: - - $ ./configure --with-fftw=$HOME/local - -Configure should now find FFTW, and search for the NetCDF library. If -configure finishes successfully, then skip to the next section, but if -you see a message ``NetCDF support disabled`` then configure couldn’t -find the NetCDF library. This will be followed by a message -``ERROR: At least one file format must be supported``. Check that you have -NetCDF installed (See the previous section on :ref:`installing dependencies ` ). - -Like the FFTW-3 library, if NetCDF is installed in a non-standard location then -you can specify the directory with the ``--with-netcdf=`` option e.g.:: - - $ ./configure --with-fftw=$HOME/local --with-netcdf=$HOME/local - -which should now finish successfully, printing a summary of the -configuration:: - - Configuration summary - PETSc support: no - SLEPc support: no - IDA support: yes - CVODE support: yes - ARKODE support: yes - NetCDF support: yes - Parallel-NetCDF support: no - -If not, see :ref:`sec-advancedinstall` for some things you can try to -resolve common problems. Working with an active ``conda`` environment ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From e9dda7bf251bf3fd573b2632ab016c8d81302e02 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 12 Oct 2023 17:33:58 +0100 Subject: [PATCH 100/412] Remove all autoconf files --- autoconf_build_defines.hxx.in | 102 - configure | 17273 ---------------- configure.ac | 1499 -- examples/2Dturbulence_multigrid/makefile | 6 - examples/6field-simple/makefile | 6 - examples/IMEX/advection-diffusion/makefile | 6 - examples/IMEX/advection-reaction/makefile | 6 - examples/IMEX/diffusion-nl/makefile | 6 - examples/IMEX/drift-wave-constraint/makefile | 6 - examples/IMEX/drift-wave/makefile | 6 - examples/advdiff/makefile | 6 - examples/advdiff2/makefile | 7 - examples/backtrace/makefile | 11 - examples/blob2d-laplacexz/makefile | 6 - examples/blob2d-outerloop/makefile | 6 - examples/blob2d/makefile | 6 - .../boundary-conditions/advection/makefile | 6 - examples/conducting-wall-mode/makefile | 6 - 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src/invert/laplace/impls/petsc3damg/makefile | 8 - src/invert/laplace/impls/serial_band/makefile | 8 - src/invert/laplace/impls/serial_tri/makefile | 8 - src/invert/laplace/impls/spt/makefile | 8 - src/invert/laplace/makefile | 9 - src/invert/laplacexy/makefile | 7 - src/invert/laplacexy2/makefile | 7 - src/invert/laplacexz/impls/cyclic/makefile | 7 - src/invert/laplacexz/impls/makefile | 7 - src/invert/laplacexz/impls/petsc/makefile | 7 - src/invert/laplacexz/makefile | 8 - src/invert/makefile | 9 - src/invert/parderiv/impls/cyclic/makefile | 8 - src/invert/parderiv/impls/makefile | 7 - src/invert/parderiv/makefile | 9 - src/invert/pardiv/impls/cyclic/makefile | 8 - src/invert/pardiv/impls/makefile | 7 - src/invert/pardiv/makefile | 8 - src/makefile.in | 96 - src/mesh/data/makefile | 8 - src/mesh/impls/bout/makefile | 8 - src/mesh/impls/makefile | 7 - src/mesh/interpolation/makefile | 10 - src/mesh/makefile | 14 - src/mesh/parallel/makefile | 8 - src/physics/makefile | 8 - src/solver/impls/adams_bashforth/makefile | 8 - src/solver/impls/arkode/makefile | 8 - src/solver/impls/cvode/makefile | 8 - src/solver/impls/euler/makefile | 8 - src/solver/impls/ida/makefile | 8 - src/solver/impls/imex-bdf2/makefile | 8 - src/solver/impls/makefile | 13 - src/solver/impls/petsc/makefile | 8 - src/solver/impls/power/makefile | 8 - src/solver/impls/pvode/makefile | 8 - src/solver/impls/rk3-ssp/makefile | 8 - src/solver/impls/rk4/makefile | 8 - .../impls/rkgeneric/impls/cashkarp/makefile | 8 - src/solver/impls/rkgeneric/impls/makefile | 7 - .../impls/rkgeneric/impls/rk4simple/makefile | 8 - .../impls/rkgeneric/impls/rkf34/makefile | 8 - .../impls/rkgeneric/impls/rkf45/makefile | 8 - src/solver/impls/rkgeneric/makefile | 9 - src/solver/impls/slepc/makefile | 8 - src/solver/impls/snes/makefile | 8 - src/solver/impls/split-rk/makefile | 8 - src/solver/makefile | 8 - src/sys/makefile | 14 - src/sys/options/makefile | 7 - 143 files changed, 22417 deletions(-) delete mode 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If not, see . -# -##################################################################### -# -# Process this file with autoreconf to produce a configure script. -# -# $ autoreconf -if -# -# Changelog: -# -# 2010-03-09 Ben Dudson -# * Changing to always require FFTW (removing NR routines) -# 2015-08-08 David Schwörer -# * Searching for libs in lib and lib64 -# - -AC_PREREQ([2.69]) -AC_INIT([BOUT++],[5.1.0],[bd512@york.ac.uk]) -AC_CONFIG_AUX_DIR([build-aux]) -AC_CONFIG_MACRO_DIR([m4]) - -AC_MSG_WARN([./configure is deprecated and will be removed in a future version, please use CMake instead]) - -AC_ARG_WITH(netcdf, [AS_HELP_STRING([--with-netcdf], - [Enable support for netCDF files])],,[]) -AC_ARG_WITH(pnetcdf, [AS_HELP_STRING([--with-pnetcdf], - [Set path to Parallel NetCDF library])],,[]) -AC_ARG_WITH(ida, [AS_HELP_STRING([--with-ida=/path/to/ida], - [Use the SUNDIALS IDA solver])],,[]) -AC_ARG_WITH(cvode, [AS_HELP_STRING([--with-cvode], - [Use the SUNDIALS CVODE solver])],,[]) -AC_ARG_WITH(sundials, [AS_HELP_STRING([--with-sundials], - [Use CVODE and IDA])],,[]) -AC_ARG_WITH(fftw, [AS_HELP_STRING([--with-fftw], - [Set directory of FFTW3 library])],,[]) -AC_ARG_WITH(lapack, [AS_HELP_STRING([--with-lapack], - [Use the LAPACK library])],,[with_lapack=guess]) -AC_ARG_WITH(petsc, [AS_HELP_STRING([--with-petsc], - [Enable PETSc interface])],,[with_petsc=no]) -AC_ARG_WITH(slepc, [AS_HELP_STRING([--with-slepc], - [Enable SLEPc interface])],,[with_slepc=no]) -AC_ARG_WITH(pvode, [AS_HELP_STRING([--with-pvode], - [Build and enable PVODE 98 (DEFAULT)])],,[]) -AC_ARG_WITH(arkode, [AS_HELP_STRING([--with-arkode], - [Use the SUNDIALS ARKODE solver])],,[]) -AC_ARG_WITH(scorep, [AS_HELP_STRING([--with-scorep], - [Enable support for scorep based instrumentation])],,[with_scorep=no]) -AC_ARG_WITH(hypre, [AS_HELP_STRING([--with-hypre], - [Enable support for HYPRE])],,[with_hypre=no]) - -dnl --with-hdf5 flags are set in AX_LIB_{PARALLEL}HDF5 -AC_ARG_WITH(system_mpark, [AS_HELP_STRING([--with-system-mpark], - [Use mpark.variant already installed rather then the bundled one])],,[with_system_mpark=auto]) -AC_ARG_WITH(system_uuid, [AS_HELP_STRING([--with-system-uuid], - [Use libuuid to generate UUIDs])],,[with_system_uuid=auto]) - -AC_ARG_ENABLE(warnings, [AS_HELP_STRING([--disable-warnings], - [Disable compiler warnings])],,[]) -AC_ARG_ENABLE(checks, [AS_HELP_STRING([--enable-checks=no/1/2/3], - [Set run-time checking level])],,[enable_checks=default]) -AC_ARG_ENABLE(msgstack, [AS_HELP_STRING([--enable-msgstack=no/yes], - [Enable MstStack for backtrace. 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-NCCONF="" # Configuration script - -BOUT_HAS_NETCDF=no -BOUT_HAS_LEGACY_NETCDF=no -AS_IF([test "x$with_netcdf" != "xno"], -[ - ########################################## - # Try to find a valid NetCDF configuration - # - # at first, try to find ncconf script - - # Search for NetCDF config scripts, prefer ncxx4-config over nc-config - # Check if the path to the config script has been supplied directly, otherwise - # check the path provided by --with-netcdf, appending "/bin" if need - # be, then check system path - # Set NCCONF to the full path of the found scropt - AS_CASE([`basename $with_netcdf 2> /dev/null`], - ["ncxx4-config"], [NCCONF=$with_netcdf], - ["nc-config"], [NCCONF=$with_netcdf], - [AC_PATH_PROGS([NCCONF], [ncxx4-config nc-config], [], - [$with_netcdf$PATH_SEPARATOR$with_netcdf/bin$PATH_SEPARATOR$PATH])]) - - ########################################## - # Get configuration - AS_IF([test "x$NCCONF" != "x" ], - [ - # If we found nc-config rather than ncxx4-config, we need to check if it supports C++ - AS_IF([test `basename $NCCONF` = 'nc-config'], - [AC_MSG_CHECKING([if $NCCONF has C++4 support]) - nc_has_cpp4=`$NCCONF --has-c++4` - AC_MSG_RESULT([$nc_has_cpp4]) - AC_MSG_CHECKING([if $NCCONF has C++ support]) - nc_has_cpp=`$NCCONF --has-c++` - AC_MSG_RESULT([$nc_has_cpp]) - ], [ - nc_has_cpp4="yes" - ]) - - NCINC=`$NCCONF --cflags` - EXTRA_INCS="$EXTRA_INCS $NCINC" - AS_IF([test "x$nc_has_cpp4" = "xyes"], - [ - NCLIB=`$NCCONF --libs` - BOUT_HAS_NETCDF=yes - AC_MSG_NOTICE([ -> NetCDF-4 support enabled]) - ], [ - # nc-config might not *say* it has C++ support, but we can try anyway - AC_MSG_CHECKING([if we can compile NetCDF with C++]) - # Note netcdf_c++ needed - NCLIB=`$NCCONF --libs | sed s/-lnetcdf/-lnetcdf_c++\ -lnetcdf/` - - save_LIBS=$LIBS - save_LDFLAGS=$LDFLAGS - save_CXXFLAGS=$CXXFLAGS - AC_LANG_PUSH([C++]) - LIBS="$save_LIBS $NCLIB" - LDFLAGS="$save_LDFLAGS $NCLIB" - CXXFLAGS="$save_CXXFLAGS $NCINC" - AC_LINK_IFELSE( - [AC_LANG_PROGRAM([ - #include - ], [NcFile file("foo.nc");])], - [AC_MSG_RESULT([yes]) - AC_MSG_NOTICE([ -> Legacy NetCDF support enabled])], - [AC_MSG_RESULT([no]) - AC_MSG_FAILURE([*** Could not compile NetCDF C++ program!])]) - AC_LANG_POP([C++]) - LIBS=$save_LIBS - LDFLAGS=$save_LDFLAGS - CXXFLAGS="$save_CXXFLAGS" - BOUT_HAS_NETCDF=yes - BOUT_HAS_LEGACY_NETCDF=yes - ]) - EXTRA_LIBS="$EXTRA_LIBS $NCLIB" - - file_formats="$file_formats netCDF" - NCPATH="found" - NCFOUND=yes - ], [ - # if nc-config / ncxx4-config is not found, try to find library directly - BOUT_MSG_DEBUG([calling bout addpath]) - BOUT_ADDPATH_CHECK_HEADER(netcdfcpp.h, - BOUT_ADDPATH_CHECK_LIB(netcdf, nc_get_att, - BOUT_ADDPATH_CHECK_LIB(netcdf_c++, nc_close, NCFOUND=yes, NCFOUND=no, [$with_netcdf]), - NCFOUND=no, [$with_netcdf]), - NCFOUND=no, [$with_netcdf]) - - AS_IF([test "x$NCFOUND" = "xyes"], - [ - file_formats="$file_formats netCDF" - AC_MSG_NOTICE([ -> Legacy NetCDF support enabled]) - NCPATH="found" - BOUT_HAS_NETCDF=yes - BOUT_HAS_LEGACY_NETCDF=yes - ], []) - ]) - - AS_IF([test $with_netcdf && test "x$NCFOUND" != "xyes" ], AC_MSG_ERROR([NetCDF requested but not found]), []) - AS_IF([test "x$NCFOUND" != "xyes"], [AC_MSG_NOTICE([ -> NetCDF support disabled])], []) -], []) - -############################################################# -# Parallel NetCDF support -############################################################# - -PNCPATH="" -AS_IF([test "$with_pnetcdf" != "no" && test "x$with_pnetcdf" != "x" ], [ - AC_MSG_NOTICE([Searching for Parallel-NetCDF library]) - - AS_IF([test "x$with_pnetcdf" != "xyes"], [ - # Given a path to the library - AC_CHECK_FILES([$with_pnetcdf/include/pnetcdf.h], [PNCPATH=$with_pnetcdf], - AC_MSG_NOTICE([parallel-netcdf not found in given directory]) - ) - ]) - - # Find the utilities included with pnetcdf - AS_IF([test "x$PNCPATH" = "x"], [ - AS_IF([test "x$with_pnetcdf" = "xyes"], [ - AC_PATH_PROG([NCMPIDUMP_PATH], [ncmpidump]) - ], [ - AC_PATH_PROG([NCMPIDUMP_PATH], [ncmpidump], [$with_pnetcdf$PATH_SEPARATOR$PATH]) - ]) - AS_IF([test "$NCMPIDUMP_PATH" != ""], [ - AC_CHECK_FILES([$NCMPIDUMP_PATH/../include/pnetcdf.h], [PNCPATH=$NCMPIDUMP_PATH/../]) - ]) - ]) - - AS_IF([test "x$PNCPATH" != "x"], [ - AC_CHECK_FILES($path/lib/libpnetcdf.a, PNCPATHLIB='lib', - AC_CHECK_FILES($path/lib64/libpnetcdf.a, PNCPATHLIB='lib64', PNCPATH='')) - ]) - - AS_IF([test "x$PNCPATH" = "x" && test "x$with_pnetcdf" != "x"], [ - AC_MSG_FAILURE([*** Parallel-NetCDF requested but not found]) - ]) -]) - -AS_IF([test "x$PNCPATH" = "x"], [ - AC_MSG_NOTICE([Parallel-NetCDF support disabled]) -], [ - # Set a compile-time flag - CXXFLAGS="$CXXFLAGS -DPNCDF" - EXTRA_INCS="$EXTRA_INCS -I$PNCPATH/include" - EXTRA_LIBS="$EXTRA_LIBS -L$PNCPATH/$PNCPATHLIB -lpnetcdf" - - file_formats="$file_formats Parallel-NetCDF" - AC_MSG_NOTICE([Parallel-NetCDF support enabled]) -]) - -############################################################# -# Check file formats -############################################################# - -AS_IF([test "x$file_formats" = "x"], [ - AC_MSG_ERROR([*** At least one file format must be supported]) -], [ - AC_MSG_NOTICE([Supported file formats:$file_formats]) -]) - -############################################################# -# LAPACK routines (Used for tri- and band-diagonal solvers) -############################################################# - -BOUT_HAS_LAPACK="no" -AS_IF([test "x$with_lapack" != "xno"], [ - AS_IF([test "x$with_lapack" = "xguess" || test "x$with_lapack" = "x" ], - [lapack_path=""], - [AS_IF([test "x$with_lapack" != xyes], - [lapack_path=$with_lapack - with_lapack=yes], - [lapack_path=""]) - ]) - BOUT_ADDPATH_CHECK_LIB(blas, zgemm_, - [BOUT_HAS_BLAS=yes], - [AS_IF([test "x$with_lapack" = "xyes"], - AC_MSG_ERROR([LAPACK requested but couldn't find BLAS]))], - $lapack_path) - BOUT_ADDPATH_CHECK_LIB(lapack, zgbsv_, - [BOUT_HAS_LAPACK=yes - AC_MSG_NOTICE([Using LAPACK]) - ], - [AS_IF([test "x$with_lapack" = "xyes"], - AC_MSG_ERROR([LAPACK requested but not found]))], - $lapack_path) -]) - -############################################################# -# PETSc library -############################################################# - -AS_IF([test "x$with_petsc" != "x" && test "$with_petsc" != "no"], [ - -# Supplying an argument to "--with-petsc" only works if PETSC_ARCH -# *should* be empty. If it should be non-empty, THIS WILL NOT WORK - AS_IF([test "$with_petsc" != "yes"], [ - PETSC_DIR="$with_petsc" - PETSC_ARCH= - ]) - - AC_MSG_NOTICE([Using PETSC_DIR=$PETSC_DIR, PETSC_ARCH=$PETSC_ARCH]) - -# Define a macro for a nice error message that preserves the -# formatting. Use like: -# -# PETSC_ERROR_MESSAGE -# -# with no identation - m4_define(PETSC_ERROR_MESSAGE, - [ You may need to specify PETSC_DIR and PETSC_ARCH like so: - --with-petsc PETSC_DIR=\$PETSC_DIR PETSC_ARCH=\$PETSC_ARCH - Also see the help online: - http://bout-dev.readthedocs.io/en/latest/user_docs/advanced_install.html#petsc - ]) - -# PETSc changed the location of the conf directory in 3.5, so we -# need to check both locations -# If we find nether, try to fall back to pkg-conf - PETSC_PKGCONF=no - AC_CHECK_FILE($PETSC_DIR/$PETSC_ARCH/conf, [ - PETSC_CONFDIR=${PETSC_DIR}/conf - ], [ - AC_CHECK_FILE($PETSC_DIR/$PETSC_ARCH/lib/petsc/conf, [ - PETSC_CONFDIR=${PETSC_DIR}/lib/petsc/conf - ], [ - PKG_CHECK_MODULES(PETSC, PETSc >= 3.4.0 , - PETSC_PKGCONF=yes, [ - PKG_CHECK_MODULES(PETSC, petsc >= 3.4.0 , - PETSC_PKGCONF=yes, [ - AC_MSG_ERROR([--with-petsc was specified but could not find PETSc distribution. -PETSC_ERROR_MESSAGE]) - ]) - ]) - ]) - ]) - - AS_IF([test $PETSC_PKGCONF = no] , - [ -# We've found an installation, need to check we can use it. First we -# need to be able to check the version number, for which we need -# petscverion.h - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$PETSC_DIR/include" - AC_CHECK_HEADER([petscversion.h], - [FOUND_PETSC_HEADER=yes], - [FOUND_PETSC_HEADER=no] - ) - -# This is a terrible hack for some Linux distributions (Fedora) that -# install PETSc in a non-supported fashion. This is really the fault -# of PETSc for their weird method of installation - AS_IF([test $FOUND_PETSC_HEADER = no], [ - AC_CHECK_FILE([${PETSC_CONFDIR}/petscvariables], [], [ - AC_MSG_ERROR([Unable to find either petscversion.h or petscvariables -PETSC_ERROR_MESSAGE]) - ]) - -# This relies on the assumption that PETSC_ARCH is empty - PETSC_CC_INCLUDES=$(grep ^PETSC_CC_INCLUDES ${PETSC_CONFDIR}/petscvariables | cut -d= -f 2-) - - AC_MSG_NOTICE([Looking for petscverion.h using $PETSC_CC_INCLUDES from ${PETSC_CONFDIR}/petscvariables]) - - # This is the cache variable set by the previous call to - # AC_CHECK_HEADER. We need to unset it so we can call the macro - # again, but now with different CPPFLAGS - AS_UNSET([ac_cv_header_petscversion_h]) - - CPPFLAGS="$CPPFLAGS $PETSC_CC_INCLUDES" - AC_CHECK_HEADER([petscversion.h], [], [ - AC_MSG_ERROR([Couldn't find or include petscversion.h. -PETSC_ERROR_MESSAGE]) - ]) - ], []) - -# Now we have the header we want, we can check the version number - AC_MSG_CHECKING([PETSc is at least 3.4.0]) - AC_EGREP_CPP([yes], [ - #include - #if PETSC_VERSION_GE(3, 4, 0) - yes - #endif - ], [PETSC_VERSION_OK="yes"], - [PETSC_VERSION_OK="no"]) - AC_MSG_RESULT([$PETSC_VERSION_OK]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test $PETSC_VERSION_OK = no], [ - AC_MSG_ERROR([PETSc version must be at least 3.4.0]) - ]) - -# Check if PETSc was compiled with SUNDIALS - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$PETSC_DIR/$PETSC_ARCH/include" - AC_MSG_CHECKING([PETSc has SUNDIALS support]) - AC_EGREP_CPP([yes], [ - #include - #ifdef PETSC_HAVE_SUNDIALS - yes - #endif - ], [PETSC_HAS_SUNDIALS="yes"], - [PETSC_HAS_SUNDIALS="no"]) - AC_MSG_RESULT([$PETSC_HAS_SUNDIALS]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test "$PETSC_HAS_SUNDIALS" = "yes"], [ - CXXFLAGS="$CXXFLAGS -DPETSC_HAS_SUNDIALS " - ]) - - # Set the line to be included in the make.conf file - PETSC_MAKE_INCLUDE="include ${PETSC_CONFDIR}/variables" - - BOUT_HAS_PETSC="yes" - - EXTRA_INCS="$EXTRA_INCS \$(PETSC_CC_INCLUDES)" - EXTRA_LIBS="$EXTRA_LIBS \$(PETSC_LIB)" - ], [ dnl pkg-config version - - # Check if PETSc was compiled with SUNDIALS - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS $PETSC_CFLAGS" - AC_MSG_CHECKING([PETSc has SUNDIALS support]) - AC_EGREP_CPP([yes], [ - #include - #ifdef PETSC_HAVE_SUNDIALS - yes - #endif - ], [PETSC_HAS_SUNDIALS="yes"], - [PETSC_HAS_SUNDIALS="no"]) - AC_MSG_RESULT([$PETSC_HAS_SUNDIALS]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test "$PETSC_HAS_SUNDIALS" = "yes"], [ - CXXFLAGS="$CXXFLAGS -DPETSC_HAS_SUNDIALS " - ]) - PETSC_MAKE_INCLUDE= - BOUT_HAS_PETSC="yes" - - EXTRA_INCS="$EXTRA_INCS $PETSC_CFLAGS" - EXTRA_LIBS="$PETSC_LIBS $EXTRA_LIBS" - ]) -], [ - PETSC_MAKE_INCLUDE= - BOUT_HAS_PETSC="no" - PETSC_HAS_SUNDIALS="no" -]) - -############################################################# -# SLEPc library -############################################################# - -AS_IF([test "x$with_slepc" != "x" && test "$with_slepc" != "no"], [ - - AS_IF([test $BOUT_HAS_PETSC = "no"], [ - AC_MSG_ERROR([--with-slepc specified, but no PETSc detected. Please reconfigure and specify --with-petsc -PETSC_ERROR_MESSAGE]) - ]) - -# Supplying an argument to "--with-slepc" only works if SLEPC_ARCH -# *should* be empty. If it should be non-empty, THIS WILL NOT WORK - AS_IF([test "$with_slepc" != "yes"], [ - SLEPC_DIR="$with_slepc" - SLEPC_ARCH= - ]) - - AC_MSG_NOTICE([Using SLEPC_DIR=$SLEPC_DIR, SLEPC_ARCH=$SLEPC_ARCH]) - -# Define a macro for a nice error message that preserves the -# formatting. Use like: -# -# SLEPC_ERROR_MESSAGE -# -# with no identation - m4_define(SLEPC_ERROR_MESSAGE, - [ You may need to specify SLEPC_DIR and SLEPC_ARCH like so: - --with-slepc SLEPC_DIR=\$SLEPC_DIR SLEPC_ARCH=\$SLEPC_ARCH - Also see the help online: - http://bout-dev.readthedocs.io/en/latest/user_docs/advanced_install.html#slepc - ]) - -# Slepc changed the location of the conf directory in 3.5, so we -# need to check both locations - AC_CHECK_FILE($SLEPC_DIR/$SLEPC_ARCH/conf, [ - SLEPC_CONFDIR=${SLEPC_DIR}/conf - ], [ - AC_CHECK_FILE($SLEPC_DIR/$SLEPC_ARCH/lib/slepc/conf, [ - SLEPC_CONFDIR=${SLEPC_DIR}/lib/slepc/conf - ], [ - AC_MSG_ERROR([--with-slepc was specified but could not find Slepc distribution. -SLEPC_ERROR_MESSAGE]) - ]) - ]) - -# We've found an installation, need to check we can use it. First we -# need to be able to check the version number, for which we need -# slepcverion.h - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$SLEPC_DIR/include" - AC_CHECK_HEADER([slepcversion.h], - [FOUND_SLEPC_HEADER=yes], - [FOUND_SLEPC_HEADER=no] - ) - -# This is a terrible hack for some Linux distributions (Fedora) that -# install Slepc in a non-supported fashion. This is really the fault -# of Slepc for their weird method of installation - AS_IF([test $FOUND_SLEPC_HEADER = no], [ - AC_CHECK_FILE([${SLEPC_CONFDIR}/slepc_variables], [], [ - AC_MSG_ERROR([Unable to find either slepcversion.h or slepc_variables -SLEPC_ERROR_MESSAGE]) - ]) - -# This relies on the assumption that SLEPC_ARCH is empty - SLEPC_CC_INCLUDES=$(grep ^SLEPC_CC_INCLUDES ${SLEPC_CONFDIR}/slepc_variables | cut -d= -f 2-) - - AC_MSG_NOTICE([Looking for slepcverion.h using $SLEPC_CC_INCLUDES from ${SLEPC_CONFDIR}/slepc_variables]) - - # This is the cache variable set by the previous call to - # AC_CHECK_HEADER. We need to unset it so we can call the macro - # again, but now with different CPPFLAGS - AS_UNSET([ac_cv_header_slepcversion_h]) - - CPPFLAGS="$CPPFLAGS $SLEPC_CC_INCLUDES" - AC_CHECK_HEADER([slepcversion.h], [], [ - AC_MSG_ERROR([Couldn't find or include slepcversion.h. -SLEPC_ERROR_MESSAGE]) - ]) - ], []) - -# Now we have the header we want, we can check the version number - AC_MSG_CHECKING([Slepc is at least 3.4.0]) - AC_EGREP_CPP([yes], [ - #include - #if SLEPC_VERSION_GE(3, 4, 0) - yes - #endif - ], [SLEPC_VERSION_OK="yes"], - [SLEPC_VERSION_OK="no"]) - AC_MSG_RESULT([$SLEPC_VERSION_OK]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test $SLEPC_VERSION_OK = no], [ - AC_MSG_ERROR([Slepc version must be at least 3.4.0]) - ]) - -# Check if Slepc was compiled with SUNDIALS - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$SLEPC_DIR/$SLEPC_ARCH/include" - - # Set the line to be included in the make.conf file - SLEPC_MAKE_INCLUDE="include ${SLEPC_CONFDIR}/slepc_variables" - - BOUT_HAS_SLEPC="yes" - - EXTRA_INCS="$EXTRA_INCS \$(SLEPC_INCLUDE)" - EXTRA_LIBS="$EXTRA_LIBS \$(SLEPC_LIB)" - -], [ - SLEPC_MAKE_INCLUDE= - BOUT_HAS_SLEPC="no" -]) - -############################################################# -# Solver choice: SUNDIALS' IDA, SUNDIALS' CVODE, PVODE -############################################################# - -BOUT_HAS_SUNDIALS=no -AS_IF([test "x$with_sundials" != "x" && test "x$with_sundials" != "xno"], [ - - # Now follows a few different checks for the version of SUNDIALS. - # We need the sundials_config.h header, which comes with all the - # versions we care about - - # If we've been given a path, look in there first - AS_IF([test "x$with_sundials" != "xyes"], [ - AC_CHECK_FILE([$with_sundials/include/sundials/sundials_config.h], - [SUNDIALS_INC=$with_sundials/include], [SUNDIALS_INC=""]) - ]) - - # If we've got one, add the include dir to the preprocessor flags - save_CPPFLAGS=$CPPFLAGS - AS_IF([test "x$SUNDIALS_INC" != "x"], [CPPFLAGS="-I$SUNDIALS_INC"]) - - AC_MSG_CHECKING([for SUNDIALS config header]) - AC_COMPILE_IFELSE([ - AC_LANG_PROGRAM([ - #include "sundials/sundials_config.h" - ], [])], - [AC_MSG_RESULT([yes])], - [AC_MSG_RESULT([no]) - AC_MSG_FAILURE([*** Could not determine SUNDIALS version])]) - - AC_MSG_CHECKING([for SUNDIALS minor version]) - AC_EGREP_CPP([^ *\"? *[12]\.[0-5]\.], [ - #include "sundials/sundials_config.h" - #ifdef SUNDIALS_PACKAGE_VERSION - SUNDIALS_PACKAGE_VERSION - #endif - ], [sundials_minor_ver="too low"], [sundials_minor_ver=ok]) - AC_MSG_RESULT([$sundials_minor_ver]) - - CPPFLAGS=$save_CPPFLAGS - - AS_IF([test "$sundials_minor_ver" = "too low"], [ - AC_MSG_FAILURE([*** Unsupported SUNDIALS version: Requires at least 2.6]) - ]) - - # Set both IDA and CVODE if not set already - AS_IF([test "x$with_ida" = "x"], [ - with_ida=$with_sundials - ]) - - AS_IF([test "x$with_cvode" = "x"], [ - with_cvode=$with_sundials - ]) - - AS_IF([test "x$with_arkode" = "x"], [ - with_arkode=$with_sundials - ]) - BOUT_HAS_SUNDIALS=yes -]) - -AS_IF([test "x$with_ida" != "x" && test "x$with_ida" != "xno"], [ - BOUT_FIND_SUNDIALS_MODULE([ida], [ - #include - #include - extern void foo(N_Vector); - ], [IDACreate();]) -]) - -AS_IF([test "x$with_cvode" != "x" && test "x$with_cvode" != "xno"], [ - BOUT_FIND_SUNDIALS_MODULE([cvode], [ - #include - #include - extern void foo(N_Vector); - ], [ - #if SUNDIALS_VERSION_MAJOR >= 4 - CVodeCreate(0); - #else - CVodeCreate(0, 0); - #endif - ]) -]) - -AS_IF([test "x$with_arkode" != "x" && test "x$with_arkode" != "xno"], [ - BOUT_FIND_SUNDIALS_MODULE([arkode], [ - #include - #if SUNDIALS_VERSION_MAJOR >= 4 - #include - #else - #include - #endif - extern void foo(N_Vector); - ], [ - #if SUNDIALS_VERSION_MAJOR >= 4 - ARKStepCreate(0, 0, 0, 0); - #else - ARKodeCreate(); - #endif - ]) -]) - -############################################################# -# HYPRE -############################################################# - -BOUT_HAS_HYPRE="no" -AS_IF([test "$with_hypre" != "no"], [ - BOUT_ADDPATH_CHECK_HEADER(HYPRE.h, - BOUT_ADDPATH_CHECK_LIB(HYPRE, HYPRE_IJVectorCreate, - [ - BOUT_HAS_HYPRE="yes" - ], - AC_MSG_ERROR([HYPRE requested but not found]), - $with_hypre), - AC_MSG_ERROR([HYPRE requested but not found]), - $with_hypre - ) -]) - -############################################################# -# Scorep setup -############################################################# - -BOUT_HAS_SCOREP="no" -AS_IF([test "$with_scorep" != "no"], [ - - AS_IF([test "$with_scorep" != "yes"], [ - AC_MSG_NOTICE([Searching for Scorep executable in $with_scorep]) - AC_PATH_PROG([SCOREPPATH], [scorep], [], [$with_scorep]) - ], [ - AC_MSG_NOTICE([Searching for Scorep executable]) - AC_PATH_PROG([SCOREPPATH], [scorep], []) - ]) - - AS_IF([test "$SCOREPPATH" = ""], [ - AC_MSG_FAILURE([*** Scorep requested, but executable not found. -Please supply the path using --with-scorep=/path/to/scorep]) - ],[ - CXX="$SCOREPPATH --user --nocompiler $CXX" - BOUT_HAS_SCOREP="yes" - AC_MSG_NOTICE([Scorep support enabled]) - ]) - - ],[ - AC_MSG_NOTICE([Scorep support disabled]) -]) - -############################################################# -# Check for mpark.variant -############################################################# - -AS_IF([test ".$with_system_mpark" = "no"], [ - SYSTEM_HAS_MPARK=no -], [ - AC_MSG_CHECKING([for mpark.variant]) - AC_COMPILE_IFELSE([ - AC_LANG_PROGRAM([ - #include "mpark/variant.hpp" - ], [])], - [AC_MSG_RESULT([yes]) - SYSTEM_HAS_MPARK=yes], - [AC_MSG_RESULT([no]) - SYSTEM_HAS_MPARK=no - AS_IF([test "$with_system_mpark" = "yes"], [ - AC_MSG_FAILURE([*** System mpark.variant not found - but requested to use]) - ])]) -]) - -AS_IF([test "$SYSTEM_HAS_MPARK" = "yes"], [ - MPARK_VARIANT_INCLUDE_PATH= - MPARK_INCLUDE= - OWN_MPARK= -], [ - AS_IF([test -d externalpackages/mpark.variant/include], [], - [ AS_IF([test -d .git && which git], [ - make -f makefile.submodules mpark_submodule || \ - AC_MSG_FAILURE([*** Could not download mpark.variant]) - ], [ - AC_MSG_FAILURE([mpark.variant not found. Please install mpark.variant or use the official releases.]) - ]) - ]) - - MPARK_VARIANT_INCLUDE_PATH="$PWD/externalpackages/mpark.variant/include" - MPARK_INCLUDE="-I$MPARK_VARIANT_INCLUDE_PATH" - OWN_MPARK=yes -]) - -############################################################# -# Check for libuuid -############################################################# - -AS_IF([test ".$with_system_uuid" = "no"], [ - BOUT_HAS_UUID_SYSTEM_GENERATOR=no -], [ - BOUT_ADDPATH_CHECK_HEADER(uuid/uuid.h, - BOUT_ADDPATH_CHECK_LIB(uuid, uuid_generate, - BOUT_HAS_UUID_SYSTEM_GENERATOR=yes, - BOUT_HAS_UUID_SYSTEM_GENERATOR=no, - [$with_system_uuid]), - BOUT_HAS_UUID_SYSTEM_GENERATOR=no, - [$with_system_uuid]) - AS_IF([test "$with_system_uuid" = "yes"], [ - AC_MSG_FAILURE([*** System UUID generator not found, but explicitly requested]) - ]) -]) - -############################################################# -# Download + Build PVODE '98 -############################################################# - -AS_MKDIR_P(externalpackages) -AS_MKDIR_P(lib) -AS_MKDIR_P(include) - -BOUT_HAS_PVODE="no" -AS_IF([test "$with_pvode" != "no"], [ - AS_IF([test "$enable_pvode_openmp" != "no" ], [ - AS_IF([test "$enable_openmp" != "no" ], [ - PVODE_FLAGS="$CXXFLAGS $OPENMP_CXXFLAGS" - AC_MSG_NOTICE([PVODE being built with OpenMP support]) - ], [ - AC_MSG_ERROR([Cannot enable openmp in PVODE as configuring with OpenMP disabled]) - ]) - ], [ - PVODE_FLAGS="$CXXFLAGS" - AC_MSG_NOTICE([PVODE being built without OpenMP support]) - ]) - # Clean PVODE - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE clean -C externalpackages/PVODE/precon/ >> config-build.log 2>&1 - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE clean -C externalpackages/PVODE/source/ >> config-build.log 2>&1 - - AC_MSG_NOTICE([Building PVODE]) - echo "* Building PVODE" >> config-build.log - echo "*************************************************************" >> config-build.log - - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE -C externalpackages/PVODE/precon/ >> config-build.log 2>&1 - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE -C externalpackages/PVODE/source/ >> config-build.log 2>&1 - - AS_IF([test -f externalpackages/PVODE/lib/libpvode.a && test -f externalpackages/PVODE/lib/libpvpre.a], [ - AC_MSG_NOTICE([Successfully built PVODE]) - AC_MSG_NOTICE([Installing PVODE into BOUT++ sourcetree]) - - echo "*************************************************************" >> config-build.log - echo "* Successfully built PVODE" >> config-build.log - echo "*************************************************************" >> config-build.log - echo "* Installing PVODE into BOUT++ sourcetree" >> config-build.log - echo "*************************************************************" >> config-build.log - ], [ - AC_MSG_ERROR(Could not build PVODE. See config-build.log for errors) - ]) - - # Set the correct libraries and copy them to bout - AS_MKDIR_P(include/pvode) - cp -r externalpackages/PVODE/include/pvode include - cp externalpackages/PVODE/lib/*.a lib/ - EXTRA_LIBS="$EXTRA_LIBS -L\$(BOUT_LIB_PATH) -lpvode -lpvpre" - BOUT_HAS_PVODE="yes" -]) - -############################################################# -# Localisation (i18n) with gettext -############################################################# - -BOUT_HAS_GETTEXT="no" -# Use macro to test if Natural Language Support (gettext) is available. -# If available sets: -# - USE_NLS to "yes" -# - LIBINTL to the linker options -# - Modifies CPPFLAGS if needed -AM_GNU_GETTEXT([external]) -AS_IF([test "$USE_NLS" = "yes"], [ - AC_MSG_NOTICE([Enabling language support with gettext]) - # Turn the .po files into .mo files - $MAKE -C locale | tee -a config-build.log 2>&1 - - # Note: BOUT_LOCALE_PATH is defined in make.config, and may be changed by `make install`. - CXXFLAGS="$CXXFLAGS -DBOUT_LOCALE_PATH=\$(BOUT_LOCALE_PATH)" - - EXTRA_LIBS="$EXTRA_LIBS $LIBINTL" - - # Set variable substituted into bout-config - BOUT_HAS_GETTEXT="yes" -],[ - AC_MSG_NOTICE([Language support with gettext not available]) -]) - -############################################################# -# Sort out fmt -############################################################# - -dnl If in a git repo, get submodule, unless BOUT_DONT_UPDATE_GIT_SUBMODULE is set -AC_CHECK_FILE([.git], [ - AS_IF([test "x$BOUT_DONT_UPDATE_GIT_SUBMODULE" == "x"], [ - git submodule update --init externalpackages/fmt - ]) -]) - -dnl Copy the one file we need to somewhere else -AC_CONFIG_LINKS(src/fmt/format.cxx:externalpackages/fmt/src/format.cc) - -############################################################# -# Check environment -############################################################# - -AS_IF([test "$CXXINCLUDE" != ""], [ - AC_MSG_NOTICE([================================================]) - AC_MSG_NOTICE([ WARNING: CXXINCLUDE environment variable set to:]) - AC_MSG_NOTICE([$CXXINCLUDE]) - AC_MSG_NOTICE([ => This will be added to compile commands]) - AC_MSG_NOTICE([ If this is not intended, then run]) - AC_MSG_NOTICE([ export CXXINCLUDE='']) - AC_MSG_NOTICE([ before making BOUT++]) - AC_MSG_NOTICE([================================================]) -]) - -############################################################# -# Gather configuration info for bout-config -############################################################# - -EXTRA_INCS="${EXTRA_INCS} ${CPPFLAGS}" - -PREFIX=$PWD -IDLCONFIGPATH=$PWD/tools/idllib -PYTHONCONFIGPATH=$PWD/tools/pylib - -BOUT_HAS_IDA="yes" -if test "$IDALIBS" = "" -then - BOUT_HAS_IDA="no" -fi - -BOUT_HAS_CVODE="yes" -if test "$CVODELIBS" = "" -then - BOUT_HAS_CVODE="no" -fi - -BOUT_HAS_ARKODE="yes" -if test "$ARKODELIBS" = "" -then - BOUT_HAS_ARKODE="no" -fi - -BOUT_HAS_PNETCDF="yes" -if test "$PNCPATH" = "" -then - BOUT_HAS_PNETCDF="no" -fi - -# Only make.config is altered by configure -AC_CONFIG_FILES([make.config]) -AC_OUTPUT - -############################################################# -# Use a dummy Makefile to get the cflags and ldflags -# -# This is to capture flags from external libraries such -# as PETSc -############################################################# - -CONFIG_CFLAGS=`$MAKE cflags -f output.make` -CONFIG_LDFLAGS=`$MAKE ldflags -f output.make` - -############################################################# -# Defines which are supported by CMake build but not autoconf - -BOUT_HAS_CUDA="no" -BOUT_HAS_RAJA="no" -BOUT_HAS_UMPIRE="no" -BOUT_HAS_CALIPER="no" - -BOUT_DEFINE_SUBST(BOUT_HAS_CUDA, [Enable CUDA]) -BOUT_DEFINE_SUBST(BOUT_HAS_RAJA, [RAJA support]) -BOUT_DEFINE_SUBST(BOUT_HAS_UMPIRE, [Umpire support]) -BOUT_DEFINE_SUBST(BOUT_HAS_CALIPER, [Caliper support]) - -############################################################# -# Write configuration to bout-config -############################################################# - -AC_SUBST(CONFIG_CFLAGS) -AC_SUBST(CONFIG_LDFLAGS) - -# Set path to lib and include here. -# If make install is run then that replaces these paths -BOUT_LIB_PATH=$PWD/lib -BOUT_INCLUDE_PATH=$PWD/include -FMT_INCLUDE_PATH=$PWD/externalpackages/fmt/include -AC_SUBST(BOUT_LIB_PATH) -AC_SUBST(BOUT_INCLUDE_PATH) -AC_SUBST(FMT_INCLUDE_PATH) -AC_SUBST(MPARK_VARIANT_INCLUDE_PATH) -AC_SUBST(MPARK_INCLUDE) -AC_SUBST(OWN_MPARK) - -AC_SUBST(PREFIX) -AC_SUBST(IDLCONFIGPATH) -AC_SUBST(PYTHONCONFIGPATH) -AC_SUBST(LIB_TO_BUILD) -AC_SUBST(STATIC_EXTRA) -AC_SUBST(SHARED_EXTRA) - -AC_SUBST(BOUT_VERSION) -AC_SUBST(BOUT_VERSION_MAJOR) -AC_SUBST(BOUT_VERSION_MINOR) -AC_SUBST(BOUT_VERSION_PATCH) -AC_SUBST(BOUT_VERSION_TAG) -AC_SUBST(BOUT_REVISION) - -AC_SUBST(BOUT_CHECK_LEVEL) -AC_DEFINE_UNQUOTED(BOUT_CHECK_LEVEL, [$BOUT_CHECK_LEVEL], [Runtime error checking level]) - -AC_SUBST(BOUT_OPENMP_SCHEDULE) -AC_DEFINE_UNQUOTED(BOUT_OPENMP_SCHEDULE, [$BOUT_OPENMP_SCHEDULE], [OpenMP schedule]) - -BOUT_DEFINE_SUBST(BOUT_HAS_ARKODE, [ARKODE support]) -BOUT_DEFINE_SUBST(BOUT_HAS_CVODE, [CVODE support]) -BOUT_DEFINE_SUBST(BOUT_HAS_FFTW, [FFTW support]) -BOUT_DEFINE_SUBST(BOUT_HAS_GETTEXT, [NLS support]) -BOUT_DEFINE_SUBST(BOUT_HAS_IDA, [IDA support]) -BOUT_DEFINE_SUBST(BOUT_HAS_LAPACK, [LAPACK support]) -BOUT_DEFINE_SUBST(BOUT_HAS_NETCDF, [NETCDF support]) -BOUT_DEFINE_SUBST(BOUT_HAS_LEGACY_NETCDF, [NETCDF support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PETSC, [PETSc support]) -BOUT_DEFINE_SUBST(BOUT_HAS_HYPRE, [Hypre support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PNETCDF, [PNETCDF support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PRETTY_FUNCTION, [Compiler PRETTYFUNCTION support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PVODE, [PVODE support]) -BOUT_DEFINE_SUBST(BOUT_HAS_SCOREP, [Score-P support]) -BOUT_DEFINE_SUBST(BOUT_HAS_SLEPC, [SLEPc support]) -BOUT_DEFINE_SUBST(BOUT_HAS_SUNDIALS, [SUNDIALS support]) -BOUT_DEFINE_SUBST(BOUT_HAS_UUID_SYSTEM_GENERATOR, [Use libuuid for UUID generation]) -BOUT_DEFINE_SUBST(BOUT_USE_BACKTRACE, [Enable backtrace in exceptions]) -BOUT_DEFINE_SUBST(BOUT_USE_COLOR, [Enable color logs option]) -BOUT_DEFINE_SUBST(BOUT_USE_OUTPUT_DEBUG, [Enabled extra debug output]) -BOUT_DEFINE_SUBST(BOUT_USE_OPENMP, [Enable OpenMP]) -BOUT_DEFINE_SUBST(BOUT_USE_SIGFPE, [Enable floating point exceptions]) -BOUT_DEFINE_SUBST(BOUT_USE_SIGNAL, [Enable signal handlers]) -BOUT_DEFINE_SUBST(BOUT_USE_TRACK, [Enable field name tracking]) -BOUT_DEFINE_SUBST(BOUT_USE_MSGSTACK, [Enable MsgStack for traces]) -AC_DEFINE_UNQUOTED([BOUT_METRIC_TYPE], $BOUT_METRIC_TYPE, [Type of the metric fields]) -BOUT_METRIC_3D=$(test $BOUT_METRIC_TYPE != 3D ; echo $?) -AC_DEFINE_UNQUOTED([BOUT_USE_METRIC_3D], $BOUT_METRIC_3D, [Is the metric field 3D]) -AC_SUBST(BOUT_METRIC_TYPE) - -AC_SUBST(PETSC_HAS_SUNDIALS) -AC_SUBST(PETSC_MAKE_INCLUDE) -AC_SUBST(PETSC_DIR) -AC_SUBST(PETSC_ARCH) -AC_SUBST(SLEPC_MAKE_INCLUDE) -AC_SUBST(SLEPC_DIR) -AC_SUBST(SLEPC_ARCH) - - -AC_CONFIG_HEADERS([include/bout/build_defines.hxx:autoconf_build_defines.hxx.in]) -AC_CONFIG_FILES([include/bout/version.hxx]) -AC_CONFIG_FILES([include/bout/revision.hxx]) -AC_CONFIG_FILES([bin/bout-config]) -AC_CONFIG_FILES([src/makefile]) -AC_CONFIG_FILES([tools/pylib/boutconfig/__init__.py]) -AC_OUTPUT -chmod a+x bin/bout-config - -############################################################# -# Print configuration info -############################################################# - -AC_MSG_NOTICE([-------------------------]) -AC_MSG_NOTICE([ Configuration summary ]) -AC_MSG_NOTICE([-------------------------]) - -AC_MSG_NOTICE([ PETSc support : $BOUT_HAS_PETSC (has SUNDIALS: $PETSC_HAS_SUNDIALS)]) -AC_MSG_NOTICE([ SLEPc support : $BOUT_HAS_SLEPC]) -AC_MSG_NOTICE([ IDA support : $BOUT_HAS_IDA]) -AC_MSG_NOTICE([ CVODE support : $BOUT_HAS_CVODE]) -AC_MSG_NOTICE([ ARKODE support : $BOUT_HAS_ARKODE]) -AC_MSG_NOTICE([ FFTW support : $BOUT_HAS_FFTW]) -AC_MSG_NOTICE([ NetCDF support : $BOUT_HAS_NETCDF (legacy: $BOUT_HAS_LEGACY_NETCDF)]) -AC_MSG_NOTICE([ Parallel-NetCDF support : $BOUT_HAS_PNETCDF]) -AC_MSG_NOTICE([ Lapack support : $BOUT_HAS_LAPACK]) -AC_MSG_NOTICE([ Scorep support : $BOUT_HAS_SCOREP]) -AC_MSG_NOTICE([ OpenMP support : $BOUT_USE_OPENMP (schedule: $OPENMP_SCHEDULE)]) -AC_MSG_NOTICE([ Natural language support: $BOUT_HAS_GETTEXT (path: $localedir)]) -AC_MSG_NOTICE([ HYPRE support : $BOUT_HAS_HYPRE]) -AC_MSG_NOTICE([ System UUID generator : $BOUT_HAS_UUID_SYSTEM_GENERATOR]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([ Enable backtrace : $BOUT_USE_BACKTRACE]) -AC_MSG_NOTICE([ Enable color logs : $BOUT_USE_COLOR]) -AC_MSG_NOTICE([ Enable more debug output: $BOUT_USE_OUTPUT_DEBUG]) -AC_MSG_NOTICE([ Enable OpenMP : $BOUT_USE_OPENMP]) -AC_MSG_NOTICE([ Enable FP exceptions : $BOUT_USE_SIGFPE]) -AC_MSG_NOTICE([ Enable signal handlers : $BOUT_USE_SIGNAL]) -AC_MSG_NOTICE([ Enable field names : $BOUT_USE_TRACK]) -AC_MSG_NOTICE([ Metric type : $BOUT_METRIC_TYPE]) - -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([-------------------------------]) -AC_MSG_NOTICE([ Data analysis configuration ]) -AC_MSG_NOTICE([-------------------------------]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([=== IDL ===]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([Make sure that the tools/idllib directory is in your IDL_PATH]) -AC_MSG_NOTICE([e.g. by adding to your ~/.bashrc file]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([ export IDL_PATH=+$PWD/tools/idllib:'':\$IDL_PATH]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([=== Python ===]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([Make sure that the tools/pylib directory is in your PYTHONPATH]) -AC_MSG_NOTICE([e.g. by adding to your ~/.bashrc file]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([ export PYTHONPATH=$PWD/tools/pylib/:\$PYTHONPATH]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([*** Now run '$MAKE' to compile BOUT++ ***]) -AC_MSG_NOTICE([]) -AC_MSG_WARN([./configure is deprecated and will be removed in a future version, please use CMake instead]) diff --git a/examples/2Dturbulence_multigrid/makefile b/examples/2Dturbulence_multigrid/makefile deleted file mode 100644 index f67cb0d1ba..0000000000 --- a/examples/2Dturbulence_multigrid/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../ - -SOURCEC = esel.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/6field-simple/makefile b/examples/6field-simple/makefile deleted file mode 100644 index 6f70c9d751..0000000000 --- a/examples/6field-simple/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../ - -SOURCEC = elm_6f.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/IMEX/advection-diffusion/makefile b/examples/IMEX/advection-diffusion/makefile deleted file mode 100644 index 588242e834..0000000000 --- a/examples/IMEX/advection-diffusion/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = imex.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/IMEX/advection-reaction/makefile b/examples/IMEX/advection-reaction/makefile deleted file mode 100644 index 689fd0c614..0000000000 --- a/examples/IMEX/advection-reaction/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = split_operator.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/IMEX/diffusion-nl/makefile b/examples/IMEX/diffusion-nl/makefile deleted file mode 100644 index 8dcd38cc0b..0000000000 --- a/examples/IMEX/diffusion-nl/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = diffusion-nl.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/IMEX/drift-wave-constraint/makefile b/examples/IMEX/drift-wave-constraint/makefile deleted file mode 100644 index fdf3abccc9..0000000000 --- a/examples/IMEX/drift-wave-constraint/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = test-drift.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/IMEX/drift-wave/makefile b/examples/IMEX/drift-wave/makefile deleted file mode 100644 index fdf3abccc9..0000000000 --- a/examples/IMEX/drift-wave/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = test-drift.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/advdiff/makefile b/examples/advdiff/makefile deleted file mode 100644 index 15bffe5c29..0000000000 --- a/examples/advdiff/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = advdiff.cxx - -include $(BOUT_TOP)/make.config \ No newline at end of file diff --git a/examples/advdiff2/makefile b/examples/advdiff2/makefile deleted file mode 100644 index e17c2c3c7a..0000000000 --- a/examples/advdiff2/makefile +++ /dev/null @@ -1,7 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = init.cxx rhs.cxx - -TARGET = advdiff - -include $(BOUT_TOP)/make.config diff --git a/examples/backtrace/makefile b/examples/backtrace/makefile deleted file mode 100644 index cb5c651884..0000000000 --- a/examples/backtrace/makefile +++ /dev/null @@ -1,11 +0,0 @@ -BOUT_TOP ?= ../.. - -TARGET=backtrace - -SOURCEC = $(TARGET).cxx - -include $(BOUT_TOP)/make.config - -$(TARGET).o: $(TARGET).cxx - @echo " Compiling " $< - @$(CXX) $(BOUT_INCLUDE) $(BOUT_FLAGS) -c $< -g -o $@ diff --git a/examples/blob2d-laplacexz/makefile b/examples/blob2d-laplacexz/makefile deleted file mode 100644 index ca2f949a73..0000000000 --- a/examples/blob2d-laplacexz/makefile +++ /dev/null @@ -1,6 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = blob2d.cxx - -include $(BOUT_TOP)/make.config - diff --git a/examples/blob2d-outerloop/makefile b/examples/blob2d-outerloop/makefile deleted file mode 100644 index 1ab6de5387..0000000000 --- a/examples/blob2d-outerloop/makefile +++ /dev/null @@ -1,6 +0,0 @@ -BOUT_TOP = ../.. - -SOURCEC = blob2d.cxx - -include $(BOUT_TOP)/make.config - diff --git a/examples/blob2d/makefile b/examples/blob2d/makefile deleted file mode 100644 index ca2f949a73..0000000000 --- a/examples/blob2d/makefile +++ /dev/null @@ -1,6 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = blob2d.cxx - -include $(BOUT_TOP)/make.config - diff --git a/examples/boundary-conditions/advection/makefile b/examples/boundary-conditions/advection/makefile deleted file mode 100644 index 962ca894c2..0000000000 --- a/examples/boundary-conditions/advection/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = advection.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/conducting-wall-mode/makefile b/examples/conducting-wall-mode/makefile deleted file mode 100644 index e3375e06d9..0000000000 --- a/examples/conducting-wall-mode/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = cwm.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/conduction-snb/makefile b/examples/conduction-snb/makefile deleted file mode 100644 index 90ecf242d8..0000000000 --- a/examples/conduction-snb/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = conduction-snb.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/conduction/makefile b/examples/conduction/makefile deleted file mode 100644 index 26a2d2686e..0000000000 --- a/examples/conduction/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = conduction.cxx - -include $(BOUT_TOP)/make.config \ No newline at end of file diff --git a/examples/constraints/alfven-wave/makefile b/examples/constraints/alfven-wave/makefile deleted file mode 100644 index cc53facb8e..0000000000 --- a/examples/constraints/alfven-wave/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = alfven.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/constraints/laplace-dae/makefile b/examples/constraints/laplace-dae/makefile deleted file mode 100644 index 224a696106..0000000000 --- a/examples/constraints/laplace-dae/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = laplace_dae.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/dalf3/doc/makefile b/examples/dalf3/doc/makefile deleted file mode 100644 index 6812b687f9..0000000000 --- a/examples/dalf3/doc/makefile +++ /dev/null @@ -1,11 +0,0 @@ - -DOCS=dalf3.pdf - -all:$(DOCS) - -%.pdf: %.tex - latexmk -pdf $< -interaction=batchmode - -.PHONY: clean -clean: - latexmk -C diff --git a/examples/dalf3/makefile b/examples/dalf3/makefile deleted file mode 100644 index 3c9eed60c1..0000000000 --- a/examples/dalf3/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = dalf3.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/eigen-box/makefile b/examples/eigen-box/makefile deleted file mode 100644 index 53855e725b..0000000000 --- a/examples/eigen-box/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = eigen-box.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/elm-pb-outerloop/makefile b/examples/elm-pb-outerloop/makefile deleted file mode 100644 index 5d9b045742..0000000000 --- a/examples/elm-pb-outerloop/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../ - -SOURCEC = elm_pb_outerloop.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/elm-pb/doc/makefile b/examples/elm-pb/doc/makefile deleted file mode 100644 index 66f9cd76f8..0000000000 --- a/examples/elm-pb/doc/makefile +++ /dev/null @@ -1,14 +0,0 @@ -# Makefile for the reference and user manuals - -.PHONY:all - -all: elm_pb.pdf - -%.pdf: %.tex - latexmk -pdf $(@F:.pdf=) -interaction=batchmode - -.PHONY:clean - -clean: - latexmk -C - diff --git a/examples/elm-pb/makefile b/examples/elm-pb/makefile deleted file mode 100644 index ea19cf6f83..0000000000 --- a/examples/elm-pb/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../ - -SOURCEC = elm_pb.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/em-drift/makefile b/examples/em-drift/makefile deleted file mode 100644 index e9c69ca443..0000000000 --- a/examples/em-drift/makefile +++ /dev/null @@ -1,5 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = 2fluid.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/fci-wave-logn/makefile b/examples/fci-wave-logn/makefile deleted file mode 100644 index 24c0928db5..0000000000 --- a/examples/fci-wave-logn/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = fci-wave.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/fci-wave/makefile b/examples/fci-wave/makefile deleted file mode 100644 index 24c0928db5..0000000000 --- a/examples/fci-wave/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = fci-wave.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/finite-volume/diffusion/makefile b/examples/finite-volume/diffusion/makefile deleted file mode 100644 index c633a109d9..0000000000 --- a/examples/finite-volume/diffusion/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = diffusion.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/finite-volume/fluid/makefile b/examples/finite-volume/fluid/makefile deleted file mode 100644 index 4effb80b45..0000000000 --- a/examples/finite-volume/fluid/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = fluid.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/finite-volume/test/makefile b/examples/finite-volume/test/makefile deleted file mode 100644 index 96b5469333..0000000000 --- a/examples/finite-volume/test/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = finite_volume.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/gas-compress/makefile b/examples/gas-compress/makefile deleted file mode 100644 index 029f9335a1..0000000000 --- a/examples/gas-compress/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = gas_compress.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/gravity_reduced/makefile b/examples/gravity_reduced/makefile deleted file mode 100644 index eb5a62641a..0000000000 --- a/examples/gravity_reduced/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = gravity_reduced.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/gyro-gem/doc/makefile b/examples/gyro-gem/doc/makefile deleted file mode 100644 index 95a4b4d896..0000000000 --- a/examples/gyro-gem/doc/makefile +++ /dev/null @@ -1,11 +0,0 @@ - -DOCS=gem.pdf - -all:$(DOCS) - -%.pdf: %.tex - latexmk -pdf $< -interaction=batchmode - -.PHONY: clean -clean: - latexmk -C diff --git a/examples/gyro-gem/makefile b/examples/gyro-gem/makefile deleted file mode 100644 index 709cf2d5fa..0000000000 --- a/examples/gyro-gem/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = gem.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/hasegawa-wakatani-3d/makefile b/examples/hasegawa-wakatani-3d/makefile deleted file mode 100644 index 8f33b716b9..0000000000 --- a/examples/hasegawa-wakatani-3d/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP = ../.. - -SOURCEC = hw.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/hasegawa-wakatani/makefile b/examples/hasegawa-wakatani/makefile deleted file mode 100644 index 34395b1bf0..0000000000 --- a/examples/hasegawa-wakatani/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = hw.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/invertable_operator/makefile b/examples/invertable_operator/makefile deleted file mode 100644 index ff5ec8c809..0000000000 --- a/examples/invertable_operator/makefile +++ /dev/null @@ -1,11 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = invertable_operator.cxx - -target: requires_petsc invertable_operator - -requires_petsc: - @test $$($(BOUT_TOP)/bin/bout-config --has-petsc ) = yes || \ - (echo "ERROR: This example requires PETSc. Please compile BOUT++ with PETSc." ; exit 1) - -include $(BOUT_TOP)/make.config diff --git a/examples/jorek-compare/doc/makefile b/examples/jorek-compare/doc/makefile deleted file mode 100644 index 66c36824ae..0000000000 --- a/examples/jorek-compare/doc/makefile +++ /dev/null @@ -1,11 +0,0 @@ - -DOCS=jorek_compare.pdf - -all:$(DOCS) - -%.pdf: %.tex - latexmk -pdf $< -interaction=batchmode - -.PHONY: clean -clean: - latexmk -C diff --git a/examples/jorek-compare/makefile b/examples/jorek-compare/makefile deleted file mode 100644 index 4d0898da1e..0000000000 --- a/examples/jorek-compare/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = jorek_compare.cxx - -include $(BOUT_TOP)/make.config \ No newline at end of file diff --git a/examples/lapd-drift/makefile b/examples/lapd-drift/makefile deleted file mode 100644 index abb567e24b..0000000000 --- a/examples/lapd-drift/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = lapd_drift.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/laplace-petsc3d/makefile b/examples/laplace-petsc3d/makefile deleted file mode 100644 index ad943fe51c..0000000000 --- a/examples/laplace-petsc3d/makefile +++ /dev/null @@ -1,5 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = test-laplace3d.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/laplace-petsc3d/makefile.create-initial-profiles b/examples/laplace-petsc3d/makefile.create-initial-profiles deleted file mode 100644 index 1e0f564626..0000000000 --- a/examples/laplace-petsc3d/makefile.create-initial-profiles +++ /dev/null @@ -1,5 +0,0 @@ -BOUT_TOP ?= ../.. - -SOURCEC = create-initial-profiles.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/laplacexy/alfven-wave/makefile b/examples/laplacexy/alfven-wave/makefile deleted file mode 100644 index cc53facb8e..0000000000 --- a/examples/laplacexy/alfven-wave/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = alfven.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/laplacexy/laplace_perp/makefile b/examples/laplacexy/laplace_perp/makefile deleted file mode 100644 index 76f2d7cc5b..0000000000 --- a/examples/laplacexy/laplace_perp/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = test.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/laplacexy/simple/makefile b/examples/laplacexy/simple/makefile deleted file mode 100644 index d3da2c0196..0000000000 --- a/examples/laplacexy/simple/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = test-laplacexy.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/monitor-newapi/makefile b/examples/monitor-newapi/makefile deleted file mode 100644 index 0ec013a133..0000000000 --- a/examples/monitor-newapi/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = monitor.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/monitor/makefile b/examples/monitor/makefile deleted file mode 100644 index 0ec013a133..0000000000 --- a/examples/monitor/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = monitor.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/orszag-tang/makefile b/examples/orszag-tang/makefile deleted file mode 100644 index 9796b1c7a7..0000000000 --- a/examples/orszag-tang/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = mhd.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/arithmetic/makefile b/examples/performance/arithmetic/makefile deleted file mode 100644 index c9e6f1e69c..0000000000 --- a/examples/performance/arithmetic/makefile +++ /dev/null @@ -1,10 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = arithmetic.cxx - -include $(BOUT_TOP)/make.config - - -run:arithmetic - ./arithmetic -q -q -q diff --git a/examples/performance/arithmetic_3d2d/makefile b/examples/performance/arithmetic_3d2d/makefile deleted file mode 100644 index 386ab242e6..0000000000 --- a/examples/performance/arithmetic_3d2d/makefile +++ /dev/null @@ -1,10 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = arithmetic_3d2d.cxx - -include $(BOUT_TOP)/make.config - - -run:arithmetic_3d2d - ./arithmetic_3d2d -q -q -q diff --git a/examples/performance/bracket/makefile b/examples/performance/bracket/makefile deleted file mode 100644 index 3559c27e2d..0000000000 --- a/examples/performance/bracket/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = bracket.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/communications/makefile b/examples/performance/communications/makefile deleted file mode 100644 index 80cdd9062f..0000000000 --- a/examples/performance/communications/makefile +++ /dev/null @@ -1,5 +0,0 @@ -BOUT_TOP ?= ../../.. - -SOURCEC = communications.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/ddx/makefile b/examples/performance/ddx/makefile deleted file mode 100644 index 52f6ed7dc0..0000000000 --- a/examples/performance/ddx/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = ddx.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/ddy/makefile b/examples/performance/ddy/makefile deleted file mode 100644 index 57b502450a..0000000000 --- a/examples/performance/ddy/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = ddy.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/ddz/makefile b/examples/performance/ddz/makefile deleted file mode 100644 index 5f7aefa6cc..0000000000 --- a/examples/performance/ddz/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = ddz.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/iterator-offsets/makefile b/examples/performance/iterator-offsets/makefile deleted file mode 100644 index 94dac859f6..0000000000 --- a/examples/performance/iterator-offsets/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = iterator-offsets.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/iterator/makefile b/examples/performance/iterator/makefile deleted file mode 100644 index 33a11d30be..0000000000 --- a/examples/performance/iterator/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = iterator.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/laplace/makefile b/examples/performance/laplace/makefile deleted file mode 100644 index 3ff28a130e..0000000000 --- a/examples/performance/laplace/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = laplace.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/performance/tuning_regionblocksize/makefile b/examples/performance/tuning_regionblocksize/makefile deleted file mode 100644 index 6f906e3793..0000000000 --- a/examples/performance/tuning_regionblocksize/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = tuning_regionblocksize.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/preconditioning/wave/makefile b/examples/preconditioning/wave/makefile deleted file mode 100644 index 095c893d8e..0000000000 --- a/examples/preconditioning/wave/makefile +++ /dev/null @@ -1,5 +0,0 @@ -BOUT_TOP ?= ../../.. - -SOURCEC = test_precon.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/reconnect-2field/makefile b/examples/reconnect-2field/makefile deleted file mode 100644 index 0b7745f5af..0000000000 --- a/examples/reconnect-2field/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = 2field.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/shear-alfven-wave/makefile b/examples/shear-alfven-wave/makefile deleted file mode 100644 index 92ac3ce50d..0000000000 --- a/examples/shear-alfven-wave/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = 2fluid.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/staggered_grid/makefile b/examples/staggered_grid/makefile deleted file mode 100644 index e00eaecd74..0000000000 --- a/examples/staggered_grid/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = test_staggered.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/subsampling/makefile b/examples/subsampling/makefile deleted file mode 100644 index 0ec013a133..0000000000 --- a/examples/subsampling/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = monitor.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/tokamak-2fluid/makefile b/examples/tokamak-2fluid/makefile deleted file mode 100644 index 92ac3ce50d..0000000000 --- a/examples/tokamak-2fluid/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = 2fluid.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/uedge-benchmark/makefile b/examples/uedge-benchmark/makefile deleted file mode 100644 index 4c8a72d394..0000000000 --- a/examples/uedge-benchmark/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = ue_bmark.cxx - -include $(BOUT_TOP)/make.config diff --git a/examples/wave-slab/makefile b/examples/wave-slab/makefile deleted file mode 100644 index b20fcf6c8e..0000000000 --- a/examples/wave-slab/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../.. - -SOURCEC = wave_slab.cxx - -include $(BOUT_TOP)/make.config diff --git a/m4/ax_append_compile_flags.m4 b/m4/ax_append_compile_flags.m4 deleted file mode 100644 index 5b6f1af51d..0000000000 --- a/m4/ax_append_compile_flags.m4 +++ /dev/null @@ -1,67 +0,0 @@ -# ============================================================================ -# https://www.gnu.org/software/autoconf-archive/ax_append_compile_flags.html -# ============================================================================ -# -# SYNOPSIS -# -# AX_APPEND_COMPILE_FLAGS([FLAG1 FLAG2 ...], [FLAGS-VARIABLE], [EXTRA-FLAGS], [INPUT]) -# -# DESCRIPTION -# -# For every FLAG1, FLAG2 it is checked whether the compiler works with the -# flag. If it does, the flag is added FLAGS-VARIABLE -# -# If FLAGS-VARIABLE is not specified, the current language's flags (e.g. -# CFLAGS) is used. During the check the flag is always added to the -# current language's flags. -# -# If EXTRA-FLAGS is defined, it is added to the current language's default -# flags (e.g. CFLAGS) when the check is done. The check is thus made with -# the flags: "CFLAGS EXTRA-FLAGS FLAG". This can for example be used to -# force the compiler to issue an error when a bad flag is given. -# -# INPUT gives an alternative input source to AC_COMPILE_IFELSE. -# -# NOTE: This macro depends on the AX_APPEND_FLAG and -# AX_CHECK_COMPILE_FLAG. Please keep this macro in sync with -# AX_APPEND_LINK_FLAGS. -# -# LICENSE -# -# Copyright (c) 2011 Maarten Bosmans -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -# Public License for more details. -# -# You should have received a copy of the GNU General Public License along -# with this program. If not, see . -# -# As a special exception, the respective Autoconf Macro's copyright owner -# gives unlimited permission to copy, distribute and modify the configure -# scripts that are the output of Autoconf when processing the Macro. You -# need not follow the terms of the GNU General Public License when using -# or distributing such scripts, even though portions of the text of the -# Macro appear in them. The GNU General Public License (GPL) does govern -# all other use of the material that constitutes the Autoconf Macro. -# -# This special exception to the GPL applies to versions of the Autoconf -# Macro released by the Autoconf Archive. When you make and distribute a -# modified version of the Autoconf Macro, you may extend this special -# exception to the GPL to apply to your modified version as well. - -#serial 6 - -AC_DEFUN([AX_APPEND_COMPILE_FLAGS], -[AX_REQUIRE_DEFINED([AX_CHECK_COMPILE_FLAG]) -AX_REQUIRE_DEFINED([AX_APPEND_FLAG]) -for flag in $1; do - AX_CHECK_COMPILE_FLAG([$flag], [AX_APPEND_FLAG([$flag], [$2])], [], [$3], [$4]) -done -])dnl AX_APPEND_COMPILE_FLAGS diff --git a/m4/ax_append_flag.m4 b/m4/ax_append_flag.m4 deleted file mode 100644 index e8c5312af6..0000000000 --- a/m4/ax_append_flag.m4 +++ /dev/null @@ -1,71 +0,0 @@ -# =========================================================================== -# https://www.gnu.org/software/autoconf-archive/ax_append_flag.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_APPEND_FLAG(FLAG, [FLAGS-VARIABLE]) -# -# DESCRIPTION -# -# FLAG is appended to the FLAGS-VARIABLE shell variable, with a space -# added in between. -# -# If FLAGS-VARIABLE is not specified, the current language's flags (e.g. -# CFLAGS) is used. FLAGS-VARIABLE is not changed if it already contains -# FLAG. If FLAGS-VARIABLE is unset in the shell, it is set to exactly -# FLAG. -# -# NOTE: Implementation based on AX_CFLAGS_GCC_OPTION. -# -# LICENSE -# -# Copyright (c) 2008 Guido U. Draheim -# Copyright (c) 2011 Maarten Bosmans -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -# Public License for more details. -# -# You should have received a copy of the GNU General Public License along -# with this program. If not, see . -# -# As a special exception, the respective Autoconf Macro's copyright owner -# gives unlimited permission to copy, distribute and modify the configure -# scripts that are the output of Autoconf when processing the Macro. You -# need not follow the terms of the GNU General Public License when using -# or distributing such scripts, even though portions of the text of the -# Macro appear in them. The GNU General Public License (GPL) does govern -# all other use of the material that constitutes the Autoconf Macro. -# -# This special exception to the GPL applies to versions of the Autoconf -# Macro released by the Autoconf Archive. When you make and distribute a -# modified version of the Autoconf Macro, you may extend this special -# exception to the GPL to apply to your modified version as well. - -#serial 7 - -AC_DEFUN([AX_APPEND_FLAG], -[dnl -AC_PREREQ(2.64)dnl for _AC_LANG_PREFIX and AS_VAR_SET_IF -AS_VAR_PUSHDEF([FLAGS], [m4_default($2,_AC_LANG_PREFIX[FLAGS])]) -AS_VAR_SET_IF(FLAGS,[ - AS_CASE([" AS_VAR_GET(FLAGS) "], - [*" $1 "*], [AC_RUN_LOG([: FLAGS already contains $1])], - [ - AS_VAR_APPEND(FLAGS,[" $1"]) - AC_RUN_LOG([: FLAGS="$FLAGS"]) - ]) - ], - [ - AS_VAR_SET(FLAGS,[$1]) - AC_RUN_LOG([: FLAGS="$FLAGS"]) - ]) -AS_VAR_POPDEF([FLAGS])dnl -])dnl AX_APPEND_FLAG diff --git a/m4/ax_check_compile_flag.m4 b/m4/ax_check_compile_flag.m4 deleted file mode 100644 index dcabb92a14..0000000000 --- a/m4/ax_check_compile_flag.m4 +++ /dev/null @@ -1,74 +0,0 @@ -# =========================================================================== -# https://www.gnu.org/software/autoconf-archive/ax_check_compile_flag.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_CHECK_COMPILE_FLAG(FLAG, [ACTION-SUCCESS], [ACTION-FAILURE], [EXTRA-FLAGS], [INPUT]) -# -# DESCRIPTION -# -# Check whether the given FLAG works with the current language's compiler -# or gives an error. (Warnings, however, are ignored) -# -# ACTION-SUCCESS/ACTION-FAILURE are shell commands to execute on -# success/failure. -# -# If EXTRA-FLAGS is defined, it is added to the current language's default -# flags (e.g. CFLAGS) when the check is done. The check is thus made with -# the flags: "CFLAGS EXTRA-FLAGS FLAG". This can for example be used to -# force the compiler to issue an error when a bad flag is given. -# -# INPUT gives an alternative input source to AC_COMPILE_IFELSE. -# -# NOTE: Implementation based on AX_CFLAGS_GCC_OPTION. Please keep this -# macro in sync with AX_CHECK_{PREPROC,LINK}_FLAG. -# -# LICENSE -# -# Copyright (c) 2008 Guido U. Draheim -# Copyright (c) 2011 Maarten Bosmans -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -# Public License for more details. -# -# You should have received a copy of the GNU General Public License along -# with this program. If not, see . -# -# As a special exception, the respective Autoconf Macro's copyright owner -# gives unlimited permission to copy, distribute and modify the configure -# scripts that are the output of Autoconf when processing the Macro. You -# need not follow the terms of the GNU General Public License when using -# or distributing such scripts, even though portions of the text of the -# Macro appear in them. The GNU General Public License (GPL) does govern -# all other use of the material that constitutes the Autoconf Macro. -# -# This special exception to the GPL applies to versions of the Autoconf -# Macro released by the Autoconf Archive. When you make and distribute a -# modified version of the Autoconf Macro, you may extend this special -# exception to the GPL to apply to your modified version as well. - -#serial 5 - -AC_DEFUN([AX_CHECK_COMPILE_FLAG], -[AC_PREREQ(2.64)dnl for _AC_LANG_PREFIX and AS_VAR_IF -AS_VAR_PUSHDEF([CACHEVAR],[ax_cv_check_[]_AC_LANG_ABBREV[]flags_$4_$1])dnl -AC_CACHE_CHECK([whether _AC_LANG compiler accepts $1], CACHEVAR, [ - ax_check_save_flags=$[]_AC_LANG_PREFIX[]FLAGS - _AC_LANG_PREFIX[]FLAGS="$[]_AC_LANG_PREFIX[]FLAGS $4 $1" - AC_COMPILE_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])], - [AS_VAR_SET(CACHEVAR,[yes])], - [AS_VAR_SET(CACHEVAR,[no])]) - _AC_LANG_PREFIX[]FLAGS=$ax_check_save_flags]) -AS_VAR_IF(CACHEVAR,yes, - [m4_default([$2], :)], - [m4_default([$3], :)]) -AS_VAR_POPDEF([CACHEVAR])dnl -])dnl AX_CHECK_COMPILE_FLAGS diff --git a/m4/ax_code_coverage.m4 b/m4/ax_code_coverage.m4 deleted file mode 100644 index 7a5b742b44..0000000000 --- a/m4/ax_code_coverage.m4 +++ /dev/null @@ -1,241 +0,0 @@ -# =========================================================================== -# This was modified for the BOUT++ project -# Original from: -# https://www.gnu.org/software/autoconf-archive/ax_code_coverage.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_CODE_COVERAGE() -# -# DESCRIPTION -# -# Defines CODE_COVERAGE_CPPFLAGS, CODE_COVERAGE_CFLAGS, -# CODE_COVERAGE_CXXFLAGS and CODE_COVERAGE_LIBS which should be included -# in the CPPFLAGS, CFLAGS CXXFLAGS and LIBS/LIBADD variables of every -# build target (program or library) which should be built with code -# coverage support. Also defines CODE_COVERAGE_RULES which should be -# substituted in your Makefile; and $enable_code_coverage which can be -# used in subsequent configure output. CODE_COVERAGE_ENABLED is defined -# and substituted, and corresponds to the value of the -# --enable-code-coverage option, which defaults to being disabled. -# -# Test also for gcov program and create GCOV variable that could be -# substituted. -# -# Note that all optimization flags in CFLAGS must be disabled when code -# coverage is enabled. -# -# Usage example: -# -# configure.ac: -# -# AX_CODE_COVERAGE -# -# Makefile.am: -# -# @CODE_COVERAGE_RULES@ -# my_program_LIBS = ... $(CODE_COVERAGE_LIBS) ... -# my_program_CPPFLAGS = ... $(CODE_COVERAGE_CPPFLAGS) ... -# my_program_CFLAGS = ... $(CODE_COVERAGE_CFLAGS) ... -# my_program_CXXFLAGS = ... $(CODE_COVERAGE_CXXFLAGS) ... -# -# This results in a "check-code-coverage" rule being added to any -# Makefile.am which includes "@CODE_COVERAGE_RULES@" (assuming the module -# has been configured with --enable-code-coverage). Running `make -# check-code-coverage` in that directory will run the module's test suite -# (`make check`) and build a code coverage report detailing the code which -# was touched, then print the URI for the report. -# -# In earlier versions of this macro, CODE_COVERAGE_LDFLAGS was defined -# instead of CODE_COVERAGE_LIBS. They are both still defined, but use of -# CODE_COVERAGE_LIBS is preferred for clarity; CODE_COVERAGE_LDFLAGS is -# deprecated. They have the same value. -# -# This code was derived from Makefile.decl in GLib, originally licenced -# under LGPLv2.1+. -# -# LICENSE -# -# Copyright (c) 2012, 2016 Philip Withnall -# Copyright (c) 2012 Xan Lopez -# Copyright (c) 2012 Christian Persch -# Copyright (c) 2012 Paolo Borelli -# Copyright (c) 2012 Dan Winship -# Copyright (c) 2015 Bastien ROUCARIES -# -# This library is free software; you can redistribute it and/or modify it -# under the terms of the GNU Lesser General Public License as published by -# the Free Software Foundation; either version 2.1 of the License, or (at -# your option) any later version. -# -# This library is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser -# General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public License -# along with this program. If not, see . - -#serial 24 - -AC_DEFUN([AX_CODE_COVERAGE],[ - dnl Check for --enable-code-coverage - AC_REQUIRE([AC_PROG_SED]) - - # allow to override gcov location - AC_ARG_WITH([gcov], - [AS_HELP_STRING([--with-gcov[=GCOV]], [use given GCOV for coverage (GCOV=gcov).])], - [_AX_CODE_COVERAGE_GCOV_PROG_WITH=$with_gcov], - [_AX_CODE_COVERAGE_GCOV_PROG_WITH=gcov]) - - AC_MSG_CHECKING([whether to build with code coverage support]) - AC_ARG_ENABLE([code-coverage], - AS_HELP_STRING([--enable-code-coverage], - [Whether to enable code coverage support]),, - enable_code_coverage=no) - - AM_CONDITIONAL([CODE_COVERAGE_ENABLED], [test x$enable_code_coverage = xyes]) - AC_SUBST([CODE_COVERAGE_ENABLED], [$enable_code_coverage]) - AC_MSG_RESULT($enable_code_coverage) - - AS_IF([ test "$enable_code_coverage" = "yes" ], [ - # check for gcov - AC_CHECK_TOOL([GCOV], - [$_AX_CODE_COVERAGE_GCOV_PROG_WITH], - [:]) - AS_IF([test "X$GCOV" = "X:"], - [AC_MSG_ERROR([gcov is needed to do coverage])]) - AC_SUBST([GCOV]) - - dnl Check if gcc is being used - AS_IF([ test "$GCC" = "no" ], [ - AC_MSG_ERROR([not compiling with gcc, which is required for gcov code coverage]) - ]) - - AC_CHECK_PROG([LCOV], [lcov], [lcov]) - AC_CHECK_PROG([GENHTML], [genhtml], [genhtml]) - - AS_IF([ test -z "$LCOV" ], [ - AC_MSG_ERROR([To enable code coverage reporting you must have lcov installed]) - ]) - - AS_IF([ test -z "$GENHTML" ], [ - AC_MSG_ERROR([Could not find genhtml from the lcov package]) - ]) - - dnl Build the code coverage flags - dnl Define CODE_COVERAGE_LDFLAGS for backwards compatibility - CODE_COVERAGE_CPPFLAGS="-DNDEBUG" - CODE_COVERAGE_CFLAGS="-O0 -g -fprofile-arcs -ftest-coverage" - CODE_COVERAGE_CXXFLAGS="-O0 -g -fprofile-arcs -ftest-coverage" - CODE_COVERAGE_LIBS="-lgcov" - CODE_COVERAGE_LDFLAGS="$CODE_COVERAGE_LIBS" - - AC_SUBST([CODE_COVERAGE_CPPFLAGS]) - AC_SUBST([CODE_COVERAGE_CFLAGS]) - AC_SUBST([CODE_COVERAGE_CXXFLAGS]) - AC_SUBST([CODE_COVERAGE_LIBS]) - AC_SUBST([CODE_COVERAGE_LDFLAGS]) - - [CODE_COVERAGE_RULES_CAPTURE=' - @$(LCOV) --quiet $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --capture --no-external --output-file "$(CODE_COVERAGE_OUTPUT_FILE).tmp" --no-checksum $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_OPTIONS) - @$(LCOV) --quiet $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --remove "$(CODE_COVERAGE_OUTPUT_FILE).tmp" "/tmp/*" $(CODE_COVERAGE_IGNORE_PATTERN) --output-file "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_RMOPTS) - -@rm -f $(CODE_COVERAGE_OUTPUT_FILE).tmp - @LANG=C $(GENHTML) --quiet $(addprefix --prefix ,$(CODE_COVERAGE_DIRECTORY)) --demangle-cpp --output-directory "$(CODE_COVERAGE_OUTPUT_DIRECTORY)" --title "BOUT++ Code Coverage" --legend --show-details "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_GENHTML_OPTIONS) - @$(LCOV) --summary $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_LCOV_OPTIONS) - @echo "file://$(abs_builddir)/$(CODE_COVERAGE_OUTPUT_DIRECTORY)/index.html" -'] - [CODE_COVERAGE_RULES_CLEAN=' -clean:: code-coverage-clean -distclean:: code-coverage-clean -code-coverage-clean: - -@$(LCOV) --directory $(abs_builddir) -z --quiet - -@$(RM) -rf $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_FILE).tmp $(CODE_COVERAGE_OUTPUT_DIRECTORY) - -@find . \( -name "*.gcda" -o -name "*.gcno" -o -name "*.gcov" \) -delete -'] - ], [ - [CODE_COVERAGE_RULES_CHECK=' - @echo "Need to reconfigure with --enable-code-coverage" -'] - CODE_COVERAGE_RULES_CAPTURE="$CODE_COVERAGE_RULES_CHECK" - CODE_COVERAGE_RULES_CLEAN='' - ]) - -[CODE_COVERAGE_RULES=' -# Code coverage -# -# Optional: -# - CODE_COVERAGE_DIRECTORY: Top-level directory for code coverage reporting. -# Multiple directories may be specified, separated by whitespace. -# (Default: $(top_builddir)) -# - CODE_COVERAGE_OUTPUT_FILE: Filename and path for the .info file generated -# by lcov for code coverage. (Default: -# bout-coverage.info) -# - CODE_COVERAGE_OUTPUT_DIRECTORY: Directory for generated code coverage -# reports to be created. (Default: -# bout-coverage) -# - CODE_COVERAGE_BRANCH_COVERAGE: Set to 1 to enforce branch coverage, -# set to 0 to disable it and leave empty to stay with the default. -# (Default: empty) -# - CODE_COVERAGE_LCOV_SHOPTS_DEFAULT: Extra options shared between both lcov -# instances. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE) -# - CODE_COVERAGE_LCOV_SHOPTS: Extra options to shared between both lcov -# instances. (Default: $CODE_COVERAGE_LCOV_SHOPTS_DEFAULT) -# - CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH: --gcov-tool pathtogcov -# - CODE_COVERAGE_LCOV_OPTIONS_DEFAULT: Extra options to pass to the -# collecting lcov instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH) -# - CODE_COVERAGE_LCOV_OPTIONS: Extra options to pass to the collecting lcov -# instance. 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In order to add the current git hash to the title, -# use the git-version-gen script, available online. - -# Optional variables -CODE_COVERAGE_DIRECTORY ?= $(abs_builddir) -CODE_COVERAGE_OUTPUT_FILE ?= bout-coverage.info -CODE_COVERAGE_OUTPUT_DIRECTORY ?= bout-coverage -CODE_COVERAGE_BRANCH_COVERAGE ?= -CODE_COVERAGE_LCOV_SHOPTS_DEFAULT ?= $(if $(CODE_COVERAGE_BRANCH_COVERAGE),\ ---rc lcov_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE)) -CODE_COVERAGE_LCOV_SHOPTS ?= $(CODE_COVERAGE_LCOV_SHOPTS_DEFAULT) -CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH ?= --gcov-tool "$(GCOV)" -CODE_COVERAGE_LCOV_OPTIONS_DEFAULT ?= $(CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH) -CODE_COVERAGE_LCOV_OPTIONS ?= $(CODE_COVERAGE_LCOV_OPTIONS_DEFAULT) -CODE_COVERAGE_LCOV_RMOPTS_DEFAULT ?= -CODE_COVERAGE_LCOV_RMOPTS ?= $(CODE_COVERAGE_LCOV_RMOPTS_DEFAULT) -CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT ?=\ -$(if $(CODE_COVERAGE_BRANCH_COVERAGE),\ ---rc genhtml_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE)) -CODE_COVERAGE_GENHTML_OPTIONS ?= $(CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT) -CODE_COVERAGE_IGNORE_PATTERN ?= "*test*/*" - -# Use recursive makes in order to ignore errors during check -check-code-coverage:'"$CODE_COVERAGE_RULES_CHECK"' - -# Capture code coverage data -code-coverage-capture: code-coverage-capture-hook'"$CODE_COVERAGE_RULES_CAPTURE"' - -# Hook rule executed before code-coverage-capture, overridable by the user -code-coverage-capture-hook: - -'"$CODE_COVERAGE_RULES_CLEAN"' - -GITIGNOREFILES ?= -GITIGNOREFILES += $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY) - -.PHONY: check-code-coverage code-coverage-capture code-coverage-capture-hook code-coverage-clean -'] - - AC_SUBST([CODE_COVERAGE_RULES]) -]) diff --git a/m4/ax_cxx_compile_stdcxx.m4 b/m4/ax_cxx_compile_stdcxx.m4 deleted file mode 100644 index 43087b2e68..0000000000 --- a/m4/ax_cxx_compile_stdcxx.m4 +++ /dev/null @@ -1,951 +0,0 @@ -# =========================================================================== -# https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_CXX_COMPILE_STDCXX(VERSION, [ext|noext], [mandatory|optional]) -# -# DESCRIPTION -# -# Check for baseline language coverage in the compiler for the specified -# version of the C++ standard. If necessary, add switches to CXX and -# CXXCPP to enable support. VERSION may be '11' (for the C++11 standard) -# or '14' (for the C++14 standard). -# -# The second argument, if specified, indicates whether you insist on an -# extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g. -# -std=c++11). If neither is specified, you get whatever works, with -# preference for an extended mode. -# -# The third argument, if specified 'mandatory' or if left unspecified, -# indicates that baseline support for the specified C++ standard is -# required and that the macro should error out if no mode with that -# support is found. If specified 'optional', then configuration proceeds -# regardless, after defining HAVE_CXX${VERSION} if and only if a -# supporting mode is found. -# -# LICENSE -# -# Copyright (c) 2008 Benjamin Kosnik -# Copyright (c) 2012 Zack Weinberg -# Copyright (c) 2013 Roy Stogner -# Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov -# Copyright (c) 2015 Paul Norman -# Copyright (c) 2015 Moritz Klammler -# Copyright (c) 2016, 2018 Krzesimir Nowak -# Copyright (c) 2019 Enji Cooper -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice -# and this notice are preserved. This file is offered as-is, without any -# warranty. - -#serial 11 - -dnl This macro is based on the code from the AX_CXX_COMPILE_STDCXX_11 macro -dnl (serial version number 13). - -AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl - m4_if([$1], [11], [ax_cxx_compile_alternatives="11 0x"], - [$1], [14], [ax_cxx_compile_alternatives="14 1y"], - [$1], [17], [ax_cxx_compile_alternatives="17 1z"], - [m4_fatal([invalid first argument `$1' to AX_CXX_COMPILE_STDCXX])])dnl - m4_if([$2], [], [], - [$2], [ext], [], - [$2], [noext], [], - [m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX])])dnl - m4_if([$3], [], [ax_cxx_compile_cxx$1_required=true], - [$3], [mandatory], [ax_cxx_compile_cxx$1_required=true], - [$3], [optional], [ax_cxx_compile_cxx$1_required=false], - [m4_fatal([invalid third argument `$3' to AX_CXX_COMPILE_STDCXX])]) - AC_LANG_PUSH([C++])dnl - ac_success=no - - m4_if([$2], [noext], [], [dnl - if test x$ac_success = xno; then - for alternative in ${ax_cxx_compile_alternatives}; do - switch="-std=gnu++${alternative}" - cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch]) - AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch, - $cachevar, - [ac_save_CXX="$CXX" - CXX="$CXX $switch" - AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])], - [eval $cachevar=yes], - [eval $cachevar=no]) - CXX="$ac_save_CXX"]) - if eval test x\$$cachevar = xyes; then - CXX="$CXX $switch" - if test -n "$CXXCPP" ; then - CXXCPP="$CXXCPP $switch" - fi - ac_success=yes - break - fi - done - fi]) - - m4_if([$2], [ext], [], [dnl - if test x$ac_success = xno; then - dnl HP's aCC needs +std=c++11 according to: - dnl http://h21007.www2.hp.com/portal/download/files/unprot/aCxx/PDF_Release_Notes/769149-001.pdf - dnl Cray's crayCC needs "-h std=c++11" - for alternative in ${ax_cxx_compile_alternatives}; do - for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}"; do - cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch]) - AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch, - $cachevar, - [ac_save_CXX="$CXX" - CXX="$CXX $switch" - AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])], - [eval $cachevar=yes], - [eval $cachevar=no]) - CXX="$ac_save_CXX"]) - if eval test x\$$cachevar = xyes; then - CXX="$CXX $switch" - if test -n "$CXXCPP" ; then - CXXCPP="$CXXCPP $switch" - fi - ac_success=yes - break - fi - done - if test x$ac_success = xyes; then - break - fi - done - fi]) - AC_LANG_POP([C++]) - if test x$ax_cxx_compile_cxx$1_required = xtrue; then - if test x$ac_success = xno; then - AC_MSG_ERROR([*** A compiler with support for C++$1 language features is required.]) - fi - fi - if test x$ac_success = xno; then - HAVE_CXX$1=0 - AC_MSG_NOTICE([No compiler with C++$1 support was found]) - else - HAVE_CXX$1=1 - AC_DEFINE(HAVE_CXX$1,1, - [define if the compiler supports basic C++$1 syntax]) - fi - AC_SUBST(HAVE_CXX$1) -]) - - -dnl Test body for checking C++11 support - -m4_define([_AX_CXX_COMPILE_STDCXX_testbody_11], - _AX_CXX_COMPILE_STDCXX_testbody_new_in_11 -) - - -dnl Test body for checking C++14 support - -m4_define([_AX_CXX_COMPILE_STDCXX_testbody_14], - _AX_CXX_COMPILE_STDCXX_testbody_new_in_11 - _AX_CXX_COMPILE_STDCXX_testbody_new_in_14 -) - -m4_define([_AX_CXX_COMPILE_STDCXX_testbody_17], - _AX_CXX_COMPILE_STDCXX_testbody_new_in_11 - _AX_CXX_COMPILE_STDCXX_testbody_new_in_14 - _AX_CXX_COMPILE_STDCXX_testbody_new_in_17 -) - -dnl Tests for new features in C++11 - -m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_11], [[ - -// If the compiler admits that it is not ready for C++11, why torture it? -// Hopefully, this will speed up the test. - -#ifndef __cplusplus - -#error "This is not a C++ compiler" - -#elif __cplusplus < 201103L - -#error "This is not a C++11 compiler" - -#else - -namespace cxx11 -{ - - namespace test_static_assert - { - - template - struct check - { - static_assert(sizeof(int) <= sizeof(T), "not big enough"); - }; - - } - - namespace test_final_override - { - - struct Base - { - virtual ~Base() {} - virtual void f() {} - }; - - struct Derived : public Base - { - virtual ~Derived() override {} - virtual void f() override {} - }; - - } - - namespace test_double_right_angle_brackets - { - - template < typename T > - struct check {}; - - typedef check single_type; - typedef check> double_type; - typedef check>> triple_type; - typedef check>>> quadruple_type; - - } - - namespace test_decltype - { - - int - f() - { - int a = 1; - decltype(a) b = 2; - return a + b; - } - - } - - namespace test_type_deduction - { - - template < typename T1, typename T2 > - struct is_same - { - static const bool value = false; - }; - - template < typename T > - struct is_same - { - static const bool value = true; - }; - - template < typename T1, typename T2 > - auto - add(T1 a1, T2 a2) -> decltype(a1 + a2) - { - return a1 + a2; - } - - int - test(const int c, volatile int v) - { - static_assert(is_same::value == true, ""); - static_assert(is_same::value == false, ""); - static_assert(is_same::value == false, ""); - auto ac = c; - auto av = v; - auto sumi = ac + av + 'x'; - auto sumf = ac + av + 1.0; - static_assert(is_same::value == true, ""); - static_assert(is_same::value == true, ""); - static_assert(is_same::value == true, ""); - static_assert(is_same::value == false, ""); - static_assert(is_same::value == true, ""); - return (sumf > 0.0) ? sumi : add(c, v); - } - - } - - namespace test_noexcept - { - - int f() { return 0; } - int g() noexcept { return 0; } - - static_assert(noexcept(f()) == false, ""); - static_assert(noexcept(g()) == true, ""); - - } - - namespace test_constexpr - { - - template < typename CharT > - unsigned long constexpr - strlen_c_r(const CharT *const s, const unsigned long acc) noexcept - { - return *s ? strlen_c_r(s + 1, acc + 1) : acc; - } - - template < typename CharT > - unsigned long constexpr - strlen_c(const CharT *const s) noexcept - { - return strlen_c_r(s, 0UL); - } - - static_assert(strlen_c("") == 0UL, ""); - static_assert(strlen_c("1") == 1UL, ""); - static_assert(strlen_c("example") == 7UL, ""); - static_assert(strlen_c("another\0example") == 7UL, ""); - - } - - namespace test_rvalue_references - { - - template < int N > - struct answer - { - static constexpr int value = N; - }; - - answer<1> f(int&) { return answer<1>(); } - answer<2> f(const int&) { return answer<2>(); } - answer<3> f(int&&) { return answer<3>(); } - - void - test() - { - int i = 0; - const int c = 0; - static_assert(decltype(f(i))::value == 1, ""); - static_assert(decltype(f(c))::value == 2, ""); - static_assert(decltype(f(0))::value == 3, ""); - } - - } - - namespace test_uniform_initialization - { - - struct test - { - static const int zero {}; - static const int one {1}; - }; - - static_assert(test::zero == 0, ""); - static_assert(test::one == 1, ""); - - } - - namespace test_lambdas - { - - void - test1() - { - auto lambda1 = [](){}; - auto lambda2 = lambda1; - lambda1(); - lambda2(); - } - - int - test2() - { - auto a = [](int i, int j){ return i + j; }(1, 2); - auto b = []() -> int { return '0'; }(); - auto c = [=](){ return a + b; }(); - auto d = [&](){ return c; }(); - auto e = [a, &b](int x) mutable { - const auto identity = [](int y){ return y; }; - for (auto i = 0; i < a; ++i) - a += b--; - return x + identity(a + b); - }(0); - return a + b + c + d + e; - } - - int - test3() - { - const auto nullary = [](){ return 0; }; - const auto unary = [](int x){ return x; }; - using nullary_t = decltype(nullary); - using unary_t = decltype(unary); - const auto higher1st = [](nullary_t f){ return f(); }; - const auto higher2nd = [unary](nullary_t f1){ - return [unary, f1](unary_t f2){ return f2(unary(f1())); }; - }; - return higher1st(nullary) + higher2nd(nullary)(unary); - } - - } - - namespace test_variadic_templates - { - - template - struct sum; - - template - struct sum - { - static constexpr auto value = N0 + sum::value; - }; - - template <> - struct sum<> - { - static constexpr auto value = 0; - }; - - static_assert(sum<>::value == 0, ""); - static_assert(sum<1>::value == 1, ""); - static_assert(sum<23>::value == 23, ""); - static_assert(sum<1, 2>::value == 3, ""); - static_assert(sum<5, 5, 11>::value == 21, ""); - static_assert(sum<2, 3, 5, 7, 11, 13>::value == 41, ""); - - } - - // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae - // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function - // because of this. - namespace test_template_alias_sfinae - { - - struct foo {}; - - template - using member = typename T::member_type; - - template - void func(...) {} - - template - void func(member*) {} - - void test(); - - void test() { func(0); } - - } - -} // namespace cxx11 - -#endif // __cplusplus >= 201103L - -]]) - - -dnl Tests for new features in C++14 - -m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_14], [[ - -// If the compiler admits that it is not ready for C++14, why torture it? -// Hopefully, this will speed up the test. - -#ifndef __cplusplus - -#error "This is not a C++ compiler" - -#elif __cplusplus < 201402L - -#error "This is not a C++14 compiler" - -#else - -namespace cxx14 -{ - - namespace test_polymorphic_lambdas - { - - int - test() - { - const auto lambda = [](auto&&... args){ - const auto istiny = [](auto x){ - return (sizeof(x) == 1UL) ? 1 : 0; - }; - const int aretiny[] = { istiny(args)... }; - return aretiny[0]; - }; - return lambda(1, 1L, 1.0f, '1'); - } - - } - - namespace test_binary_literals - { - - constexpr auto ivii = 0b0000000000101010; - static_assert(ivii == 42, "wrong value"); - - } - - namespace test_generalized_constexpr - { - - template < typename CharT > - constexpr unsigned long - strlen_c(const CharT *const s) noexcept - { - auto length = 0UL; - for (auto p = s; *p; ++p) - ++length; - return length; - } - - static_assert(strlen_c("") == 0UL, ""); - static_assert(strlen_c("x") == 1UL, ""); - static_assert(strlen_c("test") == 4UL, ""); - static_assert(strlen_c("another\0test") == 7UL, ""); - - } - - namespace test_lambda_init_capture - { - - int - test() - { - auto x = 0; - const auto lambda1 = [a = x](int b){ return a + b; }; - const auto lambda2 = [a = lambda1(x)](){ return a; }; - return lambda2(); - } - - } - - namespace test_digit_separators - { - - constexpr auto ten_million = 100'000'000; - static_assert(ten_million == 100000000, ""); - - } - - namespace test_return_type_deduction - { - - auto f(int& x) { return x; } - decltype(auto) g(int& x) { return x; } - - template < typename T1, typename T2 > - struct is_same - { - static constexpr auto value = false; - }; - - template < typename T > - struct is_same - { - static constexpr auto value = true; - }; - - int - test() - { - auto x = 0; - static_assert(is_same::value, ""); - static_assert(is_same::value, ""); - return x; - } - - } - -} // namespace cxx14 - -#endif // __cplusplus >= 201402L - -]]) - - -dnl Tests for new features in C++17 - -m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_17], [[ - -// If the compiler admits that it is not ready for C++17, why torture it? -// Hopefully, this will speed up the test. - -#ifndef __cplusplus - -#error "This is not a C++ compiler" - -#elif __cplusplus < 201703L - -#error "This is not a C++17 compiler" - -#else - -#include -#include -#include - -namespace cxx17 -{ - - namespace test_constexpr_lambdas - { - - constexpr int foo = [](){return 42;}(); - - } - - namespace test::nested_namespace::definitions - { - - } - - namespace test_fold_expression - { - - template - int multiply(Args... args) - { - return (args * ... * 1); - } - - template - bool all(Args... args) - { - return (args && ...); - } - - } - - namespace test_extended_static_assert - { - - static_assert (true); - - } - - namespace test_auto_brace_init_list - { - - auto foo = {5}; - auto bar {5}; - - static_assert(std::is_same, decltype(foo)>::value); - static_assert(std::is_same::value); - } - - namespace test_typename_in_template_template_parameter - { - - template typename X> struct D; - - } - - namespace test_fallthrough_nodiscard_maybe_unused_attributes - { - - int f1() - { - return 42; - } - - [[nodiscard]] int f2() - { - [[maybe_unused]] auto unused = f1(); - - switch (f1()) - { - case 17: - f1(); - [[fallthrough]]; - case 42: - f1(); - } - return f1(); - } - - } - - namespace test_extended_aggregate_initialization - { - - struct base1 - { - int b1, b2 = 42; - }; - - struct base2 - { - base2() { - b3 = 42; - } - int b3; - }; - - struct derived : base1, base2 - { - int d; - }; - - derived d1 {{1, 2}, {}, 4}; // full initialization - derived d2 {{}, {}, 4}; // value-initialized bases - - } - - namespace test_general_range_based_for_loop - { - - struct iter - { - int i; - - int& operator* () - { - return i; - } - - const int& operator* () const - { - return i; - } - - iter& operator++() - { - ++i; - return *this; - } - }; - - struct sentinel - { - int i; - }; - - bool operator== (const iter& i, const sentinel& s) - { - return i.i == s.i; - } - - bool operator!= (const iter& i, const sentinel& s) - { - return !(i == s); - } - - struct range - { - iter begin() const - { - return {0}; - } - - sentinel end() const - { - return {5}; - } - }; - - void f() - { - range r {}; - - for (auto i : r) - { - [[maybe_unused]] auto v = i; - } - } - - } - - namespace test_lambda_capture_asterisk_this_by_value - { - - struct t - { - int i; - int foo() - { - return [*this]() - { - return i; - }(); - } - }; - - } - - namespace test_enum_class_construction - { - - enum class byte : unsigned char - {}; - - byte foo {42}; - - } - - namespace test_constexpr_if - { - - template - int f () - { - if constexpr(cond) - { - return 13; - } - else - { - return 42; - } - } - - } - - namespace test_selection_statement_with_initializer - { - - int f() - { - return 13; - } - - int f2() - { - if (auto i = f(); i > 0) - { - return 3; - } - - switch (auto i = f(); i + 4) - { - case 17: - return 2; - - default: - return 1; - } - } - - } - - namespace test_template_argument_deduction_for_class_templates - { - - template - struct pair - { - pair (T1 p1, T2 p2) - : m1 {p1}, - m2 {p2} - {} - - T1 m1; - T2 m2; - }; - - void f() - { - [[maybe_unused]] auto p = pair{13, 42u}; - } - - } - - namespace test_non_type_auto_template_parameters - { - - template - struct B - {}; - - B<5> b1; - B<'a'> b2; - - } - - namespace test_structured_bindings - { - - int arr[2] = { 1, 2 }; - std::pair pr = { 1, 2 }; - - auto f1() -> int(&)[2] - { - return arr; - } - - auto f2() -> std::pair& - { - return pr; - } - - struct S - { - int x1 : 2; - volatile double y1; - }; - - S f3() - { - return {}; - } - - auto [ x1, y1 ] = f1(); - auto& [ xr1, yr1 ] = f1(); - auto [ x2, y2 ] = f2(); - auto& [ xr2, yr2 ] = f2(); - const auto [ x3, y3 ] = f3(); - - } - - namespace test_exception_spec_type_system - { - - struct Good {}; - struct Bad {}; - - void g1() noexcept; - void g2(); - - template - Bad - f(T*, T*); - - template - Good - f(T1*, T2*); - - static_assert (std::is_same_v); - - } - - namespace test_inline_variables - { - - template void f(T) - {} - - template inline T g(T) - { - return T{}; - } - - template<> inline void f<>(int) - {} - - template<> int g<>(int) - { - return 5; - } - - } - -} // namespace cxx17 - -#endif // __cplusplus < 201703L - -]]) diff --git a/m4/ax_prog_cxx_mpi.m4 b/m4/ax_prog_cxx_mpi.m4 deleted file mode 100644 index 0199928f41..0000000000 --- a/m4/ax_prog_cxx_mpi.m4 +++ /dev/null @@ -1,175 +0,0 @@ -# =========================================================================== -# http://www.gnu.org/software/autoconf-archive/ax_prog_cxx_mpi.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_PROG_CXX_MPI([MPI-WANTED-TEST[, ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]]) -# -# DESCRIPTION -# -# This macro tries to find out how to compile C++ programs that use MPI -# (Message Passing Interface), a standard API for parallel process -# communication (see http://www-unix.mcs.anl.gov/mpi/). The macro has to -# be used instead of the standard macro AC_PROG_CXX and will replace the -# standard variable CXX with the found compiler. -# -# MPI-WANTED-TEST is used to test whether MPI is actually wanted by the -# user. If MPI-WANTED_TEST is omitted or if it succeeds, the macro will -# try to find out how to use MPI, if it fails, the macro will call -# AC_PROG_CC to find a standard C compiler instead. -# -# When MPI is found, ACTION-IF-FOUND will be executed, if MPI is not found -# (or MPI-WANTED-TEST fails) ACTION-IF-NOT-FOUND is executed. If -# ACTION-IF-FOUND is not set, the macro will define HAVE_MPI. -# -# The following example demonstrates usage of the macro: -# -# # If --with-mpi=auto is used, try to find MPI, but use standard C compiler if it is not found. -# # If --with-mpi=yes is used, try to find MPI and fail if it isn't found. -# # If --with-mpi=no is used, use a standard C compiler instead. -# AC_ARG_WITH(mpi, [AS_HELP_STRING([--with-mpi], -# [compile with MPI (parallelization) support. If none is found, -# MPI is not used. Default: auto]) -# ],,[with_mpi=auto]) -# -# AX_PROG_CXX_MPI([test x"$with_mpi" != xno],[use_mpi=yes],[ -# use_mpi=no -# if test x"$with_mpi" = xyes; then -# AC_MSG_FAILURE([MPI compiler requested, but couldn't use MPI.]) -# else -# AC_MSG_WARN([No MPI compiler found, won't use MPI.]) -# fi -# ]) -# -# LICENSE -# -# Copyright (c) 2010,2011 Olaf Lenz -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU General Public License as published by the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -# Public License for more details. -# -# You should have received a copy of the GNU General Public License along -# with this program. If not, see . -# -# As a special exception, the respective Autoconf Macro's copyright owner -# gives unlimited permission to copy, distribute and modify the configure -# scripts that are the output of Autoconf when processing the Macro. You -# need not follow the terms of the GNU General Public License when using -# or distributing such scripts, even though portions of the text of the -# Macro appear in them. The GNU General Public License (GPL) does govern -# all other use of the material that constitutes the Autoconf Macro. -# -# This special exception to the GPL applies to versions of the Autoconf -# Macro released by the Autoconf Archive. When you make and distribute a -# modified version of the Autoconf Macro, you may extend this special -# exception to the GPL to apply to your modified version as well. - -#serial 2 - -AC_DEFUN([AX_PROG_CXX_MPI], [ -AC_PREREQ(2.50) - -# Check for compiler -# Needs to be split off into an extra macro to ensure right expansion -# order. -AC_REQUIRE([_AX_PROG_CXX_MPI],[_AX_PROG_CXX_MPI([$1])]) - -AS_IF([test x"$_ax_prog_cxx_mpi_mpi_wanted" = xno], - [ _ax_prog_cxx_mpi_mpi_found=no ], - [ - AC_LANG_PUSH([C++]) - - # test whether MPI_Init() is available - # We do not use AC_SEARCH_LIBS here, as it caches its outcome and - # thus disallows corresponding calls in the other AX_PROG_*_MPI - # macros. - for lib in NONE mpi mpich; do - save_LIBS=$LIBS - if test x"$lib" = xNONE; then - AC_MSG_CHECKING([for function MPI_Init]) - else - AC_MSG_CHECKING([for function MPI_Init in -l$lib]) - LIBS="-l$lib $LIBS" - fi - AC_LINK_IFELSE([ - AC_LANG_PROGRAM([ -extern "C" { void MPI_Init(); } -],[MPI_Init();])], - [ _ax_prog_cxx_mpi_mpi_found=yes ], - [ _ax_prog_cxx_mpi_mpi_found=no ]) - AC_MSG_RESULT($_ax_prog_cxx_mpi_mpi_found) - if test "x$_ax_prog_cxx_mpi_mpi_found" = "xyes"; then - break; - fi - LIBS=$save_LIBS - done - - # Check for header - AS_IF([test x"$_ax_prog_cxx_mpi_mpi_found" = xyes], [ - AC_MSG_CHECKING([for mpi.h]) - AC_COMPILE_IFELSE([AC_LANG_PROGRAM([#include ])], - [ AC_MSG_RESULT(yes)], - [ AC_MSG_RESULT(no) - _ax_prog_cxx_mpi_mpi_found=no - ]) - ]) - AC_LANG_POP([C++]) -]) - -# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: -AS_IF([test x"$_ax_prog_cxx_mpi_mpi_found" = xyes], [ - ifelse([$2],,[AC_DEFINE(HAVE_MPI,1,[Define if you have the MPI library.])],[$2]) - : -],[ - $3 - : -]) - -])dnl AX_PROG_CXX_MPI - -dnl _AX_PROG_CXX_MPI is an internal macro required by AX_PROG_CXX_MPI. -dnl To ensure the right expansion order, the main function AX_PROG_CXX_MPI -dnl has to be split into two parts. -dnl -dnl Known MPI C++ compilers: -dnl mpic++ -dnl mpicxx -dnl mpiCC -dnl sxmpic++ NEC SX -dnl hcp -dnl mpxlC_r -dnl mpxlC -dnl mpixlcxx_r -dnl mpixlcxx -dnl mpg++ -dnl mpc++ -dnl mpCC -dnl cmpic++ -dnl mpiFCC Fujitsu -dnl CC -dnl -AC_DEFUN([_AX_PROG_CXX_MPI], [ - AC_ARG_VAR(MPICXX,[MPI C++ compiler command]) - ifelse([$1],,[_ax_prog_cxx_mpi_mpi_wanted=yes],[ - AC_MSG_CHECKING([whether to compile using MPI]) - if $1; then - _ax_prog_cxx_mpi_mpi_wanted=yes - else - _ax_prog_cxx_mpi_mpi_wanted=no - fi - AC_MSG_RESULT($_ax_prog_cxx_mpi_mpi_wanted) - ]) - if test x"$_ax_prog_cxx_mpi_mpi_wanted" = xyes; then - AC_CHECK_TOOLS([MPICXX], [mpic++ mpicxx mpiCC sxmpic++ hcp mpxlC_r mpxlC mpixlcxx_r mpixlcxx mpg++ mpc++ mpCC cmpic++ mpiFCC CCicpc pgCC pathCC sxc++ xlC_r xlC bgxlC_r bgxlC openCC sunCC crayCC aCC CC g++ c++ gpp cxx cc++ cl.exe FCC KCC RCC]) - CXX="$MPICXX" - fi - AC_PROG_CXX -])dnl _AX_PROG_CXX_MPI diff --git a/m4/ax_require_defined.m4 b/m4/ax_require_defined.m4 deleted file mode 100644 index 17c3eab7da..0000000000 --- a/m4/ax_require_defined.m4 +++ /dev/null @@ -1,37 +0,0 @@ -# =========================================================================== -# https://www.gnu.org/software/autoconf-archive/ax_require_defined.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_REQUIRE_DEFINED(MACRO) -# -# DESCRIPTION -# -# AX_REQUIRE_DEFINED is a simple helper for making sure other macros have -# been defined and thus are available for use. This avoids random issues -# where a macro isn't expanded. Instead the configure script emits a -# non-fatal: -# -# ./configure: line 1673: AX_CFLAGS_WARN_ALL: command not found -# -# It's like AC_REQUIRE except it doesn't expand the required macro. -# -# Here's an example: -# -# AX_REQUIRE_DEFINED([AX_CHECK_LINK_FLAG]) -# -# LICENSE -# -# Copyright (c) 2014 Mike Frysinger -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice -# and this notice are preserved. This file is offered as-is, without any -# warranty. - -#serial 2 - -AC_DEFUN([AX_REQUIRE_DEFINED], [dnl - m4_ifndef([$1], [m4_fatal([macro ]$1[ is not defined; is a m4 file missing?])]) -])dnl AX_REQUIRE_DEFINED diff --git a/m4/bout.m4 b/m4/bout.m4 deleted file mode 100644 index a2e5a8a733..0000000000 --- a/m4/bout.m4 +++ /dev/null @@ -1,306 +0,0 @@ -dnl -*- mode: autoconf -*- -dnl Copyright 2010-2016 B D Dudson, BOUT++ Team -dnl -dnl Contact Ben Dudson, bd512@york.ac.uk -dnl -dnl This file is part of BOUT++. -dnl -dnl BOUT++ is free software: you can redistribute it and/or modify -dnl it under the terms of the GNU Lesser General Public License as published by -dnl the Free Software Foundation, either version 3 of the License, or -dnl (at your option) any later version. -dnl -dnl BOUT++ is distributed in the hope that it will be useful, -dnl but WITHOUT ANY WARRANTY; without even the implied warranty of -dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -dnl GNU Lesser General Public License for more details. -dnl -dnl You should have received a copy of the GNU Lesser General Public License -dnl along with BOUT++. 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Can be manually edited -# for the (very) rare occasions when autoconf fails - -# extra compilation flags: -# -DCHECK=lvl Enables a host of additional checks on each operation -# such as uninitialised data if lvl is > 0. -DCHECK=3 -# enables all tests, while -DCHECK=0 disables them. -# Helps when debugging -# -DTRACK Keeps track of variable names. -# Enables more useful error messages -# for SSE2: -msse2 -mfpmath=sse -# -# This must also specify one or more file formats -# -DPDBF PDB format (need to include pdb_format.cxx) -# -DNCDF NetCDF format (nc_format.cxx) - -# PETSc config variables need to be first, else they may clobber other -# options (e.g. CXX, CXXFLAGS) -PETSC_DIR ?= @PETSC_DIR@ -PETSC_ARCH ?= @PETSC_ARCH@ -@PETSC_MAKE_INCLUDE@ -SLEPC_DIR ?= @SLEPC_DIR@ -SLEPC_ARCH ?= @SLEPC_ARCH@ -@SLEPC_MAKE_INCLUDE@ - -# These lines can be replaced in "make install" to point to install directories -# They are used in the CXXFLAGS variable below rather than hard-coding the directories -BOUT_INCLUDE_PATH=$(BOUT_TOP)/include -BOUT_LIB_PATH=$(BOUT_TOP)/lib -BOUT_CONFIG_FILE=$(BOUT_TOP)/make.config - -prefix = @prefix@ -exec_prefix = @exec_prefix@ -datarootdir = @datarootdir@ - -# This path to the locale (.mo) files is hard-wired into bout++.cxx at compile time -BOUT_LOCALE_PATH=@localedir@ - -# Created this variable so that a user won't overwrite the CXXFLAGS variable -# on the command line, just add to this one -BOUT_FLAGS = $(CXXFLAGS) @CXXFLAGS@ @OPENMP_CXXFLAGS@ @COVERAGE_FLAGS@ -#Use := here to force a "static" evaluation of the current state of BOUT_FLAGS to -#avoid infinite recursion that would arise if BOUT_FLAGS appeared on both sides of = -BOUT_FLAGS := $(BOUT_FLAGS) -DBOUT_FLAGS_STRING="$(BOUT_FLAGS)" - -# Specify the MPI C++ compiler in CXX - -CXX = @CXX@ -CC = $(CXX) - -AR = ar -ARFLAGS = @ARFLAGS@ -RANLIB = @RANLIB@ -MKDIR = @MKDIR_P@ - -#################################################################### -# Do not need to alter anything below -#################################################################### - -LD = $(CXX) -LDFLAGS = @LDFLAGS@ -LIBS = @LIBS@ -CPPFLAGS = @CPPFLAGS@ - -#################################################################### -# Extra (optional) source files, includes and libs -# NOTE: EXTRA_SRC must include a solver (solver.cxx or ida_solver.cxx) -# and a file format (nc_format.cxx or pdb_format.cxx) -#################################################################### - -EXTRA_INCS = $(CPPFLAGS) @EXTRA_INCS@ -EXTRA_LIBS = $(LIBS) @EXTRA_LIBS@ @OPENMP_CXXFLAGS@ - -PRECON_SOURCE = @PRECON_SOURCE@ - -BOUT_VERSION = @PACKAGE_VERSION@ - -#################################################################### -# These are used for compiling physics modules using BOUT++ library -#################################################################### - -# Files that are needed by configure and should be dependencies for 'all' - -OBJ = $(SOURCEC:%.cxx=%.o) -ifndef RELEASED -# If this is part of an packaged and installed installation, the user cannot -# write these files, so they shouldn't be changed. Thus only set this, in -# the non installed case. -LIB_A = $(BOUT_LIB_PATH)/libbout++.a -LIB_SO = $(BOUT_LIB_PATH)/libbout++.so -LIB = @LIB_TO_BUILD@ -endif - -MPARK_VARIANT_INCLUDE_PATH=@MPARK_VARIANT_INCLUDE_PATH@ -FMT_INCLUDE_PATH=@FMT_INCLUDE_PATH@ -BOUT_INCLUDE = -I$(BOUT_INCLUDE_PATH) $(CXXINCLUDE) $(EXTRA_INCS) @MPARK_INCLUDE@ -I$(FMT_INCLUDE_PATH) -BOUT_LIBS = -lm -L$(BOUT_LIB_PATH) -lbout++ $(EXTRA_LIBS) - -CHANGED = $(shell find -f $(BOUT_TOP)/include $(BOUT_TOP)/src -type f \( -name \*.cxx -or -name \*.h \) -newer $(LIB) -print 2> /dev/null) - -# This will set a default if no TARGET is provided -TARGET ?= $(SOURCEC:%.cxx=%) - -#################################################################### -# Definining stuff for recursive make -#################################################################### - -# Phony targets since they are directory names -.PHONY: $(DIRS) lib install libfast runtest manual sphinx doxygen - -ifneq ("$(TARGET)","libfast") -all: $(BOUT_CONFIG_FILE) $(DIRS) $(TARGET) -else -all: $(BOUT_TOP)/config.status $(BOUT_CONFIG_FILE) $(DIRS) -endif -libfast: $(BOUT_CONFIG_FILE) $(DIRS) - -#################################################################### -# Recursively run make through subdirs -#################################################################### - -ifeq ("$(TARGET)" , "lib") -$(DIRS): -# make $@ slowly using the old method where parallel builds can cause -# race conditions that - @$(MAKE) -s --no-print-directory TARGET=lib -C $@ all -else -ifeq ("$(TARGET)","libfast") -$(DIRS): -# make $@ using the libfast method, where all .o files -# are only created in the end - @$(MAKE) -s --no-print-directory TARGET=$(TARGET) -C $@ $(TARGET) -else -MODULE_DIR?=$(shell pwd) -$(DIRS): -# MODULE_DIR: pass the module directory, where the libraries should be -# created. -# SUB_NAME is used for creating a library with the expected name. -# first a potential trailing slash is removed, and after that the -# directory name is extracted. This allows to e.g. specify a directory -# as fuu/bar/ and still get an archive named bar.a - @$(MAKE) -s --no-print-directory MODULE_DIR=$(MODULE_DIR) SUB_NAME=$(shell basename $@) TARGET=sub -C $@ -endif -endif - -# Create 'lib' and 'include' incase they don't exist -$(BOUT_TOP)/include $(BOUT_TOP)/lib: - $(MKDIR) $@ - -#################################################################### -# Install header files and libraries -#################################################################### - -INSTALL = @INSTALL@ -INSTALL_PROGRAM = ${INSTALL} -INSTALL_DATA = ${INSTALL} -m 644 - -INSTALL_INCLUDE_PATH = $(DESTDIR)@includedir@/bout++/ - -# A list of relative paths e.g. "fr/LC_MESSAGES/libbout.mo zh_CN/LC_MESSAGES/libbout.mo" -MO_FILES = $(shell cd locale; ls */LC_MESSAGES/libbout.mo) - -install: libfast - $(PRE_INSTALL) # Pre-install commands follow. - - $(NORMAL_INSTALL) # Normal commands follow. - $(MKDIR) $(INSTALL_INCLUDE_PATH)/{,pvode,bout/sys,bout/invert} - $(MKDIR) $(DESTDIR)/{@libdir@,@bindir@,@datadir@/bout++/idllib} - $(MKDIR) $(DESTDIR)/@datadir@/bout++/pylib/{boutdata,boututils} - $(INSTALL_DATA) include/*.hxx $(INSTALL_INCLUDE_PATH) -ifeq ("@OWN_MPARK@", "yes") - $(MKDIR) $(INSTALL_INCLUDE_PATH)/mpark - $(INSTALL_DATA) $(MPARK_VARIANT_INCLUDE_PATH)/mpark/*.hpp $(INSTALL_INCLUDE_PATH)/mpark -endif - $(INSTALL_DATA) $(FMT_INCLUDE_PATH)/fmt/*.h $(INSTALL_INCLUDE_PATH)/fmt - $(INSTALL_DATA) include/pvode/*.h $(INSTALL_INCLUDE_PATH)/pvode/ - $(INSTALL_DATA) include/bout/*.hxx $(INSTALL_INCLUDE_PATH)/bout/ - $(INSTALL_DATA) include/bout/sys/*.hxx $(INSTALL_INCLUDE_PATH)/bout/sys/ - $(INSTALL_DATA) include/bout/invert/*.hxx $(INSTALL_INCLUDE_PATH)/bout/invert/ - $(INSTALL_DATA) lib/libbout++.a $(DESTDIR)@libdir@ - $(INSTALL_DATA) lib/libpvode.a $(DESTDIR)@libdir@ - $(INSTALL_DATA) lib/libpvpre.a $(DESTDIR)@libdir@ -ifneq ("@SHARED_EXTRA@x", "x") - $(INSTALL_PROGRAM) lib/libbout++.so.$(SONAME) $(DESTDIR)@libdir@ - $(INSTALL_PROGRAM) lib/libpvode.so.* $(DESTDIR)@libdir@ - $(INSTALL_PROGRAM) lib/libpvpre.so.* $(DESTDIR)@libdir@ - rm -f $(DESTDIR)@libdir@/lib{bout++,pvode,pvpre}.so - ln -s libbout++.so.$(SONAME) $(DESTDIR)@libdir@/libbout++.so - ln -s libpvode.so.1.0.0 $(DESTDIR)@libdir@/libpvode.so - ln -s libpvpre.so.1.0.0 $(DESTDIR)@libdir@/libpvpre.so -endif - $(INSTALL_PROGRAM) bin/bout-config $(DESTDIR)@bindir@ - $(INSTALL_PROGRAM) bin/bout-log-color $(DESTDIR)@bindir@ - $(INSTALL_DATA) tools/idllib/*.pro $(DESTDIR)@datadir@/bout++/idllib/ - $(INSTALL_DATA) tools/idllib/README $(DESTDIR)@datadir@/bout++/idllib/ - $(INSTALL_DATA) tools/pylib/boutdata/*.py $(DESTDIR)@datadir@/bout++/pylib/boutdata/ - $(INSTALL_DATA) tools/pylib/boututils/*.py $(DESTDIR)@datadir@/bout++/pylib/boututils/ - $(INSTALL_DATA) make.config $(INSTALL_INCLUDE_PATH) - for mo in $(MO_FILES); do $(MKDIR) $(DESTDIR)@localedir@/`dirname $$mo`; $(INSTALL_DATA) locale/$$mo $(DESTDIR)@localedir@/$$mo; done - $(POST_INSTALL) # Post-install commands follow. - - @# Modify paths in the bout-config script - sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@includedir@/bout++/make.config|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^idlpath=.*|idlpath=@datadir@/bout++/idllib/|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^pythonpath=.*|pythonpath=@datadir@/bout++/pylib/|" $(DESTDIR)@bindir@/bout-config -ifeq ("@OWN_MPARK@", "yes") - sed -i "s|^MPARK_VARIANT_INCLUDE_PATH=.*|MPARK_VARIANT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@bindir@/bout-config -endif - sed -i "s|^FMT_INCLUDE_PATH=.*|FMT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@bindir@/bout-config - - @# Modify paths in the make.config file - sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(INSTALL_INCLUDE_PATH)/make.config - sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(INSTALL_INCLUDE_PATH)/make.config - sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@includedir@/bout++/make.config|" $(INSTALL_INCLUDE_PATH)/make.config -ifeq ("@OWN_MPARK@", "yes") - sed -i "s|^MPARK_VARIANT_INCLUDE_PATH=.*|MPARK_VARIANT_INCLUDE_PATH=@includedir@/bout++|" $(INSTALL_INCLUDE_PATH)/make.config -endif - sed -i "s|^FMT_INCLUDE_PATH=.*|FMT_INCLUDE_PATH=@includedir@/bout++|" $(INSTALL_INCLUDE_PATH)/make.config - -# Set the make.config as released, so the library isn't rebuild. This way the .a file doesn't need to be preserved/installed - sed -i '26 i RELEASED = yes' $(INSTALL_INCLUDE_PATH)/make.config - -uninstall: - $(PRE_UNINSTALL) # Pre-uninstall commands follow. - - $(NORMAL_UNINSTALL) # Normal commands follow. - $(RM) -r $(DESTDIR)@datadir@/bout++/pylib/boututils/ - $(RM) -r $(DESTDIR)@datadir@/bout++/pylib/boutdata/ - $(RM) -r $(DESTDIR)@datadir@/bout++/idllib/ - $(RM) $(DESTDIR)@bindir@/bout-config - $(RM) $(DESTDIR)@bindir@/bout-log-color - $(RM) $(DESTDIR)@libdir@/libbout++.a - $(RM) $(DESTDIR)@libdir@/libpvode.a - $(RM) $(DESTDIR)@libdir@/libpvpre.a - $(RM) -r $(DESTDIR)@includedir@/bout++/ - $(RM) $(DESTDIR)@localedir@/*/LC_MESSAGES/libbout.mo - - $(POST_UNINSTALL) # Post-uninstall commands follow. - -#################################################################### -# Builds the library with $(OBJ) which is defined from the SOURCEC variable -#################################################################### - -# Rules for downloading submodules --include $(BOUT_TOP)/makefile.submodules - -ifeq ("$(TARGET)", "libfast") -libfast: makefile $(BOUT_CONFIG_FILE) $(BOUT_TOP)/include $(OBJ) $(DIRS) -endif - -ifeq ("$(TARGET)", "lib") -lib: makefile $(BOUT_CONFIG_FILE) $(BOUT_TOP)/include $(BOUT_TOP)/lib $(OBJ) -ifneq ("$(OBJ)foo", "foo") - @echo " Adding $(OBJ) to libbout++.a" - @$(AR) $(ARFLAGS) $(LIB_A) $(OBJ) - @$(RANLIB) $(LIB) -endif -endif - - -ifeq ("$(TARGET)", "sub") -LIB=$(MODULE_DIR)/$(SUB_NAME).a -sub:$(LIB) - -$(LIB): makefile $(BOUT_CONFIG_FILE) $(BOUT_TOP)/include $(BOUT_TOP)/lib $(OBJ) -ifneq ("$(OBJ)foo", "foo") - @echo " Adding $(OBJ) to $(LIB)" - @LIBT=$(LIB).$$$$.a && \ - $(AR) $(ARFLAGS) $${LIBT} $(OBJ) && \ - $(RANLIB) $${LIBT} && \ - mv $${LIBT} $(LIB) -endif -endif - -runtest: - ./runtest - - -ifneq ("$(TARGET)", "sub") -ifneq ("$(TARGET)", "libfast") -ifneq ("$(TARGET)", "lib") -ifneq ("$(TARGET)", "runtest") - -#################################################################### -# Make libbout++.a if it doesn't exist with the checklib target -#################################################################### -libbout++.a: - @echo "Rebuilding out-of-date bout++ library" - @$(MAKE) --no-print-directory -C $(BOUT_TOP) - -#################################################################### -# Make the target (e.g. gas_compress) -#################################################################### -# first we remove a trailing slash, if present. Note that currently we -# dont support several trailing slashes, as in fuu/bar/// -DIRS_=$(DIRS:%/=%) -# then we extract the directory name, in case it is a longer path -# We are not in a recipe, so # needs to be escaped -# $$ is an escaped $ -DIRS__=$(shell for d in $(DIRS_) ; do basename $$d;done) -# now we can generate a list of libraries -SUB_LIBS=$(DIRS__:%=%.a) -$(SUB_LIBS):$(DIRS__) - -$(SOURCEC): checklib -$(SOURCEC:%.cxx=%.o): $(LIB) -$(TARGET): | $(DIRS) -$(TARGET): makefile $(BOUT_CONFIG_FILE) $(OBJ) $(SUB_LIBS) - @echo " Linking" $(TARGET) - @$(LD) -o $(TARGET) $(OBJ) $(SUB_LIBS) $(BOUT_LIBS) $(LDFLAGS) - -checklib: -ifneq ("$(CHANGED)foo", "foo") - @echo "Rebuilding out-of-date bout++ library" - @$(MAKE) --no-print-directory -C $(BOUT_TOP) -endif - -endif -endif -endif -endif - -# Ignore missing requirement files --include .*.mk - -# If it is a libfast target, track changes to rebuild library if needed -# -# Further track dependencies using gcc's -M feature: -# -MF write the generated dependency rule to a file -# -MG assume missing headers will be generated and don't stop with an error -# -MM generate dependency rule for prerequisite, skipping system headers -# -MP add phony target for each header to prevent errors when header is missing -# -MT add a target to the generated dependency -# Ignore failure, in case some compiler does not support this -%.o: $(BOUT_CONFIG_FILE) %.cxx - @echo " Compiling " $(@:.o=.cxx) - @$(CXX) $(BOUT_INCLUDE) $(BOUT_FLAGS) -c $(@:.o=.cxx) -o $@ -ifeq ("$(TARGET)","libfast") - @test "$@" = "bout++-time.o" || touch $(BOUT_TOP)/lib/.last.o.file -endif - -#################################################################### -# Clean target. Pretty self explanatory. -# NOTE: See that double colon (::) below? That's signifies a rule that can be added to later -# See: -# http://owen.sj.ca.us/~rk/howto/slides/make/slides/makecolon.html -#################################################################### - -clean:: - -@$(RM) -rf $(OBJ) $(DEPS) $(TARGET) - @for pp in $(DIRS) $(DIRS_CLEAN); do echo " " cleaning $$pp; $(MAKE) --no-print-directory -C $$pp clean; done - @$(RM) -f $(SUB_LIBS) - -@$(RM) .*.mk - @test -f make.config && ( find src | grep '\.o$$' && echo "WARNING: Some object files remain - which might cause issues. Clean with $(MAKE) clean-remove-object-files" ) || exit 0 - -clean-remove-object-files: - find src|grep '\.o$$' | xargs rm - - -distclean:: clean clean-tests - @echo include cleaned -# Removing the externalpackage installation. When we have more packages, need a better way - @$(RM) -rf $(BOUT_TOP)/include/pvode - @echo lib cleaned - @$(RM) -rf $(BOUT_TOP)/lib/* - -@$(RM) $(BOUT_TOP)/externalpackages/PVODE/lib/*.a - -@$(RM) $(BOUT_TOP)/externalpackages/PVODE/source/obj/*.o - -@$(RM) $(BOUT_TOP)/externalpackages/PVODE/precon/obj/*.o - -@$(RM) -rf $(BOUT_TOP)/autom4te.cache make.config - @echo externalpackages cleaned - @touch $(BOUT_TOP)/configure - @echo autom4te.cache cleaned - -@$(RM) $(BOUT_TOP)/include/bout/version.hxx - -@$(RM) $(BOUT_TOP)/include/bout/revision.hxx - -@$(RM) $(BOUT_TOP)/include/bout/build_defines.hxx - @echo generated version headers cleaned - -@$(RM) $(BOUT_TOP)/tools/pylib/boutconfig/__init__.py - @echo generated Python boutconfig module cleaned - -clean-tests: clean-unit-tests clean-integrated-tests clean-mms-tests - -clean-unit-tests: - @echo " tests/unit cleaned" - @$(MAKE) --no-print-directory -C tests/unit clean - -clean-integrated-tests: - @echo " tests/integrated cleaned" - @$(MAKE) --no-print-directory -C tests/integrated clean - -clean-mms-tests: - @echo " tests/MMS cleaned" - @$(MAKE) --no-print-directory -C tests/MMS clean - -#################################################################### -# Documentation -#################################################################### - -MANUAL_DIR=$(BOUT_TOP)/manual - -doxygen: - $(MAKE) -C $(MANUAL_DIR) doxygen - -breathe-autogen: - $(MAKE) -C $(MANUAL_DIR) breathe_autogen - -sphinx-docs-html: - $(MAKE) -C $(MANUAL_DIR) sphinx-html - -sphinx-docs-latex: - $(MAKE) -C $(MANUAL_DIR) sphinx-pdf - -manual: - $(MAKE) -C $(MANUAL_DIR) - -manual-html: - $(MAKE) -C $(MANUAL_DIR) html - -manual-pdf: - $(MAKE) -C $(MANUAL_DIR) pdf - -python: libfast - $(MAKE) -C tools/pylib python3 - -python2: libfast - $(MAKE) -C tools/pylib python2 - -python-all:python python2 - -###################################################################### -# Code coverage -###################################################################### - -GCOV = @GCOV@ -LCOV = @LCOV@ -GENHTML = @GENHTML@ -abs_builddir = @abs_builddir@ - -@CODE_COVERAGE_RULES@ diff --git a/makefile b/makefile deleted file mode 100644 index 10949da529..0000000000 --- a/makefile +++ /dev/null @@ -1,117 +0,0 @@ -BOUT_TOP = $(PWD) - -DIRS = src - -DIRS_CLEAN = tests/integrated tests/unit tests/MMS - -TARGET ?= libfast - -include make.config - -# For compatibility ignore shared -shared: libfast - -###################################################################### -# Tests -###################################################################### - -check-unit-tests: libfast - @export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH}; $(MAKE) --no-print-directory -C tests/unit check - -check-mms-tests: libfast - +@cd tests/MMS; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite_make - +@cd tests/MMS; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite - -check-mms-tests-all: libfast - +@cd tests/MMS; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite_make --all - +@cd tests/MMS; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite --all - -check-integrated-tests: libfast - +@cd tests/integrated; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite_make - +@cd tests/integrated; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite - -check-integrated-tests-all: libfast - +@cd tests/integrated; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite_make --all - +@cd tests/integrated; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite --all - - -check: build-check - +@cd tests; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite -check-all: build-check-all - +@cd tests; export LD_LIBRARY_PATH=${PWD}/lib:${LD_LIBRARY_PATH} ; \ - PYTHONPATH=${PWD}/tools/pylib/:${PYTHONPATH} \ - OMPI_MCA_rmaps_base_oversubscribe=yes ./test_suite --all - -build-check-unit-tests: libfast - @$(MAKE) --no-print-directory -C tests/unit - -build-check-mms-tests: libfast - $(MAKE) --no-print-directory -C tests/MMS -build-check-mms-tests-all: libfast - $(MAKE) --no-print-directory -C tests/MMS all-all - -build-check-integrated-tests: libfast - $(MAKE) --no-print-directory -C tests/integrated -build-check-integrated-tests-all: libfast - $(MAKE) --no-print-directory -C tests/integrated all-all - - -build-check: build-check-integrated-tests build-check-mms-tests build-check-unit-tests -build-check-all: build-check-integrated-tests-all build-check-mms-tests-all build-check-unit-tests - -# Build the .mo files needed for Natural Language Support (gettext) -.PHONY: locale -locale: - $(MAKE) -C locale - -###################################################################### -# Releases -###################################################################### - -.PHONY: dist changelog - -# Makes the tarball BOUT++-v.tar.gz -dist: - @bin/bout-archive-helper.sh v$(BOUT_VERSION) - -CHANGELOG_ERR_MESSAGE := "Run like: make changelog TOKEN= LAST_VERSION=vX.Y.Z RELEASE_BRANCH=master|next" - -# Updates CHANGELOG.md, needs some arguments: -# -# make changelog TOKEN= LAST_VERSION=vX.Y.Z RELEASE_BRANCH=master|next -# -# Note: You should probably only run this if you are a maintainer (and -# also know what you're doing)! -changelog: -ifndef TOKEN - $(error $(CHANGELOG_ERR_MESSAGE)) -endif -ifndef LAST_VERSION - $(error $(CHANGELOG_ERR_MESSAGE)) -endif -ifndef RELEASE_BRANCH - $(error $(CHANGELOG_ERR_MESSAGE)) -endif - github_changelog_generator -t $(TOKEN) --since-tag \ - $(LAST_VERSION) --no-issues --max-issues 700 \ - --base CHANGELOG.md --future-release v$(BOUT_VERSION) \ - --release-branch $(RELEASE_BRANCH) \ - --user boutproject --project BOUT-dev diff --git a/makefile.submodules b/makefile.submodules deleted file mode 100644 index d590e0e72e..0000000000 --- a/makefile.submodules +++ /dev/null @@ -1,15 +0,0 @@ -# This is in a separate file so that we can download the submodules at -# configure-time, as well as exposing a nice target if things go wrong -# afterwards (for example, after changing branches) - -submodules: sub_all - -mpark_submodule: - @echo "Downloading mpark.variant" - git submodule update --init --recursive ./externalpackages/mpark.variant - -sub_all: - @for d in $$(ls externalpackages | grep -v PVODE) ; do echo "Downloading $$d" ; git submodule update --init --recursive ./externalpackages/$$d ; done - -python_submodules: - @for d in boututils boutdata ; do echo "Downloading $$d" ; git submodule update --init --recursive ./externalpackages/$$d ; done \ No newline at end of file diff --git a/src/field/makefile b/src/field/makefile deleted file mode 100644 index acefa6bbce..0000000000 --- a/src/field/makefile +++ /dev/null @@ -1,23 +0,0 @@ - -BOUT_TOP = ../.. - -SOURCEC = field.cxx field2d.cxx field3d.cxx fieldperp.cxx field_data.cxx \ - fieldgroup.cxx field_factory.cxx fieldgenerators.cxx \ - initialprofiles.cxx vecops.cxx vector2d.cxx vector3d.cxx \ - where.cxx globalfield.cxx generated_fieldops.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) field_data.hxx -TARGET = lib - - -include $(BOUT_TOP)/make.config - -# The C++ source file depends on both the Python driver and the Jinja -# template files. If either have changed, run the driver (first -# dependency), dumping the output in the C++ target file. We then try -# to apply clang-format to this file in-place, but don't worry if the -# formatting fails -generated_fieldops.cxx: gen_fieldops.py gen_fieldops.jinja - @echo " Generating $@" - @./$< --filename $@.tmp || (fail=$?; echo "touch $@ to ignore failed generation" ; exit $fail) - @mv $@.tmp $@ - @clang-format -i $@ || echo "Formatting failed" diff --git a/src/fmt/makefile b/src/fmt/makefile deleted file mode 100644 index 96c557e412..0000000000 --- a/src/fmt/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../.. - -SOURCEC = format.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/cyclic/makefile b/src/invert/laplace/impls/cyclic/makefile deleted file mode 100644 index f819d70781..0000000000 --- a/src/invert/laplace/impls/cyclic/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = cyclic_laplace.cxx -SOURCEH = cyclic_laplace.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/hypre3d/makefile b/src/invert/laplace/impls/hypre3d/makefile deleted file mode 100644 index 5181eebf98..0000000000 --- a/src/invert/laplace/impls/hypre3d/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = hypre3d_laplace.cxx -SOURCEH = hypre3d_laplace.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/iterative_parallel_tri/makefile b/src/invert/laplace/impls/iterative_parallel_tri/makefile deleted file mode 100644 index 78e2dac08d..0000000000 --- a/src/invert/laplace/impls/iterative_parallel_tri/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = iterative_parallel_tri.cxx -SOURCEH = iterative_parallel_tri.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/makefile b/src/invert/laplace/impls/makefile deleted file mode 100644 index 5f151c263a..0000000000 --- a/src/invert/laplace/impls/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP = ../../../.. - -DIRS = serial_tri serial_band spt petsc cyclic multigrid naulin petsc3damg iterative_parallel_tri pcr pcr_thomas hypre3d - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/multigrid/makefile b/src/invert/laplace/impls/multigrid/makefile deleted file mode 100644 index 41c049a79e..0000000000 --- a/src/invert/laplace/impls/multigrid/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = multigrid_laplace.cxx multigrid_alg.cxx multigrid_solver.cxx -SOURCEH = multigrid_laplace.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/naulin/makefile b/src/invert/laplace/impls/naulin/makefile deleted file mode 100644 index 6ce4495e8e..0000000000 --- a/src/invert/laplace/impls/naulin/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = naulin_laplace.cxx -SOURCEH = naulin_laplace.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/pcr/makefile b/src/invert/laplace/impls/pcr/makefile deleted file mode 100644 index c15f57aea5..0000000000 --- a/src/invert/laplace/impls/pcr/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = pcr.cxx -SOURCEH = pcr.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/pcr_thomas/makefile b/src/invert/laplace/impls/pcr_thomas/makefile deleted file mode 100644 index 6370a5bd5e..0000000000 --- a/src/invert/laplace/impls/pcr_thomas/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = pcr_thomas.cxx -SOURCEH = pcr_thomas.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/petsc/makefile b/src/invert/laplace/impls/petsc/makefile deleted file mode 100644 index e60d45292c..0000000000 --- a/src/invert/laplace/impls/petsc/makefile +++ /dev/null @@ -1,10 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = petsc_laplace.cxx -SOURCEH = petsc_laplace.hxx -TARGET = lib - -CXXFLAGS +=-g - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/petsc3damg/makefile b/src/invert/laplace/impls/petsc3damg/makefile deleted file mode 100644 index 124b2cc607..0000000000 --- a/src/invert/laplace/impls/petsc3damg/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = petsc3damg.cxx -SOURCEH = petsc3damg.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/serial_band/makefile b/src/invert/laplace/impls/serial_band/makefile deleted file mode 100644 index 2adf384942..0000000000 --- a/src/invert/laplace/impls/serial_band/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = serial_band.cxx -SOURCEH = serial_band.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/serial_tri/makefile b/src/invert/laplace/impls/serial_tri/makefile deleted file mode 100644 index 771b7c9ea6..0000000000 --- a/src/invert/laplace/impls/serial_tri/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = serial_tri.cxx -SOURCEH = serial_tri.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/impls/spt/makefile b/src/invert/laplace/impls/spt/makefile deleted file mode 100644 index 41d0b54d64..0000000000 --- a/src/invert/laplace/impls/spt/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = spt.cxx -SOURCEH = spt.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplace/makefile b/src/invert/laplace/makefile deleted file mode 100644 index baa2f806bc..0000000000 --- a/src/invert/laplace/makefile +++ /dev/null @@ -1,9 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = impls -SOURCEC = invert_laplace.cxx -SOURCEH = invert_laplace.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplacexy/makefile b/src/invert/laplacexy/makefile deleted file mode 100644 index 241d03c302..0000000000 --- a/src/invert/laplacexy/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../.. - -SOURCEC = laplacexy.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplacexy2/makefile b/src/invert/laplacexy2/makefile deleted file mode 100644 index c785581f2f..0000000000 --- a/src/invert/laplacexy2/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../.. - -SOURCEC = laplacexy2.cxx laplacexy2_hypre.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplacexz/impls/cyclic/makefile b/src/invert/laplacexz/impls/cyclic/makefile deleted file mode 100644 index da426eb84a..0000000000 --- a/src/invert/laplacexz/impls/cyclic/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = laplacexz-cyclic.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplacexz/impls/makefile b/src/invert/laplacexz/impls/makefile deleted file mode 100644 index cf12301782..0000000000 --- a/src/invert/laplacexz/impls/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../../.. - -DIRS = cyclic petsc -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplacexz/impls/petsc/makefile b/src/invert/laplacexz/impls/petsc/makefile deleted file mode 100644 index d6826dd574..0000000000 --- a/src/invert/laplacexz/impls/petsc/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = laplacexz-petsc.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/laplacexz/makefile b/src/invert/laplacexz/makefile deleted file mode 100644 index 42022dd0b6..0000000000 --- a/src/invert/laplacexz/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = impls -SOURCEC = laplacexz.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/makefile b/src/invert/makefile deleted file mode 100644 index 7deae4cdc5..0000000000 --- a/src/invert/makefile +++ /dev/null @@ -1,9 +0,0 @@ - -BOUT_TOP = ../.. - -DIRS = parderiv pardiv laplace laplacexy laplacexz laplacexy2 -SOURCEC = fft_fftw.cxx lapack_routines.cxx -SOURCEH = fft.hxx invert_parderiv.hxx lapack_routines.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/parderiv/impls/cyclic/makefile b/src/invert/parderiv/impls/cyclic/makefile deleted file mode 100644 index 7617df09d5..0000000000 --- a/src/invert/parderiv/impls/cyclic/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = cyclic.cxx -SOURCEH = cyclic.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/parderiv/impls/makefile b/src/invert/parderiv/impls/makefile deleted file mode 100644 index 2f417f8106..0000000000 --- a/src/invert/parderiv/impls/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../../.. - -DIRS = cyclic -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/parderiv/makefile b/src/invert/parderiv/makefile deleted file mode 100644 index 93bad386bc..0000000000 --- a/src/invert/parderiv/makefile +++ /dev/null @@ -1,9 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = impls -SOURCEC = invert_parderiv.cxx -SOURCEH = invert_parderiv.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/pardiv/impls/cyclic/makefile b/src/invert/pardiv/impls/cyclic/makefile deleted file mode 100644 index 0fa26267b9..0000000000 --- a/src/invert/pardiv/impls/cyclic/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../.. - -SOURCEC = pardiv_cyclic.cxx -SOURCEH = pardiv_cyclic.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/pardiv/impls/makefile b/src/invert/pardiv/impls/makefile deleted file mode 100644 index 2f417f8106..0000000000 --- a/src/invert/pardiv/impls/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../../.. - -DIRS = cyclic -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/invert/pardiv/makefile b/src/invert/pardiv/makefile deleted file mode 100644 index 0fe293644b..0000000000 --- a/src/invert/pardiv/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = impls -SOURCEC = invert_pardiv.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/makefile.in b/src/makefile.in deleted file mode 100644 index 136f5b68c9..0000000000 --- a/src/makefile.in +++ /dev/null @@ -1,96 +0,0 @@ - -BOUT_TOP = .. - -DIRS = field invert mesh physics solver sys fmt - -SOURCEC = bout++.cxx bout++-time.cxx -SOURCEH = bout.hxx -CXXFLAGS += -DMD5SUM=$(CHECKSUM) -DBOUT_REVISION="$(BOUT_REVISION)" -TARGET ?= lib - -# Checksum passed to bout++.cxx -CHECKSUM := $(shell cat $(foreach DIR,$(DIRS),$(wildcard $(DIR)/*.cxx $(DIR)/*.hxx)) | md5sum | head -c 32 ) - -# Git revision passed to bout++.cxx -BOUT_REVISION := $(shell git rev-parse HEAD 2> /dev/null || hg id -n 2> /dev/null || { echo "Unknown"; } ) - -# From the legacy build script: -# This is a little obscure, so here is an explanation: -# the first 'all: initial_message' sets the prerequisite 'inital_message' -# to be the first one called -all: initial_message - -# Then the config file is included, which has all the other -# prerequisites for 'all' -include $(BOUT_TOP)/make.config - -# Rebuild bout++-time to get the correct time of the build - but only if -# any other file was rebuild -bout++-time.o: $(BOUT_LIB_PATH)/.last.o.file | $(DIRS) bout++.o - -# The recipie could be removed, as it only catches the case of -# out-of-date make.config -# The rest is needed to tell make that .last.o.file will be created -$(BOUT_LIB_PATH)/.last.o.file: | $(DIRS) - @test -f $@ || \ - echo "make.config is out of date - run ./configure" - @test -f $@ || \ - exit 1 - -libfast: | @LIB_TO_BUILD@ - -$(BOUT_LIB_PATH)/libbout++.a: bout++-time.o - @echo "Recreating libbout++.a" - @rm -f $(LIB_A) - @$(AR) $(ARFLAGS) $(LIB_A) $(shell find $(BOUT_TOP)/src -name \*.o -type f -print 2> /dev/null) || rm -f $(LIB_A) - @touch .libfast - @#$(RANLIB) $(LIB) - @@STATIC_EXTRA@ - -$(BOUT_LIB_PATH)/libbout++.so: bout++-time.o - @echo "Creating libbout++.so" - @echo $(BOUT_FLAGS) | grep -qi pic || (echo "not compiled with PIC support - reconfigure with --enable-shared" ;exit 1) - @$(RM) $(BOUT_LIB_PATH)/*.so* - @$(CXX) -shared -Wl,-soname,libbout++.so.$(BOUT_VERSION) -o $(LIB_SO).$(BOUT_VERSION) \ - $(shell find $(BOUT_TOP)/src -name \*.o -type f -print 2> /dev/null) \ - $(LDFLAGS) - @$(CXX) -shared -Wl,-soname,libpvode.so.1.0.0 -o $(BOUT_LIB_PATH)/libpvode_.so \ - -L $(BOUT_LIB_PATH) -Wl,--whole-archive -lpvode -Wl,--no-whole-archive \ - $(LDFLAGS) - @$(CXX) -shared -Wl,-soname,libpvpre.so.1.0.0 -o $(BOUT_LIB_PATH)/libpvpre_.so \ - -L $(BOUT_LIB_PATH) -Wl,--whole-archive -lpvpre -Wl,--no-whole-archive \ - $(LDFLAGS) - @mv $(BOUT_LIB_PATH)/libpvode_.so $(BOUT_LIB_PATH)/libpvode.so.1.0.0 - @mv $(BOUT_LIB_PATH)/libpvpre_.so $(BOUT_LIB_PATH)/libpvpre.so.1.0.0 - @ln -s libbout++.so.$(BOUT_VERSION) $(LIB_SO) - @ln -s libpvode.so.1.0.0 $(BOUT_LIB_PATH)/libpvode.so - @ln -s libpvpre.so.1.0.0 $(BOUT_LIB_PATH)/libpvpre.so - @@SHARED_EXTRA@ - -# From the legacy build script: -# Then set the last two preqrequisites for 'all' -all: lib end_message - -# Only needed for legacy build script -ifneq ("$(TARGET)","libfast") -# This to make sure build time is always printed correctly -.PHONY: bout++-time.cxx -endif - -checksum: - @echo $(CHECKSUM) - -# From the legacy build script -initial_message: - @echo "" - @echo "----- Compiling BOUT++ -----" - @echo "CXX = " $(CXX) - @echo "FLAGS = " $(BOUT_FLAGS) - @echo "CHECKSUM = " $(CHECKSUM) - @echo "INCLUDE = " $(BOUT_INCLUDE) - @rm -f $(BOUT_LIB_PATH)/libbout++.a - -# From the legacy build script -end_message: - @echo "Finished" - @echo "" diff --git a/src/mesh/data/makefile b/src/mesh/data/makefile deleted file mode 100644 index 28d8eb22a9..0000000000 --- a/src/mesh/data/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../.. - -SOURCEC = gridfromoptions.cxx gridfromfile.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/mesh/impls/bout/makefile b/src/mesh/impls/bout/makefile deleted file mode 100644 index 2d8ca5ae5c..0000000000 --- a/src/mesh/impls/bout/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = boutmesh.cxx -SOURCEH = boutmesh.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/mesh/impls/makefile b/src/mesh/impls/makefile deleted file mode 100644 index ed641625de..0000000000 --- a/src/mesh/impls/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = bout -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/mesh/interpolation/makefile b/src/mesh/interpolation/makefile deleted file mode 100644 index e0c3a434eb..0000000000 --- a/src/mesh/interpolation/makefile +++ /dev/null @@ -1,10 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = -SOURCEC = bilinear_xz.cxx hermite_spline_xz.cxx \ - monotonic_hermite_spline_xz.cxx lagrange_4pt_xz.cxx \ - hermite_spline_z.cxx interpolation_z.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/mesh/makefile b/src/mesh/makefile deleted file mode 100644 index c88bc28d8c..0000000000 --- a/src/mesh/makefile +++ /dev/null @@ -1,14 +0,0 @@ - -BOUT_TOP = ../.. - - -DIRS = impls parallel data interpolation -SOURCEC = difops.cxx interpolation_xz.cxx mesh.cxx boundary_standard.cxx \ - boundary_factory.cxx boundary_region.cxx \ - surfaceiter.cxx coordinates.cxx index_derivs.cxx \ - parallel_boundary_region.cxx parallel_boundary_op.cxx fv_ops.cxx \ - coordinates_accessor.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/mesh/parallel/makefile b/src/mesh/parallel/makefile deleted file mode 100644 index 9bbfd1a910..0000000000 --- a/src/mesh/parallel/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = -SOURCEC = shiftedmetric.cxx shiftedmetricinterp.cxx fci.cxx identity.cxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/physics/makefile b/src/physics/makefile deleted file mode 100644 index 388cda9c8f..0000000000 --- a/src/physics/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../.. - -SOURCEC = physicsmodel.cxx smoothing.cxx sourcex.cxx gyro_average.cxx snb.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/adams_bashforth/makefile b/src/solver/impls/adams_bashforth/makefile deleted file mode 100644 index 5349d55f48..0000000000 --- a/src/solver/impls/adams_bashforth/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = adams_bashforth.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/arkode/makefile b/src/solver/impls/arkode/makefile deleted file mode 100644 index 3726417df3..0000000000 --- a/src/solver/impls/arkode/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = arkode.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/cvode/makefile b/src/solver/impls/cvode/makefile deleted file mode 100644 index 7c12eb1e64..0000000000 --- a/src/solver/impls/cvode/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = cvode.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/euler/makefile b/src/solver/impls/euler/makefile deleted file mode 100644 index 77576b9250..0000000000 --- a/src/solver/impls/euler/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = euler.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/ida/makefile b/src/solver/impls/ida/makefile deleted file mode 100644 index 87d2322a11..0000000000 --- a/src/solver/impls/ida/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = ida.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/imex-bdf2/makefile b/src/solver/impls/imex-bdf2/makefile deleted file mode 100644 index 845ade8ae4..0000000000 --- a/src/solver/impls/imex-bdf2/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = imex-bdf2.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/makefile b/src/solver/impls/makefile deleted file mode 100644 index 25729c1641..0000000000 --- a/src/solver/impls/makefile +++ /dev/null @@ -1,13 +0,0 @@ - -BOUT_TOP = ../../.. - -DIRS = arkode \ - pvode cvode ida \ - petsc \ - snes imex-bdf2 \ - power slepc adams_bashforth \ - rk4 euler rk3-ssp rkgeneric split-rk - -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/petsc/makefile b/src/solver/impls/petsc/makefile deleted file mode 100644 index ac2218bc76..0000000000 --- a/src/solver/impls/petsc/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = petsc.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/power/makefile b/src/solver/impls/power/makefile deleted file mode 100644 index b2fef299d8..0000000000 --- a/src/solver/impls/power/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = power.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/pvode/makefile b/src/solver/impls/pvode/makefile deleted file mode 100644 index 72d132b150..0000000000 --- a/src/solver/impls/pvode/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = pvode.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rk3-ssp/makefile b/src/solver/impls/rk3-ssp/makefile deleted file mode 100644 index 8cae9d3c25..0000000000 --- a/src/solver/impls/rk3-ssp/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = rk3-ssp.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rk4/makefile b/src/solver/impls/rk4/makefile deleted file mode 100644 index 04fad4a71f..0000000000 --- a/src/solver/impls/rk4/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = rk4.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rkgeneric/impls/cashkarp/makefile b/src/solver/impls/rkgeneric/impls/cashkarp/makefile deleted file mode 100644 index 92a372d753..0000000000 --- a/src/solver/impls/rkgeneric/impls/cashkarp/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../../.. - -SOURCEC = cashkarp.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rkgeneric/impls/makefile b/src/solver/impls/rkgeneric/impls/makefile deleted file mode 100644 index 62e5253110..0000000000 --- a/src/solver/impls/rkgeneric/impls/makefile +++ /dev/null @@ -1,7 +0,0 @@ - -BOUT_TOP = ../../../../.. - -DIRS = rkf45 cashkarp rk4simple rkf34 -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rkgeneric/impls/rk4simple/makefile b/src/solver/impls/rkgeneric/impls/rk4simple/makefile deleted file mode 100644 index f0cf42ae7a..0000000000 --- a/src/solver/impls/rkgeneric/impls/rk4simple/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../../.. - -SOURCEC = rk4simple.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rkgeneric/impls/rkf34/makefile b/src/solver/impls/rkgeneric/impls/rkf34/makefile deleted file mode 100644 index d7c13604e2..0000000000 --- a/src/solver/impls/rkgeneric/impls/rkf34/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../../.. - -SOURCEC = rkf34.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rkgeneric/impls/rkf45/makefile b/src/solver/impls/rkgeneric/impls/rkf45/makefile deleted file mode 100644 index 6f5095b504..0000000000 --- a/src/solver/impls/rkgeneric/impls/rkf45/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../../../.. - -SOURCEC = rkf45.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/rkgeneric/makefile b/src/solver/impls/rkgeneric/makefile deleted file mode 100644 index 02e443a7d9..0000000000 --- a/src/solver/impls/rkgeneric/makefile +++ /dev/null @@ -1,9 +0,0 @@ - -BOUT_TOP = ../../../.. - -DIRS = impls -SOURCEC = rkgeneric.cxx rkscheme.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/slepc/makefile b/src/solver/impls/slepc/makefile deleted file mode 100644 index ae9b7b43e4..0000000000 --- a/src/solver/impls/slepc/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = slepc.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/snes/makefile b/src/solver/impls/snes/makefile deleted file mode 100644 index 8228444a5e..0000000000 --- a/src/solver/impls/snes/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = snes.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/impls/split-rk/makefile b/src/solver/impls/split-rk/makefile deleted file mode 100644 index 4d8153a3b5..0000000000 --- a/src/solver/impls/split-rk/makefile +++ /dev/null @@ -1,8 +0,0 @@ - -BOUT_TOP = ../../../.. - -SOURCEC = split-rk.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/solver/makefile b/src/solver/makefile deleted file mode 100644 index 7aa0327328..0000000000 --- a/src/solver/makefile +++ /dev/null @@ -1,8 +0,0 @@ -BOUT_TOP = ../.. - -DIRS = impls -SOURCEC = solver.cxx -SOURCEH = $(SOURCEC:%.cxx=%.hxx) -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/sys/makefile b/src/sys/makefile deleted file mode 100644 index 04d39971cf..0000000000 --- a/src/sys/makefile +++ /dev/null @@ -1,14 +0,0 @@ - -BOUT_TOP = ../.. -DIRS = options -SOURCEC = bout_types.cxx boutexception.cxx derivs.cxx \ - msg_stack.cxx options.cxx output.cxx \ - utils.cxx optionsreader.cxx boutcomm.cxx \ - timer.cxx range.cxx petsclib.cxx expressionparser.cxx \ - slepclib.cxx type_name.cxx generator_context.cxx \ - hyprelib.cxx - -SOURCEH = $(SOURCEC:%.cxx=%.hxx) globals.hxx bout_types.hxx multiostream.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config diff --git a/src/sys/options/makefile b/src/sys/options/makefile deleted file mode 100644 index e38608b68c..0000000000 --- a/src/sys/options/makefile +++ /dev/null @@ -1,7 +0,0 @@ -BOUT_TOP = ../../.. -SOURCEC = options_ini.cxx options_netcdf.cxx - -SOURCEH = $(SOURCEC:%.cxx=%.hxx) globals.hxx bout_types.hxx multiostream.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config From faa4ba6622a74d3e69c9cee83aa25f19aabb9283 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 12 Oct 2023 17:35:53 +0100 Subject: [PATCH 101/412] Docs: Note removal of `./configure` build system Also fix links for previous versions in changelog [skip ci] --- CHANGELOG.md | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d20a10f78..656b284b9d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,14 @@ # Changelog -## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0 +## [v6.0.0](https://github.com/boutproject/BOUT-dev/tree/next) +[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...next) +### Breaking changes + +- The autotools `./configure` build system has been removed + + +## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0) [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.0.0...v5.1.0) - Update RELEASE_HOWTO.md [\#2741][https://github.com/boutproject/BOUT-dev/pull/2741] ([dschwoerer][https://github.com/dschwoerer]) @@ -44,8 +51,8 @@ - Merge v5 into next - resolve conflicts [\#2658][https://github.com/boutproject/BOUT-dev/pull/2658] ([dschwoerer][https://github.com/dschwoerer]) - Update bundled boututils and boutdata [\#2657][https://github.com/boutproject/BOUT-dev/pull/2657] ([dschwoerer][https://github.com/dschwoerer]) -## [v5.0.0](https://github.com/boutproject/BOUT-dev/tree/next) -[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.2...next) +## [v5.0.0](https://github.com/boutproject/BOUT-dev/tree/v5.0.0) +[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.2...v5.0.0) ### Breaking changes From 106164fe1089faa176433fab8bdc77ca00a46fe9 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 28 Apr 2023 16:40:25 +0100 Subject: [PATCH 102/412] Fix lots of clang-tidy issues in PETSc interface --- include/bout/petsc_interface.hxx | 112 ++++++++++++++++--------------- 1 file changed, 58 insertions(+), 54 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 8e7d44c67d..34ac641eb4 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -74,43 +74,42 @@ public: /// Default constructor does nothing PetscVector() : vector(new Vec(), VectorDeleter()) {} + ~PetscVector() = default; /// Copy constructor - PetscVector(const PetscVector& v) : vector(new Vec(), VectorDeleter()) { + PetscVector(const PetscVector& v) + : vector(new Vec(), VectorDeleter()), indexConverter(v.indexConverter), + location(v.location), initialised(v.initialised) { VecDuplicate(*v.vector, vector.get()); VecCopy(*v.vector, *vector); - indexConverter = v.indexConverter; - location = v.location; - initialised = v.initialised; } /// Move constrcutor - PetscVector(PetscVector&& v) { + PetscVector(PetscVector&& v) noexcept + : indexConverter(v.indexConverter), location(v.location), + initialised(v.initialised) { std::swap(vector, v.vector); - indexConverter = v.indexConverter; - location = v.location; - initialised = v.initialised; v.initialised = false; } /// Construct from a field, copying over the field values - PetscVector(const T& f, IndexerPtr indConverter) - : vector(new Vec(), VectorDeleter()), indexConverter(indConverter) { - ASSERT1(indConverter->getMesh() == f.getMesh()); - const MPI_Comm comm = - std::is_same::value ? f.getMesh()->getXcomm() : BoutComm::get(); + PetscVector(const T& field, IndexerPtr indConverter) + : vector(new Vec(), VectorDeleter()), indexConverter(indConverter), + location(field.getLocation()), initialised(true)) { + ASSERT1(indConverter->getMesh() == field.getMesh()); + MPI_Comm comm = + std::is_same::value ? field.getMesh()->getXcomm() : BoutComm::get(); const int size = indexConverter->size(); VecCreateMPI(comm, size, PETSC_DECIDE, vector.get()); - location = f.getLocation(); - initialised = true; - *this = f; + *this = field; } /// Construct a vector like v, but using data from a raw PETSc /// Vec. That Vec (not a copy) will then be owned by the new object. PetscVector(const PetscVector& v, Vec* vec) { #if CHECKLEVEL >= 2 - int fsize = v.indexConverter->size(), msize; + int fsize = v.indexConverter->size(); + int msize = 0; VecGetLocalSize(*vec, &msize); ASSERT2(fsize == msize); #endif @@ -122,11 +121,12 @@ public: /// Copy assignment PetscVector& operator=(const PetscVector& rhs) { - return *this = PetscVector(rhs); + *this = PetscVector(rhs); + return *this; } /// Move assignment - PetscVector& operator=(PetscVector&& rhs) { + PetscVector& operator=(PetscVector&& rhs) noexcept { swap(*this, rhs); return *this; } @@ -163,9 +163,12 @@ public: class Element { public: Element() = delete; + ~Element() = default; + Element(Element&&) = delete; + Element& operator=(Element&&) = delete; Element(const Element& other) = default; Element(Vec* vector, int index) : petscVector(vector), petscIndex(index) { - int status; + int status = 0; BOUT_OMP(critical) status = VecGetValues(*petscVector, 1, &petscIndex, &value); if (status != 0) { @@ -179,7 +182,7 @@ public: Element& operator=(BoutReal val) { ASSERT3(finite(val)); value = val; - int status; + int status = 0; BOUT_OMP(critical) status = VecSetValue(*petscVector, petscIndex, val, INSERT_VALUES); if (status != 0) { @@ -191,7 +194,7 @@ public: ASSERT3(finite(val)); value += val; ASSERT3(finite(value)); - int status; + int status = 0; BOUT_OMP(critical) status = VecSetValue(*petscVector, petscIndex, val, ADD_VALUES); if (status != 0) { @@ -234,8 +237,8 @@ public: throw BoutException("Request to return invalid vector element"); } #endif - BoutReal value; - int status; + BoutReal value = BoutNaN; + int status = 0; BOUT_OMP(critical) status = VecGetValues(*get(), 1, &global, &value); if (status != 0) { @@ -265,7 +268,7 @@ public: // Note that this only populates boundaries to a depth of 1 BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { PetscInt ind = indexConverter->getGlobal(i); - PetscScalar val; + PetscScalar val = BoutNaN; VecGetValues(*vector, 1, &ind, &val); result[i] = val; } @@ -277,10 +280,10 @@ public: const Vec* get() const { return vector.get(); } private: - PetscLib lib; + PetscLib lib{}; std::unique_ptr vector = nullptr; IndexerPtr indexConverter; - CELL_LOC location; + CELL_LOC location = CELL_LOC::deflt; bool initialised = false; }; @@ -309,32 +312,30 @@ public: /// Default constructor does nothing PetscMatrix() : matrix(new Mat(), MatrixDeleter()) {} + ~PetscMatrix() = default; /// Copy constructor - PetscMatrix(const PetscMatrix& m) : matrix(new Mat(), MatrixDeleter()), pt(m.pt) { + PetscMatrix(const PetscMatrix& m) + : matrix(new Mat(), MatrixDeleter()), indexConverter(m.indexConverter), pt(m.pt), + yoffset(m.yoffset), initialised(m.initialised) { MatDuplicate(*m.matrix, MAT_COPY_VALUES, matrix.get()); - indexConverter = m.indexConverter; - yoffset = m.yoffset; - initialised = m.initialised; } /// Move constrcutor - PetscMatrix(PetscMatrix&& m) : pt(m.pt) { - matrix = m.matrix; - indexConverter = m.indexConverter; - yoffset = m.yoffset; - initialised = m.initialised; + PetscMatrix(PetscMatrix&& m) noexcept + : matrix(m.matrix), indexConverter(m.indexConverter), pt(m.pt), yoffset(m.yoffset), + initialised(m.initialised) { m.initialised = false; } // Construct a matrix capable of operating on the specified field, // preallocating memory if requeted and possible. PetscMatrix(IndexerPtr indConverter, bool preallocate = true) - : matrix(new Mat(), MatrixDeleter()), indexConverter(indConverter) { - const MPI_Comm comm = std::is_same::value - ? indConverter->getMesh()->getXcomm() - : BoutComm::get(); - pt = &indConverter->getMesh()->getCoordinates()->getParallelTransform(); + : matrix(new Mat(), MatrixDeleter()), indexConverter(indConverter), + pt(&indConverter->getMesh()->getCoordinates()->getParallelTransform()) { + MPI_Comm comm = std::is_same::value + ? indConverter->getMesh()->getXcomm() + : BoutComm::get(); const int size = indexConverter->size(); MatCreate(comm, matrix.get()); @@ -358,7 +359,7 @@ public: return *this; } /// Move assignment - PetscMatrix& operator=(PetscMatrix&& rhs) { + PetscMatrix& operator=(PetscMatrix&& rhs) noexcept { matrix = rhs.matrix; indexConverter = rhs.indexConverter; pt = rhs.pt; @@ -384,6 +385,9 @@ public: class Element { public: Element() = delete; + ~Element() = default; + Element(Element&&) = delete; + Element& operator=(Element&&) = delete; Element(const Element& other) = default; Element(Mat* matrix, PetscInt row, PetscInt col, std::vector p = {}, std::vector w = {}) @@ -441,7 +445,7 @@ public: std::transform(weights.begin(), weights.end(), std::back_inserter(values), [&val](BoutReal weight) -> PetscScalar { return weight * val; }); - int status; + int status = 0; BOUT_OMP(critical) status = MatSetValues(*petscMatrix, 1, &petscRow, positions.size(), positions.data(), values.data(), mode); @@ -457,8 +461,8 @@ public: }; Element operator()(const ind_type& index1, const ind_type& index2) { - const int global1 = indexConverter->getGlobal(index1), - global2 = indexConverter->getGlobal(index2); + const int global1 = indexConverter->getGlobal(index1); + const int global2 = indexConverter->getGlobal(index2); #if CHECKLEVEL >= 1 if (!initialised) { throw BoutException("Can not return element of uninitialised matrix"); @@ -475,12 +479,12 @@ public: const auto pw = [this, &index1, &index2]() { if (this->yoffset == -1) { return pt->getWeightsForYDownApproximation(index2.x(), index1.y(), index2.z()); - } else if (this->yoffset == 1) { + } + if (this->yoffset == 1) { return pt->getWeightsForYUpApproximation(index2.x(), index1.y(), index2.z()); - } else { - return pt->getWeightsForYApproximation(index2.x(), index1.y(), index2.z(), - this->yoffset); } + return pt->getWeightsForYApproximation(index2.x(), index1.y(), index2.z(), + this->yoffset); }(); const int ny = @@ -504,8 +508,8 @@ public: BoutReal operator()(const ind_type& index1, const ind_type& index2) const { ASSERT2(yoffset == 0); - const int global1 = indexConverter->getGlobal(index1), - global2 = indexConverter->getGlobal(index2); + const int global1 = indexConverter->getGlobal(index1); + const int global2 = indexConverter->getGlobal(index2); #if CHECKLEVEL >= 1 if (!initialised) { throw BoutException("Can not return element of uninitialised matrix"); @@ -515,8 +519,8 @@ public: throw BoutException("Request to return invalid matrix element"); } #endif - BoutReal value; - int status; + BoutReal value = BoutNaN; + int status = 0; BOUT_OMP(critical) status = MatGetValues(*get(), 1, &global1, 1, &global2, &value); if (status != 0) { @@ -570,7 +574,7 @@ private: PetscLib lib; std::shared_ptr matrix = nullptr; IndexerPtr indexConverter; - ParallelTransform* pt; + ParallelTransform* pt{}; int yoffset = 0; bool initialised = false; }; From 42dfd009a20a98e915e1ba2483596544b37ce662 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 28 Apr 2023 17:58:50 +0100 Subject: [PATCH 103/412] WIP convert petscvector --- include/bout/petsc_interface.hxx | 81 ++---------- .../unit/include/bout/test_petsc_setters.cxx | 124 +++++++++--------- 2 files changed, 76 insertions(+), 129 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 34ac641eb4..0f1e6e6ae9 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -34,6 +34,7 @@ #include #include +#include #include #include @@ -79,7 +80,8 @@ public: /// Copy constructor PetscVector(const PetscVector& v) : vector(new Vec(), VectorDeleter()), indexConverter(v.indexConverter), - location(v.location), initialised(v.initialised) { + location(v.location), initialised(v.initialised), vector_values(v.vector_values), + vector_indices(v.vector_indices) { VecDuplicate(*v.vector, vector.get()); VecCopy(*v.vector, *vector); } @@ -87,7 +89,8 @@ public: /// Move constrcutor PetscVector(PetscVector&& v) noexcept : indexConverter(v.indexConverter), location(v.location), - initialised(v.initialised) { + initialised(v.initialised), vector_values(std::move(v.vector_values)), + vector_indices(std::move(v.vector_indices)) { std::swap(vector, v.vector); v.initialised = false; } @@ -95,7 +98,8 @@ public: /// Construct from a field, copying over the field values PetscVector(const T& field, IndexerPtr indConverter) : vector(new Vec(), VectorDeleter()), indexConverter(indConverter), - location(field.getLocation()), initialised(true)) { + location(field.getLocation()), initialised(true), + vector_values(indexConverter->size()), vector_indices(indexConverter->size()) { ASSERT1(indConverter->getMesh() == field.getMesh()); MPI_Comm comm = std::is_same::value ? field.getMesh()->getXcomm() : BoutComm::get(); @@ -148,69 +152,7 @@ public: friend void swap(PetscVector& first, PetscVector& second); - /*! - * A class which is used to assign to a particular element of a PETSc - * vector. It is meant to be transient and will be destroyed immediately - * after use. In general you should not try to assign an instance to a - * variable. - * - * The Element object will store a copy of the value which has been - * assigned to it. This is because mixing calls to the PETSc - * function VecGetValues() and VecSetValues() without intermediate - * vector assembly will cause errors. Thus, if the user wishes to - * get the value of the vector, it must be stored here. - */ - class Element { - public: - Element() = delete; - ~Element() = default; - Element(Element&&) = delete; - Element& operator=(Element&&) = delete; - Element(const Element& other) = default; - Element(Vec* vector, int index) : petscVector(vector), petscIndex(index) { - int status = 0; - BOUT_OMP(critical) - status = VecGetValues(*petscVector, 1, &petscIndex, &value); - if (status != 0) { - value = 0.; - } - } - Element& operator=(const Element& other) { - ASSERT3(finite(static_cast(other))); - return *this = static_cast(other); - } - Element& operator=(BoutReal val) { - ASSERT3(finite(val)); - value = val; - int status = 0; - BOUT_OMP(critical) - status = VecSetValue(*petscVector, petscIndex, val, INSERT_VALUES); - if (status != 0) { - throw BoutException("Error when setting elements of a PETSc vector."); - } - return *this; - } - Element& operator+=(BoutReal val) { - ASSERT3(finite(val)); - value += val; - ASSERT3(finite(value)); - int status = 0; - BOUT_OMP(critical) - status = VecSetValue(*petscVector, petscIndex, val, ADD_VALUES); - if (status != 0) { - throw BoutException("Error when setting elements of a PETSc vector."); - } - return *this; - } - operator BoutReal() const { return value; } - - private: - Vec* petscVector = nullptr; - PetscInt petscIndex; - PetscScalar value; - }; - - Element operator()(const ind_type& index) { + BoutReal& operator()(const ind_type& index) { #if CHECKLEVEL >= 1 if (!initialised) { throw BoutException("Can not return element of uninitialised vector"); @@ -222,7 +164,9 @@ public: throw BoutException("Request to return invalid vector element"); } #endif - return Element(vector.get(), global); + const auto index_as_int = static_cast(index); + vector_indices[index_as_int] = global; + return vector_values[index_as_int]; } BoutReal operator()(const ind_type& index) const { @@ -248,6 +192,7 @@ public: } void assemble() { + VecSetValues(*vector, vector_indices.size(), vector_indices.begin(), vector_values.begin(), INSERT_VALUES); VecAssemblyBegin(*vector); VecAssemblyEnd(*vector); } @@ -283,6 +228,8 @@ private: PetscLib lib{}; std::unique_ptr vector = nullptr; IndexerPtr indexConverter; + Array vector_values{}; + Array vector_indices{}; CELL_LOC location = CELL_LOC::deflt; bool initialised = false; }; diff --git a/tests/unit/include/bout/test_petsc_setters.cxx b/tests/unit/include/bout/test_petsc_setters.cxx index 3a916f59e0..7ffbad819a 100644 --- a/tests/unit/include/bout/test_petsc_setters.cxx +++ b/tests/unit/include/bout/test_petsc_setters.cxx @@ -30,68 +30,68 @@ class PetscVectorElementTest : public ::testing::Test { virtual ~PetscVectorElementTest() { VecDestroy(&v); } }; -TEST_F(PetscVectorElementTest, AssignInsert) { - PetscVector::Element v1(&v, 1), v2(&v, 2), v3(&v, 3), v3b(&v, 3), v9(&v, 9); - v1 = 1.5; - v2 = 2.5; - v3 = 3.5; - v3b = 4.0; // Should overwrite previous call - v9 = 9.5; - VecAssemblyBegin(v); - VecAssemblyEnd(v); - PetscScalar* vecContents; - VecGetArray(v, &vecContents); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[0]); - EXPECT_DOUBLE_EQ(1.5, vecContents[1]); - EXPECT_DOUBLE_EQ(2.5, vecContents[2]); - EXPECT_DOUBLE_EQ(4.0, vecContents[3]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[4]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[5]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[6]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[7]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[8]); - EXPECT_DOUBLE_EQ(9.5, vecContents[9]); -} - -TEST_F(PetscVectorElementTest, AssignElement) { - PetscVector::Element v1(&v, 1), v2(&v, 2); - v2 = v1 = 1.5; - VecAssemblyBegin(v); - VecAssemblyEnd(v); - PetscScalar* vecContents; - VecGetArray(v, &vecContents); - EXPECT_DOUBLE_EQ(1.5, vecContents[1]); - EXPECT_DOUBLE_EQ(1.5, vecContents[2]); -} - -TEST_F(PetscVectorElementTest, AssignAdd) { - PetscVector::Element v1(&v, 1), v2(&v, 2), v3(&v, 3), v3b(&v, 3), v9(&v, 9); - v1 += 1.5; - v2 += 2.5; - v3 += 3.5; - v3b += 4.0; - v9 += 9.5; - VecAssemblyBegin(v); - VecAssemblyEnd(v); - PetscScalar* vecContents; - VecGetArray(v, &vecContents); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[0]); - EXPECT_DOUBLE_EQ(2.5, vecContents[1]); - EXPECT_DOUBLE_EQ(3.5, vecContents[2]); - EXPECT_DOUBLE_EQ(8.5, vecContents[3]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[4]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[5]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[6]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[7]); - EXPECT_DOUBLE_EQ(defaultVal, vecContents[8]); - EXPECT_DOUBLE_EQ(10.5, vecContents[9]); -} - -TEST_F(PetscVectorElementTest, ConvertToBoutReal) { - PetscVector::Element v1(&v, 1); - BoutReal val = v1; - EXPECT_DOUBLE_EQ(defaultVal, val); -} +// TEST_F(PetscVectorElementTest, AssignInsert) { +// PetscVector::Element v1(&v, 1), v2(&v, 2), v3(&v, 3), v3b(&v, 3), v9(&v, 9); +// v1 = 1.5; +// v2 = 2.5; +// v3 = 3.5; +// v3b = 4.0; // Should overwrite previous call +// v9 = 9.5; +// VecAssemblyBegin(v); +// VecAssemblyEnd(v); +// PetscScalar* vecContents; +// VecGetArray(v, &vecContents); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[0]); +// EXPECT_DOUBLE_EQ(1.5, vecContents[1]); +// EXPECT_DOUBLE_EQ(2.5, vecContents[2]); +// EXPECT_DOUBLE_EQ(4.0, vecContents[3]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[4]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[5]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[6]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[7]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[8]); +// EXPECT_DOUBLE_EQ(9.5, vecContents[9]); +// } + +// TEST_F(PetscVectorElementTest, AssignElement) { +// PetscVector::Element v1(&v, 1), v2(&v, 2); +// v2 = v1 = 1.5; +// VecAssemblyBegin(v); +// VecAssemblyEnd(v); +// PetscScalar* vecContents; +// VecGetArray(v, &vecContents); +// EXPECT_DOUBLE_EQ(1.5, vecContents[1]); +// EXPECT_DOUBLE_EQ(1.5, vecContents[2]); +// } + +// TEST_F(PetscVectorElementTest, AssignAdd) { +// PetscVector::Element v1(&v, 1), v2(&v, 2), v3(&v, 3), v3b(&v, 3), v9(&v, 9); +// v1 += 1.5; +// v2 += 2.5; +// v3 += 3.5; +// v3b += 4.0; +// v9 += 9.5; +// VecAssemblyBegin(v); +// VecAssemblyEnd(v); +// PetscScalar* vecContents; +// VecGetArray(v, &vecContents); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[0]); +// EXPECT_DOUBLE_EQ(2.5, vecContents[1]); +// EXPECT_DOUBLE_EQ(3.5, vecContents[2]); +// EXPECT_DOUBLE_EQ(8.5, vecContents[3]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[4]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[5]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[6]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[7]); +// EXPECT_DOUBLE_EQ(defaultVal, vecContents[8]); +// EXPECT_DOUBLE_EQ(10.5, vecContents[9]); +// } + +// TEST_F(PetscVectorElementTest, ConvertToBoutReal) { +// PetscVector::Element v1(&v, 1); +// BoutReal val = v1; +// EXPECT_DOUBLE_EQ(defaultVal, val); +// } ///////////////// Test PetscMatrixElement ///////////////// From 6510a19a9b8a3237ab8e43beb072078df2968a59 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 10:20:15 +0100 Subject: [PATCH 104/412] Use default constructor for `Vec/Mat` deleters --- include/bout/petsc_interface.hxx | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 0f1e6e6ae9..839c1021e3 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -74,12 +74,12 @@ public: }; /// Default constructor does nothing - PetscVector() : vector(new Vec(), VectorDeleter()) {} + PetscVector() : vector(new Vec{}) {} ~PetscVector() = default; /// Copy constructor PetscVector(const PetscVector& v) - : vector(new Vec(), VectorDeleter()), indexConverter(v.indexConverter), + : vector(new Vec()), indexConverter(v.indexConverter), location(v.location), initialised(v.initialised), vector_values(v.vector_values), vector_indices(v.vector_indices) { VecDuplicate(*v.vector, vector.get()); @@ -97,7 +97,7 @@ public: /// Construct from a field, copying over the field values PetscVector(const T& field, IndexerPtr indConverter) - : vector(new Vec(), VectorDeleter()), indexConverter(indConverter), + : vector(new Vec()), indexConverter(indConverter), location(field.getLocation()), initialised(true), vector_values(indexConverter->size()), vector_indices(indexConverter->size()) { ASSERT1(indConverter->getMesh() == field.getMesh()); @@ -258,12 +258,12 @@ public: }; /// Default constructor does nothing - PetscMatrix() : matrix(new Mat(), MatrixDeleter()) {} + PetscMatrix() : matrix(new Mat()) {} ~PetscMatrix() = default; /// Copy constructor PetscMatrix(const PetscMatrix& m) - : matrix(new Mat(), MatrixDeleter()), indexConverter(m.indexConverter), pt(m.pt), + : matrix(new Mat()), indexConverter(m.indexConverter), pt(m.pt), yoffset(m.yoffset), initialised(m.initialised) { MatDuplicate(*m.matrix, MAT_COPY_VALUES, matrix.get()); } @@ -278,7 +278,7 @@ public: // Construct a matrix capable of operating on the specified field, // preallocating memory if requeted and possible. PetscMatrix(IndexerPtr indConverter, bool preallocate = true) - : matrix(new Mat(), MatrixDeleter()), indexConverter(indConverter), + : matrix(new Mat()), indexConverter(indConverter), pt(&indConverter->getMesh()->getCoordinates()->getParallelTransform()) { MPI_Comm comm = std::is_same::value ? indConverter->getMesh()->getXcomm() From 76d912dc9fb50e520f8cdcf8857f227eba388f95 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 10:43:11 +0100 Subject: [PATCH 105/412] Use `BoutException` formatted message instead of `std::cout` --- include/bout/petsc_interface.hxx | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 839c1021e3..be89abb5c3 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -413,10 +413,11 @@ public: #if CHECKLEVEL >= 1 if (!initialised) { throw BoutException("Can not return element of uninitialised matrix"); - } else if (global1 == -1 || global2 == -1) { - std::cout << "(" << index1.x() << ", " << index1.y() << ", " << index1.z() << ") "; - std::cout << "(" << index2.x() << ", " << index2.y() << ", " << index2.z() << ")\n"; - throw BoutException("Request to return invalid matrix element"); + } + if (global1 == -1 || global2 == -1) { + throw BoutException( + "Request to return invalid matrix element: (({}, {}, {}), ({}, {}, {}))", + index1.x(), index1.y(), index1.z(), index2.x(), index2.y(), index2.z()); } #endif std::vector positions; @@ -460,10 +461,11 @@ public: #if CHECKLEVEL >= 1 if (!initialised) { throw BoutException("Can not return element of uninitialised matrix"); - } else if (global1 == -1 || global2 == -1) { - std::cout << "(" << index1.x() << ", " << index1.y() << ", " << index1.z() << ") "; - std::cout << "(" << index2.x() << ", " << index2.y() << ", " << index2.z() << ")\n"; - throw BoutException("Request to return invalid matrix element"); + } + if (global1 == -1 || global2 == -1) { + throw BoutException( + "Request to return invalid matrix element: (({}, {}, {}), ({}, {}, {}))", + index1.x(), index1.y(), index1.z(), index2.x(), index2.y(), index2.z()); } #endif BoutReal value = BoutNaN; From 5413c2ab9efe27833670b0fc15c093e96599fbcc Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 15:21:15 +0100 Subject: [PATCH 106/412] Simplify getting parallel slice interpolation weights We don't need to call the YUp/YDown specific versions, we can just use the general one --- include/bout/petsc_interface.hxx | 13 ++---------- src/mesh/parallel/shiftedmetricinterp.hxx | 9 ++------- tests/unit/include/bout/test_petsc_matrix.cxx | 20 +++++++++++-------- 3 files changed, 16 insertions(+), 26 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index be89abb5c3..ce7e0f64d3 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -424,17 +424,8 @@ public: std::vector weights; if (yoffset != 0) { ASSERT1(yoffset == index2.y() - index1.y()); - const auto pw = [this, &index1, &index2]() { - if (this->yoffset == -1) { - return pt->getWeightsForYDownApproximation(index2.x(), index1.y(), index2.z()); - } - if (this->yoffset == 1) { - return pt->getWeightsForYUpApproximation(index2.x(), index1.y(), index2.z()); - } - return pt->getWeightsForYApproximation(index2.x(), index1.y(), index2.z(), - this->yoffset); - }(); - + const auto pw = + pt->getWeightsForYApproximation(index2.x(), index1.y(), index2.z(), yoffset); const int ny = std::is_same::value ? 1 : indexConverter->getMesh()->LocalNy; const int nz = diff --git a/src/mesh/parallel/shiftedmetricinterp.hxx b/src/mesh/parallel/shiftedmetricinterp.hxx index 86ecfac853..928341827a 100644 --- a/src/mesh/parallel/shiftedmetricinterp.hxx +++ b/src/mesh/parallel/shiftedmetricinterp.hxx @@ -78,14 +78,9 @@ public: bool canToFromFieldAligned() const override { return true; } std::vector - getWeightsForYUpApproximation(int i, int j, int k) override { + getWeightsForYApproximation(int i, int j, int k, int y_offset) override { return parallel_slice_interpolators[yup_index]->getWeightsForYApproximation(i, j, k, - 1); - } - std::vector - getWeightsForYDownApproximation(int i, int j, int k) override { - return parallel_slice_interpolators[ydown_index]->getWeightsForYApproximation(i, j, k, - -1); + y_offset); } bool requiresTwistShift(bool twist_shift_enabled, YDirectionType ytype) override { diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index d55f384b9c..d97fff9b52 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -31,6 +31,8 @@ using ::testing::Return; class MockTransform : public ParallelTransformIdentity { public: MockTransform(Mesh& mesh_in) : ParallelTransformIdentity(mesh_in){}; + MOCK_METHOD(std::vector, getWeightsForYApproximation, + (int i, int j, int k, int y_offset), (override)); MOCK_METHOD(std::vector, getWeightsForYUpApproximation, (int i, int j, int k), (override)); MOCK_METHOD(std::vector, getWeightsForYDownApproximation, @@ -273,8 +275,9 @@ TYPED_TEST(PetscMatrixTest, TestYUp) { if (std::is_same::value) { expected(this->indexA, this->indexB) = val; } else if (std::is_same::value) { - EXPECT_CALL(*transform, getWeightsForYUpApproximation( - this->indexB.x(), this->indexA.y(), this->indexB.z())) + EXPECT_CALL(*transform, + getWeightsForYApproximation(this->indexB.x(), this->indexA.y(), + this->indexB.z(), 1)) .WillOnce(Return(this->yUpWeights)); expected(this->indexA, this->iWU0) = this->yUpWeights[0].weight * val; expected(this->indexA, this->iWU1) = this->yUpWeights[1].weight * val; @@ -302,8 +305,9 @@ TYPED_TEST(PetscMatrixTest, TestYDown) { if (std::is_same::value) { expected(this->indexB, this->indexA) = val; } else if (std::is_same::value) { - EXPECT_CALL(*transform, getWeightsForYDownApproximation( - this->indexA.x(), this->indexB.y(), this->indexA.z())) + EXPECT_CALL(*transform, + getWeightsForYApproximation(this->indexA.x(), this->indexB.y(), + this->indexA.z(), -1)) .WillOnce(Return(this->yDownWeights)); expected(this->indexB, this->iWD0) = this->yDownWeights[0].weight * val; expected(this->indexB, this->iWD1) = this->yDownWeights[1].weight * val; @@ -344,8 +348,8 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { EXPECT_THROW(matrix.ynext(1), BoutException); } else { if (std::is_same::value) { - EXPECT_CALL(*transform, getWeightsForYUpApproximation( - this->indexB.x(), this->indexA.y(), this->indexB.z())) + EXPECT_CALL(*transform, getWeightsForYApproximation( + this->indexB.x(), this->indexA.y(), this->indexB.z(), 1)) .Times(2) .WillRepeatedly(Return(this->yDownWeights)); } @@ -370,8 +374,8 @@ TYPED_TEST(PetscMatrixTest, TestYNextNeg) { EXPECT_THROW(matrix.ynext(-1), BoutException); } else { if (std::is_same::value) { - EXPECT_CALL(*transform, getWeightsForYDownApproximation( - this->indexA.x(), this->indexB.y(), this->indexA.z())) + EXPECT_CALL(*transform, getWeightsForYApproximation( + this->indexA.x(), this->indexB.y(), this->indexA.z(), -1)) .Times(2) .WillRepeatedly(Return(this->yDownWeights)); } From 2c0feeb71aa8d079bf2183ca4457056c8a558f2a Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 15:22:22 +0100 Subject: [PATCH 107/412] Add `size()` method to Fields to get total number of points --- include/bout/field.hxx | 3 +++ include/bout/field2d.hxx | 1 + include/bout/field3d.hxx | 2 ++ include/bout/fieldperp.hxx | 2 ++ tests/unit/field/test_field.cxx | 1 + 5 files changed, 9 insertions(+) diff --git a/include/bout/field.hxx b/include/bout/field.hxx index be347f60d0..9a425942c1 100644 --- a/include/bout/field.hxx +++ b/include/bout/field.hxx @@ -122,6 +122,9 @@ public: */ virtual int getNz() const; + /// Get the total number of points + virtual int size() const = 0; + friend void swap(Field& first, Field& second) noexcept { using std::swap; swap(static_cast(first), static_cast(second)); diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index 1c1169a175..ec89547925 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -277,6 +277,7 @@ public: friend void swap(Field2D& first, Field2D& second) noexcept; + int size() const override { return nx * ny; }; /// Internal data array. Handles allocation/freeing of memory Array data; diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx index 8213742248..4e6510f8a6 100644 --- a/include/bout/field3d.hxx +++ b/include/bout/field3d.hxx @@ -489,6 +489,8 @@ public: friend void swap(Field3D& first, Field3D& second) noexcept; + int size() const override { return nx * ny * nz; }; + private: /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null int nx{-1}, ny{-1}, nz{-1}; diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx index 4433463e8f..3b6e0567d8 100644 --- a/include/bout/fieldperp.hxx +++ b/include/bout/fieldperp.hxx @@ -287,6 +287,8 @@ public: friend void swap(FieldPerp& first, FieldPerp& second) noexcept; + int size() const override { return nx * nz; }; + private: /// The Y index at which this FieldPerp is defined int yindex{-1}; diff --git a/tests/unit/field/test_field.cxx b/tests/unit/field/test_field.cxx index b237ee3006..f458ffd6bc 100644 --- a/tests/unit/field/test_field.cxx +++ b/tests/unit/field/test_field.cxx @@ -33,6 +33,7 @@ class FieldSubClass : public Field { : Field(localmesh, location_in, directions_in) {} bool is3D() const override { return false; } + int size() const override { return 42; } }; } // namespace From 75adac99eeb9e81ccc0d2046c41ffbca88017c9a Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 15:24:04 +0100 Subject: [PATCH 108/412] Collect all test failures for petsc3d --- tests/integrated/test-laplace-petsc3d/runtest | 35 ++++++++++++------- 1 file changed, 22 insertions(+), 13 deletions(-) diff --git a/tests/integrated/test-laplace-petsc3d/runtest b/tests/integrated/test-laplace-petsc3d/runtest index 88f9d76c62..7b0d55f357 100755 --- a/tests/integrated/test-laplace-petsc3d/runtest +++ b/tests/integrated/test-laplace-petsc3d/runtest @@ -3,7 +3,7 @@ # requires: petsc from boutdata import collect -from boututils.run_wrapper import launch_safe, build_and_log +from boututils.run_wrapper import launch, build_and_log from sys import exit test_directories = [ @@ -18,21 +18,30 @@ tolerance = 1.0e-6 build_and_log("Laplace 3D with PETSc") success = True +errors = {} + for directory, nproc in test_directories: - command = "./test-laplace3d -d " + directory + command = f"./test-laplace3d -d {directory}" print("running on", nproc, "processors:", command) - launch_safe(command, nproc=nproc) + status, output = launch(command, nproc=nproc, pipe=True) - error_max = collect("error_max", path=directory, info=False) + if status: + print("FAILED") + print(output) + errors[directory] = "" + continue + error_max = collect("error_max", path=directory, info=False) if error_max > tolerance: - print(directory + " failed with maximum error {}".format(error_max)) - success = False - else: - print(directory + " passed with maximum error {}".format(error_max)) - -if success: - print("All passed") - exit(0) -else: + errors[directory] = error_max + +print("**********") + +if errors: + print("Some failures:") + for name, error in errors.items(): + print(f"{name}, max error: {error}") exit(1) + +print("All passed") +exit(0) From d3216ab1ab7659c3b7c6e911d7efd22d96dcd7b5 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 15:32:50 +0100 Subject: [PATCH 109/412] Make `Field2D::data` private --- include/bout/field2d.hxx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index ec89547925..a36f899692 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -278,10 +278,11 @@ public: friend void swap(Field2D& first, Field2D& second) noexcept; int size() const override { return nx * ny; }; + +private: /// Internal data array. Handles allocation/freeing of memory Array data; -private: /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null int nx{-1}, ny{-1}; From c85793fc7b61f8d3fc69e1eba95f56b56cc9da36 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 15:33:42 +0100 Subject: [PATCH 110/412] Replace direct calls to `VecSetValue` with buffered calls Now calls `VecSetValues` with whole vector at once --- include/bout/globalindexer.hxx | 17 ++++- include/bout/petsc_interface.hxx | 68 ++++++++++--------- tests/unit/include/bout/test_petsc_vector.cxx | 52 ++++++++------ 3 files changed, 84 insertions(+), 53 deletions(-) diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index a061f387dc..bd0a451687 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -45,7 +45,8 @@ public: bool autoInitialise = true) : fieldmesh(localmesh), indices(-1., localmesh), stencils(std::move(stencil)) { - Region allCandidate, bndryCandidate; + Region allCandidate; + Region bndryCandidate; if (stencils.getNumParts() > 0) { std::set allIndices(getRegionNobndry().getIndices().begin(), getRegionNobndry().getIndices().end()); @@ -105,7 +106,13 @@ public: /// Finish setting up the indexer, communicating indices across /// processes and, if possible, calculating the sparsity pattern of /// any matrices. - void initialise() { fieldmesh->communicate(indices); } + void initialise() { + fieldmesh->communicate(indices); + int_indices.reallocate(indices.size()); + BOUT_FOR(index, indices.getRegion("RGN_ALL")) { + int_indices[index.ind] = static_cast(indices[index]); + } + } Mesh* getMesh() const { return fieldmesh; } @@ -157,6 +164,10 @@ public: int size() const { return regionAll.size(); } + const Array& getIntIndices() const { + return int_indices; + } + protected: // Must not be const as the index field needs to be mutable in order // to fake parallel communication in the unit tests. @@ -206,6 +217,8 @@ private: /// Fields containing the indices for each element (as reals) T indices; + /// Indices as integers + Array int_indices; /// The first and last global index on this processor (inclusive in /// both cases) int globalStart, globalEnd; diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index ce7e0f64d3..ab6d775237 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -33,8 +33,10 @@ #include "bout/build_config.hxx" #include +#include #include #include +#include #include #include @@ -60,6 +62,16 @@ class PetscVector; template void swap(PetscVector& first, PetscVector& second); +template +inline MPI_Comm getComm([[maybe_unused]] const T& field) { + return BoutComm::get(); +} + +template <> +inline MPI_Comm getComm([[maybe_unused]] const FieldPerp& field) { + return field.getMesh()->getXcomm(); +} + template class PetscVector { public: @@ -73,24 +85,19 @@ public: } }; - /// Default constructor does nothing PetscVector() : vector(new Vec{}) {} ~PetscVector() = default; - /// Copy constructor PetscVector(const PetscVector& v) : vector(new Vec()), indexConverter(v.indexConverter), - location(v.location), initialised(v.initialised), vector_values(v.vector_values), - vector_indices(v.vector_indices) { + location(v.location), initialised(v.initialised), vector_values(v.vector_values) { VecDuplicate(*v.vector, vector.get()); VecCopy(*v.vector, *vector); } - /// Move constrcutor PetscVector(PetscVector&& v) noexcept : indexConverter(v.indexConverter), location(v.location), - initialised(v.initialised), vector_values(std::move(v.vector_values)), - vector_indices(std::move(v.vector_indices)) { + initialised(v.initialised), vector_values(std::move(v.vector_values)) { std::swap(vector, v.vector); v.initialised = false; } @@ -99,12 +106,14 @@ public: PetscVector(const T& field, IndexerPtr indConverter) : vector(new Vec()), indexConverter(indConverter), location(field.getLocation()), initialised(true), - vector_values(indexConverter->size()), vector_indices(indexConverter->size()) { + vector_values(field.size()) { ASSERT1(indConverter->getMesh() == field.getMesh()); - MPI_Comm comm = - std::is_same::value ? field.getMesh()->getXcomm() : BoutComm::get(); + MPI_Comm comm = getComm(field); + const int size = indexConverter->size(); VecCreateMPI(comm, size, PETSC_DECIDE, vector.get()); + // This allows us to pass negative indices + VecSetOption(*vector, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE); *this = field; } @@ -138,13 +147,7 @@ public: PetscVector& operator=(const T& f) { ASSERT1(indexConverter); // Needs to have index set BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { - const PetscInt ind = indexConverter->getGlobal(i); - if (ind != -1) { - // TODO: consider how VecSetValues() could be used where there - // are continuous stretches of field data which should be - // copied into the vector. - VecSetValue(*vector, ind, f[i], INSERT_VALUES); - } + (*this)(i) = f[i]; } assemble(); return *this; @@ -158,15 +161,7 @@ public: throw BoutException("Can not return element of uninitialised vector"); } #endif - const int global = indexConverter->getGlobal(index); -#if CHECKLEVEL >= 1 - if (global == -1) { - throw BoutException("Request to return invalid vector element"); - } -#endif - const auto index_as_int = static_cast(index); - vector_indices[index_as_int] = global; - return vector_values[index_as_int]; + return vector_values[index.ind]; } BoutReal operator()(const ind_type& index) const { @@ -192,9 +187,21 @@ public: } void assemble() { - VecSetValues(*vector, vector_indices.size(), vector_indices.begin(), vector_values.begin(), INSERT_VALUES); - VecAssemblyBegin(*vector); - VecAssemblyEnd(*vector); + auto ierr = VecSetValues(*vector, vector_values.size(), + indexConverter->getIntIndices().begin(), + vector_values.begin(), INSERT_VALUES); + if (ierr < 0) { + throw BoutException("PETSc error"); + } + + ierr = VecAssemblyBegin(*vector); + if (ierr < 0) { + throw BoutException("PETSc error"); + } + ierr = VecAssemblyEnd(*vector); + if (ierr < 0) { + throw BoutException("PETSc error"); + } } void destroy() { @@ -228,10 +235,9 @@ private: PetscLib lib{}; std::unique_ptr vector = nullptr; IndexerPtr indexConverter; - Array vector_values{}; - Array vector_indices{}; CELL_LOC location = CELL_LOC::deflt; bool initialised = false; + Array vector_values{}; }; /*! diff --git a/tests/unit/include/bout/test_petsc_vector.cxx b/tests/unit/include/bout/test_petsc_vector.cxx index 101fb9480d..f031977bb4 100644 --- a/tests/unit/include/bout/test_petsc_vector.cxx +++ b/tests/unit/include/bout/test_petsc_vector.cxx @@ -139,18 +139,39 @@ TYPED_TEST(PetscVectorTest, MoveAssignment) { EXPECT_EQ(vectorPtr, movedPtr); } +TYPED_TEST(PetscVectorTest, SetElement) { + SCOPED_TRACE("FieldAssignment"); + PetscVector vector(this->field, this->indexer); + const TypeParam val(-10.); + + BOUT_FOR(index, val.getRegion("RGN_ALL")) { + vector(index) = val[index]; + } + vector.assemble(); + + Vec* vectorPtr = vector.get(); + PetscScalar* vecContents = nullptr; + PetscInt size = 0; + VecGetArray(*vectorPtr, &vecContents); + VecGetLocalSize(*vectorPtr, &size); + ASSERT_EQ(size, this->field.size()); + TypeParam result = vector.toField(); + BOUT_FOR(i, this->field.getRegion("RGN_NOY")) { EXPECT_EQ(result[i], val[i]); } +} + // Test getting elements TYPED_TEST(PetscVectorTest, TestGetElements) { PetscVector vector(this->field, this->indexer); BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { vector(i) = (2.5 * this->field[i] - 1.0); } + vector.assemble(); + TypeParam result = vector.toField(); Vec* rawvec = vector.get(); - PetscScalar* vecContents; + PetscScalar* vecContents = nullptr; VecAssemblyBegin(*rawvec); VecAssemblyEnd(*rawvec); VecGetArray(*rawvec, &vecContents); - TypeParam result = vector.toField(); BOUT_FOR(i, this->field.getRegion("RGN_NOBNDRY")) { EXPECT_EQ(result[i], 2.5 * this->field[i] - 1.0); } @@ -165,19 +186,6 @@ TYPED_TEST(PetscVectorTest, TestGetElementsConst) { } } -// Test assemble -TYPED_TEST(PetscVectorTest, TestAssemble) { - PetscVector vector(this->field, this->indexer); - Vec* rawvec = vector.get(); - const PetscInt i = 4; - const PetscScalar r = 3.141592; - VecSetValues(*rawvec, 1, &i, &r, INSERT_VALUES); - vector.assemble(); - PetscScalar* vecContents; - VecGetArray(*rawvec, &vecContents); - ASSERT_EQ(vecContents[i], r); -} - #ifdef PETSC_USE_DEBUG // Test trying to get an element from an uninitialised vector @@ -201,14 +209,18 @@ TYPED_TEST(PetscVectorTest, TestGetOutOfBounds) { } #endif // CHECKLEVEL >= 3 -// Test trying to use both INSERT_VALUES and ADD_VALUES TYPED_TEST(PetscVectorTest, TestMixedSetting) { PetscVector vector(this->field, this->indexer); - typename TypeParam::ind_type i = *(this->field.getRegion("RGN_NOBNDRY").begin()); - typename TypeParam::ind_type j(i.ind + 1); + typename TypeParam::ind_type index1 = *(this->field.getRegion("RGN_NOBNDRY").begin()); + typename TypeParam::ind_type index2(index1.ind + 1); const PetscScalar r = 3.141592; - vector(i) = r; - EXPECT_THROW(vector(j) += r, BoutException); + vector(index1) = r; + vector(index2) += r; + vector.assemble(); + PetscScalar* vecContents = nullptr; + VecGetArray(*(vector.get()), &vecContents); + ASSERT_EQ(vecContents[index1.ind], r); + ASSERT_EQ(vecContents[index2.ind], this->field[index2] + r); } // Test destroy From 713144964cc475b8ad46d8e93fe3935c7bffd7f0 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 3 May 2023 15:34:49 +0100 Subject: [PATCH 111/412] Fix some clang-tidy issues, mostly multiple declarations on one line --- .../laplace/impls/petsc3damg/petsc3damg.cxx | 3 +- tests/unit/include/bout/test_petsc_matrix.cxx | 49 ++++++++++++------- tests/unit/include/bout/test_petsc_vector.cxx | 7 ++- 3 files changed, 36 insertions(+), 23 deletions(-) diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 633e938ccc..29fdd2c937 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -204,7 +204,8 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { if (updateRequired) { updateMatrix3D(); } - PetscVector rhs(b_in, indexer), guess(x0, indexer); + PetscVector rhs(b_in, indexer); + PetscVector guess(x0, indexer); // Adjust vectors to represent boundary conditions and check that // boundary cells are finite diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index d97fff9b52..8684ed7823 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -265,13 +265,14 @@ TYPED_TEST(PetscMatrixTest, TestDestroy) { // Test getting yup TYPED_TEST(PetscMatrixTest, TestYUp) { - PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); + PetscMatrix matrix(this->indexer, false); + PetscMatrix expected(this->indexer, false); MockTransform* transform = this->pt; SCOPED_TRACE("YUp"); if (std::is_same::value) { EXPECT_THROW(matrix.yup(), BoutException); } else { - BoutReal val = 3.141592; + const BoutReal val = 3.141592; if (std::is_same::value) { expected(this->indexA, this->indexB) = val; } else if (std::is_same::value) { @@ -284,7 +285,8 @@ TYPED_TEST(PetscMatrixTest, TestYUp) { expected(this->indexA, this->iWU2) = this->yUpWeights[2].weight * val; } matrix.yup()(this->indexA, this->indexB) = val; - Mat *rawmat = matrix.get(), *rawexp = expected.get(); + Mat* rawmat = matrix.get(); + Mat* rawexp = expected.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(*rawexp, MAT_FINAL_ASSEMBLY); @@ -295,8 +297,9 @@ TYPED_TEST(PetscMatrixTest, TestYUp) { // Test getting ydown TYPED_TEST(PetscMatrixTest, TestYDown) { - PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); - BoutReal val = 3.141592; + PetscMatrix matrix(this->indexer, false); + PetscMatrix expected(this->indexer, false); + const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YDown"); if (std::is_same::value) { @@ -314,7 +317,8 @@ TYPED_TEST(PetscMatrixTest, TestYDown) { expected(this->indexB, this->iWD2) = this->yDownWeights[2].weight * val; } matrix.ydown()(this->indexB, this->indexA) = val; - Mat *rawmat = matrix.get(), *rawexp = expected.get(); + Mat* rawmat = matrix.get(); + Mat* rawexp = expected.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(*rawexp, MAT_FINAL_ASSEMBLY); @@ -325,12 +329,14 @@ TYPED_TEST(PetscMatrixTest, TestYDown) { // Test getting ynext(0) TYPED_TEST(PetscMatrixTest, TestYNext0) { - PetscMatrix matrix(this->indexer), expected(this->indexer); - BoutReal val = 3.141592; + PetscMatrix matrix(this->indexer); + PetscMatrix expected(this->indexer); + const BoutReal val = 3.141592; SCOPED_TRACE("YNext0"); matrix.ynext(0)(this->indexA, this->indexB) = val; expected(this->indexA, this->indexB) = val; - Mat rawmat = *matrix.get(), rawexp = *expected.get(); + Mat rawmat = *matrix.get(); + Mat rawexp = *expected.get(); MatAssemblyBegin(rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(rawexp, MAT_FINAL_ASSEMBLY); @@ -340,8 +346,9 @@ TYPED_TEST(PetscMatrixTest, TestYNext0) { // Test getting ynext(1) TYPED_TEST(PetscMatrixTest, TestYNextPos) { - PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); - BoutReal val = 3.141592; + PetscMatrix matrix(this->indexer, false); + PetscMatrix expected(this->indexer, false); + const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextPos"); if (std::is_same::value) { @@ -355,7 +362,8 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { } matrix.ynext(1)(this->indexA, this->indexB) = val; expected.yup()(this->indexA, this->indexB) = val; - Mat *rawmat = matrix.get(), *rawexp = expected.get(); + Mat *rawmat = matrix.get(); + Mat *rawexp = expected.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(*rawexp, MAT_FINAL_ASSEMBLY); @@ -366,8 +374,9 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { // Test getting ynext(-1) TYPED_TEST(PetscMatrixTest, TestYNextNeg) { - PetscMatrix matrix(this->indexer, false), expected(this->indexer, false); - BoutReal val = 3.141592; + PetscMatrix matrix(this->indexer, false); + PetscMatrix expected(this->indexer, false); + const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextNeg"); if (std::is_same::value) { @@ -381,7 +390,8 @@ TYPED_TEST(PetscMatrixTest, TestYNextNeg) { } matrix.ynext(-1)(this->indexB, this->indexA) = val; expected.ydown()(this->indexB, this->indexA) = val; - Mat *rawmat = matrix.get(), *rawexp = expected.get(); + Mat *rawmat = matrix.get(); + Mat *rawexp = expected.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(*rawexp, MAT_FINAL_ASSEMBLY); @@ -392,12 +402,15 @@ TYPED_TEST(PetscMatrixTest, TestYNextNeg) { // Test swap TYPED_TEST(PetscMatrixTest, TestSwap) { - PetscMatrix lhs(this->indexer), rhs(this->indexer); - Mat l0 = *lhs.get(), r0 = *rhs.get(); + PetscMatrix lhs(this->indexer); + PetscMatrix rhs(this->indexer); + Mat l0 = *lhs.get(); + Mat r0 = *rhs.get(); EXPECT_NE(l0, nullptr); EXPECT_NE(r0, nullptr); swap(lhs, rhs); - Mat l1 = *lhs.get(), r1 = *rhs.get(); + Mat l1 = *lhs.get(); + Mat r1 = *rhs.get(); EXPECT_NE(l0, l1); EXPECT_NE(r0, r1); EXPECT_EQ(l0, r1); diff --git a/tests/unit/include/bout/test_petsc_vector.cxx b/tests/unit/include/bout/test_petsc_vector.cxx index f031977bb4..8e1cb53731 100644 --- a/tests/unit/include/bout/test_petsc_vector.cxx +++ b/tests/unit/include/bout/test_petsc_vector.cxx @@ -36,11 +36,9 @@ class PetscVectorTest : public FakeMeshFixture { IndexerPtr indexer; PetscVectorTest() - : FakeMeshFixture(), field(bout::globals::mesh), + : FakeMeshFixture(), field(1.5, bout::globals::mesh), stencil(squareStencil(bout::globals::mesh)), indexer(std::make_shared>(bout::globals::mesh, stencil)) { - field.allocate(); - field = 1.5; PetscErrorPrintf = PetscErrorPrintfNone; } @@ -124,7 +122,8 @@ TYPED_TEST(PetscVectorTest, CopyAssignment) { SCOPED_TRACE("CopyAssignment"); PetscVector vector(this->field, this->indexer); PetscVector copy = vector; - Vec *vectorPtr = vector.get(), *copyPtr = copy.get(); + Vec *vectorPtr = vector.get(); + Vec *copyPtr = copy.get(); EXPECT_NE(vectorPtr, copyPtr); testVectorsEqual(vectorPtr, copyPtr); } From 390be68359406f9d17a4cdb4710a00ba478e1131 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 4 May 2023 11:07:25 +0100 Subject: [PATCH 112/412] Make sure guard cells in PetscVector buffer are -1 --- include/bout/globalindexer.hxx | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index bd0a451687..cacafa298f 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -107,11 +107,19 @@ public: /// processes and, if possible, calculating the sparsity pattern of /// any matrices. void initialise() { - fieldmesh->communicate(indices); + // We need to ensure any _guard_ cells are -1 so we don't include them int_indices.reallocate(indices.size()); - BOUT_FOR(index, indices.getRegion("RGN_ALL")) { + BOUT_FOR(index, indices.getRegion("RGN_GUARDS")) { + int_indices[index.ind] = -1; + } + // Now we can communicate to get global indices from neighbouring processes + fieldmesh->communicate(indices); + // Finally, we fill in the global indices including in the + // _boundaries_ (*not* guards) + BOUT_FOR(index, regionAll) { int_indices[index.ind] = static_cast(indices[index]); } + } Mesh* getMesh() const { return fieldmesh; } From c60bf2e2088045648b63531a86f9583e1a3a8174 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 4 May 2023 17:10:11 +0100 Subject: [PATCH 113/412] Add a utility function for checking flags in bitsets --- include/bout/utils.hxx | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 450d3eaf87..834c269f23 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -690,4 +690,11 @@ T* pointer(T& val) { #define BOUT_CONCAT(A, B) BOUT_CONCAT_(A, B) #endif +namespace bout { +namespace utils { +/// Check that \p flag is set in \p bitset +inline bool flagSet(int bitset, int flag) { return (bitset & flag) != 0; } +} +} + #endif // __UTILS_H__ From 28ec7395ae336450154b38f6fe6fc2e68376e6d5 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 4 May 2023 17:11:47 +0100 Subject: [PATCH 114/412] Print error in laplace-petsc3d test --- tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx b/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx index a1231a6cdf..a865f04e2f 100644 --- a/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx +++ b/tests/integrated/test-laplace-petsc3d/test-laplace3d.cxx @@ -126,6 +126,7 @@ int main(int argc, char** argv) { Field3D rhs_check = D * Laplace_perp(f) + Grad_perp(C2) * Grad_perp(f) / C1 + A * f; Field3D error = rhs_check - rhs; BoutReal error_max = max(abs(error), true); + output.write("error_max = {}\n", error_max); Options dump; dump["f"] = f; From b18e1b044a90692286305bf34eb2516ed945e4ad Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 4 May 2023 17:21:16 +0100 Subject: [PATCH 115/412] Set LaplacePetsc3damg options in initialiser list --- .../laplace/impls/petsc3damg/petsc3damg.cxx | 64 +++++++------------ .../laplace/impls/petsc3damg/petsc3damg.hxx | 6 +- 2 files changed, 27 insertions(+), 43 deletions(-) diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 29fdd2c937..cd5347f66d 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -39,14 +39,35 @@ #include #include +#ifdef PETSC_HAVE_HYPRE +static constexpr auto DEFAULT_PC_TYPE = PCHYPRE; +#else +static constexpr auto DEFAULT_PC_TYPE = PCGAMG; +#endif // PETSC_HAVE_HYPRE + LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED(solver)) : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0), Ex(0.0), Ez(0.0), + opts(opt == nullptr ? &(Options::root()["laplace"]) : opt), + lower_boundary_flags((*opts)["lower_boundary_flags"].withDefault(0)), + upper_boundary_flags((*opts)["upper_boundary_flags"].withDefault(0)), + ksptype((*opts)["ksptype"].doc("KSP solver type").withDefault(KSPGMRES)), + pctype((*opts)["pctype"].doc("PC type").withDefault(DEFAULT_PC_TYPE)), + richardson_damping_factor((*opts)["richardson_damping_factor"].withDefault(1.0)), + chebyshev_max((*opts)["chebyshev_max"].withDefault(100.0)), + chebyshev_min((*opts)["chebyshev_min"].withDefault(0.01)), + gmres_max_steps((*opts)["gmres_max_steps"].withDefault(30)), + rtol((*opts)["rtol"].doc("Relative tolerance for KSP solver").withDefault(1e-5)), + atol((*opts)["atol"].doc("Absolute tolerance for KSP solver").withDefault(1e-5)), + dtol((*opts)["dtol"].doc("Divergence tolerance for KSP solver").withDefault(1e6)), + maxits( + (*opts)["maxits"].doc("Maximum number of KSP iterations").withDefault(100000)), + direct((*opts)["direct"].doc("Use direct (LU) solver?").withDefault(false)), lowerY(localmesh->iterateBndryLowerY()), upperY(localmesh->iterateBndryUpperY()), indexer(std::make_shared>( localmesh, getStencil(localmesh, lowerY, upperY))), - operator3D(indexer), kspInitialised(false), - lib(opt == nullptr ? &(Options::root()["laplace"]) : opt) { + operator3D(indexer), lib(opts) { + // Provide basic initialisation of field coefficients, etc. // Get relevent options from user input // Initialise PETSc objects @@ -57,16 +78,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes Ex.setLocation(location); Ez.setLocation(location); - // Get Options in Laplace Section - if (!opt) { - opts = Options::getRoot()->getSection("laplace"); - } else { - opts = opt; - } - // Get y boundary flags - lower_boundary_flags = (*opts)["lower_boundary_flags"].withDefault(0); - upper_boundary_flags = (*opts)["upper_boundary_flags"].withDefault(0); #if CHECK > 0 // Checking flags are set to something which is not implemented @@ -103,36 +115,8 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes } #endif - // Get Tolerances for KSP solver - rtol = (*opts)["rtol"].doc("Relative tolerance for KSP solver").withDefault(1e-5); - atol = (*opts)["atol"].doc("Absolute tolerance for KSP solver").withDefault(1e-5); - dtol = (*opts)["dtol"].doc("Divergence tolerance for KSP solver").withDefault(1e6); - maxits = (*opts)["maxits"].doc("Maximum number of KSP iterations").withDefault(100000); - - richardson_damping_factor = (*opts)["richardson_damping_factor"].withDefault(1.0); - chebyshev_max = (*opts)["chebyshev_max"].withDefault(100.0); - chebyshev_min = (*opts)["chebyshev_min"].withDefault(0.01); - gmres_max_steps = (*opts)["gmres_max_steps"].withDefault(30); - - // Get KSP Solver Type (Generalizes Minimal RESidual is the default) - ksptype = (*opts)["ksptype"].doc("KSP solver type").withDefault(KSPGMRES); - - // Get preconditioner type -#ifdef PETSC_HAVE_HYPRE - // PETSc was compiled with Hypre - pctype = (*opts)["pctype"].doc("PC type").withDefault(PCHYPRE); -#else - // Hypre not available - pctype = (*opts)["pctype"].doc("PC type").withDefault(PCGAMG); -#endif // PETSC_HAVE_HYPRE - - // Get direct solver switch - direct = (*opts)["direct"].doc("Use direct (LU) solver?").withDefault(false); if (direct) { - output << "\n" - << "Using LU decompostion for direct solution of system" - << "\n" - << "\n"; + output.write("\nUsing LU decompostion for direct solution of system\n\n"); } // Set up boundary conditions in operator diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx index 93dc88d768..60d767aa24 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx @@ -194,10 +194,10 @@ private: bool issetC = false; bool issetE = false; bool updateRequired = true; - int lower_boundary_flags; - int upper_boundary_flags; Options* opts; // Laplace Section Options Object + int lower_boundary_flags; + int upper_boundary_flags; std::string ksptype; ///< KSP solver type std::string pctype; ///< Preconditioner type @@ -217,7 +217,7 @@ private: IndexerPtr indexer; PetscMatrix operator3D; KSP ksp; - bool kspInitialised; + bool kspInitialised = false; PetscLib lib; // These are the implemented flags From 335a83763c21e575d2f43ac3bd58f3151662f177 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 4 May 2023 17:38:08 +0100 Subject: [PATCH 116/412] Refactor setting boundary conditions in LaplacePetsc3dAmg --- .../laplace/impls/petsc3damg/petsc3damg.cxx | 160 +++++++----------- 1 file changed, 61 insertions(+), 99 deletions(-) diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index cd5347f66d..3cf0f3d3ef 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -39,6 +39,8 @@ #include #include +using bout::utils::flagSet; + #ifdef PETSC_HAVE_HYPRE static constexpr auto DEFAULT_PC_TYPE = PCHYPRE; #else @@ -78,36 +80,32 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes Ex.setLocation(location); Ez.setLocation(location); - // Get y boundary flags - #if CHECK > 0 // Checking flags are set to something which is not implemented // This is done binary (which is possible as each flag is a power of 2) - if ((global_flags & ~implemented_flags) != 0) { - if ((global_flags & INVERT_4TH_ORDER) != 0) { - output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " - "setting INVERT_4TH_ORDER flag" - << "\n"; - } - throw BoutException("Attempted to set Laplacian inversion flag that is not " - "implemented in petsc_laplace.cxx"); - } - if ((inner_boundary_flags & ~implemented_boundary_flags) != 0) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); + if (flagSet(global_flags, INVERT_4TH_ORDER)) { + output.write("For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " + "setting INVERT_4TH_ORDER flag\n"); } - if ((outer_boundary_flags & ~implemented_boundary_flags) != 0) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); - } - if ((lower_boundary_flags & ~implemented_boundary_flags) != 0) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); - } - if ((upper_boundary_flags & ~implemented_boundary_flags) != 0) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + + if (flagSet(global_flags, ~implemented_flags)) { + throw BoutException("Attempted to set global Laplacian inversion flag that is not " "implemented in petsc_laplace.cxx"); } + + auto unimplementedBoundaryFlag = [](int boundary_flag, + const std::string& name) -> void { + if (flagSet(boundary_flag, ~implemented_boundary_flags)) { + throw BoutException("Attempted to set Laplacian inversion {} boundary flag " + "that is not implemented in petsc3damg.cxx", + name); + } + }; + unimplementedBoundaryFlag(inner_boundary_flags, "inner"); + unimplementedBoundaryFlag(outer_boundary_flags, "outer"); + unimplementedBoundaryFlag(lower_boundary_flags, "lower"); + unimplementedBoundaryFlag(upper_boundary_flags, "upper"); + if (localmesh->periodicX) { throw BoutException("LaplacePetsc3dAmg does not work with periodicity in the x " "direction (localmesh->PeriodicX == true). Change boundary " @@ -120,52 +118,40 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes } // Set up boundary conditions in operator + const bool inner_X_neumann = flagSet(inner_boundary_flags, INVERT_AC_GRAD); + const auto inner_X_BC = inner_X_neumann ? -1. / coords->dx / sqrt(coords->g_11) : 0.5; + const auto inner_X_BC_plus = inner_X_neumann ? -inner_X_BC : 0.5; + BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) { - if ((inner_boundary_flags & INVERT_AC_GRAD) != 0) { - // Neumann on inner X boundary - operator3D(i, i) = -1. / coords->dx[i] / sqrt(coords->g_11[i]); - operator3D(i, i.xp()) = 1. / coords->dx[i] / sqrt(coords->g_11[i]); - } else { - // Dirichlet on inner X boundary - operator3D(i, i) = 0.5; - operator3D(i, i.xp()) = 0.5; - } + operator3D(i, i) = inner_X_BC[i]; + operator3D(i, i.xp()) = inner_X_BC_plus[i]; } + const bool outer_X_neumann = flagSet(outer_boundary_flags, INVERT_AC_GRAD); + const auto outer_X_BC = outer_X_neumann ? 1. / coords->dx / sqrt(coords->g_11) : 0.5; + const auto outer_X_BC_minus = outer_X_neumann ? -outer_X_BC : 0.5; + BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) { - if ((outer_boundary_flags & INVERT_AC_GRAD) != 0) { - // Neumann on outer X boundary - operator3D(i, i) = 1. / coords->dx[i] / sqrt(coords->g_11[i]); - operator3D(i, i.xm()) = -1. / coords->dx[i] / sqrt(coords->g_11[i]); - } else { - // Dirichlet on outer X boundary - operator3D(i, i) = 0.5; - operator3D(i, i.xm()) = 0.5; - } + operator3D(i, i) = outer_X_BC[i]; + operator3D(i, i.xm()) = outer_X_BC_minus[i]; } + const bool lower_Y_neumann = flagSet(lower_boundary_flags, INVERT_AC_GRAD); + const auto lower_Y_BC = lower_Y_neumann ? -1. / coords->dy / sqrt(coords->g_22) : 0.5; + const auto lower_Y_BC_plus = lower_Y_neumann ? -lower_Y_BC : 0.5; + BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) { - if ((lower_boundary_flags & INVERT_AC_GRAD) != 0) { - // Neumann on lower Y boundary - operator3D(i, i) = -1. / coords->dy[i] / sqrt(coords->g_22[i]); - operator3D(i, i.yp()) = 1. / coords->dy[i] / sqrt(coords->g_22[i]); - } else { - // Dirichlet on lower Y boundary - operator3D(i, i) = 0.5; - operator3D(i, i.yp()) = 0.5; - } + operator3D(i, i) = lower_Y_BC[i]; + operator3D(i, i.yp()) = lower_Y_BC_plus[i]; } + const bool upper_Y_neumann = flagSet(upper_boundary_flags, INVERT_AC_GRAD); + const auto upper_Y_BC = upper_Y_neumann ? 1. / coords->dy / sqrt(coords->g_22) : 0.5; + const auto upper_Y_BC_minus = upper_Y_neumann ? -upper_Y_BC : 0.5; + BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) { - if ((upper_boundary_flags & INVERT_AC_GRAD) != 0) { - // Neumann on upper Y boundary - operator3D(i, i) = 1. / coords->dy[i] / sqrt(coords->g_22[i]); - operator3D(i, i.ym()) = -1. / coords->dy[i] / sqrt(coords->g_22[i]); - } else { - // Dirichlet on upper Y boundary - operator3D(i, i) = 0.5; - operator3D(i, i.ym()) = 0.5; - } + operator3D(i, i) = upper_Y_BC[i]; + operator3D(i, i.ym()) = upper_Y_BC_minus[i]; } } @@ -175,6 +161,17 @@ LaplacePetsc3dAmg::~LaplacePetsc3dAmg() { } } +void setBC(PetscVector& rhs, const Field3D& b_in, + const Region& region, int boundary_flags, + const Field3D& x0) { + if (flagSet(boundary_flags, INVERT_RHS)) { + BOUT_FOR(index, region) { ASSERT1(std::isfinite(b_in[index])); } + } else { + const auto& outer_X_BC = (flagSet(boundary_flags, INVERT_SET)) ? x0 : 0.0; + BOUT_FOR_SERIAL(index, region) { rhs(index) = outer_X_BC[index]; } + } +} + Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { AUTO_TRACE(); @@ -193,45 +190,10 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Adjust vectors to represent boundary conditions and check that // boundary cells are finite - BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) { - const BoutReal val = (inner_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(std::isfinite(x0[i])); - if (!(inner_boundary_flags & INVERT_RHS)) { - rhs(i) = val; - } else { - ASSERT1(std::isfinite(b_in[i])); - } - } - - BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) { - const BoutReal val = (outer_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(std::isfinite(x0[i])); - if (!(outer_boundary_flags & INVERT_RHS)) { - rhs(i) = val; - } else { - ASSERT1(std::isfinite(b_in[i])); - } - } - - BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) { - const BoutReal val = (lower_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(std::isfinite(x0[i])); - if (!(lower_boundary_flags & INVERT_RHS)) { - rhs(i) = val; - } else { - ASSERT1(std::isfinite(b_in[i])); - } - } - - BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) { - const BoutReal val = (upper_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(std::isfinite(x0[i])); - if (!(upper_boundary_flags & INVERT_RHS)) { - rhs(i) = val; - } else { - ASSERT1(std::isfinite(b_in[i])); - } - } + setBC(rhs, b_in, indexer->getRegionInnerX(), inner_boundary_flags, x0); + setBC(rhs, b_in, indexer->getRegionOuterX(), outer_boundary_flags, x0); + setBC(rhs, b_in, indexer->getRegionLowerY(), lower_boundary_flags, x0); + setBC(rhs, b_in, indexer->getRegionUpperY(), upper_boundary_flags, x0); rhs.assemble(); guess.assemble(); From acbb92af2e4cce358661d8e4fb22314cfdce378d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 4 May 2023 17:46:05 +0100 Subject: [PATCH 117/412] Delete unneeded PetscVectorElement test --- .../unit/include/bout/test_petsc_setters.cxx | 83 ------------------- 1 file changed, 83 deletions(-) diff --git a/tests/unit/include/bout/test_petsc_setters.cxx b/tests/unit/include/bout/test_petsc_setters.cxx index 7ffbad819a..d3d95280c0 100644 --- a/tests/unit/include/bout/test_petsc_setters.cxx +++ b/tests/unit/include/bout/test_petsc_setters.cxx @@ -10,89 +10,6 @@ #if BOUT_HAS_PETSC -///////////////// Test PetscVector::Element ///////////////// - -class PetscVectorElementTest : public ::testing::Test { -public: - WithQuietOutput all{output}; - Vec v; - PetscInt n = 10; - PetscScalar defaultVal = 1.; - PetscLib lib; - - PetscVectorElementTest() { - VecCreateMPI(MPI_COMM_WORLD, n, PETSC_DETERMINE, &v); - VecSet(v, defaultVal); - VecAssemblyBegin(v); - VecAssemblyEnd(v); - } - - virtual ~PetscVectorElementTest() { VecDestroy(&v); } -}; - -// TEST_F(PetscVectorElementTest, AssignInsert) { -// PetscVector::Element v1(&v, 1), v2(&v, 2), v3(&v, 3), v3b(&v, 3), v9(&v, 9); -// v1 = 1.5; -// v2 = 2.5; -// v3 = 3.5; -// v3b = 4.0; // Should overwrite previous call -// v9 = 9.5; -// VecAssemblyBegin(v); -// VecAssemblyEnd(v); -// PetscScalar* vecContents; -// VecGetArray(v, &vecContents); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[0]); -// EXPECT_DOUBLE_EQ(1.5, vecContents[1]); -// EXPECT_DOUBLE_EQ(2.5, vecContents[2]); -// EXPECT_DOUBLE_EQ(4.0, vecContents[3]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[4]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[5]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[6]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[7]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[8]); -// EXPECT_DOUBLE_EQ(9.5, vecContents[9]); -// } - -// TEST_F(PetscVectorElementTest, AssignElement) { -// PetscVector::Element v1(&v, 1), v2(&v, 2); -// v2 = v1 = 1.5; -// VecAssemblyBegin(v); -// VecAssemblyEnd(v); -// PetscScalar* vecContents; -// VecGetArray(v, &vecContents); -// EXPECT_DOUBLE_EQ(1.5, vecContents[1]); -// EXPECT_DOUBLE_EQ(1.5, vecContents[2]); -// } - -// TEST_F(PetscVectorElementTest, AssignAdd) { -// PetscVector::Element v1(&v, 1), v2(&v, 2), v3(&v, 3), v3b(&v, 3), v9(&v, 9); -// v1 += 1.5; -// v2 += 2.5; -// v3 += 3.5; -// v3b += 4.0; -// v9 += 9.5; -// VecAssemblyBegin(v); -// VecAssemblyEnd(v); -// PetscScalar* vecContents; -// VecGetArray(v, &vecContents); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[0]); -// EXPECT_DOUBLE_EQ(2.5, vecContents[1]); -// EXPECT_DOUBLE_EQ(3.5, vecContents[2]); -// EXPECT_DOUBLE_EQ(8.5, vecContents[3]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[4]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[5]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[6]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[7]); -// EXPECT_DOUBLE_EQ(defaultVal, vecContents[8]); -// EXPECT_DOUBLE_EQ(10.5, vecContents[9]); -// } - -// TEST_F(PetscVectorElementTest, ConvertToBoutReal) { -// PetscVector::Element v1(&v, 1); -// BoutReal val = v1; -// EXPECT_DOUBLE_EQ(defaultVal, val); -// } - ///////////////// Test PetscMatrixElement ///////////////// class PetscMatrixElementTest : public ::testing::Test { From b1af791bf4f19b961c30bdcfb10732cedaa5f405 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Thu, 4 May 2023 16:53:14 +0000 Subject: [PATCH 118/412] Apply clang-format changes --- include/bout/globalindexer.hxx | 9 ++------ include/bout/petsc_interface.hxx | 21 ++++++++----------- include/bout/utils.hxx | 4 ++-- tests/unit/include/bout/test_petsc_matrix.cxx | 18 +++++++++------- tests/unit/include/bout/test_petsc_vector.cxx | 10 ++++----- 5 files changed, 27 insertions(+), 35 deletions(-) diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index cacafa298f..3d0ef21cea 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -109,9 +109,7 @@ public: void initialise() { // We need to ensure any _guard_ cells are -1 so we don't include them int_indices.reallocate(indices.size()); - BOUT_FOR(index, indices.getRegion("RGN_GUARDS")) { - int_indices[index.ind] = -1; - } + BOUT_FOR(index, indices.getRegion("RGN_GUARDS")) { int_indices[index.ind] = -1; } // Now we can communicate to get global indices from neighbouring processes fieldmesh->communicate(indices); // Finally, we fill in the global indices including in the @@ -119,7 +117,6 @@ public: BOUT_FOR(index, regionAll) { int_indices[index.ind] = static_cast(indices[index]); } - } Mesh* getMesh() const { return fieldmesh; } @@ -172,9 +169,7 @@ public: int size() const { return regionAll.size(); } - const Array& getIntIndices() const { - return int_indices; - } + const Array& getIntIndices() const { return int_indices; } protected: // Must not be const as the index field needs to be mutable in order diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index ab6d775237..f6113ecdc3 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -89,8 +89,8 @@ public: ~PetscVector() = default; PetscVector(const PetscVector& v) - : vector(new Vec()), indexConverter(v.indexConverter), - location(v.location), initialised(v.initialised), vector_values(v.vector_values) { + : vector(new Vec()), indexConverter(v.indexConverter), location(v.location), + initialised(v.initialised), vector_values(v.vector_values) { VecDuplicate(*v.vector, vector.get()); VecCopy(*v.vector, *vector); } @@ -104,9 +104,8 @@ public: /// Construct from a field, copying over the field values PetscVector(const T& field, IndexerPtr indConverter) - : vector(new Vec()), indexConverter(indConverter), - location(field.getLocation()), initialised(true), - vector_values(field.size()) { + : vector(new Vec()), indexConverter(indConverter), location(field.getLocation()), + initialised(true), vector_values(field.size()) { ASSERT1(indConverter->getMesh() == field.getMesh()); MPI_Comm comm = getComm(field); @@ -139,16 +138,14 @@ public: } /// Move assignment - PetscVector& operator=(PetscVector&& rhs) noexcept { + PetscVector& operator=(PetscVector&& rhs) noexcept { swap(*this, rhs); return *this; } PetscVector& operator=(const T& f) { ASSERT1(indexConverter); // Needs to have index set - BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { - (*this)(i) = f[i]; - } + BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { (*this)(i) = f[i]; } assemble(); return *this; } @@ -269,8 +266,8 @@ public: /// Copy constructor PetscMatrix(const PetscMatrix& m) - : matrix(new Mat()), indexConverter(m.indexConverter), pt(m.pt), - yoffset(m.yoffset), initialised(m.initialised) { + : matrix(new Mat()), indexConverter(m.indexConverter), pt(m.pt), yoffset(m.yoffset), + initialised(m.initialised) { MatDuplicate(*m.matrix, MAT_COPY_VALUES, matrix.get()); } @@ -312,7 +309,7 @@ public: return *this; } /// Move assignment - PetscMatrix& operator=(PetscMatrix&& rhs) noexcept { + PetscMatrix& operator=(PetscMatrix&& rhs) noexcept { matrix = rhs.matrix; indexConverter = rhs.indexConverter; pt = rhs.pt; diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 834c269f23..126fd15d37 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -694,7 +694,7 @@ namespace bout { namespace utils { /// Check that \p flag is set in \p bitset inline bool flagSet(int bitset, int flag) { return (bitset & flag) != 0; } -} -} +} // namespace utils +} // namespace bout #endif // __UTILS_H__ diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index 8684ed7823..1fabd93a51 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -355,15 +355,16 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { EXPECT_THROW(matrix.ynext(1), BoutException); } else { if (std::is_same::value) { - EXPECT_CALL(*transform, getWeightsForYApproximation( - this->indexB.x(), this->indexA.y(), this->indexB.z(), 1)) + EXPECT_CALL(*transform, + getWeightsForYApproximation(this->indexB.x(), this->indexA.y(), + this->indexB.z(), 1)) .Times(2) .WillRepeatedly(Return(this->yDownWeights)); } matrix.ynext(1)(this->indexA, this->indexB) = val; expected.yup()(this->indexA, this->indexB) = val; - Mat *rawmat = matrix.get(); - Mat *rawexp = expected.get(); + Mat* rawmat = matrix.get(); + Mat* rawexp = expected.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(*rawexp, MAT_FINAL_ASSEMBLY); @@ -383,15 +384,16 @@ TYPED_TEST(PetscMatrixTest, TestYNextNeg) { EXPECT_THROW(matrix.ynext(-1), BoutException); } else { if (std::is_same::value) { - EXPECT_CALL(*transform, getWeightsForYApproximation( - this->indexA.x(), this->indexB.y(), this->indexA.z(), -1)) + EXPECT_CALL(*transform, + getWeightsForYApproximation(this->indexA.x(), this->indexB.y(), + this->indexA.z(), -1)) .Times(2) .WillRepeatedly(Return(this->yDownWeights)); } matrix.ynext(-1)(this->indexB, this->indexA) = val; expected.ydown()(this->indexB, this->indexA) = val; - Mat *rawmat = matrix.get(); - Mat *rawexp = expected.get(); + Mat* rawmat = matrix.get(); + Mat* rawexp = expected.get(); MatAssemblyBegin(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(*rawmat, MAT_FINAL_ASSEMBLY); MatAssemblyBegin(*rawexp, MAT_FINAL_ASSEMBLY); diff --git a/tests/unit/include/bout/test_petsc_vector.cxx b/tests/unit/include/bout/test_petsc_vector.cxx index 8e1cb53731..c478557ff4 100644 --- a/tests/unit/include/bout/test_petsc_vector.cxx +++ b/tests/unit/include/bout/test_petsc_vector.cxx @@ -36,7 +36,7 @@ class PetscVectorTest : public FakeMeshFixture { IndexerPtr indexer; PetscVectorTest() - : FakeMeshFixture(), field(1.5, bout::globals::mesh), + : FakeMeshFixture(), field(1.5, bout::globals::mesh), stencil(squareStencil(bout::globals::mesh)), indexer(std::make_shared>(bout::globals::mesh, stencil)) { PetscErrorPrintf = PetscErrorPrintfNone; @@ -122,8 +122,8 @@ TYPED_TEST(PetscVectorTest, CopyAssignment) { SCOPED_TRACE("CopyAssignment"); PetscVector vector(this->field, this->indexer); PetscVector copy = vector; - Vec *vectorPtr = vector.get(); - Vec *copyPtr = copy.get(); + Vec* vectorPtr = vector.get(); + Vec* copyPtr = copy.get(); EXPECT_NE(vectorPtr, copyPtr); testVectorsEqual(vectorPtr, copyPtr); } @@ -143,9 +143,7 @@ TYPED_TEST(PetscVectorTest, SetElement) { PetscVector vector(this->field, this->indexer); const TypeParam val(-10.); - BOUT_FOR(index, val.getRegion("RGN_ALL")) { - vector(index) = val[index]; - } + BOUT_FOR(index, val.getRegion("RGN_ALL")) { vector(index) = val[index]; } vector.assemble(); Vec* vectorPtr = vector.get(); From a2de8f29bb3bfc95ab575c88679f65c648c11af5 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 11 Oct 2023 15:38:40 +0100 Subject: [PATCH 119/412] Change some variable names to keep clang-tidy happy --- include/bout/petsc_interface.hxx | 84 ++++++++++++++++---------------- 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index f6113ecdc3..04d97c2acd 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -79,27 +79,27 @@ public: using ind_type = typename T::ind_type; struct VectorDeleter { - void operator()(Vec* v) const { - VecDestroy(v); - delete v; + void operator()(Vec* vec) const { + VecDestroy(vec); + delete vec; } }; PetscVector() : vector(new Vec{}) {} ~PetscVector() = default; - PetscVector(const PetscVector& v) - : vector(new Vec()), indexConverter(v.indexConverter), location(v.location), - initialised(v.initialised), vector_values(v.vector_values) { - VecDuplicate(*v.vector, vector.get()); - VecCopy(*v.vector, *vector); + PetscVector(const PetscVector& vec) + : vector(new Vec()), indexConverter(vec.indexConverter), location(vec.location), + initialised(vec.initialised), vector_values(vec.vector_values) { + VecDuplicate(*vec.vector, vector.get()); + VecCopy(*vec.vector, *vector); } - PetscVector(PetscVector&& v) noexcept - : indexConverter(v.indexConverter), location(v.location), - initialised(v.initialised), vector_values(std::move(v.vector_values)) { - std::swap(vector, v.vector); - v.initialised = false; + PetscVector(PetscVector&& vec) noexcept + : indexConverter(vec.indexConverter), location(vec.location), + initialised(vec.initialised), vector_values(std::move(vec.vector_values)) { + std::swap(vector, vec.vector); + vec.initialised = false; } /// Construct from a field, copying over the field values @@ -118,16 +118,16 @@ public: /// Construct a vector like v, but using data from a raw PETSc /// Vec. That Vec (not a copy) will then be owned by the new object. - PetscVector(const PetscVector& v, Vec* vec) { + PetscVector(const PetscVector& other, Vec* vec) { #if CHECKLEVEL >= 2 - int fsize = v.indexConverter->size(); + int fsize = other.indexConverter->size(); int msize = 0; VecGetLocalSize(*vec, &msize); ASSERT2(fsize == msize); #endif vector.reset(vec); - indexConverter = v.indexConverter; - location = v.location; + indexConverter = other.indexConverter; + location = other.location; initialised = true; } @@ -143,9 +143,9 @@ public: return *this; } - PetscVector& operator=(const T& f) { + PetscVector& operator=(const T& field) { ASSERT1(indexConverter); // Needs to have index set - BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { (*this)(i) = f[i]; } + BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { (*this)(i) = field[i]; } assemble(); return *this; } @@ -254,9 +254,9 @@ public: using ind_type = typename T::ind_type; struct MatrixDeleter { - void operator()(Mat* m) const { - MatDestroy(m); - delete m; + void operator()(Mat* mat) const { + MatDestroy(mat); + delete mat; } }; @@ -265,17 +265,17 @@ public: ~PetscMatrix() = default; /// Copy constructor - PetscMatrix(const PetscMatrix& m) - : matrix(new Mat()), indexConverter(m.indexConverter), pt(m.pt), yoffset(m.yoffset), - initialised(m.initialised) { - MatDuplicate(*m.matrix, MAT_COPY_VALUES, matrix.get()); + PetscMatrix(const PetscMatrix& mat) + : matrix(new Mat()), indexConverter(mat.indexConverter), pt(mat.pt), yoffset(mat.yoffset), + initialised(mat.initialised) { + MatDuplicate(*mat.matrix, MAT_COPY_VALUES, matrix.get()); } /// Move constrcutor - PetscMatrix(PetscMatrix&& m) noexcept - : matrix(m.matrix), indexConverter(m.indexConverter), pt(m.pt), yoffset(m.yoffset), - initialised(m.initialised) { - m.initialised = false; + PetscMatrix(PetscMatrix&& mat) noexcept + : matrix(mat.matrix), indexConverter(mat.indexConverter), pt(mat.pt), yoffset(mat.yoffset), + initialised(mat.initialised) { + mat.initialised = false; } // Construct a matrix capable of operating on the specified field, @@ -339,9 +339,9 @@ public: Element(Element&&) = delete; Element& operator=(Element&&) = delete; Element(const Element& other) = default; - Element(Mat* matrix, PetscInt row, PetscInt col, std::vector p = {}, - std::vector w = {}) - : petscMatrix(matrix), petscRow(row), petscCol(col), positions(p), weights(w) { + Element(Mat* matrix, PetscInt row, PetscInt col, std::vector position = {}, + std::vector weight = {}) + : petscMatrix(matrix), petscRow(row), petscCol(col), positions(std::move(position)), weights(std::move(weight)) { ASSERT2(positions.size() == weights.size()); #if CHECK > 2 for (const auto val : weights) { @@ -378,8 +378,8 @@ public: ASSERT3(finite(val)); auto columnPosition = std::find(positions.begin(), positions.end(), petscCol); if (columnPosition != positions.end()) { - int i = std::distance(positions.begin(), columnPosition); - value += weights[i] * val; + const int index = std::distance(positions.begin(), columnPosition); + value += weights[index] * val; ASSERT3(finite(value)); } setValues(val, ADD_VALUES); @@ -427,7 +427,7 @@ public: std::vector weights; if (yoffset != 0) { ASSERT1(yoffset == index2.y() - index1.y()); - const auto pw = + const auto pws = pt->getWeightsForYApproximation(index2.x(), index1.y(), index2.z(), yoffset); const int ny = std::is_same::value ? 1 : indexConverter->getMesh()->LocalNy; @@ -435,14 +435,14 @@ public: std::is_same::value ? 1 : indexConverter->getMesh()->LocalNz; std::transform( - pw.begin(), pw.end(), std::back_inserter(positions), - [this, ny, nz](ParallelTransform::PositionsAndWeights p) -> PetscInt { + pws.begin(), pws.end(), std::back_inserter(positions), + [this, ny, nz](ParallelTransform::PositionsAndWeights pos) -> PetscInt { return this->indexConverter->getGlobal( - ind_type(p.i * ny * nz + p.j * nz + p.k, ny, nz)); + ind_type(pos.i * ny * nz + pos.j * nz + pos.k, ny, nz)); }); - std::transform(pw.begin(), pw.end(), std::back_inserter(weights), - [](ParallelTransform::PositionsAndWeights p) -> PetscScalar { - return p.weight; + std::transform(pws.begin(), pws.end(), std::back_inserter(weights), + [](ParallelTransform::PositionsAndWeights pos) -> PetscScalar { + return pos.weight; }); } return Element(matrix.get(), global1, global2, positions, weights); From dfda3c9790baec1b1065aa44d7f6b100f3535e8e Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 11 Oct 2023 15:38:55 +0100 Subject: [PATCH 120/412] Stop clang-tidy complaining about some short names --- .clang-tidy | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.clang-tidy b/.clang-tidy index 7a1c58af80..b52a287a8d 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -359,5 +359,11 @@ CheckOptions: value: 'false' - key: readability-simplify-subscript-expr.Types value: '::std::basic_string;::std::basic_string_view;::std::vector;::std::array' + - key: readability-identifier-length.IgnoredVariableNames + value: '^n?[xyz]$' + - key: readability-identifier-length.IgnoredParameterNames + value: '^[ijkxyz][01]?$' + - key: readability-identifier-length.IgnoredLoopCounterNames + value: '^[ijkxyz_]$' ... From 5d413e9e66e27f3f02885b6e82ec73fe90eb15d7 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 12 Oct 2023 16:24:12 +0100 Subject: [PATCH 121/412] Fix getting correct parallel slice for `getWeightsForYApproximation` Previous change to generalise `ShiftedMetricInterp::getWeightsForYApproximation` didn't get correct parallel slice for `y_offset` --- src/mesh/parallel/shiftedmetricinterp.hxx | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/src/mesh/parallel/shiftedmetricinterp.hxx b/src/mesh/parallel/shiftedmetricinterp.hxx index 928341827a..93ea2f07be 100644 --- a/src/mesh/parallel/shiftedmetricinterp.hxx +++ b/src/mesh/parallel/shiftedmetricinterp.hxx @@ -29,6 +29,7 @@ #include #include +#include /*! * Shifted metric method @@ -79,8 +80,16 @@ public: std::vector getWeightsForYApproximation(int i, int j, int k, int y_offset) override { - return parallel_slice_interpolators[yup_index]->getWeightsForYApproximation(i, j, k, - y_offset); +#if CHECK > 0 + if (y_offset == 0) { + throw BoutException("Cannot get ShiftedMetricInterp parallel slice at zero offset"); + } +#endif + const auto index = static_cast(std::abs(y_offset) - 1) + + ((y_offset > 0) ? yup_index : ydown_index); + + return parallel_slice_interpolators[index]->getWeightsForYApproximation(i, j, k, + y_offset); } bool requiresTwistShift(bool twist_shift_enabled, YDirectionType ytype) override { From 73be372fe50ed3a94cf394eae8a388bd099f3a4b Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 13 Oct 2023 09:30:52 +0100 Subject: [PATCH 122/412] Add defaulted move ctor/assignment for `PetscMatrix::Element` --- include/bout/petsc_interface.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 04d97c2acd..1c6900acd4 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -336,8 +336,8 @@ public: public: Element() = delete; ~Element() = default; - Element(Element&&) = delete; - Element& operator=(Element&&) = delete; + Element(Element&&) noexcept = default; + Element& operator=(Element&&) noexcept = default; Element(const Element& other) = default; Element(Mat* matrix, PetscInt row, PetscInt col, std::vector position = {}, std::vector weight = {}) From 295966b2b97852f3d6061d5006d00da7e5443aee Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 13 Oct 2023 09:31:19 +0100 Subject: [PATCH 123/412] Apply clang-format --- include/bout/petsc_interface.hxx | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 1c6900acd4..94a89c6835 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -266,15 +266,15 @@ public: /// Copy constructor PetscMatrix(const PetscMatrix& mat) - : matrix(new Mat()), indexConverter(mat.indexConverter), pt(mat.pt), yoffset(mat.yoffset), - initialised(mat.initialised) { + : matrix(new Mat()), indexConverter(mat.indexConverter), pt(mat.pt), + yoffset(mat.yoffset), initialised(mat.initialised) { MatDuplicate(*mat.matrix, MAT_COPY_VALUES, matrix.get()); } /// Move constrcutor PetscMatrix(PetscMatrix&& mat) noexcept - : matrix(mat.matrix), indexConverter(mat.indexConverter), pt(mat.pt), yoffset(mat.yoffset), - initialised(mat.initialised) { + : matrix(mat.matrix), indexConverter(mat.indexConverter), pt(mat.pt), + yoffset(mat.yoffset), initialised(mat.initialised) { mat.initialised = false; } @@ -341,7 +341,8 @@ public: Element(const Element& other) = default; Element(Mat* matrix, PetscInt row, PetscInt col, std::vector position = {}, std::vector weight = {}) - : petscMatrix(matrix), petscRow(row), petscCol(col), positions(std::move(position)), weights(std::move(weight)) { + : petscMatrix(matrix), petscRow(row), petscCol(col), + positions(std::move(position)), weights(std::move(weight)) { ASSERT2(positions.size() == weights.size()); #if CHECK > 2 for (const auto val : weights) { From 7cd0d766c6d2bdf2f46c7ee688ead0590b9c3336 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 13 Oct 2023 09:45:09 +0100 Subject: [PATCH 124/412] Fix a whole bunch of clang-tidy issues in petsc interface/AMG solver --- include/bout/petsc_interface.hxx | 26 +++--- .../laplace/impls/petsc3damg/petsc3damg.cxx | 88 ++++++++++--------- .../laplace/impls/petsc3damg/petsc3damg.hxx | 2 +- 3 files changed, 61 insertions(+), 55 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 94a89c6835..3d3035f577 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -27,8 +27,8 @@ * **************************************************************************/ -#ifndef __PETSC_INTERFACE_H__ -#define __PETSC_INTERFACE_H__ +#ifndef BOUT_PETSC_INTERFACE_H +#define BOUT_PETSC_INTERFACE_H #include "bout/build_config.hxx" @@ -216,7 +216,7 @@ public: result.setLocation(location); // Note that this only populates boundaries to a depth of 1 BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) { - PetscInt ind = indexConverter->getGlobal(i); + const PetscInt ind = indexConverter->getGlobal(i); PetscScalar val = BoutNaN; VecGetValues(*vector, 1, &ind, &val); result[i] = val; @@ -231,7 +231,7 @@ public: private: PetscLib lib{}; std::unique_ptr vector = nullptr; - IndexerPtr indexConverter; + IndexerPtr indexConverter{}; CELL_LOC location = CELL_LOC::deflt; bool initialised = false; Array vector_values{}; @@ -273,7 +273,7 @@ public: /// Move constrcutor PetscMatrix(PetscMatrix&& mat) noexcept - : matrix(mat.matrix), indexConverter(mat.indexConverter), pt(mat.pt), + : matrix(std::move(mat.matrix)), indexConverter(std::move(mat.indexConverter)), pt(mat.pt), yoffset(mat.yoffset), initialised(mat.initialised) { mat.initialised = false; } @@ -349,11 +349,11 @@ public: ASSERT3(finite(val)); } #endif - if (positions.size() == 0) { + if (positions.empty()) { positions = {col}; weights = {1.0}; } - PetscBool assembled; + PetscBool assembled = PETSC_FALSE; MatAssembled(*petscMatrix, &assembled); if (assembled == PETSC_TRUE) { BOUT_OMP(critical) @@ -364,8 +364,12 @@ public: } Element& operator=(const Element& other) { AUTO_TRACE(); + if (this == &other) { + return *this; + } ASSERT3(finite(static_cast(other))); - return *this = static_cast(other); + *this = static_cast(other); + return *this; } Element& operator=(BoutReal val) { AUTO_TRACE(); @@ -517,7 +521,7 @@ public: private: PetscLib lib; std::shared_ptr matrix = nullptr; - IndexerPtr indexConverter; + IndexerPtr indexConverter{}; ParallelTransform* pt{}; int yoffset = 0; bool initialised = false; @@ -553,7 +557,7 @@ void swap(PetscMatrix& first, PetscMatrix& second) { */ template PetscVector operator*(const PetscMatrix& mat, const PetscVector& vec) { - const Vec rhs = *vec.get(); + Vec rhs = *vec.get(); Vec* result = new Vec(); VecDuplicate(rhs, result); VecAssemblyBegin(*result); @@ -565,4 +569,4 @@ PetscVector operator*(const PetscMatrix& mat, const PetscVector& vec) { #endif // BOUT_HAS_PETSC -#endif // __PETSC_INTERFACE_H__ +#endif // BOUT_PETSC_INTERFACE_H diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 3cf0f3d3ef..6ec5c21c22 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -24,6 +24,7 @@ * along with BOUT++. If not, see . * **************************************************************************/ +#include "bout/bout_types.hxx" #include "bout/build_config.hxx" #if BOUT_HAS_PETSC @@ -178,7 +179,7 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Timing reported in the log files. Includes any matrix construction. // The timing for just the solve phase can be retrieved from the "petscsolve" // timer if desired. - Timer timer("invert"); + const Timer timer("invert"); // If necessary, update the values in the matrix operator and initialise // the Krylov solver @@ -200,7 +201,7 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Invoke solver { - Timer timer("petscsolve"); + const Timer timer("petscsolve"); KSPSolve(ksp, *rhs.get(), *guess.get()); } @@ -223,11 +224,11 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { if (solution.hasParallelSlices()) { BOUT_FOR(i, indexer->getRegionLowerY()) { solution.ydown()[i] = solution[i]; } BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup()[i] = solution[i]; } - for (int b = 1; b < localmesh->ystart; b++) { + for (int boundary = 1; boundary < localmesh->ystart; boundary++) { BOUT_FOR(i, indexer->getRegionLowerY()) { - solution.ydown(b)[i.ym(b)] = solution[i]; + solution.ydown(boundary)[i.ym(boundary)] = solution[i]; } - BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup(b)[i.yp(b)] = solution[i]; } + BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup(boundary)[i.yp(boundary)] = solution[i]; } } } @@ -236,9 +237,9 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Note: RegionInnerX is the set of points just outside the domain // (in the first boundary cell) so one boundary cell is already set BOUT_FOR(i, indexer->getRegionInnerX()) { - for (int b = 1; b < localmesh->xstart; b++) { - solution[i.xm(b)] = - 3. * solution[i.xm(b - 1)] - 3. * solution[i.xm(b - 2)] + solution[i.xm(b - 3)]; + for (int boundary = 1; boundary < localmesh->xstart; boundary++) { + solution[i.xm(boundary)] = + 3. * solution[i.xm(boundary - 1)] - 3. * solution[i.xm(boundary - 2)] + solution[i.xm(boundary - 3)]; } } @@ -246,9 +247,9 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Note: RegionOuterX is the set of points just outside the domain // (in the first boundary cell) so one boundary cell is already set BOUT_FOR(i, indexer->getRegionOuterX()) { - for (int b = 1; b < localmesh->xstart; b++) { - solution[i.xp(b)] = - 3. * solution[i.xp(b - 1)] - 3. * solution[i.xp(b - 2)] + solution[i.xp(b - 3)]; + for (int boundary = 1; boundary < localmesh->xstart; boundary++) { + solution[i.xp(boundary)] = + 3. * solution[i.xp(boundary - 1)] - 3. * solution[i.xp(boundary - 2)] + solution[i.xp(boundary - 3)]; } } @@ -279,7 +280,8 @@ void LaplacePetsc3dAmg::updateMatrix3D() { // avoid confusing it with the x-index. // Calculate coefficients for the terms in the differential operator - BoutReal C_df_dx = coords->G1[l], C_df_dz = coords->G3[l]; + BoutReal C_df_dx = coords->G1[l]; + BoutReal C_df_dz = coords->G3[l]; if (issetD) { C_df_dx *= D[l]; C_df_dz *= D[l]; @@ -297,9 +299,9 @@ void LaplacePetsc3dAmg::updateMatrix3D() { C_df_dz += Ez[l]; } - BoutReal C_d2f_dx2 = coords->g11[l], - C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]), - C_d2f_dz2 = coords->g33[l]; + BoutReal C_d2f_dx2 = coords->g11[l]; + BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]); + BoutReal C_d2f_dz2 = coords->g33[l]; if (issetD) { C_d2f_dx2 *= D[l]; C_d2f_dy2 *= D[l]; @@ -336,8 +338,8 @@ void LaplacePetsc3dAmg::updateMatrix3D() { // The values stored in the y-boundary are already interpolated // up/down, so we don't want the matrix to do any such // interpolation there. - const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0, - ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0; + const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0; + const int ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0; operator3D.yup(yup)(l, l.yp()) = 0.0; operator3D.ydown(ydown)(l, l.ym()) = 0.0; operator3D.yup(yup)(l, l.xp().yp()) = 0.0; @@ -370,7 +372,8 @@ void LaplacePetsc3dAmg::updateMatrix3D() { C_d2f_dy2 *= D[l]; } - BoutReal C_d2f_dxdy = 2 * coords->g12[l], C_d2f_dydz = 2 * coords->g23[l]; + BoutReal C_d2f_dxdy = 2 * coords->g12[l]; + BoutReal C_d2f_dydz = 2 * coords->g23[l]; if (issetD) { C_d2f_dxdy *= D[l]; C_d2f_dydz *= D[l]; @@ -391,8 +394,8 @@ void LaplacePetsc3dAmg::updateMatrix3D() { // The values stored in the y-boundary are already interpolated // up/down, so we don't want the matrix to do any such // interpolation there. - const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0, - ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0; + const int yup = (l.y() == localmesh->yend && upperY.intersects(l.x())) ? -1 : 0; + const int ydown = (l.y() == localmesh->ystart && lowerY.intersects(l.x())) ? -1 : 0; operator3D.yup(yup)(l, l.yp()) += C_df_dy + C_d2f_dy2; operator3D.ydown(ydown)(l, l.ym()) += -C_df_dy + C_d2f_dy2; @@ -420,7 +423,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() { KSPSetOperators(ksp, *operator3D.get(), *operator3D.get(), DIFFERENT_NONZERO_PATTERN); #endif - PC pc; + PC pc = nullptr; KSPGetPC(ksp, &pc); if (direct) { @@ -475,33 +478,32 @@ OperatorStencil LaplacePetsc3dAmg::getStencil(Mesh* localmesh, // Get the pattern used for interpolation. This is assumed to be the // same across the whole grid. - const auto pw = + const auto positions_weights = localmesh->getCoordinates()->getParallelTransform().getWeightsForYDownApproximation( localmesh->xstart, localmesh->ystart + 1, localmesh->zstart); std::vector interpPattern; - std::transform(pw.begin(), pw.end(), std::back_inserter(interpPattern), - [localmesh](ParallelTransform::PositionsAndWeights p) -> OffsetInd3D { - return {localmesh->xstart - p.i, localmesh->ystart - p.j, - localmesh->LocalNz - p.k < p.k ? p.k - localmesh->LocalNz - : p.k}; - }); - - OffsetInd3D zero; + std::transform( + positions_weights.begin(), positions_weights.end(), + std::back_inserter(interpPattern), + [localmesh](ParallelTransform::PositionsAndWeights position) -> OffsetInd3D { + return {localmesh->xstart - position.i, localmesh->ystart - position.j, + ((localmesh->LocalNz - position.k) < position.k) + ? position.k - localmesh->LocalNz + : position.k}; + }); + + const OffsetInd3D zero; // Add interior cells - const std::vector interpolatedUpElements = {zero.yp(), zero.xp().yp(), - zero.xm().yp(), zero.yp().zp(), - zero.yp().zm()}, - interpolatedDownElements = { - zero.ym(), zero.xp().ym(), zero.xm().ym(), - zero.ym().zp(), zero.ym().zm()}; - std::set interiorStencil = {zero, zero.xp(), - zero.xm(), zero.zp(), - zero.zm(), zero.xp().zp(), - zero.xp().zm(), zero.xm().zp(), - zero.xm().zm()}, - lowerEdgeStencil = interiorStencil, - upperEdgeStencil = interiorStencil; + const std::vector interpolatedUpElements = { + zero.yp(), zero.xp().yp(), zero.xm().yp(), zero.yp().zp(), zero.yp().zm()}; + const std::vector interpolatedDownElements = { + zero.ym(), zero.xp().ym(), zero.xm().ym(), zero.ym().zp(), zero.ym().zm()}; + std::set interiorStencil = { + zero, zero.xp(), zero.xm(), zero.zp(), zero.zm(), + zero.xp().zp(), zero.xp().zm(), zero.xm().zp(), zero.xm().zm()}; + std::set lowerEdgeStencil = interiorStencil; + std::set upperEdgeStencil = interiorStencil; for (const auto& i : interpolatedDownElements) { for (auto& j : interpPattern) { diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx index 60d767aa24..99a04bd2dd 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx @@ -216,7 +216,7 @@ private: IndexerPtr indexer; PetscMatrix operator3D; - KSP ksp; + KSP ksp = nullptr; bool kspInitialised = false; PetscLib lib; From 5c201339f38f4d140b459be14a59f3619e51e307 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Fri, 13 Oct 2023 08:46:28 +0000 Subject: [PATCH 125/412] Apply clang-format changes --- include/bout/petsc_interface.hxx | 4 ++-- src/invert/laplace/impls/petsc3damg/petsc3damg.cxx | 14 +++++++++----- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 3d3035f577..450cf456f9 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -273,8 +273,8 @@ public: /// Move constrcutor PetscMatrix(PetscMatrix&& mat) noexcept - : matrix(std::move(mat.matrix)), indexConverter(std::move(mat.indexConverter)), pt(mat.pt), - yoffset(mat.yoffset), initialised(mat.initialised) { + : matrix(std::move(mat.matrix)), indexConverter(std::move(mat.indexConverter)), + pt(mat.pt), yoffset(mat.yoffset), initialised(mat.initialised) { mat.initialised = false; } diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 6ec5c21c22..d1e2207725 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -228,7 +228,9 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { BOUT_FOR(i, indexer->getRegionLowerY()) { solution.ydown(boundary)[i.ym(boundary)] = solution[i]; } - BOUT_FOR(i, indexer->getRegionUpperY()) { solution.yup(boundary)[i.yp(boundary)] = solution[i]; } + BOUT_FOR(i, indexer->getRegionUpperY()) { + solution.yup(boundary)[i.yp(boundary)] = solution[i]; + } } } @@ -238,8 +240,9 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // (in the first boundary cell) so one boundary cell is already set BOUT_FOR(i, indexer->getRegionInnerX()) { for (int boundary = 1; boundary < localmesh->xstart; boundary++) { - solution[i.xm(boundary)] = - 3. * solution[i.xm(boundary - 1)] - 3. * solution[i.xm(boundary - 2)] + solution[i.xm(boundary - 3)]; + solution[i.xm(boundary)] = 3. * solution[i.xm(boundary - 1)] + - 3. * solution[i.xm(boundary - 2)] + + solution[i.xm(boundary - 3)]; } } @@ -248,8 +251,9 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // (in the first boundary cell) so one boundary cell is already set BOUT_FOR(i, indexer->getRegionOuterX()) { for (int boundary = 1; boundary < localmesh->xstart; boundary++) { - solution[i.xp(boundary)] = - 3. * solution[i.xp(boundary - 1)] - 3. * solution[i.xp(boundary - 2)] + solution[i.xp(boundary - 3)]; + solution[i.xp(boundary)] = 3. * solution[i.xp(boundary - 1)] + - 3. * solution[i.xp(boundary - 2)] + + solution[i.xp(boundary - 3)]; } } From 8e3f75b9b35f998c58e0e5b65737126a6054736e Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 13 Oct 2023 10:21:09 +0100 Subject: [PATCH 126/412] Don't include headers for petsc interface if we're not building it --- include/bout/petsc_interface.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 450cf456f9..0698b2ec11 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -32,6 +32,8 @@ #include "bout/build_config.hxx" +#if BOUT_HAS_PETSC + #include #include #include @@ -50,8 +52,6 @@ #include #include -#if BOUT_HAS_PETSC - /*! * A class which wraps PETSc vector objects, allowing them to be * indexed using the BOUT++ scheme. Note that boundaries are only From 694c245be5474fc65448369ed8896092d79ca218 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 13 Oct 2023 10:22:38 +0100 Subject: [PATCH 127/412] Increase MG levels for Petsc3DAMG test Change in PETSc 3.20 default options caused diverged dtol, this counteracts that. Fixes #2755 --- .../test-laplace-petsc3d/data_circular_core-sol/BOUT.inp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp b/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp index d69cb51166..da1918dcc7 100644 --- a/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp +++ b/tests/integrated/test-laplace-petsc3d/data_circular_core-sol/BOUT.inp @@ -77,7 +77,7 @@ rtol = 1e-10 atol = 1e-13 [laplace:petsc] -mg_levels_ksp_max_it = 3 +mg_levels_ksp_max_it = 5 [input] transform_from_field_aligned = false From 15b271bb8cd36cdd12ec34e1c92f543636a3e3da Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 18 Oct 2023 14:42:38 +0200 Subject: [PATCH 128/412] Allow pip to break cmake --- .github/workflows/clang-tidy-review.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml index d546ce3af2..84cc85ee54 100644 --- a/.github/workflows/clang-tidy-review.yml +++ b/.github/workflows/clang-tidy-review.yml @@ -32,7 +32,7 @@ jobs: # the unit tests until they're fixed or ignored upstream exclude: "tests/unit/*cxx" cmake_command: | - pip install cmake && \ + pip install cmake --break-system-packages && \ cmake --version && \ git config --global --add safe.directory "$GITHUB_WORKSPACE" && \ cmake . -B build -DBUILD_SHARED_LIBS=ON \ From 77a6b6c975a76980fd029184fd60567f1b8c234f Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 18 Oct 2023 16:58:58 +0200 Subject: [PATCH 129/412] Rename getIntersection to intersection --- include/bout/globalindexer.hxx | 8 ++++---- include/bout/interpolation_xz.hxx | 2 +- include/bout/region.hxx | 4 ++-- src/mesh/mesh.cxx | 6 +++--- tests/unit/include/bout/test_region.cxx | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-) diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index 3d0ef21cea..ab1c927832 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -70,14 +70,14 @@ public: bndryCandidate = mask(allCandidate, getRegionNobndry()); - regionInnerX = getIntersection(bndryCandidate, indices.getRegion("RGN_INNER_X")); - regionOuterX = getIntersection(bndryCandidate, indices.getRegion("RGN_OUTER_X")); + regionInnerX = intersection(bndryCandidate, indices.getRegion("RGN_INNER_X")); + regionOuterX = intersection(bndryCandidate, indices.getRegion("RGN_OUTER_X")); if (std::is_same::value) { regionLowerY = Region({}); regionUpperY = Region({}); } else { - regionLowerY = getIntersection(bndryCandidate, indices.getRegion("RGN_LOWER_Y")); - regionUpperY = getIntersection(bndryCandidate, indices.getRegion("RGN_UPPER_Y")); + regionLowerY = intersection(bndryCandidate, indices.getRegion("RGN_LOWER_Y")); + regionUpperY = intersection(bndryCandidate, indices.getRegion("RGN_UPPER_Y")); } regionBndry = regionLowerY + regionInnerX + regionOuterX + regionUpperY; regionAll = getRegionNobndry() + regionBndry; diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 963033064a..89524f8056 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -88,7 +88,7 @@ public: const bool has_region = !region_name.empty() or this->region != nullptr; if (!region.empty() and region != "RGN_ALL") { if (has_region) { - return getIntersection(localmesh->getRegion(region), getRegion()); + return intersection(localmesh->getRegion(region), getRegion()); } return localmesh->getRegion(region); } diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 0f015595ff..24c39aeb28 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -696,7 +696,7 @@ public: return *this; // To allow command chaining }; - /// Returns a modified region including only indices that are also in the region. + /// Get a new region including only indices that are in both regions. Region getIntersection(const Region& otherRegion) { // Get other indices and sort as we're going to be searching through // this vector so if it's sorted we can be more efficient @@ -953,7 +953,7 @@ Region mask(const Region& region, const Region& mask) { /// Return the intersection of two regions template -Region getIntersection(const Region& region, const Region& otherRegion) { +Region intersection(const Region& region, const Region& otherRegion) { auto result = region; return result.getIntersection(otherRegion); } diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 68b815823d..c0b57d5627 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -784,7 +784,7 @@ int Mesh::getCommonRegion(int lhs, int rhs) { */ const size_t pos = (high * (high - 1)) / 2 + low; if (region3Dintersect.size() <= pos) { - BOUT_OMP(critical(mesh_getIntersection_realloc)) + BOUT_OMP(critical(mesh_intersection_realloc)) #if BOUT_USE_OPENMP if (region3Dintersect.size() <= pos) #endif @@ -796,12 +796,12 @@ int Mesh::getCommonRegion(int lhs, int rhs) { return region3Dintersect[pos]; } { - BOUT_OMP(critical(mesh_getIntersection)) + BOUT_OMP(critical(mesh_intersection)) #if BOUT_USE_OPENMP if (region3Dintersect[pos] == -1) #endif { - auto common = getIntersection(region3D[low], region3D[high]); + auto common = intersection(region3D[low], region3D[high]); for (size_t i = 0; i < region3D.size(); ++i) { if (common == region3D[i]) { region3Dintersect[pos] = i; diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index e16b7aa863..02b5bf0535 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -298,7 +298,7 @@ TEST_F(RegionTest, regionIntersection) { EXPECT_EQ(count1, nmesh); EXPECT_GT(count1, count2); - const auto& region3 = getIntersection(region1, region2); + const auto& region3 = intersection(region1, region2); int count3 = region_count_helper(region3); count1 = region_count_helper(region1); From 4facadfe9e00fcc1a870395101a5d18a804cb9af Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 20 Oct 2023 20:16:40 +0200 Subject: [PATCH 130/412] Prefer const --- src/mesh/mesh.cxx | 4 ++-- src/mesh/parallel/fci.cxx | 10 +++++----- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index c0b57d5627..a2d9b5e6c8 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -765,8 +765,8 @@ int Mesh::getCommonRegion(int lhs, int rhs) { if (lhs == rhs) { return lhs; } - int low = std::min(lhs, rhs); - int high = std::max(lhs, rhs); + const int low = std::min(lhs, rhs); + const int high = std::max(lhs, rhs); if (low == -1) { return high; } diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 2c245cd132..23b2b91eab 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -265,7 +265,7 @@ Field3D FCIMap::integrate(Field3D& f) const { BOUT_FOR(i, region_no_boundary) { const auto inext = i.yp(offset); - BoutReal f_c = centre[inext]; + const BoutReal f_c = centre[inext]; const auto izm = i.zm(); const int x = i.x(); const int y = i.y(); @@ -279,10 +279,10 @@ Field3D FCIMap::integrate(Field3D& f) const { // currently applied to corners. result[inext] = f_c; } else { - BoutReal f_pp = corner[inext]; // (x+1/2, z+1/2) - BoutReal f_mp = corner[inext.xm()]; // (x-1/2, z+1/2) - BoutReal f_pm = corner[inext.zm()]; // (x+1/2, z-1/2) - BoutReal f_mm = corner[inext.xm().zm()]; // (x-1/2, z-1/2) + const BoutReal f_pp = corner[inext]; // (x+1/2, z+1/2) + const BoutReal f_mp = corner[inext.xm()]; // (x-1/2, z+1/2) + const BoutReal f_pm = corner[inext.zm()]; // (x+1/2, z-1/2) + const BoutReal f_mm = corner[inext.xm().zm()]; // (x-1/2, z-1/2) // This uses a simple weighted average of centre and corners // A more sophisticated approach might be to use e.g. Gauss-Lobatto points From da19e714fe38f5ca68c78a24a21af94b82c68771 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 20 Oct 2023 20:16:51 +0200 Subject: [PATCH 131/412] Simplify unit test --- tests/unit/include/bout/test_region.cxx | 26 +++++-------------------- 1 file changed, 5 insertions(+), 21 deletions(-) diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index 02b5bf0535..fa46fed769 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -274,38 +274,22 @@ TEST_F(RegionTest, regionLoopAllSection) { EXPECT_EQ(count, nmesh); } -int region_count_helper(Region region) { - int count = 0; - BOUT_OMP(parallel) - { - BOUT_FOR_OMP(i, region, for reduction(+:count)) { - ++count; - } - } - return count; -} - TEST_F(RegionTest, regionIntersection) { auto& region1 = mesh->getRegion3D("RGN_ALL"); auto& region2 = mesh->getRegion3D("RGN_NOBNDRY"); - int count1 = region_count_helper(region1); - int count2 = region_count_helper(region2); - const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz; - EXPECT_EQ(count1, nmesh); - EXPECT_GT(count1, count2); + EXPECT_EQ(region1.size(), nmesh); + EXPECT_GT(region1.size(), region2.size()); const auto& region3 = intersection(region1, region2); - int count3 = region_count_helper(region3); - count1 = region_count_helper(region1); - EXPECT_EQ(count2, count3); + EXPECT_EQ(region2.size(), region3.size()); // Ensure this did not change - EXPECT_EQ(count1, nmesh); - EXPECT_EQ(region_count_helper(mesh->getRegion3D("RGN_ALL")), nmesh); + EXPECT_EQ(region1.size(), nmesh); + EXPECT_EQ(mesh->getRegion3D("RGN_ALL").size(), nmesh); } TEST_F(RegionTest, regionLoopNoBndrySection) { From e444b86254c426e7b42d1bf2016719cfc0c433da Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 25 Oct 2023 15:07:18 -0700 Subject: [PATCH 132/412] hypre3d: Remove reference to datafile Removed, replaced with OptionsNetCDF method. --- src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx index f99a8a8020..c3e9c5b90c 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx @@ -39,7 +39,6 @@ #include #include #include -#include LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* solver) @@ -146,14 +145,12 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, } // FIXME: This needs to be converted to outputVars - if (solver == nullptr or dump == nullptr) { - output_warn << "Warning: Need to pass both a Solver and a Datafile to " + if (solver == nullptr) { + output_warn << "Warning: Need to pass a Solver to " "Laplacian::create() to get iteration counts in the output." << endl; } else { solver->addMonitor(&monitor); - auto name = opt->name(); - dump->addRepeat(average_iterations, name + "_average_iterations"); } } From 546fbb6601e020d305133fdb3476be929526bb97 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 25 Oct 2023 15:11:38 -0700 Subject: [PATCH 133/412] hypre3d: Replace finite() with std::isfinite() Deprecated, Clang prints warnings on MacOS --- .../laplace/impls/hypre3d/hypre3d_laplace.cxx | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx index c3e9c5b90c..c74e184be3 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx @@ -40,6 +40,8 @@ #include #include +#include + LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* solver) : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0), Ex(0.0), Ez(0.0), @@ -179,41 +181,41 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) { // boundary cells are finite BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) { const BoutReal val = (inner_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(finite(val)); + ASSERT1(std::isfinite(val)); if (!(inner_boundary_flags & INVERT_RHS)) { b[i] = val; } else { - ASSERT1(finite(b[i])); + ASSERT1(std::isfinite(b[i])); } } BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) { const BoutReal val = (outer_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(finite(val)); + ASSERT1(std::isfinite(val)); if (!(outer_boundary_flags & INVERT_RHS)) { b[i] = val; } else { - ASSERT1(finite(b[i])); + ASSERT1(std::isfinite(b[i])); } } BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) { const BoutReal val = (lower_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(finite(val)); + ASSERT1(std::isfinite(val)); if (!(lower_boundary_flags & INVERT_RHS)) { b[i] = val; } else { - ASSERT1(finite(b[i])); + ASSERT1(std::isfinite(b[i])); } } BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) { const BoutReal val = (upper_boundary_flags & INVERT_SET) ? x0[i] : 0.; - ASSERT1(finite(val)); + ASSERT1(std::isfinite(val)); if (!(upper_boundary_flags & INVERT_RHS)) { b[i] = val; } else { - ASSERT1(finite(b[i])); + ASSERT1(std::isfinite(b[i])); } } CALI_MARK_END("LaplaceHypre3d_solve:AdjustBoundary"); From 78919ecca10ed317aadeb74601adb2d0976fb9fc Mon Sep 17 00:00:00 2001 From: Giorgis Georgakoudis Date: Wed, 8 Nov 2023 12:56:59 -0800 Subject: [PATCH 134/412] Add BOUT_HOST_DEVICE to accessor operators for GPU --- include/bout/field_accessor.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx index 16661a0e75..69b58da979 100644 --- a/include/bout/field_accessor.hxx +++ b/include/bout/field_accessor.hxx @@ -39,9 +39,9 @@ struct BoutRealArray { /// Cast operators, so can be assigned to a raw pointer /// Note: Not explicit, so can be cast implicitly - operator BoutReal*() { return data; } + BOUT_HOST_DEVICE operator BoutReal*() { return data; } - operator const BoutReal*() const { return data; } + BOUT_HOST_DEVICE operator const BoutReal*() const { return data; } }; /// Thin wrapper around field data, for fast but unsafe access From 052ac97a1089e3d068ee370a908ae038b639ce5b Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 13 Nov 2023 10:29:24 -0800 Subject: [PATCH 135/412] elm_pb: whitespace changes Matching versions of elm_pb example code, separating out whitespace changes first. --- examples/elm-pb/elm_pb.cxx | 56 ++++++++++++++++---------------------- 1 file changed, 24 insertions(+), 32 deletions(-) diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index 6232c72d52..48595ebaa6 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -37,11 +37,11 @@ BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xout", "none"); class ELMpb : public PhysicsModel { private: // 2D inital profiles - Field2D J0, P0; // Current and pressure - Vector2D b0xcv; // Curvature term - Field2D beta; // Used for Vpar terms + Field2D J0, P0; // Current and pressure + Vector2D b0xcv; // Curvature term + Field2D beta; // Used for Vpar terms Coordinates::FieldMetric gradparB; - Field2D phi0; // When diamagnetic terms used + Field2D phi0; // When diamagnetic terms used Field2D Psixy, x; Coordinates::FieldMetric U0; // 0th vorticity of equilibrium flow, // radial flux coordinate, normalized radial flux coordinate @@ -205,13 +205,13 @@ class ELMpb : public PhysicsModel { bool phi_constraint; // Solver for phi using a solver constraint - bool include_rmp; // Include RMP coil perturbation - bool simple_rmp; // Just use a simple form for the perturbation + bool include_rmp; // Include RMP coil perturbation + bool simple_rmp; // Just use a simple form for the perturbation - BoutReal rmp_factor; // Multiply amplitude by this factor - BoutReal rmp_ramp; // Ramp-up time for RMP [s]. negative -> instant - BoutReal rmp_freq; // Amplitude oscillation frequency [Hz] (negative -> no oscillation) - BoutReal rmp_rotate; // Rotation rate [Hz] + BoutReal rmp_factor; // Multiply amplitude by this factor + BoutReal rmp_ramp; // Ramp-up time for RMP [s]. negative -> instant + BoutReal rmp_freq; // Amplitude oscillation frequency [Hz] (negative -> no oscillation) + BoutReal rmp_rotate; // Rotation rate [Hz] bool rmp_vac_mask; Field3D rmp_Psi0; // Parallel vector potential from Resonant Magnetic Perturbation (RMP) // coils @@ -371,8 +371,9 @@ class ELMpb : public PhysicsModel { density = options["density"].doc("Number density [m^-3]").withDefault(1.0e19); - evolve_jpar = - options["evolve_jpar"].doc("If true, evolve J raher than Psi").withDefault(false); + evolve_jpar = options["evolve_jpar"] + .doc("If true, evolve J rather than Psi") + .withDefault(false); phi_constraint = options["phi_constraint"] .doc("Use solver constraint for phi?") .withDefault(false); @@ -536,8 +537,7 @@ class ELMpb : public PhysicsModel { .withDefault(false); // Parallel differencing - parallel_lr_diff = - options["parallel_lr_diff"] + parallel_lr_diff = options["parallel_lr_diff"] .doc("Use left and right shifted stencils for parallel differences?") .withDefault(false); @@ -546,28 +546,23 @@ class ELMpb : public PhysicsModel { .doc("Read RMP field rmp_A from grid?") .withDefault(false); - simple_rmp = - options["simple_rmp"].doc("Include a simple RMP model?").withDefault(false); + simple_rmp = options["simple_rmp"].doc("Include a simple RMP model?").withDefault(false); rmp_factor = options["rmp_factor"].withDefault(1.0); rmp_ramp = options["rmp_ramp"].withDefault(-1.0); rmp_freq = options["rmp_freq"].withDefault(-1.0); rmp_rotate = options["rmp_rotate"].withDefault(0.0); // Vacuum region control - vacuum_pressure = - options["vacuum_pressure"] + vacuum_pressure = options["vacuum_pressure"] .doc("Fraction of peak pressure, below which is considered vacuum.") .withDefault(0.02); - vacuum_trans = - options["vacuum_trans"] + vacuum_trans = options["vacuum_trans"] .doc("Vacuum boundary transition width, as fraction of peak pressure.") .withDefault(0.005); // Resistivity and hyper-resistivity options - vac_lund = - options["vac_lund"].doc("Lundquist number in vacuum region").withDefault(0.0); - core_lund = - options["core_lund"].doc("Lundquist number in core region").withDefault(0.0); + vac_lund = options["vac_lund"].doc("Lundquist number in vacuum region").withDefault(0.0); + core_lund = options["core_lund"].doc("Lundquist number in core region").withDefault(0.0); hyperresist = options["hyperresist"].withDefault(-1.0); ehyperviscos = options["ehyperviscos"].withDefault(-1.0); spitzer_resist = options["spitzer_resist"] @@ -579,8 +574,7 @@ class ELMpb : public PhysicsModel { damp_width = options["damp_width"] .doc("Width of the radial damping regions, in grid cells") .withDefault(0); - damp_t_const = - options["damp_t_const"] + damp_t_const = options["damp_t_const"] .doc("Time constant for damping in radial regions. Normalised time units.") .withDefault(0.1); @@ -589,8 +583,7 @@ class ELMpb : public PhysicsModel { viscos_perp = options["viscos_perp"].doc("Perpendicular viscosity").withDefault(-1.0); hyperviscos = options["hyperviscos"].doc("Radial hyperviscosity").withDefault(-1.0); - diffusion_par = - options["diffusion_par"].doc("Parallel pressure diffusion").withDefault(-1.0); + diffusion_par = options["diffusion_par"].doc("Parallel pressure diffusion").withDefault(-1.0); diffusion_p4 = options["diffusion_p4"] .doc("parallel hyper-viscous diffusion for pressure") .withDefault(-1.0); @@ -642,8 +635,7 @@ class ELMpb : public PhysicsModel { su_lengthr = options["su_lengthr"].withDefault(0.15); // Compressional terms - phi_curv = - options["phi_curv"].doc("ExB compression in P equation?").withDefault(true); + phi_curv = options["phi_curv"].doc("ExB compression in P equation?").withDefault(true); g = options["gamma"].doc("Ratio of specific heats").withDefault(5.0 / 3.0); x = (Psixy - Psiaxis) / (Psibndry - Psiaxis); @@ -1548,7 +1540,7 @@ class ELMpb : public PhysicsModel { ddt(U) += b0xcv * Grad(P); // curvature term - if (!nogradparj) { // Parallel current term + if (!nogradparj) { // Parallel current term ddt(U) -= SQ(B0) * Grad_parP(Jpar, CELL_CENTRE); // b dot grad j } @@ -1708,7 +1700,7 @@ class ELMpb : public PhysicsModel { * D2DX2(P) * (Tbar / Lbar / Lbar); // radial diffusion } - if (sink_P > 0.0) { // sink terms + if (sink_P > 0.0) { // sink terms ddt(P) -= sink_P * sink_tanhxr(P0, P, sp_width, sp_length) * Tbar; // sink } From 9cc63b1eb804d26b127ecbb068b30880f776cfdb Mon Sep 17 00:00:00 2001 From: Nami Li Date: Mon, 13 Nov 2023 10:32:59 -0800 Subject: [PATCH 136/412] elm_pb: Add missing B0 factors These factors bring the linear growth rates in line with BOUT++ v3.x There are still unexplained oscillations and mode coupling to investigate. --- examples/elm-pb/elm_pb.cxx | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index 48595ebaa6..b1034c6107 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -1479,15 +1479,16 @@ class ELMpb : public PhysicsModel { } } else { // Vector potential - ddt(Psi) = -Grad_parP(phi, loc) + eta * Jpar; + ddt(Psi) = -Grad_parP(phi * B0, loc) / B0 + eta * Jpar; if (eHall) { // electron parallel pressure ddt(Psi) += 0.25 * delta_i - * (Grad_parP(P, loc) + bracket(interp_to(P0, loc), Psi, bm_mag)); + * (Grad_parP(B0*P, loc) / B0 + + bracket(interp_to(P0, loc), Psi, bm_mag) * B0); } if (diamag_phi0) { // Equilibrium flow - ddt(Psi) -= bracket(interp_to(phi0, loc), Psi, bm_exb); + ddt(Psi) -= bracket(interp_to(phi0, loc), Psi, bm_exb) * B0; } if (withflow) { // net flow From 2b13e0ec8f45ff61bf01076cb8448ebb6b053489 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 13 Nov 2023 20:15:57 -0800 Subject: [PATCH 137/412] elm_pb: Update input, add plot_linear.py script Plots an analysis of linear growth rate. --- examples/elm-pb/data/BOUT.inp | 12 ++--- examples/elm-pb/plot_linear.py | 85 ++++++++++++++++++++++++++++++++++ 2 files changed, 88 insertions(+), 9 deletions(-) create mode 100644 examples/elm-pb/plot_linear.py diff --git a/examples/elm-pb/data/BOUT.inp b/examples/elm-pb/data/BOUT.inp index 69d8bb0976..55a4a30c06 100644 --- a/examples/elm-pb/data/BOUT.inp +++ b/examples/elm-pb/data/BOUT.inp @@ -12,21 +12,18 @@ zperiod = 15 # Fraction of a torus to simulate MZ = 16 # Number of points in Z grid = "cbm18_dens8.grid_nx68ny64.nc" # Grid file -restart_format = "nc" # Restart file format [mesh] staggergrids = false # Use staggered grids [mesh:paralleltransform] - type = shifted # Use shifted metric method ################################################## # derivative methods [mesh:ddx] - first = C4 # order of first x derivatives second = C4 # order of second x derivatives upwind = W3 # order of upwinding method W3 = Weno3 @@ -42,9 +39,6 @@ first = C4 # Z derivatives can be done using FFT second = C4 upwind = W3 -[output] -shiftoutput = true # Put the output into field-aligned coordinates - ################################################## # FFTs @@ -58,8 +52,8 @@ fft_measurement_flag = measure # If using FFTW, perform tests to determine fast [solver] # mudq, mldq, mukeep, mlkeep preconditioner options -atol = 1e-08 # absolute tolerance -rtol = 1e-05 # relative tolerance +atol = 1.0e-8 # absolute tolerance +rtol = 1.0e-5 # relative tolerance use_precon = false # Use preconditioner: User-supplied or BBD @@ -160,7 +154,7 @@ damp_t_const = 1e-2 # Damping time constant diffusion_par = -1.0 # Parallel pressure diffusion (< 0 = none) diffusion_p4 = -1e-05 # parallel hyper-viscous diffusion for pressure (< 0 = none) -diffusion_u4 = 1e-05 # parallel hyper-viscous diffusion for vorticity (< 0 = none) +diffusion_u4 = -1e-05 # parallel hyper-viscous diffusion for vorticity (< 0 = none) diffusion_a4 = -1e-05 # parallel hyper-viscous diffusion for vector potential (< 0 = none) ## heat source in pressure in watts diff --git a/examples/elm-pb/plot_linear.py b/examples/elm-pb/plot_linear.py new file mode 100644 index 0000000000..42047ec5dc --- /dev/null +++ b/examples/elm-pb/plot_linear.py @@ -0,0 +1,85 @@ +# Plots an analysis of the linear growth rate +# +# Input argument is the directory containing data files. +# +# Example: +# $ python plot_linear.py data/ +# + +from boutdata import collect +import numpy as np +import matplotlib.pyplot as plt +import os +import sys + +if len(sys.argv) != 2: + raise ValueError(f"Usage: {sys.argv[0]} path") + +# Path to the data +path = sys.argv[1] + +# Read pressure at last time point, to find peak +p = collect("P", path=path, tind=-1).squeeze() +prms = np.sqrt(np.mean(p**2, axis=-1)) + +pyprof = np.amax(prms, axis=0) +yind = np.argmax(pyprof) +pxprof = prms[:, yind] +xind = np.argmax(pxprof) +print(f"Peak amplitude at x = {xind}, y = {yind}") + +# Read pressure time history at index of peak amplitude +p = collect("P", path=path, xind=xind, yind=yind).squeeze() + +# p = p[:,:-1] # Remove point in Z + +prms = np.sqrt(np.mean(p**2, axis=-1)) + +t = collect("t_array", path=path) +dt = t[1] - t[0] + +gamma = np.gradient(np.log(prms)) / dt +growth_rate = np.mean(gamma[len(gamma) // 2 :]) +growth_rate_std = np.std(gamma[len(gamma) // 2 :]) + +print(f"Mean growth rate: {growth_rate} +/- {growth_rate_std}") + +fig, axs = plt.subplots(2, 2) + +ax = axs[0, 0] +ax.plot(pyprof) +ax.set_xlabel("Y index") +ax.set_ylabel("RMS pressure") +ax.axvline(yind, linestyle="--", color="k") +ax.text(yind, 0.5 * pyprof[yind], f"y = {yind}") + +ax = axs[0, 1] +ax.plot(pxprof) +ax.set_xlabel("X index") +ax.set_ylabel("RMS pressure") +ax.axvline(xind, linestyle="--", color="k") +ax.text(xind, 0.5 * pxprof[xind], f"x = {xind}") + +ax = axs[1, 0] +ax.plot(t, prms) +ax.set_xlabel(r"Time [$\tau_A$]") +ax.set_ylabel("RMS pressure") +ax.set_yscale("log") +ax.plot(t, prms[-1] * np.exp(growth_rate * (t - t[-1])), "--k") + +ax = axs[1, 1] +ax.plot(t, gamma) +ax.set_xlabel(r"Time [$\tau_A$]") +ax.set_ylabel("Growth rate [$\omega_A$]") +ax.axhline(growth_rate, linestyle="--", color="k") +ax.text( + (t[-1] + t[0]) / 4, + growth_rate * 1.2, + rf"$\gamma = {growth_rate:.3f}\pm {growth_rate_std:.3f} \omega_A$", +) + +plt.savefig(os.path.join(path, "linear_growth.pdf")) +plt.savefig(os.path.join(path, "linear_growth.png")) + +plt.tight_layout() +plt.show() From f6f41c2124dd0ea805ae73cc8a5bd6d216ccbb8a Mon Sep 17 00:00:00 2001 From: bendudson Date: Tue, 14 Nov 2023 04:22:45 +0000 Subject: [PATCH 138/412] Apply clang-format changes --- examples/elm-pb/elm_pb.cxx | 57 ++++++++++++++++++++++---------------- 1 file changed, 33 insertions(+), 24 deletions(-) diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index b1034c6107..e81742747a 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -37,11 +37,11 @@ BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xout", "none"); class ELMpb : public PhysicsModel { private: // 2D inital profiles - Field2D J0, P0; // Current and pressure - Vector2D b0xcv; // Curvature term - Field2D beta; // Used for Vpar terms + Field2D J0, P0; // Current and pressure + Vector2D b0xcv; // Curvature term + Field2D beta; // Used for Vpar terms Coordinates::FieldMetric gradparB; - Field2D phi0; // When diamagnetic terms used + Field2D phi0; // When diamagnetic terms used Field2D Psixy, x; Coordinates::FieldMetric U0; // 0th vorticity of equilibrium flow, // radial flux coordinate, normalized radial flux coordinate @@ -205,13 +205,13 @@ class ELMpb : public PhysicsModel { bool phi_constraint; // Solver for phi using a solver constraint - bool include_rmp; // Include RMP coil perturbation - bool simple_rmp; // Just use a simple form for the perturbation + bool include_rmp; // Include RMP coil perturbation + bool simple_rmp; // Just use a simple form for the perturbation - BoutReal rmp_factor; // Multiply amplitude by this factor - BoutReal rmp_ramp; // Ramp-up time for RMP [s]. negative -> instant - BoutReal rmp_freq; // Amplitude oscillation frequency [Hz] (negative -> no oscillation) - BoutReal rmp_rotate; // Rotation rate [Hz] + BoutReal rmp_factor; // Multiply amplitude by this factor + BoutReal rmp_ramp; // Ramp-up time for RMP [s]. negative -> instant + BoutReal rmp_freq; // Amplitude oscillation frequency [Hz] (negative -> no oscillation) + BoutReal rmp_rotate; // Rotation rate [Hz] bool rmp_vac_mask; Field3D rmp_Psi0; // Parallel vector potential from Resonant Magnetic Perturbation (RMP) // coils @@ -372,8 +372,8 @@ class ELMpb : public PhysicsModel { density = options["density"].doc("Number density [m^-3]").withDefault(1.0e19); evolve_jpar = options["evolve_jpar"] - .doc("If true, evolve J rather than Psi") - .withDefault(false); + .doc("If true, evolve J rather than Psi") + .withDefault(false); phi_constraint = options["phi_constraint"] .doc("Use solver constraint for phi?") .withDefault(false); @@ -537,7 +537,8 @@ class ELMpb : public PhysicsModel { .withDefault(false); // Parallel differencing - parallel_lr_diff = options["parallel_lr_diff"] + parallel_lr_diff = + options["parallel_lr_diff"] .doc("Use left and right shifted stencils for parallel differences?") .withDefault(false); @@ -546,23 +547,28 @@ class ELMpb : public PhysicsModel { .doc("Read RMP field rmp_A from grid?") .withDefault(false); - simple_rmp = options["simple_rmp"].doc("Include a simple RMP model?").withDefault(false); + simple_rmp = + options["simple_rmp"].doc("Include a simple RMP model?").withDefault(false); rmp_factor = options["rmp_factor"].withDefault(1.0); rmp_ramp = options["rmp_ramp"].withDefault(-1.0); rmp_freq = options["rmp_freq"].withDefault(-1.0); rmp_rotate = options["rmp_rotate"].withDefault(0.0); // Vacuum region control - vacuum_pressure = options["vacuum_pressure"] + vacuum_pressure = + options["vacuum_pressure"] .doc("Fraction of peak pressure, below which is considered vacuum.") .withDefault(0.02); - vacuum_trans = options["vacuum_trans"] + vacuum_trans = + options["vacuum_trans"] .doc("Vacuum boundary transition width, as fraction of peak pressure.") .withDefault(0.005); // Resistivity and hyper-resistivity options - vac_lund = options["vac_lund"].doc("Lundquist number in vacuum region").withDefault(0.0); - core_lund = options["core_lund"].doc("Lundquist number in core region").withDefault(0.0); + vac_lund = + options["vac_lund"].doc("Lundquist number in vacuum region").withDefault(0.0); + core_lund = + options["core_lund"].doc("Lundquist number in core region").withDefault(0.0); hyperresist = options["hyperresist"].withDefault(-1.0); ehyperviscos = options["ehyperviscos"].withDefault(-1.0); spitzer_resist = options["spitzer_resist"] @@ -574,7 +580,8 @@ class ELMpb : public PhysicsModel { damp_width = options["damp_width"] .doc("Width of the radial damping regions, in grid cells") .withDefault(0); - damp_t_const = options["damp_t_const"] + damp_t_const = + options["damp_t_const"] .doc("Time constant for damping in radial regions. Normalised time units.") .withDefault(0.1); @@ -583,7 +590,8 @@ class ELMpb : public PhysicsModel { viscos_perp = options["viscos_perp"].doc("Perpendicular viscosity").withDefault(-1.0); hyperviscos = options["hyperviscos"].doc("Radial hyperviscosity").withDefault(-1.0); - diffusion_par = options["diffusion_par"].doc("Parallel pressure diffusion").withDefault(-1.0); + diffusion_par = + options["diffusion_par"].doc("Parallel pressure diffusion").withDefault(-1.0); diffusion_p4 = options["diffusion_p4"] .doc("parallel hyper-viscous diffusion for pressure") .withDefault(-1.0); @@ -635,7 +643,8 @@ class ELMpb : public PhysicsModel { su_lengthr = options["su_lengthr"].withDefault(0.15); // Compressional terms - phi_curv = options["phi_curv"].doc("ExB compression in P equation?").withDefault(true); + phi_curv = + options["phi_curv"].doc("ExB compression in P equation?").withDefault(true); g = options["gamma"].doc("Ratio of specific heats").withDefault(5.0 / 3.0); x = (Psixy - Psiaxis) / (Psibndry - Psiaxis); @@ -1483,7 +1492,7 @@ class ELMpb : public PhysicsModel { if (eHall) { // electron parallel pressure ddt(Psi) += 0.25 * delta_i - * (Grad_parP(B0*P, loc) / B0 + * (Grad_parP(B0 * P, loc) / B0 + bracket(interp_to(P0, loc), Psi, bm_mag) * B0); } @@ -1541,7 +1550,7 @@ class ELMpb : public PhysicsModel { ddt(U) += b0xcv * Grad(P); // curvature term - if (!nogradparj) { // Parallel current term + if (!nogradparj) { // Parallel current term ddt(U) -= SQ(B0) * Grad_parP(Jpar, CELL_CENTRE); // b dot grad j } @@ -1701,7 +1710,7 @@ class ELMpb : public PhysicsModel { * D2DX2(P) * (Tbar / Lbar / Lbar); // radial diffusion } - if (sink_P > 0.0) { // sink terms + if (sink_P > 0.0) { // sink terms ddt(P) -= sink_P * sink_tanhxr(P0, P, sp_width, sp_length) * Tbar; // sink } From 6b47853d8884fd5865eb798bef6994ca88cb28f8 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 30 Oct 2023 09:39:22 +0000 Subject: [PATCH 139/412] CI: Replace pip script with requirements.txt - Don't pin pip and setuptools versions - Bump netcdf4 and Cython - Install boututils and boutdata --- .github/workflows/tests.yml | 5 ++--- .pip_install_for_ci.sh | 20 -------------------- requirements.txt | 6 ++++-- 3 files changed, 6 insertions(+), 25 deletions(-) delete mode 100755 .pip_install_for_ci.sh diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6aaedb5804..148b6e17db 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -185,9 +185,8 @@ jobs: - name: Install pip packages run: | - ./.pip_install_for_ci.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' zoidberg fastcov - # Add the pip install location to the runner's PATH - echo ~/.local/bin >> $GITHUB_PATH + python -m pip install --upgrade pip setuptools + python -m pip install -r requirements.txt - name: Cache SUNDIALS build uses: actions/cache@v3 diff --git a/.pip_install_for_ci.sh b/.pip_install_for_ci.sh deleted file mode 100755 index 4a5258cc2d..0000000000 --- a/.pip_install_for_ci.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env bash - -set -e - -export PATH=${HOME}/.local/bin:${PATH} -pip3 install --user --upgrade pip~=20.0 setuptools~=46.1 -pip3 install --user --upgrade scipy~=1.4 numpy~=1.18 natsort~=8.1.0 -for package in $@ -do - if test $package == "cython" - then - # fast install Cython - pip3 install --user Cython --install-option="--no-cython-compile" - elif test $package == "something_else" - then - pip3 install what_we_need - else - pip3 install --user $package - fi -done diff --git a/requirements.txt b/requirements.txt index 03f43a92d2..75358b10db 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,8 @@ Jinja2>=2.11.3 numpy>=1.14.1 scipy>=1.0.0 -netcdf4>=1.3.1 +netcdf4~=1.6.0 matplotlib>=2.0.0 -Cython>=0.29.0 +Cython~=3.0.0 +boututils~=0.2.1 +boutdata~=0.2.1 From 8ce97599c34edd77659455e731c027b0748ce42c Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 6 Nov 2023 17:04:13 +0100 Subject: [PATCH 140/412] Set oversubscribe flags for openmpi 5 --- .ci_fedora.sh | 1 + .github/workflows/tests.yml | 1 + 2 files changed, 2 insertions(+) diff --git a/.ci_fedora.sh b/.ci_fedora.sh index 0774000b9c..452afb4b7e 100755 --- a/.ci_fedora.sh +++ b/.ci_fedora.sh @@ -56,6 +56,7 @@ else . /etc/profile.d/modules.sh module load mpi/${1}-x86_64 export OMPI_MCA_rmaps_base_oversubscribe=yes + export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe export TRAVIS=true export FLEXIBLAS=NETLIB cd diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 148b6e17db..1083c5e059 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -28,6 +28,7 @@ jobs: OMP_NUM_THREADS: ${{ matrix.config.omp_num_threads }} PYTHONPATH: ${{ github.workspace }}/tools/pylib OMPI_MCA_rmaps_base_oversubscribe: yes + PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe" MPIRUN: mpiexec -np strategy: fail-fast: true From ab07dcaf168c1c3e8957bddaab4f84c8466b7721 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 4 Dec 2023 14:03:28 -0800 Subject: [PATCH 141/412] elm-pb-outerloop: Add B0 factors Like the elm-pb example, add B0 factors so that we're solving the same equations as BOUT++ v3.x --- examples/elm-pb-outerloop/data/BOUT.inp | 6 --- .../elm-pb-outerloop/elm_pb_outerloop.cxx | 47 ++++++++++++------- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/examples/elm-pb-outerloop/data/BOUT.inp b/examples/elm-pb-outerloop/data/BOUT.inp index d06073f838..6c9f268057 100644 --- a/examples/elm-pb-outerloop/data/BOUT.inp +++ b/examples/elm-pb-outerloop/data/BOUT.inp @@ -13,9 +13,6 @@ MZ = 16 # Number of points in Z grid = "cbm18_dens8.grid_nx68ny64.nc" # Grid file -dump_format = "nc" # Dump file format. "nc" = NetCDF, "pdb" = PDB -restart_format = "nc" # Restart file format - [mesh] staggergrids = false # Use staggered grids @@ -44,9 +41,6 @@ first = C4 # Z derivatives can be done using FFT second = C4 upwind = W3 -[output] -shiftoutput = true # Put the output into field-aligned coordinates - ################################################## # FFTs diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx index 691f4303f4..b3ad81ef1a 100644 --- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx +++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx @@ -1576,7 +1576,17 @@ class ELMpb : public PhysicsModel { Field3D B0U = B0 * U; mesh->communicate(B0U); auto B0U_acc = FieldAccessor<>(B0U); -#endif +#else + Field3D B0phi = B0 * phi; + mesh->communicate(B0phi); + auto B0phi_acc = FieldAccessor<>(B0phi); + +#if EHALL + Field3D B0P = B0 * P; + mesh->communicate(B0 * P); + auto B0P_acc = FieldAccessor<>(B0P); +#endif // EHALL +#endif // EVOLVE_JPAR #if RELAX_J_VAC auto vac_mask_acc = FieldAccessor<>(vac_mask); @@ -1612,23 +1622,24 @@ class ELMpb : public PhysicsModel { #else // Evolve vector potential ddt(psi) - ddt(Psi_acc)[i] = - -GRAD_PARP(phi_acc) + eta_acc[i] * Jpar_acc[i] + ddt(Psi_acc)[i] = -GRAD_PARP(B0phi_acc) / B0_acc[i2d] + eta_acc[i] * Jpar_acc[i] - + EVAL_IF(EHALL, // electron parallel pressure - 0.25 * delta_i * (GRAD_PARP(P_acc) + bracket(P0_acc, Psi_acc, i))) + + EVAL_IF(EHALL, // electron parallel pressure + 0.25 * delta_i + * (GRAD_PARP(B0P_acc) / B0_acc[i2d] + + bracket(P0_acc, Psi_acc, i) * B0_acc[i2d])) - - EVAL_IF(DIAMAG_PHI0, // Equilibrium flow - bracket(phi0_acc, Psi_acc, i)) + - EVAL_IF(DIAMAG_PHI0, // Equilibrium flow + bracket(phi0_acc, Psi_acc, i) * B0_acc[i2d]) - + EVAL_IF(DIAMAG_GRAD_T, // grad_par(T_e) correction - 1.71 * dnorm * 0.5 * GRAD_PARP(P_acc) / B0_acc[i2d]) + + EVAL_IF(DIAMAG_GRAD_T, // grad_par(T_e) correction + 1.71 * dnorm * 0.5 * GRAD_PARP(P_acc) / B0_acc[i2d]) - - EVAL_IF(HYPERRESIST, // Hyper-resistivity - eta_acc[i] * hyperresist * Delp2(Jpar_acc, i)) + - EVAL_IF(HYPERRESIST, // Hyper-resistivity + eta_acc[i] * hyperresist * Delp2(Jpar_acc, i)) - - EVAL_IF(EHYPERVISCOS, // electron Hyper-viscosity - eta_acc[i] * ehyperviscos * Delp2(Jpar2_acc, i)); + - EVAL_IF(EHYPERVISCOS, // electron Hyper-viscosity + eta_acc[i] * ehyperviscos * Delp2(Jpar2_acc, i)); #endif //////////////////////////////////////////////////// @@ -1669,12 +1680,12 @@ class ELMpb : public PhysicsModel { #endif }; - // Terms which are not yet single index operators - // Note: Terms which are included in the single index loop - // may be commented out here, to allow comparison/testing + // Terms which are not yet single index operators + // Note: Terms which are included in the single index loop + // may be commented out here, to allow comparison/testing - //////////////////////////////////////////////////// - // Parallel electric field + //////////////////////////////////////////////////// + // Parallel electric field #if not EVOLVE_JPAR // Vector potential From fb51ce8f423dd97be52efb1a3223e014dc177acd Mon Sep 17 00:00:00 2001 From: bendudson Date: Mon, 4 Dec 2023 22:04:52 +0000 Subject: [PATCH 142/412] Apply clang-format changes --- examples/elm-pb-outerloop/elm_pb_outerloop.cxx | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx index b3ad81ef1a..8e84901806 100644 --- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx +++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx @@ -1680,12 +1680,12 @@ class ELMpb : public PhysicsModel { #endif }; - // Terms which are not yet single index operators - // Note: Terms which are included in the single index loop - // may be commented out here, to allow comparison/testing + // Terms which are not yet single index operators + // Note: Terms which are included in the single index loop + // may be commented out here, to allow comparison/testing - //////////////////////////////////////////////////// - // Parallel electric field + //////////////////////////////////////////////////// + // Parallel electric field #if not EVOLVE_JPAR // Vector potential From ec60cd5ffa945dd2b3f382986fcca8b7441a8636 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Tue, 5 Dec 2023 11:33:38 -0500 Subject: [PATCH 143/412] remove files that are removed in next --- autoconf_build_defines.hxx.in | 217 - configure | 17331 -------------------------------- configure.ac | 1501 --- src/sys/options/makefile | 7 - 4 files changed, 19056 deletions(-) delete mode 100644 autoconf_build_defines.hxx.in delete mode 100755 configure delete mode 100644 configure.ac delete mode 100644 src/sys/options/makefile diff --git a/autoconf_build_defines.hxx.in b/autoconf_build_defines.hxx.in deleted file mode 100644 index 7dc2daf5d2..0000000000 --- a/autoconf_build_defines.hxx.in +++ /dev/null @@ -1,217 +0,0 @@ -/* autoconf_build_defines.hxx.in. 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If not, see . -# -##################################################################### -# -# Process this file with autoreconf to produce a configure script. -# -# $ autoreconf -if -# -# Changelog: -# -# 2010-03-09 Ben Dudson -# * Changing to always require FFTW (removing NR routines) -# 2015-08-08 David Schwörer -# * Searching for libs in lib and lib64 -# - -AC_PREREQ([2.69]) -AC_INIT([BOUT++],[5.1.0],[bd512@york.ac.uk]) -AC_CONFIG_AUX_DIR([build-aux]) -AC_CONFIG_MACRO_DIR([m4]) - -AC_MSG_WARN([./configure is deprecated and will be removed in a future version, please use CMake instead]) - -AC_ARG_WITH(netcdf, [AS_HELP_STRING([--with-netcdf], - [Enable support for netCDF files])],,[]) -AC_ARG_WITH(pnetcdf, [AS_HELP_STRING([--with-pnetcdf], - [Set path to Parallel NetCDF library])],,[]) -AC_ARG_WITH(ida, [AS_HELP_STRING([--with-ida=/path/to/ida], - [Use the SUNDIALS IDA solver])],,[]) -AC_ARG_WITH(cvode, [AS_HELP_STRING([--with-cvode], - [Use the SUNDIALS CVODE solver])],,[]) -AC_ARG_WITH(sundials, [AS_HELP_STRING([--with-sundials], - [Use CVODE and IDA])],,[]) -AC_ARG_WITH(fftw, [AS_HELP_STRING([--with-fftw], - [Set directory of FFTW3 library])],,[]) -AC_ARG_WITH(lapack, [AS_HELP_STRING([--with-lapack], - [Use the LAPACK library])],,[with_lapack=guess]) -AC_ARG_WITH(petsc, [AS_HELP_STRING([--with-petsc], - [Enable PETSc interface])],,[with_petsc=no]) -AC_ARG_WITH(slepc, [AS_HELP_STRING([--with-slepc], - [Enable SLEPc interface])],,[with_slepc=no]) -AC_ARG_WITH(pvode, [AS_HELP_STRING([--with-pvode], - [Build and enable PVODE 98 (DEFAULT)])],,[]) -AC_ARG_WITH(arkode, [AS_HELP_STRING([--with-arkode], - [Use the SUNDIALS ARKODE solver])],,[]) -AC_ARG_WITH(scorep, [AS_HELP_STRING([--with-scorep], - [Enable support for scorep based instrumentation])],,[with_scorep=no]) -AC_ARG_WITH(hypre, [AS_HELP_STRING([--with-hypre], - [Enable support for HYPRE])],,[with_hypre=no]) - -dnl --with-hdf5 flags are set in AX_LIB_{PARALLEL}HDF5 -AC_ARG_WITH(system_mpark, [AS_HELP_STRING([--with-system-mpark], - [Use mpark.variant already installed rather then the bundled one])],,[with_system_mpark=auto]) -AC_ARG_WITH(system_uuid, [AS_HELP_STRING([--with-system-uuid], - [Use libuuid to generate UUIDs])],,[with_system_uuid=auto]) - -AC_ARG_ENABLE(warnings, [AS_HELP_STRING([--disable-warnings], - [Disable compiler warnings])],,[]) -AC_ARG_ENABLE(checks, [AS_HELP_STRING([--enable-checks=no/1/2/3], - [Set run-time checking level])],,[enable_checks=default]) -AC_ARG_ENABLE(msgstack, [AS_HELP_STRING([--enable-msgstack=no/yes], - [Enable MstStack for backtrace. 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-NCCONF="" # Configuration script - -BOUT_HAS_NETCDF=no -BOUT_HAS_LEGACY_NETCDF=no -AS_IF([test "x$with_netcdf" != "xno"], -[ - ########################################## - # Try to find a valid NetCDF configuration - # - # at first, try to find ncconf script - - # Search for NetCDF config scripts, prefer ncxx4-config over nc-config - # Check if the path to the config script has been supplied directly, otherwise - # check the path provided by --with-netcdf, appending "/bin" if need - # be, then check system path - # Set NCCONF to the full path of the found scropt - AS_CASE([`basename $with_netcdf 2> /dev/null`], - ["ncxx4-config"], [NCCONF=$with_netcdf], - ["nc-config"], [NCCONF=$with_netcdf], - [AC_PATH_PROGS([NCCONF], [ncxx4-config nc-config], [], - [$with_netcdf$PATH_SEPARATOR$with_netcdf/bin$PATH_SEPARATOR$PATH])]) - - ########################################## - # Get configuration - AS_IF([test "x$NCCONF" != "x" ], - [ - # If we found nc-config rather than ncxx4-config, we need to check if it supports C++ - AS_IF([test `basename $NCCONF` = 'nc-config'], - [AC_MSG_CHECKING([if $NCCONF has C++4 support]) - nc_has_cpp4=`$NCCONF --has-c++4` - AC_MSG_RESULT([$nc_has_cpp4]) - AC_MSG_CHECKING([if $NCCONF has C++ support]) - nc_has_cpp=`$NCCONF --has-c++` - AC_MSG_RESULT([$nc_has_cpp]) - ], [ - nc_has_cpp4="yes" - ]) - - NCINC=`$NCCONF --cflags` - EXTRA_INCS="$EXTRA_INCS $NCINC" - AS_IF([test "x$nc_has_cpp4" = "xyes"], - [ - NCLIB=`$NCCONF --libs` - BOUT_HAS_NETCDF=yes - AC_MSG_NOTICE([ -> NetCDF-4 support enabled]) - ], [ - # nc-config might not *say* it has C++ support, but we can try anyway - AC_MSG_CHECKING([if we can compile NetCDF with C++]) - # Note netcdf_c++ needed - NCLIB=`$NCCONF --libs | sed s/-lnetcdf/-lnetcdf_c++\ -lnetcdf/` - - save_LIBS=$LIBS - save_LDFLAGS=$LDFLAGS - save_CXXFLAGS=$CXXFLAGS - AC_LANG_PUSH([C++]) - LIBS="$save_LIBS $NCLIB" - LDFLAGS="$save_LDFLAGS $NCLIB" - CXXFLAGS="$save_CXXFLAGS $NCINC" - AC_LINK_IFELSE( - [AC_LANG_PROGRAM([ - #include - ], [NcFile file("foo.nc");])], - [AC_MSG_RESULT([yes]) - AC_MSG_NOTICE([ -> Legacy NetCDF support enabled])], - [AC_MSG_RESULT([no]) - AC_MSG_FAILURE([*** Could not compile NetCDF C++ program!])]) - AC_LANG_POP([C++]) - LIBS=$save_LIBS - LDFLAGS=$save_LDFLAGS - CXXFLAGS="$save_CXXFLAGS" - BOUT_HAS_NETCDF=yes - BOUT_HAS_LEGACY_NETCDF=yes - ]) - EXTRA_LIBS="$EXTRA_LIBS $NCLIB" - - file_formats="$file_formats netCDF" - NCPATH="found" - NCFOUND=yes - ], [ - # if nc-config / ncxx4-config is not found, try to find library directly - BOUT_MSG_DEBUG([calling bout addpath]) - BOUT_ADDPATH_CHECK_HEADER(netcdfcpp.h, - BOUT_ADDPATH_CHECK_LIB(netcdf, nc_get_att, - BOUT_ADDPATH_CHECK_LIB(netcdf_c++, nc_close, NCFOUND=yes, NCFOUND=no, [$with_netcdf]), - NCFOUND=no, [$with_netcdf]), - NCFOUND=no, [$with_netcdf]) - - AS_IF([test "x$NCFOUND" = "xyes"], - [ - file_formats="$file_formats netCDF" - AC_MSG_NOTICE([ -> Legacy NetCDF support enabled]) - NCPATH="found" - BOUT_HAS_NETCDF=yes - BOUT_HAS_LEGACY_NETCDF=yes - ], []) - ]) - - AS_IF([test $with_netcdf && test "x$NCFOUND" != "xyes" ], AC_MSG_ERROR([NetCDF requested but not found]), []) - AS_IF([test "x$NCFOUND" != "xyes"], [AC_MSG_NOTICE([ -> NetCDF support disabled])], []) -], []) - -############################################################# -# Parallel NetCDF support -############################################################# - -PNCPATH="" -AS_IF([test "$with_pnetcdf" != "no" && test "x$with_pnetcdf" != "x" ], [ - AC_MSG_NOTICE([Searching for Parallel-NetCDF library]) - - AS_IF([test "x$with_pnetcdf" != "xyes"], [ - # Given a path to the library - AC_CHECK_FILES([$with_pnetcdf/include/pnetcdf.h], [PNCPATH=$with_pnetcdf], - AC_MSG_NOTICE([parallel-netcdf not found in given directory]) - ) - ]) - - # Find the utilities included with pnetcdf - AS_IF([test "x$PNCPATH" = "x"], [ - AS_IF([test "x$with_pnetcdf" = "xyes"], [ - AC_PATH_PROG([NCMPIDUMP_PATH], [ncmpidump]) - ], [ - AC_PATH_PROG([NCMPIDUMP_PATH], [ncmpidump], [$with_pnetcdf$PATH_SEPARATOR$PATH]) - ]) - AS_IF([test "$NCMPIDUMP_PATH" != ""], [ - AC_CHECK_FILES([$NCMPIDUMP_PATH/../include/pnetcdf.h], [PNCPATH=$NCMPIDUMP_PATH/../]) - ]) - ]) - - AS_IF([test "x$PNCPATH" != "x"], [ - AC_CHECK_FILES($path/lib/libpnetcdf.a, PNCPATHLIB='lib', - AC_CHECK_FILES($path/lib64/libpnetcdf.a, PNCPATHLIB='lib64', PNCPATH='')) - ]) - - AS_IF([test "x$PNCPATH" = "x" && test "x$with_pnetcdf" != "x"], [ - AC_MSG_FAILURE([*** Parallel-NetCDF requested but not found]) - ]) -]) - -AS_IF([test "x$PNCPATH" = "x"], [ - AC_MSG_NOTICE([Parallel-NetCDF support disabled]) -], [ - # Set a compile-time flag - CXXFLAGS="$CXXFLAGS -DPNCDF" - EXTRA_INCS="$EXTRA_INCS -I$PNCPATH/include" - EXTRA_LIBS="$EXTRA_LIBS -L$PNCPATH/$PNCPATHLIB -lpnetcdf" - - file_formats="$file_formats Parallel-NetCDF" - AC_MSG_NOTICE([Parallel-NetCDF support enabled]) -]) - -############################################################# -# Check file formats -############################################################# - -AS_IF([test "x$file_formats" = "x"], [ - AC_MSG_ERROR([*** At least one file format must be supported]) -], [ - AC_MSG_NOTICE([Supported file formats:$file_formats]) -]) - -############################################################# -# LAPACK routines (Used for tri- and band-diagonal solvers) -############################################################# - -BOUT_HAS_LAPACK="no" -AS_IF([test "x$with_lapack" != "xno"], [ - AS_IF([test "x$with_lapack" = "xguess" || test "x$with_lapack" = "x" ], - [lapack_path=""], - [AS_IF([test "x$with_lapack" != xyes], - [lapack_path=$with_lapack - with_lapack=yes], - [lapack_path=""]) - ]) - BOUT_ADDPATH_CHECK_LIB(blas, zgemm_, - [BOUT_HAS_BLAS=yes], - [AS_IF([test "x$with_lapack" = "xyes"], - AC_MSG_ERROR([LAPACK requested but couldn't find BLAS]))], - $lapack_path) - BOUT_ADDPATH_CHECK_LIB(lapack, zgbsv_, - [BOUT_HAS_LAPACK=yes - AC_MSG_NOTICE([Using LAPACK]) - ], - [AS_IF([test "x$with_lapack" = "xyes"], - AC_MSG_ERROR([LAPACK requested but not found]))], - $lapack_path) -]) - -############################################################# -# PETSc library -############################################################# - -AS_IF([test "x$with_petsc" != "x" && test "$with_petsc" != "no"], [ - -# Supplying an argument to "--with-petsc" only works if PETSC_ARCH -# *should* be empty. If it should be non-empty, THIS WILL NOT WORK - AS_IF([test "$with_petsc" != "yes"], [ - PETSC_DIR="$with_petsc" - PETSC_ARCH= - ]) - - AC_MSG_NOTICE([Using PETSC_DIR=$PETSC_DIR, PETSC_ARCH=$PETSC_ARCH]) - -# Define a macro for a nice error message that preserves the -# formatting. Use like: -# -# PETSC_ERROR_MESSAGE -# -# with no identation - m4_define(PETSC_ERROR_MESSAGE, - [ You may need to specify PETSC_DIR and PETSC_ARCH like so: - --with-petsc PETSC_DIR=\$PETSC_DIR PETSC_ARCH=\$PETSC_ARCH - Also see the help online: - http://bout-dev.readthedocs.io/en/latest/user_docs/advanced_install.html#petsc - ]) - -# PETSc changed the location of the conf directory in 3.5, so we -# need to check both locations -# If we find nether, try to fall back to pkg-conf - PETSC_PKGCONF=no - AC_CHECK_FILE($PETSC_DIR/$PETSC_ARCH/conf, [ - PETSC_CONFDIR=${PETSC_DIR}/conf - ], [ - AC_CHECK_FILE($PETSC_DIR/$PETSC_ARCH/lib/petsc/conf, [ - PETSC_CONFDIR=${PETSC_DIR}/lib/petsc/conf - ], [ - PKG_CHECK_MODULES(PETSC, PETSc >= 3.4.0 , - PETSC_PKGCONF=yes, [ - PKG_CHECK_MODULES(PETSC, petsc >= 3.4.0 , - PETSC_PKGCONF=yes, [ - AC_MSG_ERROR([--with-petsc was specified but could not find PETSc distribution. -PETSC_ERROR_MESSAGE]) - ]) - ]) - ]) - ]) - - AS_IF([test $PETSC_PKGCONF = no] , - [ -# We've found an installation, need to check we can use it. First we -# need to be able to check the version number, for which we need -# petscverion.h - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$PETSC_DIR/include" - AC_CHECK_HEADER([petscversion.h], - [FOUND_PETSC_HEADER=yes], - [FOUND_PETSC_HEADER=no] - ) - -# This is a terrible hack for some Linux distributions (Fedora) that -# install PETSc in a non-supported fashion. This is really the fault -# of PETSc for their weird method of installation - AS_IF([test $FOUND_PETSC_HEADER = no], [ - AC_CHECK_FILE([${PETSC_CONFDIR}/petscvariables], [], [ - AC_MSG_ERROR([Unable to find either petscversion.h or petscvariables -PETSC_ERROR_MESSAGE]) - ]) - -# This relies on the assumption that PETSC_ARCH is empty - PETSC_CC_INCLUDES=$(grep ^PETSC_CC_INCLUDES ${PETSC_CONFDIR}/petscvariables | cut -d= -f 2-) - - AC_MSG_NOTICE([Looking for petscverion.h using $PETSC_CC_INCLUDES from ${PETSC_CONFDIR}/petscvariables]) - - # This is the cache variable set by the previous call to - # AC_CHECK_HEADER. We need to unset it so we can call the macro - # again, but now with different CPPFLAGS - AS_UNSET([ac_cv_header_petscversion_h]) - - CPPFLAGS="$CPPFLAGS $PETSC_CC_INCLUDES" - AC_CHECK_HEADER([petscversion.h], [], [ - AC_MSG_ERROR([Couldn't find or include petscversion.h. -PETSC_ERROR_MESSAGE]) - ]) - ], []) - -# Now we have the header we want, we can check the version number - AC_MSG_CHECKING([PETSc is at least 3.4.0]) - AC_EGREP_CPP([yes], [ - #include - #if PETSC_VERSION_GE(3, 4, 0) - yes - #endif - ], [PETSC_VERSION_OK="yes"], - [PETSC_VERSION_OK="no"]) - AC_MSG_RESULT([$PETSC_VERSION_OK]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test $PETSC_VERSION_OK = no], [ - AC_MSG_ERROR([PETSc version must be at least 3.4.0]) - ]) - -# Check if PETSc was compiled with SUNDIALS - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$PETSC_DIR/$PETSC_ARCH/include" - AC_MSG_CHECKING([PETSc has SUNDIALS support]) - AC_EGREP_CPP([yes], [ - #include - #ifdef PETSC_HAVE_SUNDIALS - yes - #endif - ], [PETSC_HAS_SUNDIALS="yes"], - [PETSC_HAS_SUNDIALS="no"]) - AC_MSG_RESULT([$PETSC_HAS_SUNDIALS]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test "$PETSC_HAS_SUNDIALS" = "yes"], [ - CXXFLAGS="$CXXFLAGS -DPETSC_HAS_SUNDIALS " - ]) - - # Set the line to be included in the make.conf file - PETSC_MAKE_INCLUDE="include ${PETSC_CONFDIR}/variables" - - BOUT_HAS_PETSC="yes" - - EXTRA_INCS="$EXTRA_INCS \$(PETSC_CC_INCLUDES)" - EXTRA_LIBS="$EXTRA_LIBS \$(PETSC_LIB)" - ], [ dnl pkg-config version - - # Check if PETSc was compiled with SUNDIALS - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS $PETSC_CFLAGS" - AC_MSG_CHECKING([PETSc has SUNDIALS support]) - AC_EGREP_CPP([yes], [ - #include - #ifdef PETSC_HAVE_SUNDIALS - yes - #endif - ], [PETSC_HAS_SUNDIALS="yes"], - [PETSC_HAS_SUNDIALS="no"]) - AC_MSG_RESULT([$PETSC_HAS_SUNDIALS]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test "$PETSC_HAS_SUNDIALS" = "yes"], [ - CXXFLAGS="$CXXFLAGS -DPETSC_HAS_SUNDIALS " - ]) - PETSC_MAKE_INCLUDE= - BOUT_HAS_PETSC="yes" - - EXTRA_INCS="$EXTRA_INCS $PETSC_CFLAGS" - EXTRA_LIBS="$PETSC_LIBS $EXTRA_LIBS" - ]) -], [ - PETSC_MAKE_INCLUDE= - BOUT_HAS_PETSC="no" - PETSC_HAS_SUNDIALS="no" -]) - -############################################################# -# SLEPc library -############################################################# - -AS_IF([test "x$with_slepc" != "x" && test "$with_slepc" != "no"], [ - - AS_IF([test $BOUT_HAS_PETSC = "no"], [ - AC_MSG_ERROR([--with-slepc specified, but no PETSc detected. Please reconfigure and specify --with-petsc -PETSC_ERROR_MESSAGE]) - ]) - -# Supplying an argument to "--with-slepc" only works if SLEPC_ARCH -# *should* be empty. If it should be non-empty, THIS WILL NOT WORK - AS_IF([test "$with_slepc" != "yes"], [ - SLEPC_DIR="$with_slepc" - SLEPC_ARCH= - ]) - - AC_MSG_NOTICE([Using SLEPC_DIR=$SLEPC_DIR, SLEPC_ARCH=$SLEPC_ARCH]) - -# Define a macro for a nice error message that preserves the -# formatting. Use like: -# -# SLEPC_ERROR_MESSAGE -# -# with no identation - m4_define(SLEPC_ERROR_MESSAGE, - [ You may need to specify SLEPC_DIR and SLEPC_ARCH like so: - --with-slepc SLEPC_DIR=\$SLEPC_DIR SLEPC_ARCH=\$SLEPC_ARCH - Also see the help online: - http://bout-dev.readthedocs.io/en/latest/user_docs/advanced_install.html#slepc - ]) - -# Slepc changed the location of the conf directory in 3.5, so we -# need to check both locations - AC_CHECK_FILE($SLEPC_DIR/$SLEPC_ARCH/conf, [ - SLEPC_CONFDIR=${SLEPC_DIR}/conf - ], [ - AC_CHECK_FILE($SLEPC_DIR/$SLEPC_ARCH/lib/slepc/conf, [ - SLEPC_CONFDIR=${SLEPC_DIR}/lib/slepc/conf - ], [ - AC_MSG_ERROR([--with-slepc was specified but could not find Slepc distribution. -SLEPC_ERROR_MESSAGE]) - ]) - ]) - -# We've found an installation, need to check we can use it. First we -# need to be able to check the version number, for which we need -# slepcverion.h - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$SLEPC_DIR/include" - AC_CHECK_HEADER([slepcversion.h], - [FOUND_SLEPC_HEADER=yes], - [FOUND_SLEPC_HEADER=no] - ) - -# This is a terrible hack for some Linux distributions (Fedora) that -# install Slepc in a non-supported fashion. This is really the fault -# of Slepc for their weird method of installation - AS_IF([test $FOUND_SLEPC_HEADER = no], [ - AC_CHECK_FILE([${SLEPC_CONFDIR}/slepc_variables], [], [ - AC_MSG_ERROR([Unable to find either slepcversion.h or slepc_variables -SLEPC_ERROR_MESSAGE]) - ]) - -# This relies on the assumption that SLEPC_ARCH is empty - SLEPC_CC_INCLUDES=$(grep ^SLEPC_CC_INCLUDES ${SLEPC_CONFDIR}/slepc_variables | cut -d= -f 2-) - - AC_MSG_NOTICE([Looking for slepcverion.h using $SLEPC_CC_INCLUDES from ${SLEPC_CONFDIR}/slepc_variables]) - - # This is the cache variable set by the previous call to - # AC_CHECK_HEADER. We need to unset it so we can call the macro - # again, but now with different CPPFLAGS - AS_UNSET([ac_cv_header_slepcversion_h]) - - CPPFLAGS="$CPPFLAGS $SLEPC_CC_INCLUDES" - AC_CHECK_HEADER([slepcversion.h], [], [ - AC_MSG_ERROR([Couldn't find or include slepcversion.h. -SLEPC_ERROR_MESSAGE]) - ]) - ], []) - -# Now we have the header we want, we can check the version number - AC_MSG_CHECKING([Slepc is at least 3.4.0]) - AC_EGREP_CPP([yes], [ - #include - #if SLEPC_VERSION_GE(3, 4, 0) - yes - #endif - ], [SLEPC_VERSION_OK="yes"], - [SLEPC_VERSION_OK="no"]) - AC_MSG_RESULT([$SLEPC_VERSION_OK]) - CPPFLAGS="$save_CPPFLAGS" - - AS_IF([test $SLEPC_VERSION_OK = no], [ - AC_MSG_ERROR([Slepc version must be at least 3.4.0]) - ]) - -# Check if Slepc was compiled with SUNDIALS - save_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$SLEPC_DIR/$SLEPC_ARCH/include" - - # Set the line to be included in the make.conf file - SLEPC_MAKE_INCLUDE="include ${SLEPC_CONFDIR}/slepc_variables" - - BOUT_HAS_SLEPC="yes" - - EXTRA_INCS="$EXTRA_INCS \$(SLEPC_INCLUDE)" - EXTRA_LIBS="$EXTRA_LIBS \$(SLEPC_LIB)" - -], [ - SLEPC_MAKE_INCLUDE= - BOUT_HAS_SLEPC="no" -]) - -############################################################# -# Solver choice: SUNDIALS' IDA, SUNDIALS' CVODE, PVODE -############################################################# - -BOUT_HAS_SUNDIALS=no -AS_IF([test "x$with_sundials" != "x" && test "x$with_sundials" != "xno"], [ - - # Now follows a few different checks for the version of SUNDIALS. - # We need the sundials_config.h header, which comes with all the - # versions we care about - - # If we've been given a path, look in there first - AS_IF([test "x$with_sundials" != "xyes"], [ - AC_CHECK_FILE([$with_sundials/include/sundials/sundials_config.h], - [SUNDIALS_INC=$with_sundials/include], [SUNDIALS_INC=""]) - ]) - - # If we've got one, add the include dir to the preprocessor flags - save_CPPFLAGS=$CPPFLAGS - AS_IF([test "x$SUNDIALS_INC" != "x"], [CPPFLAGS="-I$SUNDIALS_INC"]) - - AC_MSG_CHECKING([for SUNDIALS config header]) - AC_COMPILE_IFELSE([ - AC_LANG_PROGRAM([ - #include "sundials/sundials_config.h" - ], [])], - [AC_MSG_RESULT([yes])], - [AC_MSG_RESULT([no]) - AC_MSG_FAILURE([*** Could not determine SUNDIALS version])]) - - AC_MSG_CHECKING([for SUNDIALS minor version]) - AC_EGREP_CPP([^ *\"? *[12]\.[0-5]\.], [ - #include "sundials/sundials_config.h" - #ifdef SUNDIALS_PACKAGE_VERSION - SUNDIALS_PACKAGE_VERSION - #endif - ], [sundials_minor_ver="too low"], [sundials_minor_ver=ok]) - AC_MSG_RESULT([$sundials_minor_ver]) - - CPPFLAGS=$save_CPPFLAGS - - AS_IF([test "$sundials_minor_ver" = "too low"], [ - AC_MSG_FAILURE([*** Unsupported SUNDIALS version: Requires at least 2.6]) - ]) - - # Set both IDA and CVODE if not set already - AS_IF([test "x$with_ida" = "x"], [ - with_ida=$with_sundials - ]) - - AS_IF([test "x$with_cvode" = "x"], [ - with_cvode=$with_sundials - ]) - - AS_IF([test "x$with_arkode" = "x"], [ - with_arkode=$with_sundials - ]) - BOUT_HAS_SUNDIALS=yes -]) - -AS_IF([test "x$with_ida" != "x" && test "x$with_ida" != "xno"], [ - BOUT_FIND_SUNDIALS_MODULE([ida], [ - #include - #include - extern void foo(N_Vector); - ], [IDACreate();]) -]) - -AS_IF([test "x$with_cvode" != "x" && test "x$with_cvode" != "xno"], [ - BOUT_FIND_SUNDIALS_MODULE([cvode], [ - #include - #include - extern void foo(N_Vector); - ], [ - #if SUNDIALS_VERSION_MAJOR >= 4 - CVodeCreate(0); - #else - CVodeCreate(0, 0); - #endif - ]) -]) - -AS_IF([test "x$with_arkode" != "x" && test "x$with_arkode" != "xno"], [ - BOUT_FIND_SUNDIALS_MODULE([arkode], [ - #include - #if SUNDIALS_VERSION_MAJOR >= 4 - #include - #else - #include - #endif - extern void foo(N_Vector); - ], [ - #if SUNDIALS_VERSION_MAJOR >= 4 - ARKStepCreate(0, 0, 0, 0); - #else - ARKodeCreate(); - #endif - ]) -]) - -############################################################# -# HYPRE -############################################################# - -BOUT_HAS_HYPRE="no" -AS_IF([test "$with_hypre" != "no"], [ - BOUT_ADDPATH_CHECK_HEADER(HYPRE.h, - BOUT_ADDPATH_CHECK_LIB(HYPRE, HYPRE_IJVectorCreate, - [ - BOUT_HAS_HYPRE="yes" - ], - AC_MSG_ERROR([HYPRE requested but not found]), - $with_hypre), - AC_MSG_ERROR([HYPRE requested but not found]), - $with_hypre - ) -]) - -############################################################# -# Scorep setup -############################################################# - -BOUT_HAS_SCOREP="no" -AS_IF([test "$with_scorep" != "no"], [ - - AS_IF([test "$with_scorep" != "yes"], [ - AC_MSG_NOTICE([Searching for Scorep executable in $with_scorep]) - AC_PATH_PROG([SCOREPPATH], [scorep], [], [$with_scorep]) - ], [ - AC_MSG_NOTICE([Searching for Scorep executable]) - AC_PATH_PROG([SCOREPPATH], [scorep], []) - ]) - - AS_IF([test "$SCOREPPATH" = ""], [ - AC_MSG_FAILURE([*** Scorep requested, but executable not found. -Please supply the path using --with-scorep=/path/to/scorep]) - ],[ - CXX="$SCOREPPATH --user --nocompiler $CXX" - BOUT_HAS_SCOREP="yes" - AC_MSG_NOTICE([Scorep support enabled]) - ]) - - ],[ - AC_MSG_NOTICE([Scorep support disabled]) -]) - -############################################################# -# Check for mpark.variant -############################################################# - -AS_IF([test ".$with_system_mpark" = "no"], [ - SYSTEM_HAS_MPARK=no -], [ - AC_MSG_CHECKING([for mpark.variant]) - AC_COMPILE_IFELSE([ - AC_LANG_PROGRAM([ - #include "mpark/variant.hpp" - ], [])], - [AC_MSG_RESULT([yes]) - SYSTEM_HAS_MPARK=yes], - [AC_MSG_RESULT([no]) - SYSTEM_HAS_MPARK=no - AS_IF([test "$with_system_mpark" = "yes"], [ - AC_MSG_FAILURE([*** System mpark.variant not found - but requested to use]) - ])]) -]) - -AS_IF([test "$SYSTEM_HAS_MPARK" = "yes"], [ - MPARK_VARIANT_INCLUDE_PATH= - MPARK_INCLUDE= - OWN_MPARK= -], [ - AS_IF([test -d externalpackages/mpark.variant/include], [], - [ AS_IF([test -d .git && which git], [ - make -f makefile.submodules mpark_submodule || \ - AC_MSG_FAILURE([*** Could not download mpark.variant]) - ], [ - AC_MSG_FAILURE([mpark.variant not found. Please install mpark.variant or use the official releases.]) - ]) - ]) - - MPARK_VARIANT_INCLUDE_PATH="$PWD/externalpackages/mpark.variant/include" - MPARK_INCLUDE="-I$MPARK_VARIANT_INCLUDE_PATH" - OWN_MPARK=yes -]) - -############################################################# -# Check for libuuid -############################################################# - -AS_IF([test ".$with_system_uuid" = "no"], [ - BOUT_HAS_UUID_SYSTEM_GENERATOR=no -], [ - BOUT_ADDPATH_CHECK_HEADER(uuid/uuid.h, - BOUT_ADDPATH_CHECK_LIB(uuid, uuid_generate, - BOUT_HAS_UUID_SYSTEM_GENERATOR=yes, - BOUT_HAS_UUID_SYSTEM_GENERATOR=no, - [$with_system_uuid]), - BOUT_HAS_UUID_SYSTEM_GENERATOR=no, - [$with_system_uuid]) - AS_IF([test "$with_system_uuid" = "yes"], [ - AC_MSG_FAILURE([*** System UUID generator not found, but explicitly requested]) - ]) -]) - -############################################################# -# Download + Build PVODE '98 -############################################################# - -AS_MKDIR_P(externalpackages) -AS_MKDIR_P(lib) -AS_MKDIR_P(include) - -BOUT_HAS_PVODE="no" -AS_IF([test "$with_pvode" != "no"], [ - AS_IF([test "$enable_pvode_openmp" != "no" ], [ - AS_IF([test "$enable_openmp" != "no" ], [ - PVODE_FLAGS="$CXXFLAGS $OPENMP_CXXFLAGS" - AC_MSG_NOTICE([PVODE being built with OpenMP support]) - ], [ - AC_MSG_ERROR([Cannot enable openmp in PVODE as configuring with OpenMP disabled]) - ]) - ], [ - PVODE_FLAGS="$CXXFLAGS" - AC_MSG_NOTICE([PVODE being built without OpenMP support]) - ]) - # Clean PVODE - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE clean -C externalpackages/PVODE/precon/ >> config-build.log 2>&1 - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE clean -C externalpackages/PVODE/source/ >> config-build.log 2>&1 - - AC_MSG_NOTICE([Building PVODE]) - echo "* Building PVODE" >> config-build.log - echo "*************************************************************" >> config-build.log - - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE -C externalpackages/PVODE/precon/ >> config-build.log 2>&1 - CXX="$CXX" CXXFLAGS=$PVODE_FLAGS MKDIR="$MKDIR_P" RANLIB="$RANLIB" $MAKE -C externalpackages/PVODE/source/ >> config-build.log 2>&1 - - AS_IF([test -f externalpackages/PVODE/lib/libpvode.a && test -f externalpackages/PVODE/lib/libpvpre.a], [ - AC_MSG_NOTICE([Successfully built PVODE]) - AC_MSG_NOTICE([Installing PVODE into BOUT++ sourcetree]) - - echo "*************************************************************" >> config-build.log - echo "* Successfully built PVODE" >> config-build.log - echo "*************************************************************" >> config-build.log - echo "* Installing PVODE into BOUT++ sourcetree" >> config-build.log - echo "*************************************************************" >> config-build.log - ], [ - AC_MSG_ERROR(Could not build PVODE. See config-build.log for errors) - ]) - - # Set the correct libraries and copy them to bout - AS_MKDIR_P(include/pvode) - cp -r externalpackages/PVODE/include/pvode include - cp externalpackages/PVODE/lib/*.a lib/ - EXTRA_LIBS="$EXTRA_LIBS -L\$(BOUT_LIB_PATH) -lpvode -lpvpre" - BOUT_HAS_PVODE="yes" -]) - -############################################################# -# Localisation (i18n) with gettext -############################################################# - -BOUT_HAS_GETTEXT="no" -# Use macro to test if Natural Language Support (gettext) is available. -# If available sets: -# - USE_NLS to "yes" -# - LIBINTL to the linker options -# - Modifies CPPFLAGS if needed -AM_GNU_GETTEXT([external]) -AS_IF([test "$USE_NLS" = "yes"], [ - AC_MSG_NOTICE([Enabling language support with gettext]) - # Turn the .po files into .mo files - $MAKE -C locale | tee -a config-build.log 2>&1 - - # Note: BOUT_LOCALE_PATH is defined in make.config, and may be changed by `make install`. - CXXFLAGS="$CXXFLAGS -DBOUT_LOCALE_PATH=\$(BOUT_LOCALE_PATH)" - - EXTRA_LIBS="$EXTRA_LIBS $LIBINTL" - - # Set variable substituted into bout-config - BOUT_HAS_GETTEXT="yes" -],[ - AC_MSG_NOTICE([Language support with gettext not available]) -]) - -############################################################# -# Sort out fmt -############################################################# - -dnl If in a git repo, get submodule, unless BOUT_DONT_UPDATE_GIT_SUBMODULE is set -AC_CHECK_FILE([.git], [ - AS_IF([test "x$BOUT_DONT_UPDATE_GIT_SUBMODULE" == "x"], [ - git submodule update --init externalpackages/fmt - ]) -]) - -dnl Copy the one file we need to somewhere else -AC_CONFIG_LINKS(src/fmt/format.cxx:externalpackages/fmt/src/format.cc) - -############################################################# -# Check environment -############################################################# - -AS_IF([test "$CXXINCLUDE" != ""], [ - AC_MSG_NOTICE([================================================]) - AC_MSG_NOTICE([ WARNING: CXXINCLUDE environment variable set to:]) - AC_MSG_NOTICE([$CXXINCLUDE]) - AC_MSG_NOTICE([ => This will be added to compile commands]) - AC_MSG_NOTICE([ If this is not intended, then run]) - AC_MSG_NOTICE([ export CXXINCLUDE='']) - AC_MSG_NOTICE([ before making BOUT++]) - AC_MSG_NOTICE([================================================]) -]) - -############################################################# -# Gather configuration info for bout-config -############################################################# - -EXTRA_INCS="${EXTRA_INCS} ${CPPFLAGS}" - -PREFIX=$PWD -IDLCONFIGPATH=$PWD/tools/idllib -PYTHONCONFIGPATH=$PWD/tools/pylib - -BOUT_HAS_IDA="yes" -if test "$IDALIBS" = "" -then - BOUT_HAS_IDA="no" -fi - -BOUT_HAS_CVODE="yes" -if test "$CVODELIBS" = "" -then - BOUT_HAS_CVODE="no" -fi - -BOUT_HAS_ARKODE="yes" -if test "$ARKODELIBS" = "" -then - BOUT_HAS_ARKODE="no" -fi - -BOUT_HAS_PNETCDF="yes" -if test "$PNCPATH" = "" -then - BOUT_HAS_PNETCDF="no" -fi - -# Only make.config is altered by configure -AC_CONFIG_FILES([make.config]) -AC_OUTPUT - -############################################################# -# Use a dummy Makefile to get the cflags and ldflags -# -# This is to capture flags from external libraries such -# as PETSc -############################################################# - -CONFIG_CFLAGS=`$MAKE cflags -f output.make` -CONFIG_LDFLAGS=`$MAKE ldflags -f output.make` - -############################################################# -# Defines which are supported by CMake build but not autoconf - -BOUT_HAS_CUDA="no" -BOUT_HAS_RAJA="no" -BOUT_HAS_UMPIRE="no" -BOUT_HAS_CALIPER="no" -BOUT_HAS_ADIOS="no" - -BOUT_DEFINE_SUBST(BOUT_HAS_CUDA, [Enable CUDA]) -BOUT_DEFINE_SUBST(BOUT_HAS_RAJA, [RAJA support]) -BOUT_DEFINE_SUBST(BOUT_HAS_UMPIRE, [Umpire support]) -BOUT_DEFINE_SUBST(BOUT_HAS_CALIPER, [Caliper support]) -BOUT_DEFINE_SUBST(BOUT_HAS_ADIOS, [ADIOS support]) - -############################################################# -# Write configuration to bout-config -############################################################# - -AC_SUBST(CONFIG_CFLAGS) -AC_SUBST(CONFIG_LDFLAGS) - -# Set path to lib and include here. -# If make install is run then that replaces these paths -BOUT_LIB_PATH=$PWD/lib -BOUT_INCLUDE_PATH=$PWD/include -FMT_INCLUDE_PATH=$PWD/externalpackages/fmt/include -AC_SUBST(BOUT_LIB_PATH) -AC_SUBST(BOUT_INCLUDE_PATH) -AC_SUBST(FMT_INCLUDE_PATH) -AC_SUBST(MPARK_VARIANT_INCLUDE_PATH) -AC_SUBST(MPARK_INCLUDE) -AC_SUBST(OWN_MPARK) - -AC_SUBST(PREFIX) -AC_SUBST(IDLCONFIGPATH) -AC_SUBST(PYTHONCONFIGPATH) -AC_SUBST(LIB_TO_BUILD) -AC_SUBST(STATIC_EXTRA) -AC_SUBST(SHARED_EXTRA) - -AC_SUBST(BOUT_VERSION) -AC_SUBST(BOUT_VERSION_MAJOR) -AC_SUBST(BOUT_VERSION_MINOR) -AC_SUBST(BOUT_VERSION_PATCH) -AC_SUBST(BOUT_VERSION_TAG) -AC_SUBST(BOUT_REVISION) - -AC_SUBST(BOUT_CHECK_LEVEL) -AC_DEFINE_UNQUOTED(BOUT_CHECK_LEVEL, [$BOUT_CHECK_LEVEL], [Runtime error checking level]) - -AC_SUBST(BOUT_OPENMP_SCHEDULE) -AC_DEFINE_UNQUOTED(BOUT_OPENMP_SCHEDULE, [$BOUT_OPENMP_SCHEDULE], [OpenMP schedule]) - -BOUT_DEFINE_SUBST(BOUT_HAS_ARKODE, [ARKODE support]) -BOUT_DEFINE_SUBST(BOUT_HAS_CVODE, [CVODE support]) -BOUT_DEFINE_SUBST(BOUT_HAS_FFTW, [FFTW support]) -BOUT_DEFINE_SUBST(BOUT_HAS_GETTEXT, [NLS support]) -BOUT_DEFINE_SUBST(BOUT_HAS_IDA, [IDA support]) -BOUT_DEFINE_SUBST(BOUT_HAS_LAPACK, [LAPACK support]) -BOUT_DEFINE_SUBST(BOUT_HAS_NETCDF, [NETCDF support]) -BOUT_DEFINE_SUBST(BOUT_HAS_LEGACY_NETCDF, [NETCDF support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PETSC, [PETSc support]) -BOUT_DEFINE_SUBST(BOUT_HAS_HYPRE, [Hypre support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PNETCDF, [PNETCDF support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PRETTY_FUNCTION, [Compiler PRETTYFUNCTION support]) -BOUT_DEFINE_SUBST(BOUT_HAS_PVODE, [PVODE support]) -BOUT_DEFINE_SUBST(BOUT_HAS_SCOREP, [Score-P support]) -BOUT_DEFINE_SUBST(BOUT_HAS_SLEPC, [SLEPc support]) -BOUT_DEFINE_SUBST(BOUT_HAS_SUNDIALS, [SUNDIALS support]) -BOUT_DEFINE_SUBST(BOUT_HAS_UUID_SYSTEM_GENERATOR, [Use libuuid for UUID generation]) -BOUT_DEFINE_SUBST(BOUT_USE_BACKTRACE, [Enable backtrace in exceptions]) -BOUT_DEFINE_SUBST(BOUT_USE_COLOR, [Enable color logs option]) -BOUT_DEFINE_SUBST(BOUT_USE_OUTPUT_DEBUG, [Enabled extra debug output]) -BOUT_DEFINE_SUBST(BOUT_USE_OPENMP, [Enable OpenMP]) -BOUT_DEFINE_SUBST(BOUT_USE_SIGFPE, [Enable floating point exceptions]) -BOUT_DEFINE_SUBST(BOUT_USE_SIGNAL, [Enable signal handlers]) -BOUT_DEFINE_SUBST(BOUT_USE_TRACK, [Enable field name tracking]) -BOUT_DEFINE_SUBST(BOUT_USE_MSGSTACK, [Enable MsgStack for traces]) -AC_DEFINE_UNQUOTED([BOUT_METRIC_TYPE], $BOUT_METRIC_TYPE, [Type of the metric fields]) -BOUT_METRIC_3D=$(test $BOUT_METRIC_TYPE != 3D ; echo $?) -AC_DEFINE_UNQUOTED([BOUT_USE_METRIC_3D], $BOUT_METRIC_3D, [Is the metric field 3D]) -AC_SUBST(BOUT_METRIC_TYPE) - -AC_SUBST(PETSC_HAS_SUNDIALS) -AC_SUBST(PETSC_MAKE_INCLUDE) -AC_SUBST(PETSC_DIR) -AC_SUBST(PETSC_ARCH) -AC_SUBST(SLEPC_MAKE_INCLUDE) -AC_SUBST(SLEPC_DIR) -AC_SUBST(SLEPC_ARCH) - - -AC_CONFIG_HEADERS([include/bout/build_defines.hxx:autoconf_build_defines.hxx.in]) -AC_CONFIG_FILES([include/bout/version.hxx]) -AC_CONFIG_FILES([include/bout/revision.hxx]) -AC_CONFIG_FILES([bin/bout-config]) -AC_CONFIG_FILES([src/makefile]) -AC_CONFIG_FILES([tools/pylib/boutconfig/__init__.py]) -AC_OUTPUT -chmod a+x bin/bout-config - -############################################################# -# Print configuration info -############################################################# - -AC_MSG_NOTICE([-------------------------]) -AC_MSG_NOTICE([ Configuration summary ]) -AC_MSG_NOTICE([-------------------------]) - -AC_MSG_NOTICE([ PETSc support : $BOUT_HAS_PETSC (has SUNDIALS: $PETSC_HAS_SUNDIALS)]) -AC_MSG_NOTICE([ SLEPc support : $BOUT_HAS_SLEPC]) -AC_MSG_NOTICE([ IDA support : $BOUT_HAS_IDA]) -AC_MSG_NOTICE([ CVODE support : $BOUT_HAS_CVODE]) -AC_MSG_NOTICE([ ARKODE support : $BOUT_HAS_ARKODE]) -AC_MSG_NOTICE([ FFTW support : $BOUT_HAS_FFTW]) -AC_MSG_NOTICE([ NetCDF support : $BOUT_HAS_NETCDF (legacy: $BOUT_HAS_LEGACY_NETCDF)]) -AC_MSG_NOTICE([ Parallel-NetCDF support : $BOUT_HAS_PNETCDF]) -AC_MSG_NOTICE([ Lapack support : $BOUT_HAS_LAPACK]) -AC_MSG_NOTICE([ Scorep support : $BOUT_HAS_SCOREP]) -AC_MSG_NOTICE([ OpenMP support : $BOUT_USE_OPENMP (schedule: $OPENMP_SCHEDULE)]) -AC_MSG_NOTICE([ Natural language support: $BOUT_HAS_GETTEXT (path: $localedir)]) -AC_MSG_NOTICE([ HYPRE support : $BOUT_HAS_HYPRE]) -AC_MSG_NOTICE([ System UUID generator : $BOUT_HAS_UUID_SYSTEM_GENERATOR]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([ Enable backtrace : $BOUT_USE_BACKTRACE]) -AC_MSG_NOTICE([ Enable color logs : $BOUT_USE_COLOR]) -AC_MSG_NOTICE([ Enable more debug output: $BOUT_USE_OUTPUT_DEBUG]) -AC_MSG_NOTICE([ Enable OpenMP : $BOUT_USE_OPENMP]) -AC_MSG_NOTICE([ Enable FP exceptions : $BOUT_USE_SIGFPE]) -AC_MSG_NOTICE([ Enable signal handlers : $BOUT_USE_SIGNAL]) -AC_MSG_NOTICE([ Enable field names : $BOUT_USE_TRACK]) -AC_MSG_NOTICE([ Metric type : $BOUT_METRIC_TYPE]) - -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([-------------------------------]) -AC_MSG_NOTICE([ Data analysis configuration ]) -AC_MSG_NOTICE([-------------------------------]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([=== IDL ===]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([Make sure that the tools/idllib directory is in your IDL_PATH]) -AC_MSG_NOTICE([e.g. by adding to your ~/.bashrc file]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([ export IDL_PATH=+$PWD/tools/idllib:'':\$IDL_PATH]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([=== Python ===]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([Make sure that the tools/pylib directory is in your PYTHONPATH]) -AC_MSG_NOTICE([e.g. by adding to your ~/.bashrc file]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([ export PYTHONPATH=$PWD/tools/pylib/:\$PYTHONPATH]) -AC_MSG_NOTICE([]) -AC_MSG_NOTICE([*** Now run '$MAKE' to compile BOUT++ ***]) -AC_MSG_NOTICE([]) -AC_MSG_WARN([./configure is deprecated and will be removed in a future version, please use CMake instead]) diff --git a/src/sys/options/makefile b/src/sys/options/makefile deleted file mode 100644 index f8f0c76f69..0000000000 --- a/src/sys/options/makefile +++ /dev/null @@ -1,7 +0,0 @@ -BOUT_TOP = ../../.. -SOURCEC = options_ini.cxx options_netcdf.cxx options_io.cxx - -SOURCEH = $(SOURCEC:%.cxx=%.hxx) globals.hxx bout_types.hxx multiostream.hxx -TARGET = lib - -include $(BOUT_TOP)/make.config From fb7a962fdfe212cfe3db02f15ba4305a40a172c1 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Tue, 5 Dec 2023 13:02:07 -0500 Subject: [PATCH 144/412] Build adios2 for the first ubuntu build --- .build_adios2_for_ci.sh | 62 +++++++++++++++++++++++++++++++++++++ .github/workflows/tests.yml | 6 ++++ 2 files changed, 68 insertions(+) create mode 100755 .build_adios2_for_ci.sh diff --git a/.build_adios2_for_ci.sh b/.build_adios2_for_ci.sh new file mode 100755 index 0000000000..90f4aae29a --- /dev/null +++ b/.build_adios2_for_ci.sh @@ -0,0 +1,62 @@ +#!/bin/bash + +set -e + +if test $BUILD_ADIOS2 ; then + if [[ ! -d $HOME/local/adios/include/adios2.h ]] || test $1 ; then + echo "****************************************" + echo "Building ADIOS2" + echo "****************************************" + + branch=${1:-release_29} + if [ ! -d adios2 ]; then + git clone -b $branch https://github.com/ornladios/ADIOS2.git adios2 --depth=1 + fi + + pushd adios2 + rm -rf build + mkdir -p build + pushd build + + cmake .. \ + -DCMAKE_INSTALL_PREFIX=$HOME/local/adios2 \ + -DADIOS2_USE_MPI=ON \ + -DADIOS2_USE_Fortran=OFF \ + -DADIOS2_USE_Python=OFF \ + -DADIOS2_BUILD_EXAMPLES=OFF \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_POSITION_INDEPENDENT_CODE=ON \ + -DADIOS2_BUILD_TESTING=OFF \ + -DADIOS2_USE_SST=OFF \ + -DADIOS2_USE_MGARD=OFF \ + -DADIOS2_USE_HDF5=OFF \ + -DADIOS2_USE_BZip2=OFF \ + -DADIOS2_USE_Blosc2=OFF \ + -DADIOS2_USE_SZ=OFF \ + -DADIOS2_USE_ZFP=OFF \ + -DADIOS2_USE_DAOS=OFF \ + -DADIOS2_USE_UCX=OFF \ + -DADIOS2_USE_LIBPRESSIO=OFF \ + -DADIOS2_USE_Sodium=OFF \ + -DADIOS2_USE_ZeroMQ=OFF \ + -DADIOS2_USE_MHS=OFF \ + -DADIOS2_USE_DataMan=OFF + + make -j 4 && make install + popd + + echo "****************************************" + echo " Finished building ADIOS2" + echo "****************************************" + + else + + echo "****************************************" + echo " ADIOS2 already installed" + echo "****************************************" + fi +else + echo "****************************************" + echo " ADIOS2 not requested" + echo "****************************************" +fi diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 1083c5e059..7e4df9abf8 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -47,12 +47,15 @@ jobs: -DBOUT_USE_PETSC=ON -DBOUT_USE_SLEPC=ON -DBOUT_USE_SUNDIALS=ON + -DBOUT_USE_ADIOS2=ON -DBOUT_ENABLE_PYTHON=ON + -DADIOS2_DIR=/home/runner/local/adios2 -DSUNDIALS_ROOT=/home/runner/local -DPETSC_DIR=/home/runner/local/petsc -DSLEPC_DIR=/home/runner/local/slepc" build_petsc: -petsc-main build_petsc_branch: main + build_adios2: true on_cron: true - name: "Default options, Ubuntu 20.04" @@ -201,6 +204,9 @@ jobs: - name: Build PETSc run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }} + - name: Build ADIOS2 + run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh + - name: Build BOUT++ run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }} From f4b24d71a6473a9cd3b4b1d246df383738ea36e2 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 5 Dec 2023 16:44:09 -0800 Subject: [PATCH 145/412] options_adios: Address Clang-tidy comments Mainly unused parameters, moving definitions to the header, adding override keywords. Note that there is a GCC compiler bug with [[maybe_unused]] on first argument of a constructor: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81429 --- include/bout/options_adios.hxx | 42 +++++++++++++++++-------------- include/bout/options_io.hxx | 8 +++--- src/sys/options/options_adios.cxx | 10 -------- 3 files changed, 27 insertions(+), 33 deletions(-) diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index 0c4853bc38..81e492c2e7 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -18,24 +18,27 @@ namespace bout { class OptionsADIOS : public OptionsIO { public: + OptionsADIOS() {} explicit OptionsADIOS( - const std::string& filename, - bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, - bool singleWriteFile = false) {} - OptionsADIOS(const OptionsADIOS&) = default; - OptionsADIOS(OptionsADIOS&&) = default; - OptionsADIOS& operator=(const OptionsADIOS&) = default; - OptionsADIOS& operator=(OptionsADIOS&&) = default; + const std::string& filename [[maybe_unused]], + [[maybe_unused]] bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, + [[maybe_unused]] bool singleWriteFile = false) {} + OptionsADIOS(const OptionsADIOS&) = delete; + OptionsADIOS(OptionsADIOS&&) noexcept = default; + ~OptionsADIOS() = default; + + OptionsADIOS& operator=(const OptionsADIOS&) = delete; + OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default; /// Read options from file - Options read() { throw BoutException("OptionsADIOS not available\n"); } + Options read() override { throw BoutException("OptionsADIOS not available\n"); } /// Write options to file - void write(const Options& options, const std::string& time_dim) { + void write([[maybe_unused]] const Options& options, [[maybe_unused]] const std::string& time_dim) override { throw BoutException("OptionsADIOS not available\n"); } - void verifyTimesteps() const { throw BoutException("OptionsADIOS not available\n"); } + void verifyTimesteps() const override { throw BoutException("OptionsADIOS not available\n"); } }; } // namespace bout @@ -55,27 +58,28 @@ class OptionsADIOS : public OptionsIO { public: // Constructors need to be defined in implementation due to forward // declaration of ADIOSStream - OptionsADIOS(); + OptionsADIOS() {} OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, - bool singleWriteFile = false); - ~OptionsADIOS(); + bool singleWriteFile = false) : OptionsIO(filename, mode, singleWriteFile) {} OptionsADIOS(const OptionsADIOS&) = delete; - OptionsADIOS(OptionsADIOS&&) noexcept; + OptionsADIOS(OptionsADIOS&&) noexcept = default; + ~OptionsADIOS() = default; + OptionsADIOS& operator=(const OptionsADIOS&) = delete; - OptionsADIOS& operator=(OptionsADIOS&&) noexcept; + OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default; /// Read options from file - Options read(); + Options read() override; /// Write options to file - void write(const Options& options) { write(options, "t"); } - void write(const Options& options, const std::string& time_dim); + void write(const Options& options) override { write(options, "t"); } + void write(const Options& options, const std::string& time_dim) override; /// Check that all variables with the same time dimension have the /// same size in that dimension. Throws BoutException if there are /// any differences, otherwise is silent - void verifyTimesteps() const; + void verifyTimesteps() const override; private: }; diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index b0ffdb5bb1..d8f26dc8ef 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -2,8 +2,8 @@ #pragma once -#ifndef __OPTIONS_IO_H__ -#define __OPTIONS_IO_H__ +#ifndef OPTIONS_IO_H +#define OPTIONS_IO_H #include "bout/build_config.hxx" @@ -35,7 +35,7 @@ public: OptionsIO(); OptionsIO(std::string filename, FileMode mode = FileMode::replace, bool singleWriteFile = false); - ~OptionsIO(); + virtual ~OptionsIO(); OptionsIO(const OptionsIO&) = delete; OptionsIO(OptionsIO&&) noexcept; OptionsIO& operator=(const OptionsIO&) = delete; @@ -97,4 +97,4 @@ void writeDefaultOutputFile( } // namespace bout -#endif // __OPTIONS_IO_H__ +#endif // OPTIONS_IO_H diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 04bf242d1a..a032fd1629 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -16,16 +16,6 @@ #include namespace bout { - -OptionsADIOS::OptionsADIOS() {} - -OptionsADIOS::OptionsADIOS(std::string filename, FileMode mode, bool singleWriteFile) - : OptionsIO(filename, mode, singleWriteFile) {} - -OptionsADIOS::~OptionsADIOS() = default; -OptionsADIOS::OptionsADIOS(OptionsADIOS&&) noexcept = default; -OptionsADIOS& OptionsADIOS::operator=(OptionsADIOS&&) noexcept = default; - /// Name of the attribute used to track individual variable's time indices constexpr auto current_time_index_name = "current_time_index"; From b95947360ef2f9c5ad37fae3f60e95d7fc8e7e7d Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 5 Dec 2023 16:46:45 -0800 Subject: [PATCH 146/412] options_adios: Clang format Automatic formatting --- include/bout/options_adios.hxx | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx index 81e492c2e7..7bbe421247 100644 --- a/include/bout/options_adios.hxx +++ b/include/bout/options_adios.hxx @@ -19,10 +19,10 @@ namespace bout { class OptionsADIOS : public OptionsIO { public: OptionsADIOS() {} - explicit OptionsADIOS( - const std::string& filename [[maybe_unused]], - [[maybe_unused]] bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, - [[maybe_unused]] bool singleWriteFile = false) {} + explicit OptionsADIOS(const std::string& filename [[maybe_unused]], + [[maybe_unused]] bout::OptionsIO::FileMode mode = + bout::OptionsIO::FileMode::replace, + [[maybe_unused]] bool singleWriteFile = false) {} OptionsADIOS(const OptionsADIOS&) = delete; OptionsADIOS(OptionsADIOS&&) noexcept = default; ~OptionsADIOS() = default; @@ -34,11 +34,14 @@ public: Options read() override { throw BoutException("OptionsADIOS not available\n"); } /// Write options to file - void write([[maybe_unused]] const Options& options, [[maybe_unused]] const std::string& time_dim) override { + void write([[maybe_unused]] const Options& options, + [[maybe_unused]] const std::string& time_dim) override { throw BoutException("OptionsADIOS not available\n"); } - void verifyTimesteps() const override { throw BoutException("OptionsADIOS not available\n"); } + void verifyTimesteps() const override { + throw BoutException("OptionsADIOS not available\n"); + } }; } // namespace bout @@ -61,7 +64,8 @@ public: OptionsADIOS() {} OptionsADIOS(std::string filename, bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, - bool singleWriteFile = false) : OptionsIO(filename, mode, singleWriteFile) {} + bool singleWriteFile = false) + : OptionsIO(filename, mode, singleWriteFile) {} OptionsADIOS(const OptionsADIOS&) = delete; OptionsADIOS(OptionsADIOS&&) noexcept = default; ~OptionsADIOS() = default; From d7e8865abef3a3036cd617f6169b6c9189db812b Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 6 Dec 2023 17:47:53 -0800 Subject: [PATCH 147/412] Use generic Factory for OptionsIO Sorry for the large commit; this touches quite a few places. The OptionsNetCDF and OptionsADIOS classes are now private, so that OptionsIO is now the interface to both. The generic Factory is used to implement OptionsIOFactory, and the "netcdf" and "adios" types are registered in their separate header files. The OptionsIOFactory handles the choice of default section ("restart_files" for restarts, "output" for dump/output files), and sets the default path and prefix. This simplifies both the PhysicsModel and the separate implementations by putting that logic in one place. --- CMakeLists.txt | 4 +- include/bout/bout.hxx | 10 +- include/bout/generic_factory.hxx | 6 +- include/bout/options_adios.hxx | 95 -------------- include/bout/options_io.hxx | 135 +++++++++++--------- include/bout/options_netcdf.hxx | 91 ------------- include/bout/physicsmodel.hxx | 9 +- include/bout/solver.hxx | 6 +- src/bout++.cxx | 4 +- src/mesh/data/gridfromfile.cxx | 4 +- src/physics/physicsmodel.cxx | 25 +--- src/sys/options/options_adios.cxx | 18 ++- src/sys/options/options_adios.hxx | 84 ++++++++++++ src/sys/options/options_io.cxx | 129 ++++--------------- src/sys/options/options_netcdf.cxx | 21 +-- src/sys/options/options_netcdf.hxx | 84 ++++++++++++ tools/pylib/_boutpp_build/bout_options.pxd | 18 +-- tools/pylib/_boutpp_build/boutcpp.pxd.jinja | 2 +- tools/pylib/_boutpp_build/boutpp.pyx.jinja | 4 - 19 files changed, 325 insertions(+), 424 deletions(-) delete mode 100644 include/bout/options_adios.hxx delete mode 100644 include/bout/options_netcdf.hxx create mode 100644 src/sys/options/options_adios.hxx create mode 100644 src/sys/options/options_netcdf.hxx diff --git a/CMakeLists.txt b/CMakeLists.txt index ece5d139e4..ada2e6b4c4 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -148,8 +148,6 @@ set(BOUT_SOURCES ./include/bout/operatorstencil.hxx ./include/bout/options.hxx ./include/bout/options_io.hxx - ./include/bout/options_netcdf.hxx - ./include/bout/options_adios.hxx ./include/bout/optionsreader.hxx ./include/bout/output.hxx ./include/bout/output_bout_types.hxx @@ -344,7 +342,9 @@ set(BOUT_SOURCES ./src/sys/options/options_ini.hxx ./src/sys/options/options_io.cxx ./src/sys/options/options_netcdf.cxx + ./src/sys/options/options_netcdf.hxx ./src/sys/options/options_adios.cxx + ./src/sys/options/options_adios.hxx ./src/sys/optionsreader.cxx ./src/sys/output.cxx ./src/sys/petsclib.cxx diff --git a/include/bout/bout.hxx b/include/bout/bout.hxx index 5e718dde33..d929a19c2f 100644 --- a/include/bout/bout.hxx +++ b/include/bout/bout.hxx @@ -2,8 +2,6 @@ * * @mainpage BOUT++ * - * @version 3.0 - * * @par Description * Framework for the solution of partial differential * equations, in particular fluid models in plasma physics. @@ -33,8 +31,8 @@ * **************************************************************************/ -#ifndef __BOUT_H__ -#define __BOUT_H__ +#ifndef BOUT_H +#define BOUT_H #include "bout/build_config.hxx" @@ -44,7 +42,7 @@ #include "bout/field3d.hxx" #include "bout/globals.hxx" #include "bout/mesh.hxx" -#include "bout/options_netcdf.hxx" +#include "bout/options_io.hxx" #include "bout/output.hxx" #include "bout/smoothing.hxx" // Smoothing functions #include "bout/solver.hxx" @@ -206,4 +204,4 @@ private: */ int BoutFinalise(bool write_settings = true); -#endif // __BOUT_H__ +#endif // BOUT_H diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx index 3a2a63c94c..f7a0692af8 100644 --- a/include/bout/generic_factory.hxx +++ b/include/bout/generic_factory.hxx @@ -1,8 +1,8 @@ /// Base type for factories #pragma once -#ifndef __BOUT_GENERIC_FACTORY_H__ -#define __BOUT_GENERIC_FACTORY_H__ +#ifndef BOUT_GENERIC_FACTORY_H +#define BOUT_GENERIC_FACTORY_H #include "bout/boutexception.hxx" #include "bout/options.hxx" @@ -259,4 +259,4 @@ public: }; }; -#endif // __BOUT_GENERIC_FACTORY_H__ +#endif // BOUT_GENERIC_FACTORY_H diff --git a/include/bout/options_adios.hxx b/include/bout/options_adios.hxx deleted file mode 100644 index 7bbe421247..0000000000 --- a/include/bout/options_adios.hxx +++ /dev/null @@ -1,95 +0,0 @@ - -#pragma once - -#ifndef __OPTIONS_ADIOS_H__ -#define __OPTIONS_ADIOS_H__ - -#include "bout/build_config.hxx" -#include "bout/options.hxx" -#include "bout/options_io.hxx" - -#if !BOUT_HAS_ADIOS - -#include - -#include "bout/boutexception.hxx" - -namespace bout { - -class OptionsADIOS : public OptionsIO { -public: - OptionsADIOS() {} - explicit OptionsADIOS(const std::string& filename [[maybe_unused]], - [[maybe_unused]] bout::OptionsIO::FileMode mode = - bout::OptionsIO::FileMode::replace, - [[maybe_unused]] bool singleWriteFile = false) {} - OptionsADIOS(const OptionsADIOS&) = delete; - OptionsADIOS(OptionsADIOS&&) noexcept = default; - ~OptionsADIOS() = default; - - OptionsADIOS& operator=(const OptionsADIOS&) = delete; - OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default; - - /// Read options from file - Options read() override { throw BoutException("OptionsADIOS not available\n"); } - - /// Write options to file - void write([[maybe_unused]] const Options& options, - [[maybe_unused]] const std::string& time_dim) override { - throw BoutException("OptionsADIOS not available\n"); - } - - void verifyTimesteps() const override { - throw BoutException("OptionsADIOS not available\n"); - } -}; - -} // namespace bout - -#else - -#include -#include - -namespace bout { - -/// Forward declare ADIOS file type so we don't need to depend -/// directly on ADIOS -struct ADIOSStream; - -class OptionsADIOS : public OptionsIO { -public: - // Constructors need to be defined in implementation due to forward - // declaration of ADIOSStream - OptionsADIOS() {} - OptionsADIOS(std::string filename, - bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, - bool singleWriteFile = false) - : OptionsIO(filename, mode, singleWriteFile) {} - OptionsADIOS(const OptionsADIOS&) = delete; - OptionsADIOS(OptionsADIOS&&) noexcept = default; - ~OptionsADIOS() = default; - - OptionsADIOS& operator=(const OptionsADIOS&) = delete; - OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default; - - /// Read options from file - Options read() override; - - /// Write options to file - void write(const Options& options) override { write(options, "t"); } - void write(const Options& options, const std::string& time_dim) override; - - /// Check that all variables with the same time dimension have the - /// same size in that dimension. Throws BoutException if there are - /// any differences, otherwise is silent - void verifyTimesteps() const override; - -private: -}; - -} // namespace bout - -#endif // BOUT_HAS_ADIOS - -#endif // __OPTIONS_ADIOS_H__ diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index d8f26dc8ef..0139609417 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -6,40 +6,29 @@ #define OPTIONS_IO_H #include "bout/build_config.hxx" +#include "bout/generic_factory.hxx" +#include "bout/options.hxx" #include #include -#include "bout/options.hxx" - namespace bout { class OptionsIO { public: - enum class FileMode { - replace, ///< Overwrite file when writing - append ///< Append to file when writing - }; - - enum class Library { ADIOS, NetCDF, Invalid }; - - static const Library defaultIOLibrary = -#if BOUT_HAS_ADIOS - Library::NetCDF; -#elif BOUT_HAS_NETCDF - Library::NetCDF; -#else - Library::Invalid; -#endif + /// No default constructor, as settings are required + OptionsIO() = delete; + + /// Constructor specifies the kind of file, and options to control + /// the name of file, mode of operation etc. + OptionsIO(Options&) {} + + virtual ~OptionsIO() = default; - OptionsIO(); - OptionsIO(std::string filename, FileMode mode = FileMode::replace, - bool singleWriteFile = false); - virtual ~OptionsIO(); OptionsIO(const OptionsIO&) = delete; - OptionsIO(OptionsIO&&) noexcept; + OptionsIO(OptionsIO&&) noexcept = default; OptionsIO& operator=(const OptionsIO&) = delete; - OptionsIO& operator=(OptionsIO&&) noexcept; + OptionsIO& operator=(OptionsIO&&) noexcept = default; /// Read options from file virtual Options read() = 0; @@ -54,46 +43,72 @@ public: /// ADIOS: Indicate completion of an output step. virtual void verifyTimesteps() const = 0; - /// ADIOS: close file at the end of write(). NetCDF: no effect. - /// restart file must have this true if using ADIOS - //void setSingleWriteFile(const bool flag) { singleWriteFile = flag; }; + static std::unique_ptr create(const std::string& file); +}; + +class OptionsIOFactory : public Factory { +public: + static constexpr auto type_name = "OptionsIO"; + static constexpr auto section_name = "io"; + static constexpr auto option_name = "type"; + static constexpr auto default_type = +#if BOUT_HAS_NETCDF + "netcdf"; +#elif BOUT_HAS_ADIOS + "adios"; +#else + "invalid"; +#endif -protected: - /// Name of the file on disk - std::string filename; - /// How to open the file for writing - FileMode file_mode{FileMode::replace}; - bool singleWriteFile = false; + /// Create a restart file, configured with options (if given), + /// or root "restart_files" section. + /// + /// Options: + /// - "type" The type of file e.g "netcdf" or "adios" + /// - "file" Name of the file. Default is /.[type-dependent] + /// - "path" Path to restart files. Default is root "datadir" option, + /// that defaults to "data" + /// - "prefix" Default is "BOUT.restart" + ReturnType createRestart(Options* optionsptr = nullptr) const; + + /// Create an output file for writing time history. + /// Configure with options (if given), or root "output" section. + /// + /// Options: + /// - "type" The type of file e.g "netcdf" or "adios" + /// - "file" Name of the file. Default is /.[type] + /// - "path" Path to output files. Default is root "datadir" option, + /// that defaults to "data" + /// - "prefix" Default is "BOUT.dmp" + /// - "append" Append to existing file? Default is root "append" option, + /// that defaults to false. + ReturnType createOutput(Options* optionsptr = nullptr) const; + + /// Create a single file (e.g. mesh file) of the default type + ReturnType createFile(const std::string& file) const; }; -std::shared_ptr -OptionsIOFactory(std::string filename, - OptionsIO::FileMode mode = OptionsIO::FileMode::replace, - const OptionsIO::Library library = OptionsIO::defaultIOLibrary, - const bool singleWriteFile = false); - -OptionsIO::Library getIOLibrary(Options& options); - -/// Name of the directory for restart files -std::string getRestartDirectoryName(Options& options); -/// Name of the restart file on this rank -std::string getRestartFilename(Options& options, const OptionsIO::Library library); -/// Name of the restart file on \p rank -std::string getRestartFilename(Options& options, int rank, - const OptionsIO::Library library); -/// Name of the main output file on this rank -std::string getOutputFilename(Options& options, const OptionsIO::Library library); -/// Name of the main output file on \p rank -std::string getOutputFilename(Options& options, int rank, - const OptionsIO::Library library); -/// Write `Options::root()` to the main output file, overwriting any -/// existing files -void writeDefaultOutputFile( - const OptionsIO::Library library = OptionsIO::defaultIOLibrary); -/// Write \p options to the main output file, overwriting any existing -/// files -void writeDefaultOutputFile( - Options& options, const OptionsIO::Library library = OptionsIO::defaultIOLibrary); +/// Simpler name for Factory registration helper class +/// +/// Usage: +/// +/// #include +/// namespace { +/// RegisterOptionsIO registeroptionsiomine("myoptionsio"); +/// } +template +using RegisterOptionsIO = OptionsIOFactory::RegisterInFactory; + +/// Simpler name for indicating that an OptionsIO implementation +/// is unavailable. +/// +/// Usage: +/// +/// namespace { +/// RegisterUnavailableOptionsIO +/// unavailablemyoptionsio("myoptiosio", "BOUT++ was not configured with MyOptionsIO"); +/// } +using RegisterUnavailableOptionsIO = OptionsIOFactory::RegisterUnavailableInFactory; } // namespace bout diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx deleted file mode 100644 index 5cbbf7e5fc..0000000000 --- a/include/bout/options_netcdf.hxx +++ /dev/null @@ -1,91 +0,0 @@ - -#pragma once - -#ifndef __OPTIONS_NETCDF_H__ -#define __OPTIONS_NETCDF_H__ - -#include "bout/build_config.hxx" - -#include "bout/options.hxx" -#include "bout/options_io.hxx" - -#if !BOUT_HAS_NETCDF || BOUT_HAS_LEGACY_NETCDF - -#include - -#include "bout/boutexception.hxx" -#include "bout/options.hxx" - -namespace bout { - -class OptionsNetCDF : public OptionsIO { -public: - OptionsNetCDF(const std::string& filename, - bout::OptionsIO::FileMode mode = bout::OptionsIO::FileMode::replace, - bool singleWriteFile = false) {} - OptionsNetCDF(const OptionsNetCDF&) = default; - OptionsNetCDF(OptionsNetCDF&&) = default; - OptionsNetCDF& operator=(const OptionsNetCDF&) = default; - OptionsNetCDF& operator=(OptionsNetCDF&&) = default; - - /// Read options from file - Options read() { throw BoutException("OptionsNetCDF not available\n"); } - - /// Write options to file - void write(const Options& options, const std::string& time_dim) { - throw BoutException("OptionsNetCDF not available\n"); - } - - void verifyTimesteps() const { throw BoutException("OptionsADIOS not available\n"); } -}; - -} // namespace bout - -#else - -#include -#include - -/// Forward declare netCDF file type so we don't need to depend -/// directly on netCDF -namespace netCDF { -class NcFile; -} - -namespace bout { - -class OptionsNetCDF : public OptionsIO { -public: - // Constructors need to be defined in implementation due to forward - // declaration of NcFile - OptionsNetCDF(); - OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace, - bool singleWriteFile = false); - ~OptionsNetCDF(); - OptionsNetCDF(const OptionsNetCDF&) = delete; - OptionsNetCDF(OptionsNetCDF&&) noexcept; - OptionsNetCDF& operator=(const OptionsNetCDF&) = delete; - OptionsNetCDF& operator=(OptionsNetCDF&&) noexcept; - - /// Read options from file - Options read(); - - /// Write options to file - void write(const Options& options) { write(options, "t"); } - void write(const Options& options, const std::string& time_dim); - - /// Check that all variables with the same time dimension have the - /// same size in that dimension. Throws BoutException if there are - /// any differences, otherwise is silent - void verifyTimesteps() const; - -private: - /// Pointer to netCDF file so we don't introduce direct dependence - std::unique_ptr data_file; -}; - -} // namespace bout - -#endif - -#endif // __OPTIONS_NETCDF_H__ diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index eb1bae8ae1..e0f046eb1f 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -88,9 +88,6 @@ public: void add(Vector2D* value, const std::string& name, bool save_repeat = false); void add(Vector3D* value, const std::string& name, bool save_repeat = false); - /// Write stored data to file immediately - bool write(); - private: /// Helper struct to save enough information so that we can save an /// object to file later @@ -148,7 +145,7 @@ public: bout::DataFileFacade restart{}; /*! - * Initialse the model, calling the init() and postInit() methods + * Initialise the model, calling the init() and postInit() methods * * Note: this is usually only called by the Solver */ @@ -383,13 +380,13 @@ private: /// State for outputs Options output_options; /// File to write the outputs to - std::shared_ptr output_file; + std::unique_ptr output_file; /// Should we write output files bool output_enabled{true}; /// Stores the state for restarting Options restart_options; /// File to write the restart-state to - std::shared_ptr restart_file; + std::unique_ptr restart_file; /// Should we write restart files bool restart_enabled{true}; /// Split operator model? diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index 8a3f07c27a..ef7cbe63eb 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -33,8 +33,8 @@ * **************************************************************************/ -#ifndef __SOLVER_H__ -#define __SOLVER_H__ +#ifndef SOLVER_H +#define SOLVER_H #include "bout/build_config.hxx" @@ -597,4 +597,4 @@ private: BoutReal output_timestep; }; -#endif // __SOLVER_H__ +#endif // SOLVER_H diff --git a/src/bout++.cxx b/src/bout++.cxx index a42b0dcff8..1dc93dc76d 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -4,9 +4,9 @@ * Adapted from the BOUT code by B.Dudson, University of York, Oct 2007 * ************************************************************************** - * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu + * Copyright 2010-2023 BOUT++ contributors * - * Contact Ben Dudson, bd512@york.ac.uk + * Contact Ben Dudson, dudson2@llnl.gov * * This file is part of BOUT++. * diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index 7e875bd109..aa66b145c7 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -6,7 +6,7 @@ #include #include #include -#include +#include #include #include #include @@ -14,7 +14,7 @@ #include GridFile::GridFile(std::string gridfilename) - : GridDataSource(true), data(bout::OptionsNetCDF(gridfilename).read()), + : GridDataSource(true), data(bout::OptionsIO::create(gridfilename)->read()), filename(std::move(gridfilename)) { TRACE("GridFile constructor"); diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx index 538851f4cb..9f538895ed 100644 --- a/src/physics/physicsmodel.cxx +++ b/src/physics/physicsmodel.cxx @@ -58,18 +58,6 @@ void DataFileFacade::add(Vector3D* value, const std::string& name, bool save_rep add(value->y, name_prefix + "y"s, save_repeat); add(value->z, name_prefix + "z"s, save_repeat); } - -bool DataFileFacade::write() { - for (const auto& item : data) { - bout::utils::visit(bout::OptionsConversionVisitor{Options::root(), item.name}, - item.value); - if (item.repeat) { - Options::root()[item.name].attributes["time_dimension"] = "t"; - } - } - writeDefaultOutputFile(); - return true; -} } // namespace bout PhysicsModel::PhysicsModel() @@ -81,21 +69,12 @@ PhysicsModel::PhysicsModel() .withDefault(true)) { - bout::OptionsIO::Library iolibrary = bout::getIOLibrary(Options::root()); if (output_enabled) { - std::string outputFileName = bout::getOutputFilename(Options::root(), iolibrary); - auto mode = Options::root()["append"] - .doc("Add output data to existing (dump) files?") - .withDefault(false) - ? bout::OptionsIO::FileMode::append - : bout::OptionsIO::FileMode::replace; - output_file = bout::OptionsIOFactory(outputFileName, mode, iolibrary); + output_file = bout::OptionsIOFactory::getInstance().createOutput(); } if (restart_enabled) { - std::string restartFileName = bout::getRestartFilename(Options::root(), iolibrary); - restart_file = bout::OptionsIOFactory( - restartFileName, bout::OptionsIO::FileMode::replace, iolibrary, true); + restart_file = bout::OptionsIOFactory::getInstance().createRestart(); } } diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index a032fd1629..fd8e978091 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -2,8 +2,8 @@ #if BOUT_HAS_ADIOS +#include "options_adios.hxx" #include "bout/adios_object.hxx" -#include "bout/options_adios.hxx" #include "bout/bout.hxx" #include "bout/globals.hxx" @@ -19,6 +19,22 @@ namespace bout { /// Name of the attribute used to track individual variable's time indices constexpr auto current_time_index_name = "current_time_index"; +OptionsADIOS::OptionsADIOS(Options& options) { + if (options["file"].doc("File name. Defaults to /.pb").isSet()) { + filename = options["file"].as(); + } else { + // Both path and prefix must be set + filename = fmt::format("{}/{}.bp", options["path"].as(), + options["prefix"].as()); + } + + file_mode = (options["append"].doc("Append to existing file?").withDefault(false)) + ? FileMode::append + : FileMode::replace; + + singleWriteFile = options["singleWriteFile"].withDefault(false); +} + template bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, const std::string& type, Options& result) { diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx new file mode 100644 index 0000000000..2460dfd10c --- /dev/null +++ b/src/sys/options/options_adios.hxx @@ -0,0 +1,84 @@ + +#pragma once + +#ifndef OPTIONS_ADIOS_H +#define OPTIONS_ADIOS_H + +#include "bout/build_config.hxx" +#include "bout/options.hxx" +#include "bout/options_io.hxx" + +#if !BOUT_HAS_ADIOS + +namespace { +bout::RegisterUnavailableOptionsIO + registerunavailableoptionsadios("adios", "BOUT++ was not configured with ADIOS2"); +} + +#else + +#include +#include + +namespace bout { + +/// Forward declare ADIOS file type so we don't need to depend +/// directly on ADIOS +struct ADIOSStream; + +class OptionsADIOS : public OptionsIO { +public: + // Constructors need to be defined in implementation due to forward + // declaration of ADIOSStream + OptionsADIOS() = delete; + + /// Create an OptionsADIOS + /// + /// Options: + /// - "file" The name of the file + /// If not set then "path" and "prefix" must be set, + /// and file is set to {path}/{prefix}.bp + /// - "append" + /// - "singleWriteFile" + OptionsADIOS(Options& options); + + OptionsADIOS(const OptionsADIOS&) = delete; + OptionsADIOS(OptionsADIOS&&) noexcept = default; + ~OptionsADIOS() = default; + + OptionsADIOS& operator=(const OptionsADIOS&) = delete; + OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default; + + /// Read options from file + Options read() override; + + /// Write options to file + void write(const Options& options) override { write(options, "t"); } + void write(const Options& options, const std::string& time_dim) override; + + /// Check that all variables with the same time dimension have the + /// same size in that dimension. Throws BoutException if there are + /// any differences, otherwise is silent + void verifyTimesteps() const override; + +private: + enum class FileMode { + replace, ///< Overwrite file when writing + append ///< Append to file when writing + }; + + /// Name of the file on disk + std::string filename; + /// How to open the file for writing + FileMode file_mode{FileMode::replace}; + bool singleWriteFile = false; +}; + +namespace { +RegisterOptionsIO registeroptionsadios("adios"); +} + +} // namespace bout + +#endif // BOUT_HAS_ADIOS +#endif // OPTIONS_ADIOS_H diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 514307ec59..0d25591db7 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -1,118 +1,41 @@ -#include "bout/build_config.hxx" - #include "bout/options_io.hxx" -#include "bout/bout.hxx" -#include "bout/globals.hxx" -#include "bout/mesh.hxx" -#include "bout/sys/timer.hxx" - -#include -#include -#include - -#include "bout/options_adios.hxx" -#include "bout/options_netcdf.hxx" +#include "options_adios.hxx" +#include "options_netcdf.hxx" namespace bout { - -OptionsIO::OptionsIO() {} - -OptionsIO::OptionsIO(std::string filename, FileMode mode, bool singleWriteFile) - : filename(std::move(filename)), file_mode(mode), singleWriteFile(singleWriteFile) {} - -OptionsIO::~OptionsIO() = default; -OptionsIO::OptionsIO(OptionsIO&&) noexcept = default; -OptionsIO& OptionsIO::operator=(OptionsIO&&) noexcept = default; - -OptionsIO::Library getIOLibrary(Options& options) { - if (options["iolibrary"].isSet()) { - // Solver-specific IO library - std::string iolib = options["iolibrary"]; - std::transform(iolib.begin(), iolib.end(), iolib.begin(), ::tolower); - if (iolib == "adios") - return OptionsIO::Library::ADIOS; - else if (iolib == "netcdf") - return OptionsIO::Library::NetCDF; - else - return OptionsIO::Library::Invalid; - } else { - return OptionsIO::defaultIOLibrary; - } +std::unique_ptr OptionsIO::create(const std::string& file) { + return OptionsIOFactory::getInstance().createFile(file); } -std::shared_ptr OptionsIOFactory(std::string filename, - OptionsIO::FileMode mode, - const OptionsIO::Library library, - const bool singleWriteFile) { - if (library == OptionsIO::Library::ADIOS) { - return std::make_shared(OptionsADIOS(filename, mode, singleWriteFile)); - } else if (library == OptionsIO::Library::NetCDF) { - return std::make_shared( - OptionsNetCDF(filename, mode, singleWriteFile)); - } else { - return nullptr; - } -} +OptionsIOFactory::ReturnType OptionsIOFactory::createRestart(Options* optionsptr) const { + Options& options = optionsptr ? *optionsptr : Options::root()["restart_files"]; -std::string getRestartDirectoryName(Options& options) { - if (options["restartdir"].isSet()) { - // Solver-specific restart directory - return options["restartdir"].withDefault("data"); - } - // Use the root data directory - return options["datadir"].withDefault("data"); + // Set defaults + options["path"].overrideDefault( + Options::root()["datadir"].withDefault("data")); + options["prefix"].overrideDefault("BOUT.restart"); + options["append"].overrideDefault(false); + options["singleWriteFile"].overrideDefault(true); + return create(getType(&options), options); } -std::string getRestartFilename(Options& options, const OptionsIO::Library library) { - return getRestartFilename(options, BoutComm::rank(), library); -} - -std::string getRestartFilename(Options& options, int rank, - const OptionsIO::Library library) { - if (library == OptionsIO::Library::ADIOS) - return fmt::format("{}/BOUT.restart.bp", bout::getRestartDirectoryName(options)); - else if (library == OptionsIO::Library::NetCDF) - return fmt::format("{}/BOUT.restart.{}.nc", bout::getRestartDirectoryName(options), - rank); - else - return fmt::format("{}/BOUT.restart.{}.data", bout::getRestartDirectoryName(options), - rank); -} - -std::string getOutputFilename(Options& options, const OptionsIO::Library library) { - return getOutputFilename(options, BoutComm::rank(), library); -} - -std::string getOutputFilename(Options& options, int rank, - const OptionsIO::Library library) { - if (library == OptionsIO::Library::ADIOS) - return fmt::format("{}/BOUT.dmp.bp", - options["datadir"].withDefault("data")); - else if (library == OptionsIO::Library::NetCDF) - return fmt::format("{}/BOUT.dmp.{}.nc", - options["datadir"].withDefault("data"), rank); - else - return fmt::format("{}/BOUT.dmp.{}.data", - options["datadir"].withDefault("data"), rank); -} +OptionsIOFactory::ReturnType OptionsIOFactory::createOutput(Options* optionsptr) const { + Options& options = optionsptr ? *optionsptr : Options::root()["output"]; -void writeDefaultOutputFile(const OptionsIO::Library library) { - writeDefaultOutputFile(Options::root(), library); + // Set defaults + options["path"].overrideDefault( + Options::root()["datadir"].withDefault("data")); + options["prefix"].overrideDefault("BOUT.dmp"); + options["append"].overrideDefault(Options::root()["append"] + .doc("Add output data to existing (dump) files?") + .withDefault(false)); + return create(getType(&options), options); } -void writeDefaultOutputFile(Options& options, const OptionsIO::Library library) { - bout::experimental::addBuildFlagsToOptions(options); - bout::globals::mesh->outputVars(options); - auto mode = options["append"] - .doc("Add output data to existing (dump) files?") - .withDefault(false) - ? bout::OptionsIO::FileMode::append - : bout::OptionsIO::FileMode::replace; - // Note: `options` contains the data to write. - // Get the output file from the `Options::root()` input settings. - auto io = OptionsIOFactory(getOutputFilename(Options::root(), library), mode, library); - io->write(options); +OptionsIOFactory::ReturnType OptionsIOFactory::createFile(const std::string& file) const { + Options options{{"file", file}}; + return create(getDefaultType(), options); } } // namespace bout diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx index 0262e0cbbd..eda2b0bfbd 100644 --- a/src/sys/options/options_netcdf.cxx +++ b/src/sys/options/options_netcdf.cxx @@ -2,7 +2,7 @@ #if BOUT_HAS_NETCDF && !BOUT_HAS_LEGACY_NETCDF -#include "bout/options_netcdf.hxx" +#include "options_netcdf.hxx" #include "bout/bout.hxx" #include "bout/globals.hxx" @@ -643,14 +643,19 @@ std::vector verifyTimesteps(const NcGroup& group) { namespace bout { -OptionsNetCDF::OptionsNetCDF() : data_file(nullptr) {} - -OptionsNetCDF::OptionsNetCDF(std::string filename, FileMode mode, bool singleWriteFile) - : OptionsIO(filename, mode, singleWriteFile), data_file(nullptr) {} +OptionsNetCDF::OptionsNetCDF(Options& options) : OptionsIO(options) { + if (options["file"].doc("File name. Defaults to /..nc").isSet()) { + filename = options["file"].as(); + } else { + // Both path and prefix must be set + filename = fmt::format("{}/{}.{}.nc", options["path"].as(), + options["prefix"].as(), BoutComm::rank()); + } -OptionsNetCDF::~OptionsNetCDF() = default; -OptionsNetCDF::OptionsNetCDF(OptionsNetCDF&&) noexcept = default; -OptionsNetCDF& OptionsNetCDF::operator=(OptionsNetCDF&&) noexcept = default; + file_mode = (options["append"].doc("Append to existing file?").withDefault(false)) + ? FileMode::append + : FileMode::replace; +} void OptionsNetCDF::verifyTimesteps() const { NcFile dataFile(filename, NcFile::read); diff --git a/src/sys/options/options_netcdf.hxx b/src/sys/options/options_netcdf.hxx new file mode 100644 index 0000000000..8f195c9d92 --- /dev/null +++ b/src/sys/options/options_netcdf.hxx @@ -0,0 +1,84 @@ + +#pragma once + +#ifndef OPTIONS_NETCDF_H +#define OPTIONS_NETCDF_H + +#include "bout/build_config.hxx" + +#include "bout/options.hxx" +#include "bout/options_io.hxx" + +#if !BOUT_HAS_NETCDF || BOUT_HAS_LEGACY_NETCDF + +namespace { +RegisterUnavailableOptionsIO + registerunavailableoptionsnetcdf("netcdf", "BOUT++ was not configured with NetCDF"); +} + +#else + +#include +#include +#include + +namespace bout { + +class OptionsNetCDF : public OptionsIO { +public: + // Constructors need to be defined in implementation due to forward + // declaration of NcFile + OptionsNetCDF() = delete; + + /// Create an OptionsNetCDF + /// + /// Options: + /// - "file" The name of the file + /// If not set then "path" and "prefix" options must be set, + /// and file is set to {path}/{prefix}.{rank}.nc + /// - "append" File mode, default is false + OptionsNetCDF(Options& options); + + ~OptionsNetCDF() {} + + OptionsNetCDF(const OptionsNetCDF&) = delete; + OptionsNetCDF(OptionsNetCDF&&) noexcept = default; + OptionsNetCDF& operator=(const OptionsNetCDF&) = delete; + OptionsNetCDF& operator=(OptionsNetCDF&&) noexcept = default; + + /// Read options from file + Options read(); + + /// Write options to file + void write(const Options& options) { write(options, "t"); } + void write(const Options& options, const std::string& time_dim); + + /// Check that all variables with the same time dimension have the + /// same size in that dimension. Throws BoutException if there are + /// any differences, otherwise is silent + void verifyTimesteps() const; + +private: + enum class FileMode { + replace, ///< Overwrite file when writing + append ///< Append to file when writing + }; + + /// Pointer to netCDF file so we don't introduce direct dependence + std::unique_ptr data_file = nullptr; + + /// Name of the file on disk + std::string filename; + /// How to open the file for writing + FileMode file_mode{FileMode::replace}; +}; + +namespace { +RegisterOptionsIO registeroptionsnetcdf("netcdf"); +} + +} // namespace bout + +#endif + +#endif // OPTIONS_NETCDF_H diff --git a/tools/pylib/_boutpp_build/bout_options.pxd b/tools/pylib/_boutpp_build/bout_options.pxd index ba5e64c8e3..550bfc01e1 100644 --- a/tools/pylib/_boutpp_build/bout_options.pxd +++ b/tools/pylib/_boutpp_build/bout_options.pxd @@ -8,20 +8,10 @@ cdef extern from "boutexception_helper.hxx": cdef void raise_bout_py_error() -cdef extern from "bout/options_netcdf.hxx" namespace "bout": - cdef void writeDefaultOutputFile(); - cdef void writeDefaultOutputFile(Options& options); - cppclass OptionsNetCDF: - enum FileMode: - replace - append - OptionsNetCDF() except +raise_bout_py_error - OptionsNetCDF(string filename) except +raise_bout_py_error - OptionsNetCDF(string filename, FileMode mode) except +raise_bout_py_error - OptionsNetCDF(const OptionsNetCDF&); - OptionsNetCDF(OptionsNetCDF&&); - OptionsNetCDF& operator=(const OptionsNetCDF&); - OptionsNetCDF& operator=(OptionsNetCDF&&); +cdef extern from "bout/options_io.hxx" namespace "bout": + cppclass OptionsIO: + @staticmethod + OptionsIO * create(string filename) Options read(); void write(const Options& options); void write(const Options& options, string time_dim); diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja index c94fd14a17..28633cad95 100644 --- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja +++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja @@ -5,7 +5,7 @@ from libcpp.memory cimport unique_ptr from libcpp.string cimport string cimport resolve_enum as benum -from bout_options cimport Options, OptionsReader, OptionsNetCDF, writeDefaultOutputFile +from bout_options cimport Options, OptionsReader, OptionsIO cdef extern from "boutexception_helper.hxx": cdef void raise_bout_py_error() diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja index 657e2f28c1..a8c027475a 100644 --- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja +++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja @@ -1723,10 +1723,6 @@ cdef class Options: del self.cobj self.cobj = NULL - -def writeDefaultOutputFile(options: Options): - c.writeDefaultOutputFile(deref(options.cobj)) - def print(*args, sep=" ", end="\n"): _print(sep.join([str(a) for a in args]) + end) From ffc1e94ba71c7982f1329cc95a5fb5e4e9143bb8 Mon Sep 17 00:00:00 2001 From: Norbert Podhorszki Date: Thu, 7 Dec 2023 08:37:05 -0500 Subject: [PATCH 148/412] adios2 build - turn off building testing, pass to cmake ADIOS2_ROOT instead of ADIOS2_DIR --- .build_adios2_for_ci.sh | 2 +- .github/workflows/tests.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.build_adios2_for_ci.sh b/.build_adios2_for_ci.sh index 90f4aae29a..f636252a94 100755 --- a/.build_adios2_for_ci.sh +++ b/.build_adios2_for_ci.sh @@ -26,7 +26,7 @@ if test $BUILD_ADIOS2 ; then -DADIOS2_BUILD_EXAMPLES=OFF \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_POSITION_INDEPENDENT_CODE=ON \ - -DADIOS2_BUILD_TESTING=OFF \ + -DBUILD_TESTING=OFF \ -DADIOS2_USE_SST=OFF \ -DADIOS2_USE_MGARD=OFF \ -DADIOS2_USE_HDF5=OFF \ diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7e4df9abf8..b79144c10a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -49,7 +49,7 @@ jobs: -DBOUT_USE_SUNDIALS=ON -DBOUT_USE_ADIOS2=ON -DBOUT_ENABLE_PYTHON=ON - -DADIOS2_DIR=/home/runner/local/adios2 + -DADIOS2_ROOT=/home/runner/local/adios2 -DSUNDIALS_ROOT=/home/runner/local -DPETSC_DIR=/home/runner/local/petsc -DSLEPC_DIR=/home/runner/local/slepc" From 3b2abb8cae8d28372e12a59beebe3ad5580797e1 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 7 Dec 2023 13:52:50 -0800 Subject: [PATCH 149/412] Fix compilation of OptionsADIOS Now tested with ADIOS enabled. --- src/sys/options/options_adios.cxx | 2 +- src/sys/options/options_adios.hxx | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index fd8e978091..23abcc74bc 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -19,7 +19,7 @@ namespace bout { /// Name of the attribute used to track individual variable's time indices constexpr auto current_time_index_name = "current_time_index"; -OptionsADIOS::OptionsADIOS(Options& options) { +OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) { if (options["file"].doc("File name. Defaults to /.pb").isSet()) { filename = options["file"].as(); } else { diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx index 2460dfd10c..eddb3976ff 100644 --- a/src/sys/options/options_adios.hxx +++ b/src/sys/options/options_adios.hxx @@ -53,7 +53,6 @@ public: Options read() override; /// Write options to file - void write(const Options& options) override { write(options, "t"); } void write(const Options& options, const std::string& time_dim) override; /// Check that all variables with the same time dimension have the From 180908651cd8a84fc579e6bc6b1c3ba4043061c6 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 7 Dec 2023 13:54:57 -0800 Subject: [PATCH 150/412] Add BOUT_DOWNLOAD_ADIOS CMake flag If configured with `-DBOUT_DOWNLOAD_ADIOS=ON`, CMake will download ADIOS2 from github, configure and build it with BOUT++. --- cmake/SetupBOUTThirdParty.cmake | 36 +++++++++++++++++++++++++++------ 1 file changed, 30 insertions(+), 6 deletions(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index b5470a2f46..e1d6f00cb4 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -156,6 +156,7 @@ option(BOUT_USE_NETCDF "Enable support for NetCDF output" ON) option(BOUT_DOWNLOAD_NETCDF_CXX4 "Download and build netCDF-cxx4" OFF) if (BOUT_USE_NETCDF) if (BOUT_DOWNLOAD_NETCDF_CXX4) + message(STATUS "Downloading and configuring NetCDF-cxx4") include(FetchContent) FetchContent_Declare( netcdf-cxx4 @@ -186,14 +187,37 @@ message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}") set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF}) option(BOUT_USE_ADIOS "Enable support for ADIOS output" ON) +option(BOUT_DOWNLOAD_ADIOS "Download and build ADIOS2" OFF) if (BOUT_USE_ADIOS) - find_package(ADIOS2) - if (ADIOS2_FOUND) - ENABLE_LANGUAGE(C) - find_package(MPI REQUIRED COMPONENTS C) - target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C) + if (BOUT_DOWNLOAD_ADIOS) + message(STATUS "Downloading and configuring ADIOS2") + include(FetchContent) + FetchContent_Declare( + adios2 + GIT_REPOSITORY https://github.com/ornladios/ADIOS2.git + GIT_TAG origin/master + GIT_SHALLOW 1 + ) + set(ADIOS2_USE_MPI ON CACHE BOOL "" FORCE) + set(ADIOS2_USE_Fortran OFF CACHE BOOL "" FORCE) + set(ADIOS2_USE_Python OFF CACHE BOOL "" FORCE) + set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "" FORCE) + # Disable testing, or ADIOS will try to find or install GTEST + set(BUILD_TESTING OFF CACHE BOOL "" FORCE) + # Note: SST requires but doesn't check at configure time + set(ADIOS2_USE_SST OFF CACHE BOOL "" FORCE) + FetchContent_MakeAvailable(adios2) + target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi) + message(STATUS "ADIOS2 done configuring") else() - set(BOUT_USE_ADIOS OFF) + find_package(ADIOS2) + if (ADIOS2_FOUND) + ENABLE_LANGUAGE(C) + find_package(MPI REQUIRED COMPONENTS C) + target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C) + else() + set(BOUT_USE_ADIOS OFF) + endif() endif() endif() message(STATUS "ADIOS support: ${BOUT_USE_ADIOS}") From 1399e204f8f8b67dd750efe65e70ef4c5480b34e Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 7 Dec 2023 17:36:16 -0800 Subject: [PATCH 151/412] test_options_netcdf: Change to OptionsIO interface --- include/bout/options_io.hxx | 1 + src/sys/options/options_io.cxx | 5 ++ tests/unit/sys/test_options_netcdf.cxx | 78 +++++++++++++------------- 3 files changed, 46 insertions(+), 38 deletions(-) diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 0139609417..9350c252ff 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -44,6 +44,7 @@ public: virtual void verifyTimesteps() const = 0; static std::unique_ptr create(const std::string& file); + static std::unique_ptr create(Options& config); }; class OptionsIOFactory : public Factory { diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 0d25591db7..13a8c9890a 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -8,6 +8,11 @@ std::unique_ptr OptionsIO::create(const std::string& file) { return OptionsIOFactory::getInstance().createFile(file); } +std::unique_ptr OptionsIO::create(Options& config) { + auto& factory = OptionsIOFactory::getInstance(); + return factory.create(factory.getType(&config), config); +} + OptionsIOFactory::ReturnType OptionsIOFactory::createRestart(Options* optionsptr) const { Options& options = optionsptr ? *optionsptr : Options::root()["restart_files"]; diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx index b086043822..3f32b0b7d9 100644 --- a/tests/unit/sys/test_options_netcdf.cxx +++ b/tests/unit/sys/test_options_netcdf.cxx @@ -9,9 +9,9 @@ #include "test_extras.hxx" #include "bout/field3d.hxx" #include "bout/mesh.hxx" -#include "bout/options_netcdf.hxx" +#include "bout/options_io.hxx" -using bout::OptionsNetCDF; +using bout::OptionsIO; #include @@ -39,11 +39,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteInt) { options["test"] = 42; // Write the file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read again - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["test"], 42); } @@ -54,11 +54,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteString) { options["test"] = std::string{"hello"}; // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["test"], std::string("hello")); } @@ -69,11 +69,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteField2D) { options["test"] = Field2D(1.0); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); Field2D value = data["test"].as(bout::globals::mesh); @@ -87,11 +87,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteField3D) { options["test"] = Field3D(2.4); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); Field3D value = data["test"].as(bout::globals::mesh); @@ -106,11 +106,11 @@ TEST_F(OptionsNetCDFTest, Groups) { options["test"]["key"] = 42; // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["test"]["key"], 42); } @@ -121,11 +121,11 @@ TEST_F(OptionsNetCDFTest, AttributeInt) { options["test"].attributes["thing"] = 4; // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["test"].attributes["thing"].as(), 4); } @@ -136,11 +136,11 @@ TEST_F(OptionsNetCDFTest, AttributeBoutReal) { options["test"].attributes["thing"] = 3.14; // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_DOUBLE_EQ(data["test"].attributes["thing"].as(), 3.14); } @@ -151,11 +151,11 @@ TEST_F(OptionsNetCDFTest, AttributeString) { options["test"].attributes["thing"] = "hello"; // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["test"].attributes["thing"].as(), "hello"); } @@ -165,11 +165,11 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellCentre) { options["f2d"] = Field2D(2.0); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), toString(CELL_CENTRE)); @@ -181,11 +181,11 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellYLow) { options["f2d"] = Field2D(2.0, mesh_staggered).setLocation(CELL_YLOW); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), toString(CELL_YLOW)); @@ -197,11 +197,11 @@ TEST_F(OptionsNetCDFTest, Field3DWriteCellCentre) { options["f3d"] = Field3D(2.0); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), toString(CELL_CENTRE)); @@ -213,11 +213,11 @@ TEST_F(OptionsNetCDFTest, Field3DWriteCellYLow) { options["f3d"] = Field3D(2.0, mesh_staggered).setLocation(CELL_YLOW); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), toString(CELL_YLOW)); @@ -235,11 +235,11 @@ TEST_F(OptionsNetCDFTest, FieldPerpWriteCellCentre) { fperp.getMesh()->getXcomm(); // Write file - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } // Read file - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_EQ(data["fperp"].attributes["cell_location"].as(), toString(CELL_CENTRE)); @@ -252,10 +252,10 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) { options["thing1"] = 1.0; options["thing1"].attributes["time_dimension"] = "t"; - OptionsNetCDF(filename).write(options); + OptionsIO::create(filename).write(options); } - EXPECT_NO_THROW(OptionsNetCDF(filename).verifyTimesteps()); + EXPECT_NO_THROW(OptionsIO::create(filename).verifyTimesteps()); { Options options; @@ -265,10 +265,12 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) { options["thing2"] = 3.0; options["thing2"].attributes["time_dimension"] = "t"; - OptionsNetCDF(filename, OptionsNetCDF::FileMode::append).write(options); + Optiond config{{"type", "netcdf"}, {"file", filename}, {"append", true}}; + + OptionsIO::create(config).write(options); } - EXPECT_THROW(OptionsNetCDF(filename).verifyTimesteps(), BoutException); + EXPECT_THROW(OptionsIO::create(filename).verifyTimesteps(), BoutException); } TEST_F(OptionsNetCDFTest, WriteTimeDimension) { @@ -278,10 +280,10 @@ TEST_F(OptionsNetCDFTest, WriteTimeDimension) { options["thing2"].assignRepeat(2.0, "t2"); // non-default // Only write non-default time dim - OptionsNetCDF(filename).write(options, "t2"); + OptionsIO::create(filename).write(options, "t2"); } - Options data = OptionsNetCDF(filename).read(); + Options data = OptionsIO::create(filename).read(); EXPECT_FALSE(data.isSet("thing1")); EXPECT_TRUE(data.isSet("thing2")); @@ -297,12 +299,12 @@ TEST_F(OptionsNetCDFTest, WriteMultipleTimeDimensions) { options["thing4_t2"].assignRepeat(2.0, "t2"); // non-default // Write the non-default time dim twice - OptionsNetCDF(filename).write(options, "t2"); - OptionsNetCDF(filename).write(options, "t2"); - OptionsNetCDF(filename).write(options, "t"); + OptionsIO::create(filename).write(options, "t2"); + OptionsIO::create(filename).write(options, "t2"); + OptionsIO::create(filename).write(options, "t"); } - EXPECT_NO_THROW(OptionsNetCDF(filename).verifyTimesteps()); + EXPECT_NO_THROW(OptionsIO::create(filename).verifyTimesteps()); } #endif // BOUT_HAS_NETCDF From f62b5e5bafa3877d138e14a99cb8b8dc3dab82e5 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 8 Dec 2023 11:25:26 -0800 Subject: [PATCH 152/412] Adding documentation and fixing tests Some documentation in the comments, and in the manual. --- include/bout/options_io.hxx | 64 +++++++++++++++- manual/sphinx/index.rst | 1 + manual/sphinx/user_docs/adios2.rst | 45 +++++++++++ manual/sphinx/user_docs/advanced_install.rst | 6 +- manual/sphinx/user_docs/bout_options.rst | 48 +++++------- manual/sphinx/user_docs/installing.rst | 4 + src/sys/options/options_io.cxx | 4 + .../test-options-netcdf.cxx | 23 +++--- tests/unit/sys/test_options_netcdf.cxx | 75 +++++++++---------- tools/pylib/_boutpp_build/bout_options.pxd | 1 + tools/pylib/_boutpp_build/boutcpp.pxd.jinja | 2 +- tools/pylib/_boutpp_build/boutpp.pyx.jinja | 3 + 12 files changed, 193 insertions(+), 83 deletions(-) create mode 100644 manual/sphinx/user_docs/adios2.rst diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 9350c252ff..65c3cb7dd1 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -1,4 +1,34 @@ -/* Parent class for IO/ADIOS option classes */ +/// Parent class for IO to binary files and streams +/// +/// +/// Usage: +/// +/// 1. Dump files, containing time history: +/// +/// auto dump = OptionsIOFactory::getInstance().createOutput(); +/// dump->write(data); +/// +/// where data is an Options tree. By default dump files are configured +/// with the root `output` section, or an Option tree can be passed to +/// `createOutput`. +/// +/// 2. Restart files: +/// +/// auto restart = OptionsIOFactory::getInstance().createOutput(); +/// restart->write(data); +/// +/// where data is an Options tree. By default restart files are configured +/// with the root `restart_files` section, or an Option tree can be passed to +/// `createRestart`. +/// +/// 3. Ad-hoc single files +/// Note: The caller should consider how multiple processors interact with the file. +/// +/// auto file = OptionsIOFactory::getInstance().createFile("some_file.nc"); +/// or +/// auto file = OptionsIO::create("some_file.nc"); +/// +/// #pragma once @@ -43,8 +73,35 @@ public: /// ADIOS: Indicate completion of an output step. virtual void verifyTimesteps() const = 0; + /// Create an OptionsIO for I/O to the given file. + /// This uses the default file type and default options. static std::unique_ptr create(const std::string& file); + + /// Create an OptionsIO for I/O to the given file. + /// The file will be configured using the given `config` options: + /// - "type" : string The file type e.g. "netcdf" or "adios" + /// - "file" : string Name of the file + /// - "append" : bool Append to existing data (Default is false) static std::unique_ptr create(Options& config); + + /// Create an OptionsIO for I/O to the given file. + /// The file will be configured using the given `config` options: + /// - "type" : string The file type e.g. "netcdf" or "adios" + /// - "file" : string Name of the file + /// - "append" : bool Append to existing data (Default is false) + /// + /// Example: + /// + /// auto file = OptionsIO::create({ + /// {"file", "some_file.nc"}, + /// {"type", "netcdf"}, + /// {"append", false} + /// }); + static std::unique_ptr + create(std::initializer_list> config_list) { + Options config(config_list); // Construct an Options to pass by reference + return create(config); + } }; class OptionsIOFactory : public Factory { @@ -111,6 +168,11 @@ using RegisterOptionsIO = OptionsIOFactory::RegisterInFactory; /// } using RegisterUnavailableOptionsIO = OptionsIOFactory::RegisterUnavailableInFactory; +/// Convenient wrapper function around OptionsIOFactory::createOutput +/// Opens a dump file configured with the `output` root section, +/// and writes the given `data` to the file. +void writeDefaultOutputFile(Options& data); + } // namespace bout #endif // OPTIONS_IO_H diff --git a/manual/sphinx/index.rst b/manual/sphinx/index.rst index 46728c7119..9f661ca187 100644 --- a/manual/sphinx/index.rst +++ b/manual/sphinx/index.rst @@ -42,6 +42,7 @@ The documentation is divided into the following sections: user_docs/boundary_options user_docs/testing user_docs/gpu_support + user_docs/adios2 .. toctree:: :maxdepth: 2 diff --git a/manual/sphinx/user_docs/adios2.rst b/manual/sphinx/user_docs/adios2.rst new file mode 100644 index 0000000000..8a6228cd3a --- /dev/null +++ b/manual/sphinx/user_docs/adios2.rst @@ -0,0 +1,45 @@ +.. _sec-adios2: + +ADIOS2 support +============== + +This section summarises the use of `ADIOS2 `_ in BOUT++. + +Installation +------------ + +The easiest way to configure BOUT++ with ADIOS2 is to tell CMake to download and build it +with this flag:: + + -DBOUT_DOWNLOAD_ADIOS=ON + +The ``master`` branch will be downloaded from `Github `_, +configured and built with BOUT++. + +Alternatively, if ADIOS is already installed then the following flags can be used:: + + -DBOUT_USE_ADIOS=ON -DADIOS2_ROOT=/path/to/adios2 + +Output files +------------ + +The output (dump) files are controlled with the root ``output`` options. +By default the output format is NetCDF, so to use ADIOS2 instead set +the output type in BOUT.inp:: + + [output] + type = adios + +or on the BOUT++ command line set ``output:type=adios``. The default +prefix is "BOUT.dmp" so the ADIOS file will be called "BOUT.dmp.bp". To change this, +set the ``output:prefix`` option. + +Restart files +------------- + +The restart files are contolled with the root ``restart_files`` options, +so to read and write restarts from an ADIOS dataset, put in BOUT.inp:: + + [restart_files] + type = adios + diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst index 957173b820..e25be12b4b 100644 --- a/manual/sphinx/user_docs/advanced_install.rst +++ b/manual/sphinx/user_docs/advanced_install.rst @@ -170,8 +170,10 @@ for a production run use: File formats ------------ -BOUT++ can currently use the NetCDF-4_ file format, with experimental -support for the parallel flavour. NetCDF is a widely used format and +BOUT++ can currently use the NetCDF-4_ file format and the ADIOS2 library +for high-performance parallel output. + +NetCDF is a widely used format and has many tools for viewing and manipulating files. .. _NetCDF-4: https://www.unidata.ucar.edu/software/netcdf/ diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst index 5422558ff9..976faa0544 100644 --- a/manual/sphinx/user_docs/bout_options.rst +++ b/manual/sphinx/user_docs/bout_options.rst @@ -523,6 +523,12 @@ options available are listed in table :numref:`tab-outputopts`. +-------------+----------------------------------------------------+--------------+ | enabled | Writing is enabled | true | +-------------+----------------------------------------------------+--------------+ + | type | File type e.g. "netcdf" or "adios" | "netcdf" | + +-------------+----------------------------------------------------+--------------+ + | prefix | File name prefix | "BOUT.dmp" | + +-------------+----------------------------------------------------+--------------+ + | path | Directory to write the file into | ``datadir`` | + +-------------+----------------------------------------------------+--------------+ | floats | Write floats rather than doubles | false | +-------------+----------------------------------------------------+--------------+ | flush | Flush the file to disk after each write | true | @@ -531,8 +537,6 @@ options available are listed in table :numref:`tab-outputopts`. +-------------+----------------------------------------------------+--------------+ | openclose | Re-open the file for each write, and close after | true | +-------------+----------------------------------------------------+--------------+ - | parallel | Use parallel I/O | false | - +-------------+----------------------------------------------------+--------------+ | @@ -541,20 +545,6 @@ want to exclude I/O from the timings. **floats** can be used to reduce the size of the output files: files are stored as double by default, but setting **floats = true** changes the output to single-precision floats. -To enable parallel I/O for either output or restart files, set - -.. code-block:: cfg - - parallel = true - -in the output or restart section. If you have compiled BOUT++ with a -parallel I/O library such as pnetcdf (see -:ref:`sec-advancedinstall`), then rather than outputting one file per -processor, all processors will output to the same file. For restart -files this is particularly useful, as it means that you can restart a -job with a different number of processors. Note that this feature is -still experimental, and incomplete: output dump files are not yet -supported by the collect routines. Implementation -------------- @@ -833,30 +823,30 @@ This is currently quite rudimentary and needs improving. .. _sec-options-netcdf: -Reading and writing to NetCDF ------------------------------ +Reading and writing to binary formats +------------------------------------- -The `bout::OptionsNetCDF` class provides an interface to read and -write options. Examples are in integrated test +The `bout::OptionsIO` class provides an interface to read and +write options to binary files. Examples are in integrated test ``tests/integrated/test-options-netcdf/`` To write the current `Options` tree (e.g. from ``BOUT.inp``) to a NetCDF file:: - bout::OptionsNetCDF("settings.nc").write(Options::root()); + bout::OptionsIO::create("settings.nc")->write(Options::root()); and to read it in again:: - Options data = bout::OptionsNetCDF("settings.nc").read(); + Options data = bout::OptionsIO::create("settings.nc")->read(); Fields can also be stored and written:: Options fields; fields["f2d"] = Field2D(1.0); fields["f3d"] = Field3D(2.0); - bout::OptionsNetCDF("fields.nc").write(fields); + bout::OptionsIO::create("fields.nc").write(fields); -This should allow the input settings and evolving variables to be +This allows the input settings and evolving variables to be combined into a single tree (see above on joining trees) and written to the output dump or restart files. @@ -865,7 +855,7 @@ an ``Array``, 2D as ``Matrix`` and 3D as ``Tensor``. These can be extracted directly from the ``Options`` tree, or converted to a Field:: - Options fields_in = bout::OptionsNetCDF("fields.nc").read(); + Options fields_in = bout::OptionsIO::create("fields.nc")->read(); Field2D f2d = fields_in["f2d"].as(); Field3D f3d = fields_in["f3d"].as(); @@ -907,7 +897,7 @@ automatically set the ``"time_dimension"`` attribute:: // Or use `assignRepeat` to do it automatically: data["field"].assignRepeat(Field3D(2.0)); - bout::OptionsNetCDF("time.nc").write(data); + bout::OptionsIO::create("time.nc")->write(data); // Update time-dependent values. This can be done without `force` if the time_dimension // attribute is set @@ -915,13 +905,13 @@ automatically set the ``"time_dimension"`` attribute:: data["field"] = Field3D(3.0); // Append data to file - bout::OptionsNetCDF("time.nc", bout::OptionsNetCDF::FileMode::append).write(data); + bout::OptionsIO({{"file", "time.nc"}, {"append", true}})->write(data); -.. note:: By default, `bout::OptionsNetCDF::write` will only write variables +.. note:: By default, `bout::OptionsIO::write` will only write variables with a ``"time_dimension"`` of ``"t"``. You can write variables with a different time dimension by passing it as the second argument: - ``OptionsNetCDF(filename).write(options, "t2")`` for example. + ``OptionsIO::create(filename)->write(options, "t2")`` for example. FFT diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst index fc1b2ce2da..eb155909bf 100644 --- a/manual/sphinx/user_docs/installing.rst +++ b/manual/sphinx/user_docs/installing.rst @@ -373,6 +373,10 @@ For SUNDIALS, use ``-DBOUT_DOWNLOAD_SUNDIALS=ON``. If using ``ccmake`` this opti may not appear initially. This automatically sets ``BOUT_USE_SUNDIALS=ON``, and configures SUNDIALS to use MPI. +For ADIOS2, use ``-DBOUT_DOWNLOAD_ADIOS=ON``. This will download and +configure `ADIOS2 `_, enabling BOUT++ +to read and write this high-performance parallel file format. + Bundled Dependencies ~~~~~~~~~~~~~~~~~~~~ diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 13a8c9890a..454ba77fc3 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -43,4 +43,8 @@ OptionsIOFactory::ReturnType OptionsIOFactory::createFile(const std::string& fil return create(getDefaultType(), options); } +void writeDefaultOutputFile(Options& data) { + OptionsIOFactory::getInstance().createOutput()->write(data); +} + } // namespace bout diff --git a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx index 7da6199535..f5daf8919c 100644 --- a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx +++ b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx @@ -2,18 +2,17 @@ #include "bout/bout.hxx" #include "bout/options_io.hxx" -#include "bout/options_netcdf.hxx" #include "bout/optionsreader.hxx" -using bout::OptionsNetCDF; +using bout::OptionsIO; int main(int argc, char** argv) { BoutInitialise(argc, argv); // Read values from a NetCDF file - OptionsNetCDF file("test.nc"); + auto file = OptionsIO::create("test.nc"); - auto values = file.read(); + auto values = file->read(); values.printUnused(); @@ -22,15 +21,15 @@ int main(int argc, char** argv) { reader->write(&values, "test-out.ini"); // Write to a NetCDF file - OptionsNetCDF("test-out.nc").write(values); + OptionsIO::create("test-out.nc")->write(values); /////////////////////////// // Write the BOUT.inp settings to NetCDF file - OptionsNetCDF("settings.nc").write(Options::root()); + OptionsIO::create("settings.nc")->write(Options::root()); // Read back in - auto settings = OptionsNetCDF("settings.nc").read(); + auto settings = OptionsIO::create("settings.nc")->read(); // Write to INI file reader->write(&settings, "settings.ini"); @@ -42,12 +41,12 @@ int main(int argc, char** argv) { fields["f2d"] = Field2D(1.0); fields["f3d"] = Field3D(2.0); fields["fperp"] = FieldPerp(3.0); - OptionsNetCDF("fields.nc").write(fields); + OptionsIO::create("fields.nc")->write(fields); /////////////////////////// // Read fields - Options fields_in = OptionsNetCDF("fields.nc").read(); + Options fields_in = OptionsIO::create("fields.nc")->read(); auto f2d = fields_in["f2d"].as(bout::globals::mesh); auto f3d = fields_in["f3d"].as(bout::globals::mesh); @@ -59,7 +58,7 @@ int main(int argc, char** argv) { fields2["fperp"] = fperp; // Write out again - OptionsNetCDF("fields2.nc").write(fields2); + OptionsIO::create("fields2.nc")->write(fields2); /////////////////////////// // Time dependent values @@ -71,14 +70,14 @@ int main(int argc, char** argv) { data["field"] = Field3D(2.0); data["field"].attributes["time_dimension"] = "t"; - OptionsNetCDF("time.nc").write(data); + OptionsIO::create("time.nc")->write(data); // Update time-dependent values data["scalar"] = 2.0; data["field"] = Field3D(3.0); // Append data to file - OptionsNetCDF("time.nc", bout::OptionsIO::FileMode::append).write(data); + OptionsIO::create({{"file", "time.nc"}, {"append", true}})->write(data); BoutFinalise(); }; diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx index 3f32b0b7d9..5869cf4932 100644 --- a/tests/unit/sys/test_options_netcdf.cxx +++ b/tests/unit/sys/test_options_netcdf.cxx @@ -39,11 +39,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteInt) { options["test"] = 42; // Write the file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read again - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["test"], 42); } @@ -54,11 +54,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteString) { options["test"] = std::string{"hello"}; // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["test"], std::string("hello")); } @@ -69,11 +69,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteField2D) { options["test"] = Field2D(1.0); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); Field2D value = data["test"].as(bout::globals::mesh); @@ -87,11 +87,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteField3D) { options["test"] = Field3D(2.4); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); Field3D value = data["test"].as(bout::globals::mesh); @@ -106,11 +106,11 @@ TEST_F(OptionsNetCDFTest, Groups) { options["test"]["key"] = 42; // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["test"]["key"], 42); } @@ -121,11 +121,11 @@ TEST_F(OptionsNetCDFTest, AttributeInt) { options["test"].attributes["thing"] = 4; // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["test"].attributes["thing"].as(), 4); } @@ -136,11 +136,11 @@ TEST_F(OptionsNetCDFTest, AttributeBoutReal) { options["test"].attributes["thing"] = 3.14; // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_DOUBLE_EQ(data["test"].attributes["thing"].as(), 3.14); } @@ -151,11 +151,11 @@ TEST_F(OptionsNetCDFTest, AttributeString) { options["test"].attributes["thing"] = "hello"; // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["test"].attributes["thing"].as(), "hello"); } @@ -165,11 +165,11 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellCentre) { options["f2d"] = Field2D(2.0); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), toString(CELL_CENTRE)); @@ -181,11 +181,11 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellYLow) { options["f2d"] = Field2D(2.0, mesh_staggered).setLocation(CELL_YLOW); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["f2d"].attributes["cell_location"].as(), toString(CELL_YLOW)); @@ -197,11 +197,11 @@ TEST_F(OptionsNetCDFTest, Field3DWriteCellCentre) { options["f3d"] = Field3D(2.0); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), toString(CELL_CENTRE)); @@ -213,11 +213,11 @@ TEST_F(OptionsNetCDFTest, Field3DWriteCellYLow) { options["f3d"] = Field3D(2.0, mesh_staggered).setLocation(CELL_YLOW); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["f3d"].attributes["cell_location"].as(), toString(CELL_YLOW)); @@ -235,11 +235,11 @@ TEST_F(OptionsNetCDFTest, FieldPerpWriteCellCentre) { fperp.getMesh()->getXcomm(); // Write file - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } // Read file - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_EQ(data["fperp"].attributes["cell_location"].as(), toString(CELL_CENTRE)); @@ -252,10 +252,10 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) { options["thing1"] = 1.0; options["thing1"].attributes["time_dimension"] = "t"; - OptionsIO::create(filename).write(options); + OptionsIO::create(filename)->write(options); } - EXPECT_NO_THROW(OptionsIO::create(filename).verifyTimesteps()); + EXPECT_NO_THROW(OptionsIO::create(filename)->verifyTimesteps()); { Options options; @@ -265,12 +265,11 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) { options["thing2"] = 3.0; options["thing2"].attributes["time_dimension"] = "t"; - Optiond config{{"type", "netcdf"}, {"file", filename}, {"append", true}}; - - OptionsIO::create(config).write(options); + OptionsIO::create({{"type", "netcdf"}, {"file", filename}, {"append", true}}) + ->write(options); } - EXPECT_THROW(OptionsIO::create(filename).verifyTimesteps(), BoutException); + EXPECT_THROW(OptionsIO::create(filename)->verifyTimesteps(), BoutException); } TEST_F(OptionsNetCDFTest, WriteTimeDimension) { @@ -280,10 +279,10 @@ TEST_F(OptionsNetCDFTest, WriteTimeDimension) { options["thing2"].assignRepeat(2.0, "t2"); // non-default // Only write non-default time dim - OptionsIO::create(filename).write(options, "t2"); + OptionsIO::create(filename)->write(options, "t2"); } - Options data = OptionsIO::create(filename).read(); + Options data = OptionsIO::create(filename)->read(); EXPECT_FALSE(data.isSet("thing1")); EXPECT_TRUE(data.isSet("thing2")); @@ -299,12 +298,12 @@ TEST_F(OptionsNetCDFTest, WriteMultipleTimeDimensions) { options["thing4_t2"].assignRepeat(2.0, "t2"); // non-default // Write the non-default time dim twice - OptionsIO::create(filename).write(options, "t2"); - OptionsIO::create(filename).write(options, "t2"); - OptionsIO::create(filename).write(options, "t"); + OptionsIO::create(filename)->write(options, "t2"); + OptionsIO::create(filename)->write(options, "t2"); + OptionsIO::create(filename)->write(options, "t"); } - EXPECT_NO_THROW(OptionsIO::create(filename).verifyTimesteps()); + EXPECT_NO_THROW(OptionsIO::create(filename)->verifyTimesteps()); } #endif // BOUT_HAS_NETCDF diff --git a/tools/pylib/_boutpp_build/bout_options.pxd b/tools/pylib/_boutpp_build/bout_options.pxd index 550bfc01e1..be17608cea 100644 --- a/tools/pylib/_boutpp_build/bout_options.pxd +++ b/tools/pylib/_boutpp_build/bout_options.pxd @@ -9,6 +9,7 @@ cdef extern from "boutexception_helper.hxx": cdef extern from "bout/options_io.hxx" namespace "bout": + cdef void writeDefaultOutputFile(Options& options); cppclass OptionsIO: @staticmethod OptionsIO * create(string filename) diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja index 28633cad95..12e210a5b5 100644 --- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja +++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja @@ -5,7 +5,7 @@ from libcpp.memory cimport unique_ptr from libcpp.string cimport string cimport resolve_enum as benum -from bout_options cimport Options, OptionsReader, OptionsIO +from bout_options cimport Options, OptionsReader, OptionsIO, writeDefaultOutputFile cdef extern from "boutexception_helper.hxx": cdef void raise_bout_py_error() diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja index a8c027475a..3aeb1428eb 100644 --- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja +++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja @@ -1723,6 +1723,9 @@ cdef class Options: del self.cobj self.cobj = NULL +def writeDefaultOutputFile(options: Options): + c.writeDefaultOutputFile(deref(options.cobj)) + def print(*args, sep=" ", end="\n"): _print(sep.join([str(a) for a in args]) + end) From 2c1f341b386222824c53fccd26050b959b20e6bf Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 8 Dec 2023 11:26:14 -0800 Subject: [PATCH 153/412] unit tests build gmock The unit tests require GMock, so set BUILD_GMOCK=ON by default. --- tests/unit/CMakeLists.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt index c0fd4a1e1f..c4ffa4fa75 100644 --- a/tests/unit/CMakeLists.txt +++ b/tests/unit/CMakeLists.txt @@ -19,6 +19,9 @@ if(NOT TARGET gtest) message(FATAL_ERROR "googletest not found! Have you disabled the git submodules (GIT_SUBMODULE)?") endif() +# Some unit tests require GMOCK, so make sure we build it +set(BUILD_GMOCK ON) + mark_as_advanced( BUILD_GMOCK BUILD_GTEST BUILD_SHARED_LIBS gmock_build_tests gtest_build_samples gtest_build_tests From 1725c818ab609fb51fffb122faebef5722fe93f7 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 8 Dec 2023 11:56:36 -0800 Subject: [PATCH 154/412] Fix calls to writeDefaultOutputFile Now always need to pass the data to be written, rather than implicitly writing Options::root(). --- tests/integrated/test-twistshift-staggered/test-twistshift.cxx | 2 +- tests/integrated/test-twistshift/test-twistshift.cxx | 2 +- tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx index 87b9e0a094..c9f8be7b09 100644 --- a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx +++ b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx @@ -30,7 +30,7 @@ int main(int argc, char** argv) { Options::root()["test"] = test; Options::root()["test_aligned"] = test_aligned; - bout::writeDefaultOutputFile(); + bout::writeDefaultOutputFile(Options::root()); BoutFinalise(); } diff --git a/tests/integrated/test-twistshift/test-twistshift.cxx b/tests/integrated/test-twistshift/test-twistshift.cxx index ccde8b82b6..2c0fc79563 100644 --- a/tests/integrated/test-twistshift/test-twistshift.cxx +++ b/tests/integrated/test-twistshift/test-twistshift.cxx @@ -28,7 +28,7 @@ int main(int argc, char** argv) { Options::root()["test"] = test; Options::root()["test_aligned"] = test_aligned; - bout::writeDefaultOutputFile(); + bout::writeDefaultOutputFile(Options::root()); BoutFinalise(); } diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx b/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx index 22d1fb9e07..e8a2982bfd 100644 --- a/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx +++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx @@ -70,7 +70,7 @@ int main(int argc, char** argv) { Options::root()["ddy"] = ddy; Options::root()["ddy2"] = ddy2; - bout::writeDefaultOutputFile(); + bout::writeDefaultOutputFile(Options::root()); BoutFinalise(); From eeb91777a2957a74554a5728de04798322dad179 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 8 Dec 2023 12:58:18 -0800 Subject: [PATCH 155/412] More integrated test fixes Changing from OptionsNetCDF to OptionsIO interface. --- .../test-griddata/test_griddata.cxx | 2 +- .../test-options-adios/test-options-adios.cxx | 52 ++++++++++++------- 2 files changed, 35 insertions(+), 19 deletions(-) diff --git a/tests/integrated/test-griddata/test_griddata.cxx b/tests/integrated/test-griddata/test_griddata.cxx index 9f12d48d9d..0277f9e001 100644 --- a/tests/integrated/test-griddata/test_griddata.cxx +++ b/tests/integrated/test-griddata/test_griddata.cxx @@ -13,7 +13,7 @@ int main(int argc, char** argv) { dump["Bpxy"] = Bpxy; bout::experimental::addBuildFlagsToOptions(dump); bout::globals::mesh->outputVars(dump); - bout::OptionsNetCDF("data.nc").write(dump); + bout::OptionsIO::create("data.nc")->write(dump); BoutFinalise(); return 0; diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx index efd74344c0..727172c688 100644 --- a/tests/integrated/test-options-adios/test-options-adios.cxx +++ b/tests/integrated/test-options-adios/test-options-adios.cxx @@ -1,20 +1,18 @@ #include "bout/bout.hxx" -#include "bout/options_adios.hxx" #include "bout/options_io.hxx" -#include "bout/options_netcdf.hxx" #include "bout/optionsreader.hxx" -using bout::OptionsADIOS; +using bout::OptionsIO; int main(int argc, char** argv) { BoutInitialise(argc, argv); // Read values from a NetCDF file - bout::OptionsNetCDF file("test.nc"); + auto file = bout::OptionsIO::create("test.nc"); - auto values = file.read(); + auto values = file->read(); values.printUnused(); @@ -22,17 +20,24 @@ int main(int argc, char** argv) { OptionsReader* reader = OptionsReader::getInstance(); reader->write(&values, "test-out.ini"); - // Write to ADIOS file - OptionsADIOS("test-out.bp", bout::OptionsIO::FileMode::replace, true).write(values); + // Write to ADIOS file, by setting file type "adios" + OptionsIO::create({{"file", "test-out.bp"}, + {"type", "adios"}, + {"append", false}, + {"singleWriteFile", true}}) + ->write(values); /////////////////////////// // Write the BOUT.inp settings to NetCDF file - OptionsADIOS("settings.bp", bout::OptionsIO::FileMode::replace, true) - .write(Options::root()); + OptionsIO::create({{"file", "settings.bp"}, + {"type", "adios"}, + {"append", false}, + {"singleWriteFile", true}}) + ->write(Options::root()); // Read back in - auto settings = OptionsADIOS("settings.bp").read(); + auto settings = OptionsIO::create({{"file", "settings.bp"}, {"type", "adios"}})->read(); // Write to INI file reader->write(&settings, "settings.ini"); @@ -44,19 +49,20 @@ int main(int argc, char** argv) { fields["f2d"] = Field2D(1.0); fields["f3d"] = Field3D(2.0); fields["fperp"] = FieldPerp(3.0); - auto f = OptionsADIOS("fields.bp"); + auto f = OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}}); /* write() for adios only buffers data but does not guarantee writing to disk unless singleWriteFile is set to true */ - f.write(fields); + f->write(fields); // indicate completion of step, required to get data on disk - f.verifyTimesteps(); + f->verifyTimesteps(); /////////////////////////// // Read fields - Options fields_in = OptionsADIOS("fields.bp").read(); + Options fields_in = + OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}})->read(); auto f2d = fields_in["f2d"].as(bout::globals::mesh); auto f3d = fields_in["f3d"].as(bout::globals::mesh); @@ -68,8 +74,10 @@ int main(int argc, char** argv) { fields2["fperp"] = fperp; // Write out again - auto f2 = bout::OptionsIOFactory("fields2.bp", bout::OptionsIO::FileMode::replace, - bout::OptionsIO::Library::ADIOS, true); + auto f2 = OptionsIO::create({{"file", "fields2.bp"}, + {"type", "adios"}, + {"append", false}, + {"singleWriteFile", true}}); f2->write(fields2); /////////////////////////// @@ -82,14 +90,22 @@ int main(int argc, char** argv) { data["field"] = Field3D(2.0); data["field"].attributes["time_dimension"] = "t"; - OptionsADIOS("time.bp", bout::OptionsIO::FileMode::replace, true).write(data); + OptionsIO::create({{"file", "time.bp"}, + {"type", "adios"}, + {"append", false}, + {"singleWriteFile", true}}) + ->write(data); // Update time-dependent values data["scalar"] = 2.0; data["field"] = Field3D(3.0); // Append data to file - OptionsADIOS("time.bp", bout::OptionsIO::FileMode::append, true).write(data); + OptionsIO::create({{"file", "time.bp"}, + {"type", "adios"}, + {"append", true}, + {"singleWriteFile", true}}) + ->write(data); BoutFinalise(); }; From 9ec88574ff126b193b860d095eb119f3746e41b6 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 8 Dec 2023 14:13:27 -0800 Subject: [PATCH 156/412] Fix MMS-spatial-fci test Output file needs MZ and other mesh variables for collect() to work. --- tests/MMS/spatial/fci/data/BOUT.inp | 1 + tests/MMS/spatial/fci/fci_mms.cxx | 2 ++ 2 files changed, 3 insertions(+) diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp index 5f377bbb56..802f70f99b 100644 --- a/tests/MMS/spatial/fci/data/BOUT.inp +++ b/tests/MMS/spatial/fci/data/BOUT.inp @@ -5,6 +5,7 @@ input_field = sin(y - 2*z) + sin(y - z) solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) MXG = 1 +MYG = 1 NXPE = 1 [mesh] diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx index 5a2599368e..18405a7f88 100644 --- a/tests/MMS/spatial/fci/fci_mms.cxx +++ b/tests/MMS/spatial/fci/fci_mms.cxx @@ -17,6 +17,8 @@ int main(int argc, char** argv) { Field3D error{result - solution}; Options dump; + // Add mesh geometry variables + mesh->outputVars(dump); dump["l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY")); dump["l_inf"] = max(abs(error), true, "RGN_NOBNDRY"); From 365ce5241112d46caae15551b88a80af967d8703 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 13 Dec 2023 13:57:03 -0800 Subject: [PATCH 157/412] writeDefaultOutputFile: Add mesh variables Needed in post-processing when reading data --- src/sys/options/options_io.cxx | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 454ba77fc3..025a655c1d 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -1,4 +1,6 @@ #include "bout/options_io.hxx" +#include "bout/globals.hxx" +#include "bout/mesh.hxx" #include "options_adios.hxx" #include "options_netcdf.hxx" @@ -44,6 +46,9 @@ OptionsIOFactory::ReturnType OptionsIOFactory::createFile(const std::string& fil } void writeDefaultOutputFile(Options& data) { + // Add mesh information + bout::globals::mesh->outputVars(data); + // Write to the default output file OptionsIOFactory::getInstance().createOutput()->write(data); } From 63b25413532337c2a96d37354be47f914d040c9f Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 13 Dec 2023 17:29:56 -0800 Subject: [PATCH 158/412] writeDefaultOutputFile: Add BOUT++ version and flags collect needs to know BOUT_VERSION or it assumes pre-0.2 format. --- src/sys/options/options_io.cxx | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx index 025a655c1d..6717b6b07d 100644 --- a/src/sys/options/options_io.cxx +++ b/src/sys/options/options_io.cxx @@ -1,4 +1,5 @@ #include "bout/options_io.hxx" +#include "bout/bout.hxx" #include "bout/globals.hxx" #include "bout/mesh.hxx" @@ -46,6 +47,8 @@ OptionsIOFactory::ReturnType OptionsIOFactory::createFile(const std::string& fil } void writeDefaultOutputFile(Options& data) { + // Add BOUT++ version and flags + bout::experimental::addBuildFlagsToOptions(data); // Add mesh information bout::globals::mesh->outputVars(data); // Write to the default output file From 77eb501e7310b96c466ef17e64917355f76caf8b Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 14 Dec 2023 17:53:23 -0800 Subject: [PATCH 159/412] ADIOS reading of groups, more test fixes ADIOS uses '/' as a separator, but BOUT++ options uses ':'. When reading variables, we now split on '/' separator and navigate to the correct subsection. Attributes are also named using the final part of the name after the last '/'. solver and beuler integrated tests weren't calling BoutInitialise, so failed when ADIOSFinalize is called. --- include/bout/adios_object.hxx | 11 +++ src/sys/adios_object.cxx | 16 ++-- src/sys/options/options_adios.cxx | 75 ++++++++++++------- tests/integrated/test-beuler/test_beuler.cxx | 1 + .../test-options-adios/test-options-adios.cxx | 2 +- tests/integrated/test-solver/test_solver.cxx | 1 + 6 files changed, 72 insertions(+), 34 deletions(-) mode change 100755 => 100644 src/sys/adios_object.cxx diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx index 7568810cfd..9d2f545b46 100755 --- a/include/bout/adios_object.hxx +++ b/include/bout/adios_object.hxx @@ -1,3 +1,14 @@ +/*!************************************************************************ + * Provides access to the ADIOS library, handling initialisation and + * finalisation. + * + * Usage + * ----- + * + * #include + * + **************************************************************************/ + #ifndef ADIOS_OBJECT_HXX #define ADIOS_OBJECT_HXX diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx old mode 100755 new mode 100644 index 35126090f8..c7d6dab9aa --- a/src/sys/adios_object.cxx +++ b/src/sys/adios_object.cxx @@ -3,6 +3,7 @@ #if BOUT_HAS_ADIOS #include "bout/adios_object.hxx" +#include "bout/boutexception.hxx" #include #include @@ -21,7 +22,7 @@ void ADIOSInit(const std::string configFile, MPI_Comm comm) { void ADIOSFinalize() { if (adios == nullptr) { - throw std::runtime_error( + throw BoutException( "ADIOS needs to be initialized first before calling ADIOSFinalize()"); } adiosStreams.clear(); @@ -30,7 +31,7 @@ void ADIOSFinalize() { ADIOSPtr GetADIOSPtr() { if (adios == nullptr) { - throw std::runtime_error( + throw BoutException( "ADIOS needs to be initialized first before calling GetADIOSPtr()"); } return adios; @@ -76,9 +77,9 @@ void ADIOSSetParameters(const std::string& input, const char delimKeyValue, while (std::getline(inputSS, parameter, delimItem)) { const size_t position = parameter.find(delimKeyValue); if (position == parameter.npos) { - throw std::invalid_argument("ADIOSSetParameters(): wrong format for IO parameter " - + parameter + ", format must be key" + delimKeyValue - + "value for each entry"); + throw BoutException("ADIOSSetParameters(): wrong format for IO parameter " + + parameter + ", format must be key" + delimKeyValue + + "value for each entry"); } std::string key = parameter.substr(0, position); @@ -86,9 +87,8 @@ void ADIOSSetParameters(const std::string& input, const char delimKeyValue, std::string value = parameter.substr(position + 1); lf_Trim(value); if (value.length() == 0) { - throw std::invalid_argument("ADIOS2SetParameters: empty value in IO parameter " - + parameter + ", format must be key" + delimKeyValue - + "value"); + throw BoutException("ADIOS2SetParameters: empty value in IO parameter " + parameter + + ", format must be key" + delimKeyValue + "value"); } io.SetParameter(key, value); } diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index 23abcc74bc..e93a1fea94 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -6,6 +6,7 @@ #include "bout/adios_object.hxx" #include "bout/bout.hxx" +#include "bout/boutexception.hxx" #include "bout/globals.hxx" #include "bout/mesh.hxx" #include "bout/sys/timer.hxx" @@ -36,16 +37,15 @@ OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) { } template -bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, - const std::string& type, Options& result) { +Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, + const std::string& type) { std::vector data; adios2::Variable variable = io.InquireVariable(name); if (variable.ShapeID() == adios2::ShapeID::GlobalValue) { T value; reader.Get(variable, &value, adios2::Mode::Sync); - result[name] = value; - return true; + return Options(value); } if (variable.ShapeID() == adios2::ShapeID::LocalArray) { @@ -84,51 +84,65 @@ bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& nam Array value(static_cast(dims[0])); BoutReal* data = value.begin(); reader.Get(variableD, data, adios2::Mode::Sync); - result[name] = value; - break; + return Options(value); } case 2: { Matrix value(static_cast(dims[0]), static_cast(dims[1])); BoutReal* data = value.begin(); reader.Get(variableD, data, adios2::Mode::Sync); - result[name] = value; - break; + return Options(value); } case 3: { Tensor value(static_cast(dims[0]), static_cast(dims[1]), static_cast(dims[2])); BoutReal* data = value.begin(); reader.Get(variableD, data, adios2::Mode::Sync); - result[name] = value; - break; + return Options(value); } } - - return true; + throw BoutException("ADIOS reader failed to read '{}' of dimension {} in file '{}'", + name, ndims, reader.Name()); } -bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, - const std::string& type, Options& result) { - bool ret = false; -#define declare_template_instantiation(T) \ - if (type == adios2::GetType()) { \ - ret = readVariable(reader, io, name, type, result); \ +Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, + const std::string& type) { +#define declare_template_instantiation(T) \ + if (type == adios2::GetType()) { \ + return readVariable(reader, io, name, type); \ } ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) + declare_template_instantiation(std::string) #undef declare_template_instantiation - return ret; + output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')", type, + name); + return Options{}; } bool readAttribute(adios2::IO& io, const std::string& name, const std::string& type, Options& result) { + // Attribute is the part of 'name' after the last '/' separator + std::string attrname; + auto pos = name.find_last_of('/'); + if (pos == std::string::npos) { + attrname = name; + } else { + attrname = name.substr(pos + 1); + } + #define declare_template_instantiation(T) \ if (type == adios2::GetType()) { \ adios2::Attribute a = io.InquireAttribute(name); \ - result[name] = a.Data().data(); \ + result.attributes[attrname] = *a.Data().data(); \ + return true; \ } - ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation) + // Only some types of attributes are supported + //declare_template_instantiation(bool) + declare_template_instantiation(int) declare_template_instantiation(BoutReal) + declare_template_instantiation(std::string) #undef declare_template_instantiation - return true; + output_warn.write("ADIOS readAttribute can't read type '{}' (variable '{}')", + type, name); + return false; } Options OptionsADIOS::read() { @@ -157,17 +171,27 @@ Options OptionsADIOS::read() { auto it = varpair.second.find("Type"); const std::string& var_type = it->second; - readVariable(reader, io, var_name, var_type, result); - result[var_name].attributes["source"] = filename; + Options* varptr = &result; + for (const auto& piece : strsplit(var_name, '/')) { + varptr = &(*varptr)[piece]; // Navigate to subsection if needed + } + Options& var = *varptr; + + // Note: Copying the value rather than simple assignment is used + // because the Options assignment operator overwrites full_name. + var = 0; // Setting is_section to false + var.value = readVariable(reader, io, var_name, var_type).value; + var.attributes["source"] = filename; // Get variable attributes for (const auto& attpair : io.AvailableAttributes(var_name, "/", true)) { const auto& att_name = attpair.first; // Attribute name const auto& att = attpair.second; // attribute params + auto it = att.find("Type"); const std::string& att_type = it->second; - readAttribute(io, att_name, att_type, result); + readAttribute(io, att_name, att_type, var); } } @@ -448,6 +472,7 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string& } // Write the variable + // Note: ADIOS2 uses '/' to as a group separator; BOUT++ uses ':' std::string varname = groupname.empty() ? name : groupname + "/" + name; bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value); diff --git a/tests/integrated/test-beuler/test_beuler.cxx b/tests/integrated/test-beuler/test_beuler.cxx index cfdae89eb2..2f8e082348 100644 --- a/tests/integrated/test-beuler/test_beuler.cxx +++ b/tests/integrated/test-beuler/test_beuler.cxx @@ -41,6 +41,7 @@ class TestSolver : public PhysicsModel { }; int main(int argc, char** argv) { + BoutInitialise(argc, argv); // Absolute tolerance for difference between the actual value and the // expected value diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx index 727172c688..60604e1aa3 100644 --- a/tests/integrated/test-options-adios/test-options-adios.cxx +++ b/tests/integrated/test-options-adios/test-options-adios.cxx @@ -29,7 +29,7 @@ int main(int argc, char** argv) { /////////////////////////// - // Write the BOUT.inp settings to NetCDF file + // Write the BOUT.inp settings to ADIOS file OptionsIO::create({{"file", "settings.bp"}, {"type", "adios"}, {"append", false}, diff --git a/tests/integrated/test-solver/test_solver.cxx b/tests/integrated/test-solver/test_solver.cxx index ee64c6097f..2beca7ae06 100644 --- a/tests/integrated/test-solver/test_solver.cxx +++ b/tests/integrated/test-solver/test_solver.cxx @@ -25,6 +25,7 @@ class TestSolver : public PhysicsModel { }; int main(int argc, char** argv) { + BoutInitialise(argc, argv); // The expected answer to the integral of \f$\int_0^{\pi/2}\sin^2(t)\f$ constexpr BoutReal expected = PI / 4.; From af6610f07a80ac89cf30f1b23fce41bf88a8ca59 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 14 Dec 2023 20:40:34 -0800 Subject: [PATCH 160/412] test-solver: Remove BoutInitialise and BoutFinalise BoutFinalise throws an exception when ADIOS is enabled but BoutInitialise is not called. BoutInitialise throws an exception if the "data" directory doesn't exist. For this test neither BoutInitialise nor BoutFinalise are needed, so removed. --- tests/integrated/test-solver/test_solver.cxx | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/integrated/test-solver/test_solver.cxx b/tests/integrated/test-solver/test_solver.cxx index 2beca7ae06..2e4345c8cc 100644 --- a/tests/integrated/test-solver/test_solver.cxx +++ b/tests/integrated/test-solver/test_solver.cxx @@ -25,7 +25,6 @@ class TestSolver : public PhysicsModel { }; int main(int argc, char** argv) { - BoutInitialise(argc, argv); // The expected answer to the integral of \f$\int_0^{\pi/2}\sin^2(t)\f$ constexpr BoutReal expected = PI / 4.; @@ -147,8 +146,6 @@ int main(int argc, char** argv) { } } - BoutFinalise(false); - if (!errors.empty()) { output_test << "\n => Some failed tests\n\n"; for (auto& error : errors) { From e543cd48c76bf409c3c95b909bf1408143f0372e Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 14 Dec 2023 21:16:53 -0800 Subject: [PATCH 161/412] test-beuler: Remove BoutInitialise and BoutFinalise Not required, and BoutInitialise throws an exception because the "data" directory doesn't exist. --- tests/integrated/test-beuler/test_beuler.cxx | 4 ---- 1 file changed, 4 deletions(-) diff --git a/tests/integrated/test-beuler/test_beuler.cxx b/tests/integrated/test-beuler/test_beuler.cxx index 2f8e082348..5a080767dd 100644 --- a/tests/integrated/test-beuler/test_beuler.cxx +++ b/tests/integrated/test-beuler/test_beuler.cxx @@ -41,8 +41,6 @@ class TestSolver : public PhysicsModel { }; int main(int argc, char** argv) { - BoutInitialise(argc, argv); - // Absolute tolerance for difference between the actual value and the // expected value constexpr BoutReal tolerance = 1.e-5; @@ -88,8 +86,6 @@ int main(int argc, char** argv) { solver->solve(); - BoutFinalise(false); - if (model.check_solution(tolerance)) { output_test << " PASSED\n"; return 0; From 721157a9333fed3e55de9e8ff4804ad040ebdb26 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 15 Dec 2023 11:25:52 -0800 Subject: [PATCH 162/412] CI: Change ADIOS install directory Using $HOME/local rather than $HOME/local/adios2. Hopefully cmake can find it. --- .build_adios2_for_ci.sh | 2 +- .github/workflows/tests.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.build_adios2_for_ci.sh b/.build_adios2_for_ci.sh index f636252a94..c6d4178884 100755 --- a/.build_adios2_for_ci.sh +++ b/.build_adios2_for_ci.sh @@ -19,7 +19,7 @@ if test $BUILD_ADIOS2 ; then pushd build cmake .. \ - -DCMAKE_INSTALL_PREFIX=$HOME/local/adios2 \ + -DCMAKE_INSTALL_PREFIX=$HOME/local \ -DADIOS2_USE_MPI=ON \ -DADIOS2_USE_Fortran=OFF \ -DADIOS2_USE_Python=OFF \ diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b79144c10a..c449beb4ca 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -39,7 +39,7 @@ jobs: is_cron: - ${{ github.event_name == 'cron' }} config: - - name: "CMake, PETSc unreleased" + - name: "CMake, PETSc unreleased, ADIOS" os: ubuntu-20.04 cmake_options: "-DBUILD_SHARED_LIBS=ON -DBOUT_ENABLE_METRIC_3D=ON From 81ef07db68d2c84b4b651dbe867173b521847c30 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 20 Dec 2023 10:32:31 +0100 Subject: [PATCH 163/412] CI: Work around paranoid pip --- .github/workflows/clang-tidy-review.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml index d546ce3af2..f50d5aeff7 100644 --- a/.github/workflows/clang-tidy-review.yml +++ b/.github/workflows/clang-tidy-review.yml @@ -32,7 +32,7 @@ jobs: # the unit tests until they're fixed or ignored upstream exclude: "tests/unit/*cxx" cmake_command: | - pip install cmake && \ + pip install --break-system-packages cmake && \ cmake --version && \ git config --global --add safe.directory "$GITHUB_WORKSPACE" && \ cmake . -B build -DBUILD_SHARED_LIBS=ON \ From b85362f2298c374fd13a572b5a9b7313888fb235 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 20 Dec 2023 13:47:48 -0800 Subject: [PATCH 164/412] Updating the readme file - Add newlines between equations - Update copyright notice and year - Remove out of date material --- README.md | 69 +++++++++++-------------------------------------------- 1 file changed, 13 insertions(+), 56 deletions(-) diff --git a/README.md b/README.md index fd9e6931ab..055d4f7160 100644 --- a/README.md +++ b/README.md @@ -26,8 +26,11 @@ For example, the following set of equations for magnetohydrodynamics (MHD): ![ddt_rho](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Crho%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Crho%20-%20%5Crho%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D) + ![ddt_p](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20p%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%20p%20-%20%5Cgamma%20p%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D) + ![ddt_v](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Cmathbf%7Bv%7D%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Cmathbf%7Bv%7D%20+%20%5Cfrac%7B1%7D%7B%5Crho%7D%28-%5Cnabla%20p%20+%20%28%5Cnabla%5Ctimes%5Cmathbf%7BB%7D%29%5Ctimes%5Cmathbf%7BB%7D%29) + ![ddt_B](http://latex.codecogs.com/png.latex?%7B%7B%5Cfrac%7B%5Cpartial%20%5Cmathbf%7BB%7D%7D%7B%5Cpartial%20t%7D%7D%7D%20%3D%20%5Cnabla%5Ctimes%28%5Cmathbf%7Bv%7D%5Ctimes%5Cmathbf%7BB%7D%29) can be written simply as: @@ -43,7 +46,7 @@ The full code for this example can be found in the [orszag-tang example](examples/orszag-tang/mhd.cxx). Jointly developed by University of York (UK), LLNL, CCFE, DCU, DTU, -and other international partners. +and other international partners. See the Git logs for author details. Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/) @@ -52,7 +55,6 @@ Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/) * [Requirements](#requirements) * [Usage and installation](#usage-and-installation) * [Terms of use](#terms-of-use) -* [Overview of files](#overview-of-files) * [Contributing](#contributing) * [License](#license) @@ -66,18 +68,17 @@ BOUT++ needs the following: BOUT++ has the following optional dependencies: -* FFTW3 (strongly recommended!) -* OpenMP -* PETSc -* SLEPc -* ARKODE -* IDA -* CVODE +* [FFTW3](https://www.fftw.org/) (strongly recommended!) +* [SUNDIALS](https://computing.llnl.gov/projects/sundials): CVODE, IDA, ARKODE +* [PETSc](https://petsc.org) +* [ADIOS2](https://adios2.readthedocs.io/) +* [SLEPc](https://slepc.upv.es/) * LAPACK +* OpenMP * Score-p (for performance diagnostics) ## Usage and installation -Please see the [users manual](http://bout-dev.readthedocs.io) +Please see the [users manual](http://bout-dev.readthedocs.io). ## Terms of use @@ -105,58 +106,14 @@ You can convert the CITATION.cff file into a Bibtex file as follows: pip3 install --user cffconvert cffconvert -if CITATION.cff -f bibtex -of CITATION.bib -## Overview of files - -This directory contains - -* **bin** Files for setting the BOUT++ configuration -* **examples** Example models and test codes -* **externalpackages** External packages needed for installing BOUT++ -* **include** Header files used in BOUT++ -* **manual** Manuals and documentation (also [doxygen](http://www.stack.nl/~dimitri/doxygen/) documentation) -* **src** The main code directory -* **CITATION** Contains the paper citation for BOUT++ -* **LICENSE** LGPL license -* **LICENSE.GPL** GPL license -* **tools** Tools for helping with analysis, mesh generation, and data managment - - * **archiving** Routines for managing input/output files e.g. compressing data, converting formats, and managing runs - * **cyl_and_helimak_grids** IDL codes for generating cylindrical and helimak grids - * **eigensolver** Matlab routines for solving eigenmodes - * **idllib** Analysis codes in IDL. Add this to your IDL_PATH environment variable - * **line_tracing** IDL routines for line tracing of field lines - * **line_tracing_v2** Newer version of the IDL routines for line tracing of field lines - * **mathematicalib** Library for post processing using Mathematica - * **matlablib** Library for post processing using MATLAB - * **numlib** Numerical IDL routines - * **octave** Routines for post processing using octave - * **plasmalib** IDL routines for calculation of plasma parameters - * **pdb2idl** Library to read Portable Data Binary (PDB) files into IDL - * **pylib** Analysis codes in Python - - * **boutdata** Routines to simplify accessing BOUT++ output - * **boututils** Some useful routines for accessing and plotting data - * **post_bout** Routines for post processing in BOUT++ - - * **slab** IDL routine for grid generation of a slab - * **tokamak_grids** Code to generate input grids for tokamak equilibria - - * **gridgen** Grid generator in IDL. Hypnotoad GUI for converting G-EQDSK files into a flux-aligned orthogonal grid. - * **elite** Convert ELITE .eqin files into an intermediate binary file - * **gato** Convert DSKGATO files into intermediate binary format - * **all** Convert the intermediate binary file into BOUT++ input grid - * **coils** Routines for calculating the field due to external RMP coils and adding to existing equilibria - * **cyclone** Generate cyclone test cases (concentric circle "equilibrium" for local flux-surface calculations) - * **py_gridgen** Translation" into python of the corresponding IDL routines in the folder gridgen - * **shifted_circle** Produce shifted cirle equilibria input grids ## Contributing -See [CONTRIBUTING.md](CONTRIBUTING.md). +See [CONTRIBUTING.md](CONTRIBUTING.md) and the [manual page](https://bout-dev.readthedocs.io/en/stable/developer_docs/contributing.html) ## License -Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu +Copyright 2010-2023 BOUT++ contributors BOUT++ is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by From 0567ab14d06ef75371cada71b35282ae54d405fc Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 21 Dec 2023 13:38:35 -0800 Subject: [PATCH 165/412] Changing Options string to bool behaviour Enables boolean options expressions like: ``` thing = true another = false third = thing & another ``` but breaks inputs using "yes", "False" and other strings that are not "true" or "false" for boolean settings. When converting a string to a BoutReal, Options uses an expression parser that can use variables defined in the input options. The same parser is used when converting to an integer. When converting to a bool, however, Options was doing a simple case-insensitive match to "true", "false", "yes", "no" and a few similar strings. This commit changes this behaviour, treating bools like a special case of an integer: The same parser is used, but the result must be either 1 or 0. This enables boolean quantities to behave consistently with int and BoutReal types. We now define "true" to be equal to 1, and "false" to be 0, so can be used in expressions e.g `true * 2 -> 2`, and `false * 3 -> 0`. No other variations so e.g. "yes", "no", "True" are undefined. We define operators `|` and `&` for logical `or`, and logical `and`. Due to the simplicity of the parser binary operators must be single characters. These both check that their left and right arguments are bools (i.e. either 1 or 0). Logical not (`!`) is not implemented yet, and may require changes to the parser (I guess treat like a unary `-`). --- include/bout/sys/expressionparser.hxx | 4 ++-- src/field/field_factory.cxx | 4 ++++ src/sys/expressionparser.cxx | 16 ++++++++++++++++ src/sys/options.cxx | 21 +++++++++------------ src/sys/options/options_ini.cxx | 2 +- 5 files changed, 32 insertions(+), 15 deletions(-) diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx index 0ee3a7f97b..52e250b9bc 100644 --- a/include/bout/sys/expressionparser.hxx +++ b/include/bout/sys/expressionparser.hxx @@ -3,9 +3,9 @@ * * Parses strings containing expressions, returning a tree of generators * - * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu + * Copyright 2010-2023 BOUT++ contributors * - * Contact: Ben Dudson, bd512@york.ac.uk + * Contact: Ben Dudson, dudson2@llnl.gov * * This file is part of BOUT++. * diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx index fb03c3b174..f6c929a3a3 100644 --- a/src/field/field_factory.cxx +++ b/src/field/field_factory.cxx @@ -114,6 +114,10 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt) addGenerator("pi", std::make_shared(PI)); addGenerator("π", std::make_shared(PI)); + // Boolean values + addGenerator("true", std::make_shared(1)); + addGenerator("false", std::make_shared(0)); + // Some standard functions addGenerator("sin", std::make_shared>(nullptr, "sin")); addGenerator("cos", std::make_shared>(nullptr, "cos")); diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx index 39f8d3bb71..266e15c2ff 100644 --- a/src/sys/expressionparser.cxx +++ b/src/sys/expressionparser.cxx @@ -187,7 +187,21 @@ FieldGeneratorPtr FieldBinary::clone(const list args) { BoutReal FieldBinary::generate(const Context& ctx) { BoutReal lval = lhs->generate(ctx); BoutReal rval = rhs->generate(ctx); + + // Convert a real value to a Boolean + auto toBool = [] (BoutReal rval) { + int ival = ROUND(rval); + if ((fabs(rval - static_cast(ival)) > 1e-3) or (ival < 0) or (ival > 1)) { + throw BoutException(_("Boolean operator argument {:e} is not a bool"), rval); + } + return ival == 1; + }; + switch (op) { + case '|': // Logical OR + return (toBool(lval) or toBool(rval)) ? 1.0 : 0.0; + case '&': // Logical AND + return (toBool(lval) and toBool(rval)) ? 1.0 : 0.0; case '+': return lval + rval; case '-': @@ -207,6 +221,8 @@ BoutReal FieldBinary::generate(const Context& ctx) { ExpressionParser::ExpressionParser() { // Add standard binary operations + addBinaryOp('|', std::make_shared(nullptr, nullptr, '|'), 3); + addBinaryOp('&', std::make_shared(nullptr, nullptr, '&'), 5); addBinaryOp('+', std::make_shared(nullptr, nullptr, '+'), 10); addBinaryOp('-', std::make_shared(nullptr, nullptr, '-'), 10); addBinaryOp('*', std::make_shared(nullptr, nullptr, '*'), 20); diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 8b49b1f3f1..45cacd4acc 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -433,19 +433,16 @@ bool Options::as(const bool& UNUSED(similar_to)) const { result = bout::utils::get(value); } else if (bout::utils::holds_alternative(value)) { - // case-insensitve check, so convert string to lower case - const auto strvalue = lowercase(bout::utils::get(value)); - - if ((strvalue == "y") or (strvalue == "yes") or (strvalue == "t") - or (strvalue == "true") or (strvalue == "1")) { - result = true; - } else if ((strvalue == "n") or (strvalue == "no") or (strvalue == "f") - or (strvalue == "false") or (strvalue == "0")) { - result = false; - } else { - throw BoutException(_("\tOption '{:s}': Boolean expected. Got '{:s}'\n"), full_name, - strvalue); + // Parse as floating point because that's the only type the parser understands + BoutReal rval = parseExpression(value, this, "bool", full_name); + + // Check that the result is either close to 1 (true) or close to 0 (false) + int ival = ROUND(rval); + if ((fabs(rval - static_cast(ival)) > 1e-3) or (ival < 0) or (ival > 1)) { + throw BoutException(_("Value for option {:s} = {:e} is not a bool"), full_name, + rval); } + result = ival == 1; } else { throw BoutException(_("Value for option {:s} cannot be converted to a bool"), full_name); diff --git a/src/sys/options/options_ini.cxx b/src/sys/options/options_ini.cxx index a1e9bcaeb1..d1889f993b 100644 --- a/src/sys/options/options_ini.cxx +++ b/src/sys/options/options_ini.cxx @@ -189,7 +189,7 @@ void OptionINI::parse(const string& buffer, string& key, string& value) { // Just set a flag to true // e.g. "restart" or "append" on command line key = buffer; - value = string("TRUE"); + value = string("true"); return; } From ca73b231c332f33a4fc6287d927e58c684987db3 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 21 Dec 2023 14:01:42 -0800 Subject: [PATCH 166/412] Parser Context: Remove default x,y,z,t Previously x,y,z and t were initialized to 0, but for booleans this would now have quite bad consequences: Inputs that used "y" to mean "true" would now evaluate to `0` which would be interpreted as `false`. With this change we get an exception ("y" is undefined) rather than incorrect behaviour. By removing these defaults, scalar quantities (e.g. integers, booleans) are evaluated without defining x,y,z or t. Trying to convert an expression like "x + y" to an integer or bool would previously evaluate to 0, but will now throw a BoutException. --- include/bout/sys/generator_context.hxx | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx index 3f912ec1da..528b96113d 100644 --- a/include/bout/sys/generator_context.hxx +++ b/include/bout/sys/generator_context.hxx @@ -28,10 +28,7 @@ public: Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t); /// If constructed without parameters, contains no values (null). - /// Requesting x,y,z or t should throw an exception - /// - /// NOTE: For backward compatibility, all locations are set to zero. - /// This should be changed in a future release. + /// Requesting x,y,z or t throws an exception Context() = default; /// The location on the boundary @@ -60,7 +57,13 @@ public: } /// Retrieve a value previously set - BoutReal get(const std::string& name) const { return parameters.at(name); } + BoutReal get(const std::string& name) const { + auto it = parameters.find(name); + if (it != parameters.end()) { + return it->second; + } + throw BoutException("Generator context doesn't contain '{:s}'", name); + } /// Get the mesh for this context (position) /// If the mesh is null this will throw a BoutException (if CHECK >= 1) @@ -73,8 +76,7 @@ private: Mesh* localmesh{nullptr}; ///< The mesh on which the position is defined /// Contains user-set values which can be set and retrieved - std::map parameters{ - {"x", 0.0}, {"y", 0.0}, {"z", 0.0}, {"t", 0.0}}; + std::map parameters{}; }; } // namespace generator From 3b087081fa06a688dd59584e0781c53a66fe6255 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 21 Dec 2023 14:09:17 -0800 Subject: [PATCH 167/412] Updating unit tests and integrated test inputs Reflect the change in behaviour of the boolean parser --- .../test-boutpp/collect-staggered/data/BOUT.inp | 2 +- .../test-boutpp/collect/input/BOUT.inp | 2 +- .../test-boutpp/legacy-model/data/BOUT.inp | 2 +- .../integrated/test-boutpp/mms-ddz/data/BOUT.inp | 2 +- tests/unit/mesh/data/test_gridfromoptions.cxx | 13 ++++++++----- tests/unit/sys/test_options.cxx | 16 +++++++--------- 6 files changed, 19 insertions(+), 18 deletions(-) diff --git a/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp b/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp index 6dc68a7e8b..cb1d1ec7f6 100644 --- a/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp +++ b/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp @@ -2,7 +2,7 @@ nout = 10 timestep = 0.1 [mesh] -staggergrids = True +staggergrids = true n = 1 nx = n+2*MXG ny = 16 diff --git a/tests/integrated/test-boutpp/collect/input/BOUT.inp b/tests/integrated/test-boutpp/collect/input/BOUT.inp index a390bb1891..cad2f17c52 100644 --- a/tests/integrated/test-boutpp/collect/input/BOUT.inp +++ b/tests/integrated/test-boutpp/collect/input/BOUT.inp @@ -5,7 +5,7 @@ MXG = 2 MYG = 2 [mesh] -staggergrids = True +staggergrids = true n = 1 nx = n+2*MXG ny = n diff --git a/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp b/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp index c6dd2fd761..b6b44502f6 100644 --- a/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp +++ b/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp @@ -2,7 +2,7 @@ nout = 10 timestep = 0.1 [mesh] -staggergrids = True +staggergrids = true n = 1 nx = n+2*MXG ny = n diff --git a/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp b/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp index a390bb1891..cad2f17c52 100644 --- a/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp +++ b/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp @@ -5,7 +5,7 @@ MXG = 2 MYG = 2 [mesh] -staggergrids = True +staggergrids = true n = 1 nx = n+2*MXG ny = n diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx index d2a038cb93..84f08ff47b 100644 --- a/tests/unit/mesh/data/test_gridfromoptions.cxx +++ b/tests/unit/mesh/data/test_gridfromoptions.cxx @@ -33,6 +33,8 @@ class GridFromOptionsTest : public ::testing::Test { output_progress.disable(); output_warn.disable(); options["f"] = expected_string; + options["n"] = 12; + options["r"] = 3.14; // modify mesh section in global options options["dx"] = "1."; @@ -116,10 +118,11 @@ TEST_F(GridFromOptionsTest, GetStringNone) { TEST_F(GridFromOptionsTest, GetInt) { int result{-1}; - int expected{3}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f")); - EXPECT_EQ(result, expected); + // The expression must not depend on x,y,z or t + EXPECT_THROW(griddata->get(&mesh_from_options, result, "f"), BoutException); + griddata->get(&mesh_from_options, result, "n"); + EXPECT_EQ(result, 12); } TEST_F(GridFromOptionsTest, GetIntNone) { @@ -132,9 +135,9 @@ TEST_F(GridFromOptionsTest, GetIntNone) { TEST_F(GridFromOptionsTest, GetBoutReal) { BoutReal result{-1.}; - BoutReal expected{3.}; + BoutReal expected{3.14}; - EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f")); + EXPECT_TRUE(griddata->get(&mesh_from_options, result, "r")); EXPECT_EQ(result, expected); } diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index a357923053..8ef86a0668 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -232,10 +232,9 @@ TEST_F(OptionsTest, GetBoolFromString) { EXPECT_EQ(value, true); + // "yes" is not an acceptable bool bool value2; - options.get("bool_key2", value2, false, false); - - EXPECT_EQ(value2, true); + EXPECT_THROW(options.get("bool_key2", value2, false, false), BoutException); } TEST_F(OptionsTest, DefaultValueBool) { @@ -1361,8 +1360,7 @@ TEST_P(BoolTrueTestParametrized, BoolTrueFromString) { } INSTANTIATE_TEST_CASE_P(BoolTrueTests, BoolTrueTestParametrized, - ::testing::Values("y", "Y", "yes", "Yes", "yeS", "t", "true", "T", - "True", "tRuE", "1")); + ::testing::Values("true", "1")); class BoolFalseTestParametrized : public OptionsTest, public ::testing::WithParamInterface {}; @@ -1376,8 +1374,7 @@ TEST_P(BoolFalseTestParametrized, BoolFalseFromString) { } INSTANTIATE_TEST_CASE_P(BoolFalseTests, BoolFalseTestParametrized, - ::testing::Values("n", "N", "no", "No", "nO", "f", "false", "F", - "False", "fAlSe", "0")); + ::testing::Values("false", "0")); class BoolInvalidTestParametrized : public OptionsTest, public ::testing::WithParamInterface {}; @@ -1391,6 +1388,7 @@ TEST_P(BoolInvalidTestParametrized, BoolInvalidFromString) { } INSTANTIATE_TEST_CASE_P(BoolInvalidTests, BoolInvalidTestParametrized, - ::testing::Values("a", "B", "yellow", "Yogi", "test", "truelong", + ::testing::Values("yes", "no", "True", "False", "y", "n", "a", + "B", "yellow", "Yogi", "test", "truelong", "Tim", "2", "not", "No bool", "nOno", - "falsebuttoolong", "-1")); + "falsebuttoolong", "-1", "1.1")); From 8e7279fa3cccaedced93061081c4c12ae4bf3978 Mon Sep 17 00:00:00 2001 From: bendudson Date: Thu, 21 Dec 2023 22:22:47 +0000 Subject: [PATCH 168/412] Apply clang-format changes --- src/sys/expressionparser.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx index 266e15c2ff..4182ce968e 100644 --- a/src/sys/expressionparser.cxx +++ b/src/sys/expressionparser.cxx @@ -189,7 +189,7 @@ BoutReal FieldBinary::generate(const Context& ctx) { BoutReal rval = rhs->generate(ctx); // Convert a real value to a Boolean - auto toBool = [] (BoutReal rval) { + auto toBool = [](BoutReal rval) { int ival = ROUND(rval); if ((fabs(rval - static_cast(ival)) > 1e-3) or (ival < 0) or (ival > 1)) { throw BoutException(_("Boolean operator argument {:e} is not a bool"), rval); From 30b1a56a8e55a134d8b643aff83dafc29be40096 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 2 Jan 2024 10:33:01 +0100 Subject: [PATCH 169/412] Remove comment about m4 The code has been removed a while ago with the switch to cmake --- README.md | 8 -------- 1 file changed, 8 deletions(-) diff --git a/README.md b/README.md index 055d4f7160..20b66ac397 100644 --- a/README.md +++ b/README.md @@ -128,15 +128,7 @@ GNU Lesser General Public License for more details. A copy of the LGPL license is in [LICENSE](LICENSE). Since this is based on (and refers to) the GPL, this is included in [LICENSE.GPL](LICENSE.GPL). -Some of the autoconf macros under [m4](m4) are licensed under -GPLv3. These are not necessary to either build or run BOUT++, but are -used in the creation of [configure](configure) from -[configure.ac](configure.ac), and are provided as a courtesy to -developers. You are free to substitute them with other autoconf macros -that provide equivalent functionality. - BOUT++ links by default with some GPL licensed libraries. Thus if you compile BOUT++ with any of them, BOUT++ will automatically be licensed as GPL. Thus if you want to use BOUT++ with GPL non-compatible code, make sure to compile without GPLed code. - From 0aec67c22f198c12283766acd1fe27f8eadde204 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 2 Jan 2024 08:37:25 -0800 Subject: [PATCH 170/412] Update README.md Co-authored-by: David Bold --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 20b66ac397..5f774ad337 100644 --- a/README.md +++ b/README.md @@ -113,7 +113,7 @@ You can convert the CITATION.cff file into a Bibtex file as follows: See [CONTRIBUTING.md](CONTRIBUTING.md) and the [manual page](https://bout-dev.readthedocs.io/en/stable/developer_docs/contributing.html) ## License -Copyright 2010-2023 BOUT++ contributors +Copyright 2010-2024 BOUT++ contributors BOUT++ is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by From 4fd1717af765275d786a4d8f825cc5e191ed3a61 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 2 Jan 2024 10:21:42 -0800 Subject: [PATCH 171/412] Options: Add logical NOT (!) and comparison (<,>) operators Boolean expressions can now include `!` to negate, and compare numbers using `<` and `>` comparison operators. --- include/bout/sys/expressionparser.hxx | 10 ++--- src/sys/expressionparser.cxx | 47 +++++++++++++++++++----- tests/unit/sys/test_expressionparser.cxx | 40 +++++++++++++++++++- tests/unit/sys/test_options.cxx | 45 +++++++++++++++++++++++ 4 files changed, 126 insertions(+), 16 deletions(-) diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx index 52e250b9bc..a22b41e499 100644 --- a/include/bout/sys/expressionparser.hxx +++ b/include/bout/sys/expressionparser.hxx @@ -3,7 +3,7 @@ * * Parses strings containing expressions, returning a tree of generators * - * Copyright 2010-2023 BOUT++ contributors + * Copyright 2010-2024 BOUT++ contributors * * Contact: Ben Dudson, dudson2@llnl.gov * @@ -24,8 +24,8 @@ * **************************************************************************/ -#ifndef __EXPRESSION_PARSER_H__ -#define __EXPRESSION_PARSER_H__ +#ifndef EXPRESSION_PARSER_H +#define EXPRESSION_PARSER_H #include "bout/format.hxx" #include "bout/unused.hxx" @@ -158,7 +158,7 @@ protected: /// Characters which cannot be used in symbols without escaping; /// all other allowed. In addition, whitespace cannot be used. /// Adding a binary operator adds its symbol to this string - std::string reserved_chars = "+-*/^[](){},="; + std::string reserved_chars = "+-*/^[](){},=!"; private: std::map gen; ///< Generators, addressed by name @@ -260,4 +260,4 @@ private: std::string message; }; -#endif // __EXPRESSION_PARSER_H__ +#endif // EXPRESSION_PARSER_H diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx index 4182ce968e..14c29c7c09 100644 --- a/src/sys/expressionparser.cxx +++ b/src/sys/expressionparser.cxx @@ -184,24 +184,29 @@ FieldGeneratorPtr FieldBinary::clone(const list args) { return std::make_shared(args.front(), args.back(), op); } +/// Convert a real value to a Boolean +/// Throw exception if `rval` isn't close to 0 or 1 +bool toBool(BoutReal rval) { + int ival = ROUND(rval); + if ((fabs(rval - static_cast(ival)) > 1e-3) or (ival < 0) or (ival > 1)) { + throw BoutException(_("Boolean operator argument {:e} is not a bool"), rval); + } + return ival == 1; +} + BoutReal FieldBinary::generate(const Context& ctx) { BoutReal lval = lhs->generate(ctx); BoutReal rval = rhs->generate(ctx); - // Convert a real value to a Boolean - auto toBool = [](BoutReal rval) { - int ival = ROUND(rval); - if ((fabs(rval - static_cast(ival)) > 1e-3) or (ival < 0) or (ival > 1)) { - throw BoutException(_("Boolean operator argument {:e} is not a bool"), rval); - } - return ival == 1; - }; - switch (op) { case '|': // Logical OR return (toBool(lval) or toBool(rval)) ? 1.0 : 0.0; case '&': // Logical AND return (toBool(lval) and toBool(rval)) ? 1.0 : 0.0; + case '>': // Comparison + return (lval > rval) ? 1.0 : 0.0; + case '<': + return (lval < rval) ? 1.0 : 0.0; case '+': return lval + rval; case '-': @@ -217,12 +222,31 @@ BoutReal FieldBinary::generate(const Context& ctx) { throw ParseException("Unknown binary operator '{:c}'", op); } +class LogicalNot : public FieldGenerator { +public: + /// Logically negate a boolean expression + LogicalNot(FieldGeneratorPtr expr) : expr(expr) {} + + /// Evaluate expression, check it's a bool, and return 1 or 0 + double generate(const Context& ctx) override { + return toBool(expr->generate(ctx)) ? 0.0 : 1.0; + } + + std::string str() const override { + return "!"s + expr->str(); + } +private: + FieldGeneratorPtr expr; +}; + ///////////////////////////////////////////// ExpressionParser::ExpressionParser() { // Add standard binary operations addBinaryOp('|', std::make_shared(nullptr, nullptr, '|'), 3); addBinaryOp('&', std::make_shared(nullptr, nullptr, '&'), 5); + addBinaryOp('<', std::make_shared(nullptr, nullptr, '<'), 7); + addBinaryOp('>', std::make_shared(nullptr, nullptr, '>'), 7); addBinaryOp('+', std::make_shared(nullptr, nullptr, '+'), 10); addBinaryOp('-', std::make_shared(nullptr, nullptr, '-'), 10); addBinaryOp('*', std::make_shared(nullptr, nullptr, '*'), 20); @@ -498,6 +522,11 @@ FieldGeneratorPtr ExpressionParser::parsePrimary(LexInfo& lex) const { // Don't eat the minus, and return an implicit zero return std::make_shared(0.0); } + case '!': { + // Logical not + lex.nextToken(); // Eat '!' + return std::make_shared(parsePrimary(lex)); + } case '(': { return parseParenExpr(lex); } diff --git a/tests/unit/sys/test_expressionparser.cxx b/tests/unit/sys/test_expressionparser.cxx index 00cb23c042..ae8ccea625 100644 --- a/tests/unit/sys/test_expressionparser.cxx +++ b/tests/unit/sys/test_expressionparser.cxx @@ -379,9 +379,9 @@ TEST_F(ExpressionParserTest, BadBinaryOp) { TEST_F(ExpressionParserTest, AddBinaryOp) { // Add a synonym for multiply with a lower precedence than addition - parser.addBinaryOp('&', std::make_shared(nullptr, nullptr, '*'), 5); + parser.addBinaryOp('$', std::make_shared(nullptr, nullptr, '*'), 5); - auto fieldgen = parser.parseString("2 & x + 3"); + auto fieldgen = parser.parseString("2 $ x + 3"); EXPECT_EQ(fieldgen->str(), "(2*(x+3))"); for (auto x : x_array) { @@ -679,3 +679,39 @@ TEST_F(ExpressionParserTest, FuzzyFind) { EXPECT_EQ(first_CAPS_match->name, "multiply"); EXPECT_EQ(first_CAPS_match->distance, 1); } + +TEST_F(ExpressionParserTest, LogicalOR) { + EXPECT_DOUBLE_EQ(parser.parseString("1 | 0")->generate({}), 1.0); + EXPECT_DOUBLE_EQ(parser.parseString("0 | 1")->generate({}), 1.0); + EXPECT_DOUBLE_EQ(parser.parseString("1 | 1")->generate({}), 1.0); + EXPECT_DOUBLE_EQ(parser.parseString("0 | 0")->generate({}), 0.0); +} + +TEST_F(ExpressionParserTest, LogicalAND) { + EXPECT_DOUBLE_EQ(parser.parseString("1 & 0")->generate({}), 0.0); + EXPECT_DOUBLE_EQ(parser.parseString("0 & 1")->generate({}), 0.0); + EXPECT_DOUBLE_EQ(parser.parseString("1 & 1")->generate({}), 1.0); + EXPECT_DOUBLE_EQ(parser.parseString("0 & 0")->generate({}), 0.0); +} + +TEST_F(ExpressionParserTest, LogicalNOT) { + EXPECT_DOUBLE_EQ(parser.parseString("!0")->generate({}), 1.0); + EXPECT_DOUBLE_EQ(parser.parseString("!1")->generate({}), 0.0); +} + +TEST_F(ExpressionParserTest, LogicalNOTprecedence) { + // Should bind more strongly than all binary operators + EXPECT_DOUBLE_EQ(parser.parseString("!1 & 0")->generate({}), 0.0); + EXPECT_DOUBLE_EQ(parser.parseString("1 & !0")->generate({}), 1.0); +} + +TEST_F(ExpressionParserTest, CompareGT) { + EXPECT_DOUBLE_EQ(parser.parseString("1 > 0")->generate({}), 1.0); + EXPECT_DOUBLE_EQ(parser.parseString("3 > 5")->generate({}), 0.0); +} + +TEST_F(ExpressionParserTest, CompareLT) { + EXPECT_DOUBLE_EQ(parser.parseString("1 < 0")->generate({}), 0.0); + EXPECT_DOUBLE_EQ(parser.parseString("3 < 5")->generate({}), 1.0); +} + diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index 8ef86a0668..e7067ef4d5 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -1392,3 +1392,48 @@ INSTANTIATE_TEST_CASE_P(BoolInvalidTests, BoolInvalidTestParametrized, "B", "yellow", "Yogi", "test", "truelong", "Tim", "2", "not", "No bool", "nOno", "falsebuttoolong", "-1", "1.1")); + +TEST_F(OptionsTest, BoolLogicalOR) { + ASSERT_TRUE(Options("true | false").as()); + ASSERT_TRUE(Options("false | true").as()); + ASSERT_TRUE(Options("true | true").as()); + ASSERT_FALSE(Options("false | false").as()); + ASSERT_TRUE(Options("true | false | true").as()); +} + +TEST_F(OptionsTest, BoolLogicalAND) { + ASSERT_FALSE(Options("true & false").as()); + ASSERT_FALSE(Options("false & true").as()); + ASSERT_TRUE(Options("true & true").as()); + ASSERT_FALSE(Options("false & false").as()); + ASSERT_FALSE(Options("true & false & true").as()); + + EXPECT_THROW(Options("true & 1.3").as(), BoutException); + EXPECT_THROW(Options("2 & false").as(), BoutException); +} + +TEST_F(OptionsTest, BoolLogicalNOT) { + ASSERT_FALSE(Options("!true").as()); + ASSERT_TRUE(Options("!false").as()); + ASSERT_FALSE(Options("!true & false").as()); + ASSERT_TRUE(Options("!(true & false)").as()); + ASSERT_TRUE(Options("true & !false").as()); + + EXPECT_THROW(Options("!2").as(), BoutException); + EXPECT_THROW(Options("!1.2").as(), BoutException); +} + +TEST_F(OptionsTest, BoolComparisonGT) { + ASSERT_TRUE(Options("2 > 1").as()); + ASSERT_FALSE(Options("2 > 3").as()); +} + +TEST_F(OptionsTest, BoolComparisonLT) { + ASSERT_FALSE(Options("2 < 1").as()); + ASSERT_TRUE(Options("2 < 3").as()); +} + +TEST_F(OptionsTest, BoolCompound) { + ASSERT_TRUE(Options("true & !false").as()); + ASSERT_TRUE(Options("2 > 1 & 2 < 3").as()); +} From 822fad4a556d1f90cea44ce60888b77ce21bdcd7 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 2 Jan 2024 10:24:20 -0800 Subject: [PATCH 172/412] Document boolean expresion changes - CHANGELOG entry under breaking changes - Section in manual on boolean expressions, with notes highlighting changes from previous versions. --- CHANGELOG.md | 2 + manual/sphinx/user_docs/bout_options.rst | 59 ++++++++++++++++++++---- 2 files changed, 53 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 656b284b9d..d71dc470e9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,8 @@ ### Breaking changes - The autotools `./configure` build system has been removed +- Parsing of booleans has changed [\#2828][https://github.com/boutproject/BOUT-dev/pull/2828] ([bendudson][https://github.com/bendudson]). + See the [manual page](https://bout-dev.readthedocs.io/en/stable/user_docs/bout_options.html#boolean-expressions) for details. ## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0) diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst index 976faa0544..5586f7b3b1 100644 --- a/manual/sphinx/user_docs/bout_options.rst +++ b/manual/sphinx/user_docs/bout_options.rst @@ -48,9 +48,10 @@ name in square brackets. Option names can contain almost any character except ’=’ and ’:’, including unicode. If they start with a number or ``.``, contain -arithmetic symbols (``+-*/^``), brackets (``(){}[]``), equality -(``=``), whitespace or comma ``,``, then these will need to be escaped -in expressions. See below for how this is done. +arithmetic/boolean operator symbols (``+-*/^&|!<>``), brackets +(``(){}[]``), equality (``=``), whitespace or comma ``,``, then these +will need to be escaped in expressions. See below for how this is +done. Subsections can also be used, separated by colons ’:’, e.g. @@ -87,6 +88,13 @@ operators, with the usual precedence rules. In addition to ``π``, expressions can use predefined variables ``x``, ``y``, ``z`` and ``t`` to refer to the spatial and time coordinates (for definitions of the values these variables take see :ref:`sec-expressions`). + +.. note:: The variables ``x``, ``y``, ``z`` should only be defined + when reading a 3D field; ``t`` should only be defined when reading + a time-dependent value. Earlier BOUT++ versions (v5.1.0 and earler) + defined all of these to be 0 by default e.g. when reading scalar + inputs. + A number of functions are defined, listed in table :numref:`tab-initexprfunc`. One slightly unusual feature (borrowed from `Julia `_) is that if a number comes before a symbol or an opening bracket (``(``) @@ -109,11 +117,11 @@ The convention is the same as in `Python `_: If brackets are not balanced (closed) then the expression continues on the next line. All expressions are calculated in floating point and then converted to -an integer if needed when read inside BOUT++. The conversion is done by rounding -to the nearest integer, but throws an error if the floating point -value is not within :math:`1e-3` of an integer. This is to minimise -unexpected behaviour. If you want to round any result to an integer, -use the ``round`` function: +an integer (or boolean) if needed when read inside BOUT++. The +conversion is done by rounding to the nearest integer, but throws an +error if the floating point value is not within :math:`1e-3` of an +integer. This is to minimise unexpected behaviour. If you want to +round any result to an integer, use the ``round`` function: .. code-block:: cfg @@ -125,6 +133,41 @@ number, since the type is determined by how it is used. Have a look through the examples to see how the options are used. +Boolean expressions +~~~~~~~~~~~~~~~~~~~ + +Boolean values must be either "true" or "false". Booleans can be +combined into expressions using binary operators `&` (logical AND), +`|` (logical OR), and unary operator `!` (logical NOT). For example +"true & false" evaluates to `false`; "!false" evaluates to `true`. +Like real values and integers, boolean expressions can refer to other +variables: + +.. code-block:: cfg + + switch = true + other_switch = !switch + +Boolean expressions can be formed by comparing real values using +`>` and `<` comparison operators: + +.. code-block:: cfg + + value = 3.2 + is_true = value > 3 + is_false = value < 2 + +.. note:: + Previous BOUT++ versions (v5.1.0 and earlier) were case + insensitive when reading boolean values, so would read "True" or + "yEs" as `true`, and "False" or "No" as `false`. These earlier + versions did not allow boolean expressions. + +Internally, booleans are evaluated as real values, with `true` being 1 +and `false` being 0. Logical operators (`&`, `|`, `!`) check that +their left and right arguments are either close to 0 or close to 1 +(like integers, "close to" is within 1e-3). + Special symbols in Option names ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From d0df5cdab406a351aa42290c80648527c2b9494a Mon Sep 17 00:00:00 2001 From: bendudson Date: Tue, 2 Jan 2024 18:26:16 +0000 Subject: [PATCH 173/412] Apply clang-format changes --- src/sys/expressionparser.cxx | 5 ++--- tests/unit/sys/test_expressionparser.cxx | 1 - 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx index 14c29c7c09..8290a4cae0 100644 --- a/src/sys/expressionparser.cxx +++ b/src/sys/expressionparser.cxx @@ -232,9 +232,8 @@ class LogicalNot : public FieldGenerator { return toBool(expr->generate(ctx)) ? 0.0 : 1.0; } - std::string str() const override { - return "!"s + expr->str(); - } + std::string str() const override { return "!"s + expr->str(); } + private: FieldGeneratorPtr expr; }; diff --git a/tests/unit/sys/test_expressionparser.cxx b/tests/unit/sys/test_expressionparser.cxx index ae8ccea625..c4f0ebfcf3 100644 --- a/tests/unit/sys/test_expressionparser.cxx +++ b/tests/unit/sys/test_expressionparser.cxx @@ -714,4 +714,3 @@ TEST_F(ExpressionParserTest, CompareLT) { EXPECT_DOUBLE_EQ(parser.parseString("1 < 0")->generate({}), 0.0); EXPECT_DOUBLE_EQ(parser.parseString("3 < 5")->generate({}), 1.0); } - From d52bb141f0e29a78c3c19425a7c5478cc45ab540 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 2 Jan 2024 12:31:38 -0800 Subject: [PATCH 174/412] Boolean expressions: Allow "True" and "False" again Python formats booleans with uppercase first letter, so for ease of input and command-line formatting allow these variations. Added to documentation. --- manual/sphinx/user_docs/bout_options.rst | 14 ++++++++------ src/field/field_factory.cxx | 4 ++++ tests/unit/sys/test_options.cxx | 6 +++--- 3 files changed, 15 insertions(+), 9 deletions(-) diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst index 5586f7b3b1..85a8a17d59 100644 --- a/manual/sphinx/user_docs/bout_options.rst +++ b/manual/sphinx/user_docs/bout_options.rst @@ -136,12 +136,14 @@ Have a look through the examples to see how the options are used. Boolean expressions ~~~~~~~~~~~~~~~~~~~ -Boolean values must be either "true" or "false". Booleans can be -combined into expressions using binary operators `&` (logical AND), -`|` (logical OR), and unary operator `!` (logical NOT). For example -"true & false" evaluates to `false`; "!false" evaluates to `true`. -Like real values and integers, boolean expressions can refer to other -variables: +Boolean values must be "true", "false", "True", "False", "1" or +"0". All lowercase ("true"/"false") is preferred, but the uppercase +versions are allowed to support Python string conversions. Booleans +can be combined into expressions using binary operators `&` (logical +AND), `|` (logical OR), and unary operator `!` (logical NOT). For +example "true & false" evaluates to `false`; "!false" evaluates to +`true`. Like real values and integers, boolean expressions can refer +to other variables: .. code-block:: cfg diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx index f6c929a3a3..f65e20332a 100644 --- a/src/field/field_factory.cxx +++ b/src/field/field_factory.cxx @@ -118,6 +118,10 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt) addGenerator("true", std::make_shared(1)); addGenerator("false", std::make_shared(0)); + // Python converts booleans to True/False + addGenerator("True", std::make_shared(1)); + addGenerator("False", std::make_shared(0)); + // Some standard functions addGenerator("sin", std::make_shared>(nullptr, "sin")); addGenerator("cos", std::make_shared>(nullptr, "cos")); diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index e7067ef4d5..5ba3826cf8 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -1360,7 +1360,7 @@ TEST_P(BoolTrueTestParametrized, BoolTrueFromString) { } INSTANTIATE_TEST_CASE_P(BoolTrueTests, BoolTrueTestParametrized, - ::testing::Values("true", "1")); + ::testing::Values("true", "True", "1")); class BoolFalseTestParametrized : public OptionsTest, public ::testing::WithParamInterface {}; @@ -1374,7 +1374,7 @@ TEST_P(BoolFalseTestParametrized, BoolFalseFromString) { } INSTANTIATE_TEST_CASE_P(BoolFalseTests, BoolFalseTestParametrized, - ::testing::Values("false", "0")); + ::testing::Values("false", "False", "0")); class BoolInvalidTestParametrized : public OptionsTest, public ::testing::WithParamInterface {}; @@ -1388,7 +1388,7 @@ TEST_P(BoolInvalidTestParametrized, BoolInvalidFromString) { } INSTANTIATE_TEST_CASE_P(BoolInvalidTests, BoolInvalidTestParametrized, - ::testing::Values("yes", "no", "True", "False", "y", "n", "a", + ::testing::Values("yes", "no", "y", "n", "a", "B", "yellow", "Yogi", "test", "truelong", "Tim", "2", "not", "No bool", "nOno", "falsebuttoolong", "-1", "1.1")); From 343acf465ff08b4500ccee27ea638d2fc75d99ee Mon Sep 17 00:00:00 2001 From: bendudson Date: Tue, 2 Jan 2024 20:33:51 +0000 Subject: [PATCH 175/412] Apply clang-format changes --- tests/unit/sys/test_options.cxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index 5ba3826cf8..40458757ec 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -1388,10 +1388,10 @@ TEST_P(BoolInvalidTestParametrized, BoolInvalidFromString) { } INSTANTIATE_TEST_CASE_P(BoolInvalidTests, BoolInvalidTestParametrized, - ::testing::Values("yes", "no", "y", "n", "a", - "B", "yellow", "Yogi", "test", "truelong", - "Tim", "2", "not", "No bool", "nOno", - "falsebuttoolong", "-1", "1.1")); + ::testing::Values("yes", "no", "y", "n", "a", "B", "yellow", + "Yogi", "test", "truelong", "Tim", "2", "not", + "No bool", "nOno", "falsebuttoolong", "-1", + "1.1")); TEST_F(OptionsTest, BoolLogicalOR) { ASSERT_TRUE(Options("true | false").as()); From 128797010ec78bdab8e3a82e14363ab21b0d445b Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 2 Jan 2024 15:36:03 -0800 Subject: [PATCH 176/412] FieldFactory: Use string matching for options Constructor reads a bool from options, but that now needs a FieldFactory to parse. The proper solution is probably to use ExpressionParser in more places, to avoid this circular dependency. --- src/field/field_factory.cxx | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx index f65e20332a..fbc47bb129 100644 --- a/src/field/field_factory.cxx +++ b/src/field/field_factory.cxx @@ -93,8 +93,18 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt) // Note: don't use 'options' here because 'options' is a 'const Options*' // pointer, so this would fail if the "input" section is not present. Options& nonconst_options{opt == nullptr ? Options::root() : *opt}; - transform_from_field_aligned = - nonconst_options["input"]["transform_from_field_aligned"].withDefault(true); + + // Convert from string, or FieldFactory is used to parse the string + auto str = nonconst_options["input"]["transform_from_field_aligned"].withDefault("true"); + if ((str == "true") or (str == "True")) { + transform_from_field_aligned = true; + } else if ((str == "false") or (str == "False")) { + transform_from_field_aligned = false; + } else { + throw ParseException( + "Invalid boolean given as input:transform_from_field_aligned: '{:s}'", + nonconst_options["input"]["transform_from_field_aligned"].as()); + } // Convert using stoi rather than Options, or a FieldFactory is used to parse // the string, leading to infinite loop. From 24e7d1795860f307c54899d48c3ea9c16479ca8d Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 2 Jan 2024 15:37:55 -0800 Subject: [PATCH 177/412] Fix test-twistshift-staggered Not passing mesh to create3D, causing an error. --- .../test-twistshift-staggered/test-twistshift.cxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx index c9f8be7b09..33b45b662d 100644 --- a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx +++ b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx @@ -4,11 +4,11 @@ int main(int argc, char** argv) { BoutInitialise(argc, argv); - Field3D test = FieldFactory::get()->create3D("test", nullptr, nullptr, CELL_YLOW); + using bout::globals::mesh; - Field3D test_aligned = toFieldAligned(test); + Field3D test = FieldFactory::get()->create3D("test", nullptr, mesh, CELL_YLOW); - using bout::globals::mesh; + Field3D test_aligned = toFieldAligned(test); // zero guard cells to check that communication is doing something for (int x = 0; x < mesh->LocalNx; x++) { @@ -25,7 +25,7 @@ int main(int argc, char** argv) { mesh->communicate(test_aligned); Options::root()["check"] = - FieldFactory::get()->create3D("check", nullptr, nullptr, CELL_YLOW); + FieldFactory::get()->create3D("check", nullptr, mesh, CELL_YLOW); Options::root()["test"] = test; Options::root()["test_aligned"] = test_aligned; From 1e76fa2106b9e6adffd2093c05244168cc154c47 Mon Sep 17 00:00:00 2001 From: bendudson Date: Tue, 2 Jan 2024 23:39:14 +0000 Subject: [PATCH 178/412] Apply clang-format changes --- src/field/field_factory.cxx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx index fbc47bb129..f65f2e7f55 100644 --- a/src/field/field_factory.cxx +++ b/src/field/field_factory.cxx @@ -95,7 +95,9 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt) Options& nonconst_options{opt == nullptr ? Options::root() : *opt}; // Convert from string, or FieldFactory is used to parse the string - auto str = nonconst_options["input"]["transform_from_field_aligned"].withDefault("true"); + auto str = + nonconst_options["input"]["transform_from_field_aligned"].withDefault( + "true"); if ((str == "true") or (str == "True")) { transform_from_field_aligned = true; } else if ((str == "false") or (str == "False")) { From bf3f64f74b72ab20ec3e1ed95017a7cf8b76a82d Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 11:13:05 +0100 Subject: [PATCH 179/412] rename getDefaultRegion to getValidRegionWithDefault --- include/bout/field2d.hxx | 2 +- include/bout/field3d.hxx | 2 +- include/bout/fieldperp.hxx | 2 +- src/field/field3d.cxx | 4 +- src/field/gen_fieldops.jinja | 4 +- src/field/generated_fieldops.cxx | 72 ++++++++++++++++---------------- 6 files changed, 43 insertions(+), 43 deletions(-) diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index 356c2e2896..ea61648d3f 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -174,7 +174,7 @@ public: /// Return a Region reference to use to iterate over this field const Region& getRegion(REGION region) const; const Region& getRegion(const std::string& region_name) const; - const Region& getDefaultRegion(const std::string& region_name) const { + const Region& getValidRegionWithDefault(const std::string& region_name) const { return getRegion(region_name); } diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx index 34658676c6..21484f2ea5 100644 --- a/include/bout/field3d.hxx +++ b/include/bout/field3d.hxx @@ -314,7 +314,7 @@ public: const Region& getRegion(REGION region) const; const Region& getRegion(const std::string& region_name) const; /// Use region provided by the default, and if none is set, use the provided one - const Region& getDefaultRegion(const std::string& region_name) const; + const Region& getValidRegionWithDefault(const std::string& region_name) const; void setRegion(const std::string& region_name); void resetRegion() { regionID = -1; }; void setRegion(int id) { regionID = id; }; diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx index 3295caf98d..3b8ed45db6 100644 --- a/include/bout/fieldperp.hxx +++ b/include/bout/fieldperp.hxx @@ -98,7 +98,7 @@ public: /// Return a Region reference to use to iterate over this field const Region& getRegion(REGION region) const; const Region& getRegion(const std::string& region_name) const; - const Region& getDefaultRegion(const std::string& region_name) const { + const Region& getValidRegionWithDefault(const std::string& region_name) const { return getRegion(region_name); } diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 54c3afcf02..b284e35439 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -742,7 +742,7 @@ namespace { #if CHECK > 2 void checkDataIsFiniteOnRegion(const Field3D& f, const std::string& region) { // Do full checks - BOUT_FOR_SERIAL(i, f.getDefaultRegion(region)) { + BOUT_FOR_SERIAL(i, f.getValidRegionWithDefault(region)) { if (!finite(f[i])) { throw BoutException("Field3D: Operation on non-finite data at [{:d}][{:d}][{:d}]\n", i.x(), i.y(), i.z()); @@ -820,7 +820,7 @@ void swap(Field3D& first, Field3D& second) noexcept { swap(first.ydown_fields, second.ydown_fields); } -const Region& Field3D::getDefaultRegion(const std::string& region_name) const { +const Region& Field3D::getValidRegionWithDefault(const std::string& region_name) const { if (regionID != -1) { return fieldmesh->getRegion(regionID); } diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja index 40a59172a3..ecd4e628cc 100644 --- a/src/field/gen_fieldops.jinja +++ b/src/field/gen_fieldops.jinja @@ -52,11 +52,11 @@ } {% elif (operator == "/") and (rhs == "BoutReal") %} const auto tmp = 1.0 / {{rhs.index}}; - {{region_loop}}({{index_var}}, {{out.name}}.getDefaultRegion({{region_name}})) { + {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) { {{out.index}} = {{lhs.index}} * tmp; } {% else %} - {{region_loop}}({{index_var}}, {{out.name}}.getDefaultRegion({{region_name}})) { + {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) { {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}}; } {% endif %} diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx index 2193fd4272..6b778acee3 100644 --- a/src/field/generated_fieldops.cxx +++ b/src/field/generated_fieldops.cxx @@ -16,7 +16,7 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) { result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -60,7 +60,7 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) { result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -104,7 +104,7 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) { result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -148,7 +148,7 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) { result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID())); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -481,7 +481,7 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) { result.setRegion(lhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * rhs; } @@ -522,7 +522,7 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) { result.setRegion(lhs.getRegionID()); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * tmp; } @@ -563,7 +563,7 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) { result.setRegion(lhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] + rhs; } @@ -603,7 +603,7 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) { result.setRegion(lhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] - rhs; } @@ -734,7 +734,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -770,7 +770,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -806,7 +806,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -842,7 +842,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -957,7 +957,7 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * rhs; } @@ -992,7 +992,7 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * tmp; } @@ -1027,7 +1027,7 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] + rhs; } @@ -1061,7 +1061,7 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] - rhs; } @@ -1464,7 +1464,7 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * rhs[index]; } @@ -1500,7 +1500,7 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] / rhs[index]; } @@ -1536,7 +1536,7 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] + rhs[index]; } @@ -1572,7 +1572,7 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] - rhs[index]; } @@ -1607,7 +1607,7 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * rhs; } @@ -1642,7 +1642,7 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) { checkData(rhs); const auto tmp = 1.0 / rhs; - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] * tmp; } @@ -1676,7 +1676,7 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] + rhs; } @@ -1710,7 +1710,7 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs[index] - rhs; } @@ -1746,7 +1746,7 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) { result.setRegion(rhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs * rhs[index]; } @@ -1763,7 +1763,7 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) { result.setRegion(rhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs / rhs[index]; } @@ -1780,7 +1780,7 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) { result.setRegion(rhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs + rhs[index]; } @@ -1797,7 +1797,7 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) { result.setRegion(rhs.getRegionID()); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs - rhs[index]; } @@ -1812,7 +1812,7 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs * rhs[index]; } @@ -1827,7 +1827,7 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs / rhs[index]; } @@ -1842,7 +1842,7 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs + rhs[index]; } @@ -1857,7 +1857,7 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs - rhs[index]; } @@ -1872,7 +1872,7 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs * rhs[index]; } @@ -1887,7 +1887,7 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs / rhs[index]; } @@ -1902,7 +1902,7 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs + rhs[index]; } @@ -1917,7 +1917,7 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) { checkData(lhs); checkData(rhs); - BOUT_FOR(index, result.getDefaultRegion("RGN_ALL")) { + BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) { result[index] = lhs - rhs[index]; } From 3c507287e35b7252d44cdc3f08a378a2cd573d61 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 11:13:19 +0100 Subject: [PATCH 180/412] Remove python2 compatibility --- tests/MMS/spatial/fci/mms.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py index 806441b330..1e71135c90 100755 --- a/tests/MMS/spatial/fci/mms.py +++ b/tests/MMS/spatial/fci/mms.py @@ -3,9 +3,6 @@ # Generate manufactured solution and sources for FCI test # -from __future__ import division -from __future__ import print_function - from boutdata.mms import * from sympy import sin, cos, sqrt From 0c5d41c848b870ae9407fec2ea274cefb0687c58 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 11:13:27 +0100 Subject: [PATCH 181/412] Fix escaping --- tests/MMS/spatial/fci/runtest | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest index 3db54a3870..712442a795 100755 --- a/tests/MMS/spatial/fci/runtest +++ b/tests/MMS/spatial/fci/runtest @@ -164,7 +164,7 @@ if False: dx, error_inf[nslice], "--", - label="{} $l_\inf$".format(method_orders[nslice]["name"]), + label="{} $l_\\inf$".format(method_orders[nslice]["name"]), ) ax.legend(loc="upper left") ax.grid() From 121a4abe938be3799db06e7510c97e5068d7bac9 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 11:17:10 +0100 Subject: [PATCH 182/412] Add comments on OpenMP + mutex --- src/mesh/mesh.cxx | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index a2d9b5e6c8..78eb85ce31 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -785,6 +785,10 @@ int Mesh::getCommonRegion(int lhs, int rhs) { const size_t pos = (high * (high - 1)) / 2 + low; if (region3Dintersect.size() <= pos) { BOUT_OMP(critical(mesh_intersection_realloc)) + // By default this function does not need the mutex, however, if we are + // going to allocate global memory, we need to use a mutex. + // Now that we have the mutex, we need to check again whether a + // different thread was faster and already allocated. #if BOUT_USE_OPENMP if (region3Dintersect.size() <= pos) #endif @@ -797,6 +801,7 @@ int Mesh::getCommonRegion(int lhs, int rhs) { } { BOUT_OMP(critical(mesh_intersection)) + // See comment above why we need to check again in case of OpenMP #if BOUT_USE_OPENMP if (region3Dintersect[pos] == -1) #endif From 242a6f4fab54b76c988fe39cf740c66d80b3065c Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 11:32:47 +0100 Subject: [PATCH 183/412] Add more OpenMP comments --- src/mesh/mesh.cxx | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 78eb85ce31..33cd22d40d 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -789,6 +789,10 @@ int Mesh::getCommonRegion(int lhs, int rhs) { // going to allocate global memory, we need to use a mutex. // Now that we have the mutex, we need to check again whether a // different thread was faster and already allocated. + // BOUT_OMP(single) would work in most cases, but it would fail if the + // function is called in parallel with different arguments. While BOUT++ + // is not currently doing it, other openmp parallised projects might be + // calling BOUT++ in this way. #if BOUT_USE_OPENMP if (region3Dintersect.size() <= pos) #endif From b8be3fea3919a0ca102f8e3b63904e326b693148 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 14:24:57 +0100 Subject: [PATCH 184/412] use std::optional Should make the intent much cleaner, and also raises a nice exception if a value is used, without being present. --- include/bout/field3d.hxx | 10 ++++++---- include/bout/mesh.hxx | 15 ++++++++++----- src/field/field3d.cxx | 4 ++-- src/mesh/mesh.cxx | 37 +++++++++++++++++++++---------------- 4 files changed, 39 insertions(+), 27 deletions(-) diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx index 21484f2ea5..9f5326253d 100644 --- a/include/bout/field3d.hxx +++ b/include/bout/field3d.hxx @@ -40,6 +40,7 @@ class Mesh; // #include "bout/mesh.hxx" #include "bout/utils.hxx" +#include #include /// Class for 3D X-Y-Z scalar fields @@ -316,9 +317,10 @@ public: /// Use region provided by the default, and if none is set, use the provided one const Region& getValidRegionWithDefault(const std::string& region_name) const; void setRegion(const std::string& region_name); - void resetRegion() { regionID = -1; }; - void setRegion(int id) { regionID = id; }; - int getRegionID() const { return regionID; }; + void resetRegion() { regionID.reset(); }; + void setRegion(size_t id) { regionID = id; }; + void setRegion(std::optional id) { regionID = id; }; + std::optional getRegionID() const { return regionID; }; /// Return a Region reference to use to iterate over the x- and /// y-indices of this field @@ -511,7 +513,7 @@ private: std::vector yup_fields{}, ydown_fields{}; /// RegionID over which the field is valid - int regionID{-1}; + std::optional regionID; }; // Non-member overloaded operators diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 9acf6a6b89..6633fa923a 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -74,6 +74,7 @@ class Mesh; #include #include #include +#include #include #include @@ -795,9 +796,13 @@ public: // Switch for communication of corner guard and boundary cells const bool include_corner_cells; - int getCommonRegion(int, int); - int getRegionID(const std::string& region) const; - const Region& getRegion(int RegionID) const { return region3D[RegionID]; } + std::optional getCommonRegion(std::optional, std::optional); + size_t getRegionID(const std::string& region) const; + const Region& getRegion(size_t RegionID) const { return region3D[RegionID]; } + const Region& getRegion(std::optional RegionID) const { + ASSERT1(RegionID.has_value()); + return region3D[RegionID.value()]; + } private: /// Allocates default Coordinates objects @@ -811,9 +816,9 @@ private: bool force_interpolate_from_centre = false); //Internal region related information - std::map regionMap3D; + std::map regionMap3D; std::vector> region3D; - std::vector region3Dintersect; + std::vector> region3Dintersect; std::map> regionMap2D; std::map> regionMapPerp; Array indexLookup3Dto2D; diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index b284e35439..2d62ef923a 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -821,8 +821,8 @@ void swap(Field3D& first, Field3D& second) noexcept { } const Region& Field3D::getValidRegionWithDefault(const std::string& region_name) const { - if (regionID != -1) { - return fieldmesh->getRegion(regionID); + if (regionID.has_value()) { + return fieldmesh->getRegion(regionID.value()); } return fieldmesh->getRegion(region_name); } diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 33cd22d40d..3668de6d3b 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -562,7 +562,7 @@ const Region<>& Mesh::getRegion3D(const std::string& region_name) const { return region3D[found->second]; } -int Mesh::getRegionID(const std::string& region_name) const { +size_t Mesh::getRegionID(const std::string& region_name) const { const auto found = regionMap3D.find(region_name); if (found == end(regionMap3D)) { throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name); @@ -604,19 +604,19 @@ void Mesh::addRegion3D(const std::string& region_name, const Region<>& region) { region_name); } - int id = -1; + std::optional id; for (size_t i = 0; i < region3D.size(); ++i) { if (region3D[i] == region) { id = i; break; } } - if (id == -1) { + if (!id.has_value()) { id = region3D.size(); region3D.push_back(region); } - regionMap3D[region_name] = id; + regionMap3D[region_name] = id.value(); output_verbose.write(_("Registered region 3D {:s}"), region_name); output_verbose << "\n:\t" << region.getStats() << "\n"; @@ -761,15 +761,20 @@ constexpr decltype(MeshFactory::section_name) MeshFactory::section_name; constexpr decltype(MeshFactory::option_name) MeshFactory::option_name; constexpr decltype(MeshFactory::default_type) MeshFactory::default_type; -int Mesh::getCommonRegion(int lhs, int rhs) { - if (lhs == rhs) { +std::optional Mesh::getCommonRegion(std::optional lhs, + std::optional rhs) { + if (!lhs.has_value()) { + return rhs; + } + if (!rhs.has_value()) { return lhs; } - const int low = std::min(lhs, rhs); - const int high = std::max(lhs, rhs); - if (low == -1) { - return high; + if (lhs.value() == rhs.value()) { + return lhs; } + const size_t low = std::min(lhs.value(), rhs.value()); + const size_t high = std::max(lhs.value(), rhs.value()); + /* Memory layout of indices * left is lower index, bottom is higher index * 0 1 2 3 @@ -797,17 +802,17 @@ int Mesh::getCommonRegion(int lhs, int rhs) { if (region3Dintersect.size() <= pos) #endif { - region3Dintersect.resize(pos + 1, -1); + region3Dintersect.resize(pos + 1, std::nullopt); } } - if (region3Dintersect[pos] != -1) { + if (region3Dintersect[pos].has_value()) { return region3Dintersect[pos]; } { BOUT_OMP(critical(mesh_intersection)) - // See comment above why we need to check again in case of OpenMP + // See comment above why we need to check again in case of OpenMP #if BOUT_USE_OPENMP - if (region3Dintersect[pos] == -1) + if (!region3Dintersect[pos].has_value()) #endif { auto common = intersection(region3D[low], region3D[high]); @@ -817,9 +822,9 @@ int Mesh::getCommonRegion(int lhs, int rhs) { break; } } - if (region3Dintersect[pos] == -1) { + if (!region3Dintersect[pos].has_value()) { + region3Dintersect[pos] = region3D.size(); region3D.push_back(common); - region3Dintersect[pos] = region3D.size() - 1; } } } From 433f92b7aab508ee6bbc8913c7ef88a4872908b4 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Fri, 5 Jan 2024 13:34:54 +0000 Subject: [PATCH 185/412] Apply clang-format changes --- src/field/field3d.cxx | 3 ++- src/mesh/mesh.cxx | 16 ++++++++-------- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index 2d62ef923a..b4bb0d394f 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -820,7 +820,8 @@ void swap(Field3D& first, Field3D& second) noexcept { swap(first.ydown_fields, second.ydown_fields); } -const Region& Field3D::getValidRegionWithDefault(const std::string& region_name) const { +const Region& +Field3D::getValidRegionWithDefault(const std::string& region_name) const { if (regionID.has_value()) { return fieldmesh->getRegion(regionID.value()); } diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 3668de6d3b..af9f2c38f3 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -790,14 +790,14 @@ std::optional Mesh::getCommonRegion(std::optional lhs, const size_t pos = (high * (high - 1)) / 2 + low; if (region3Dintersect.size() <= pos) { BOUT_OMP(critical(mesh_intersection_realloc)) - // By default this function does not need the mutex, however, if we are - // going to allocate global memory, we need to use a mutex. - // Now that we have the mutex, we need to check again whether a - // different thread was faster and already allocated. - // BOUT_OMP(single) would work in most cases, but it would fail if the - // function is called in parallel with different arguments. While BOUT++ - // is not currently doing it, other openmp parallised projects might be - // calling BOUT++ in this way. + // By default this function does not need the mutex, however, if we are + // going to allocate global memory, we need to use a mutex. + // Now that we have the mutex, we need to check again whether a + // different thread was faster and already allocated. + // BOUT_OMP(single) would work in most cases, but it would fail if the + // function is called in parallel with different arguments. While BOUT++ + // is not currently doing it, other openmp parallised projects might be + // calling BOUT++ in this way. #if BOUT_USE_OPENMP if (region3Dintersect.size() <= pos) #endif From 36f152dc04dd14a339a7c88376a26b0a049c163b Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 15:46:53 +0100 Subject: [PATCH 186/412] Explicitly set -std=c++17 for --cflags --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index ada2e6b4c4..88b31e8553 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -468,7 +468,7 @@ set_target_properties(bout++ PROPERTIES # Set some variables for the bout-config script set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++") set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include") -set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS}") +set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17") target_compile_features(bout++ PUBLIC cxx_std_17) set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF) From d4dab6c3f518aebae36f38a2b3dd215b135642a6 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 5 Jan 2024 15:47:08 +0100 Subject: [PATCH 187/412] Be more verbose by default --- examples/make-script/makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/make-script/makefile b/examples/make-script/makefile index ac5f4e96a4..b941125bce 100644 --- a/examples/make-script/makefile +++ b/examples/make-script/makefile @@ -22,11 +22,11 @@ LDFLAGS:=$(shell bout-config --libs) $(TARGET): makefile $(OBJ) @echo " Linking" $(TARGET) - @$(LD) -o $(TARGET) $(OBJ) $(LDFLAGS) + $(LD) -o $(TARGET) $(OBJ) $(LDFLAGS) %.o: %.cxx @echo " Compiling " $(@F:.o=.cxx) - @$(CXX) $(CFLAGS) -c $(@F:.o=.cxx) -o $@ + $(CXX) $(CFLAGS) -c $(@F:.o=.cxx) -o $@ .PHONY: clean clean: From 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zLn4wV8o78R{E(t~uK9>mCTf)SWnLP=-^>|ikNXB(44bQ2zT9k_?e;b=3y8Akh z4Opz9N8xgtH2pQ6UlH6=X+Mmf=97dx zcfss#^wT1RowV=5D=HY&yViJaBO;iB>W&o ns7KIl$%tYkuo>QRHpM6#`M>GDbr}8MZ4BDx%C7%`^Y8uxHt^j& diff --git a/tests/integrated/test-interchange-instability/orig_test.idl.dat b/tests/integrated/test-interchange-instability/orig_test.idl.dat deleted file mode 100644 index 93652ca8563239dd35cd365709fb936bea40e9b6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2612 zcmeHITWl0n7~a~2T}QStsnQCyIWee}lw>w{55fk1eH2miCX)rcmV@Y+B5 z=l|!N|Mq=nF7cSl?Q*#om&@G?c2!mxSY=?9f%2EIjJ8TTs;@=0EZ@+?*VUoAK%g0@ z@i>~KTRXCpB~O}QUB)W)OW+$aLY;zm!4{9OP4sq+s_0H(v$)A0plhX&K1ZFr6gT^r z%?~O*21TO%;m#0`!1XcVu09l(hHy;`Ted+kN+~L~5Y`fgoJEdqItf*=G62>jhDj7` zOC*aFJ!KG0vK2#z8dAb=Y-DFJqSYWSO(e~aVt5D>3nQ$j6&+)u=xJo6AWpGzT@YAE zA{c669|PBfBFk8Zt}-UMdNwASl~2kS59u-*uwb`ONn#y}2Z3L#Vcmu~s%ZPrKwt1V zKMJa9ZW;%IEhGUjf?snK0zhm7d`U(U)RJgAU7^$an1A+zYDmh1vlR_OGx~5DX+6Fq9vK zX;UCSDOtEW7qL>=#|$d~DS-i9QgviNF|62`T+E+v;Gj^}a0q3<#7X)P_|Xe0hH5Yb z!KOj%`@qWvAl8in63cKWsec1Hah^ziyZ7A(zX0yYM1W1Je$IX^Tqp0Pr(@QPiN4K?B zFWzZ=<8D#wH;dD4n@(P88y&mWHvhvb?G?+F?asQ%_Ss}2`1sC`g36wo!I{BqM~T_c zF*rKcaq7#7PS2-}o&Aq&=$w52#jc`PTf4Td|E25rm9nloV|PRC6O*CCjyv@0x{2=Q zqk-fn5dgo=iKq5epv5ZTQOTB=OgH*`Qaw*0Jc_GP#5byOC9@B2*j-o79{x&4yZ@Z0BN t^yU|$ey>N|AMX&4FSLv2wpED>xKzA86lr<*UA3jMv=b1oT_K9vKLFhc!k7R6 From a127d2b90b73944abbf325ca1e81b6e452391f24 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 12 Jan 2024 15:27:17 +0100 Subject: [PATCH 189/412] prefer std::equal Co-authored-by: Peter Hill --- include/bout/region.hxx | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 24c39aeb28..ad3e421425 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -567,16 +567,10 @@ public: Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; bool operator==(const Region& other) const { - if (this->size() != other.size()) { - return false; - } - for (auto i1 = const_cast*>(this)->begin(), i2 = other.begin(); - i1 != this->end(); ++i1, ++i2) { - if (i1 != i2) { - return false; - } - } - return true; + return std::equal( + this->begin(), this->end(), + other.begin(), other.end() + ); } /// Destructor From 204b1188c0f10af16cea00494860a05cbcb85fce Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 16 Jan 2024 12:38:38 +0100 Subject: [PATCH 190/412] Improve comment Co-authored-by: David Bold --- src/mesh/mesh.cxx | 39 ++++++++++++++++++++++++++++----------- 1 file changed, 28 insertions(+), 11 deletions(-) diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index af9f2c38f3..7f3c5195b4 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -775,17 +775,34 @@ std::optional Mesh::getCommonRegion(std::optional lhs, const size_t low = std::min(lhs.value(), rhs.value()); const size_t high = std::max(lhs.value(), rhs.value()); - /* Memory layout of indices - * left is lower index, bottom is higher index - * 0 1 2 3 - * 0 - * 1 0 - * 2 1 2 - * 3 3 4 5 - * 4 6 7 8 9 - * - * As we only need half of the square, the indices do not depend on - * the total number of elements. + /* This function finds the ID of the region corresponding to the + intersection of two regions, and caches the result. The cache is a + vector, indexed by some function of the two input IDs. Because the + intersection of two regions doesn't depend on the order, and the + intersection of a region with itself is the identity operation, we can + order the IDs numerically and use a generalised triangle number: + $[n (n - 1) / 2] + m$ to construct the cache index. This diagram shows + the result for the first few numbers: + | 0 1 2 3 + ---------------- + 0 | + 1 | 0 + 2 | 1 2 + 3 | 3 4 5 + 4 | 6 7 8 9 + + These indices might be sparse, but presumably we don't expect to store + very many intersections so this shouldn't give much overhead. + + After calculating the cache index, we look it up in the cache (possibly + reallocating to ensure it's large enough). If the index is in the cache, + we can just return it as-is, otherwise we need to do a bit more work. + + First, we need to fully compute the intersection of the two regions. We + then check if this corresponds to an existing region. If so, we cache the + ID of that region and return it. Otherwise, we need to store this new + region in `region3D` -- the index in this vector is the ID we need to + cache and return here. */ const size_t pos = (high * (high - 1)) / 2 + low; if (region3Dintersect.size() <= pos) { From 1de0d2aeec28f4df74bea30f5a8047b14614e34c Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 16 Jan 2024 12:42:43 +0100 Subject: [PATCH 191/412] Remove commented out code --- include/bout/field2d.hxx | 2 +- include/bout/field_data.hxx | 2 -- include/bout/solver.hxx | 1 - include/bout/vector2d.hxx | 2 +- include/bout/vector3d.hxx | 5 ++--- src/field/field.cxx | 2 -- src/mesh/interpolation/monotonic_hermite_spline_xz.cxx | 1 - src/solver/impls/petsc/petsc.cxx | 1 - 8 files changed, 4 insertions(+), 12 deletions(-) diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index ea61648d3f..5bac67beb2 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -33,7 +33,7 @@ class Field2D; class Mesh; #include "bout/field.hxx" #include "bout/field_data.hxx" -class Field3D; //#include "bout/field3d.hxx" +class Field3D; #include "bout/fieldperp.hxx" #include "bout/stencils.hxx" diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx index 59bd751fc4..03b9d6759b 100644 --- a/include/bout/field_data.hxx +++ b/include/bout/field_data.hxx @@ -38,8 +38,6 @@ class FieldData; #include #include -// Including the next line leads to compiler errors -//#include "bout/boundary_op.hxx" class BoundaryOp; class BoundaryOpPar; class Coordinates; diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index ef7cbe63eb..f795808f6a 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -63,7 +63,6 @@ using Jacobian = int (*)(BoutReal t); /// Solution monitor, called each timestep using TimestepMonitorFunc = int (*)(Solver* solver, BoutReal simtime, BoutReal lastdt); -//#include "bout/globals.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/generic_factory.hxx" diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx index 9ff4a69ba8..974c5f81db 100644 --- a/include/bout/vector2d.hxx +++ b/include/bout/vector2d.hxx @@ -39,7 +39,7 @@ class Vector2D; class Field2D; class Field3D; -class Vector3D; //#include "bout/vector3d.hxx" +class Vector3D; #include diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx index f3adf41ae8..93ee798663 100644 --- a/include/bout/vector3d.hxx +++ b/include/bout/vector3d.hxx @@ -33,11 +33,10 @@ class Vector3D; #ifndef __VECTOR3D_H__ #define __VECTOR3D_H__ -class Field2D; //#include "bout/field2d.hxx" +class Field2D; +class Vector2D; #include "bout/field3d.hxx" -class Vector2D; //#include "bout/vector2d.hxx" - /*! * Represents a 3D vector, with x,y,z components * stored as separate Field3D objects diff --git a/src/field/field.cxx b/src/field/field.cxx index 54883c506c..e48a8f3ef7 100644 --- a/src/field/field.cxx +++ b/src/field/field.cxx @@ -23,8 +23,6 @@ * **************************************************************************/ -//#include - #include #include #include diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx index 32b1e0be7e..abedb27733 100644 --- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx +++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx @@ -24,7 +24,6 @@ #include "bout/index_derivs_interface.hxx" #include "bout/interpolation_xz.hxx" #include "bout/mesh.hxx" -//#include "bout/output.hxx" #include diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx index 1b81ca36b6..9270848998 100644 --- a/src/solver/impls/petsc/petsc.cxx +++ b/src/solver/impls/petsc/petsc.cxx @@ -29,7 +29,6 @@ #if BOUT_HAS_PETSC -//#include #include #include From 311fd5edc3f1a0b74268fcfc6c97b92a779850fc Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Tue, 16 Jan 2024 11:47:28 +0000 Subject: [PATCH 192/412] Apply clang-format changes --- include/bout/region.hxx | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index ad3e421425..13c4a137fa 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -567,10 +567,7 @@ public: Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; bool operator==(const Region& other) const { - return std::equal( - this->begin(), this->end(), - other.begin(), other.end() - ); + return std::equal(this->begin(), this->end(), other.begin(), other.end()); } /// Destructor From 9ac43fee0744f188332e7a30e7c99b4918850b7a Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 11:50:37 +0000 Subject: [PATCH 193/412] Remove some unused header includes from options --- include/bout/options.hxx | 1 - src/sys/options.cxx | 2 -- 2 files changed, 3 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index bf1704100f..c214048ccf 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -53,7 +53,6 @@ class Options; #include #include -#include #include #include #include diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 45cacd4acc..b862456c60 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -7,8 +7,6 @@ #include #include -#include -#include /// The source label given to default values const std::string Options::DEFAULT_SOURCE{_("default")}; From 140a4d0c5e84148a68accb4be3d33051c4f46d53 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 12:05:50 +0000 Subject: [PATCH 194/412] Ensure `options.cxx` includes all relevant headers --- src/sys/options.cxx | 34 ++++++++++++++++++++++++++++------ 1 file changed, 28 insertions(+), 6 deletions(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index b862456c60..fab2bbeb0a 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -1,12 +1,34 @@ -#include -#include // Used for parsing expressions -#include -#include -#include - +#include "bout/options.hxx" + +#include "bout/array.hxx" +#include "bout/bout_types.hxx" +#include "bout/boutexception.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/field_factory.hxx" // Used for parsing expressions +#include "bout/fieldperp.hxx" +#include "bout/output.hxx" +#include "bout/sys/expressionparser.hxx" +#include "bout/sys/gettext.hxx" +#include "bout/sys/type_name.hxx" +#include "bout/sys/variant.hxx" +#include "bout/traits.hxx" +#include "bout/unused.hxx" +#include "bout/utils.hxx" + +#include #include #include +#include +#include +#include +#include +#include +#include +#include +#include +#include /// The source label given to default values const std::string Options::DEFAULT_SOURCE{_("default")}; From fe95a4c5d4cd2bf42ead97719d3b323106ff0223 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 13:52:11 +0000 Subject: [PATCH 195/412] Maint: Ignore clang-tidy recursion warning --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index b52a287a8d..48a434bc14 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -1,5 +1,5 @@ --- -Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity' +Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion' WarningsAsErrors: '' HeaderFilterRegex: '' AnalyzeTemporaryDtors: false From 0688f3298617bdba44484032fdeb15f7ff35f934 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:05:49 +0000 Subject: [PATCH 196/412] Make some local variables const-correct --- include/bout/msg_stack.hxx | 2 +- src/sys/options.cxx | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx index cc19a7b9f6..fe273c60eb 100644 --- a/include/bout/msg_stack.hxx +++ b/include/bout/msg_stack.hxx @@ -201,7 +201,7 @@ private: arguments and the optional arguments follow from there. */ #define TRACE(...) \ - MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__) + const MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__) #else #define TRACE(...) #endif diff --git a/src/sys/options.cxx b/src/sys/options.cxx index fab2bbeb0a..f1fbc3f12b 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -100,7 +100,7 @@ Options::Options(std::initializer_list> values) append_impl(children, section_name, append_impl); }; - for (auto& value : values) { + for (const auto& value : values) { (*this)[value.first] = value.second; // value.second was constructed from the "bare" `Options(T)` so // doesn't have `full_name` set. This clobbers @@ -454,10 +454,10 @@ bool Options::as(const bool& UNUSED(similar_to)) const { } else if (bout::utils::holds_alternative(value)) { // Parse as floating point because that's the only type the parser understands - BoutReal rval = parseExpression(value, this, "bool", full_name); + const BoutReal rval = parseExpression(value, this, "bool", full_name); // Check that the result is either close to 1 (true) or close to 0 (false) - int ival = ROUND(rval); + const int ival = ROUND(rval); if ((fabs(rval - static_cast(ival)) > 1e-3) or (ival < 0) or (ival > 1)) { throw BoutException(_("Value for option {:s} = {:e} is not a bool"), full_name, rval); @@ -510,7 +510,7 @@ Field3D Options::as(const Field3D& similar_to) const { if (bout::utils::holds_alternative(value) or bout::utils::holds_alternative(value)) { - BoutReal scalar_value = + const BoutReal scalar_value = bout::utils::variantStaticCastOrThrow(value); // Get metadata from similar_to, fill field with scalar_value @@ -566,7 +566,7 @@ Field2D Options::as(const Field2D& similar_to) const { if (bout::utils::holds_alternative(value) or bout::utils::holds_alternative(value)) { - BoutReal scalar_value = + const BoutReal scalar_value = bout::utils::variantStaticCastOrThrow(value); // Get metadata from similar_to, fill field with scalar_value @@ -618,7 +618,7 @@ FieldPerp Options::as(const FieldPerp& similar_to) const { if (bout::utils::holds_alternative(value) or bout::utils::holds_alternative(value)) { - BoutReal scalar_value = + const BoutReal scalar_value = bout::utils::variantStaticCastOrThrow(value); // Get metadata from similar_to, fill field with scalar_value @@ -875,7 +875,7 @@ Options Options::getUnused(const std::vector& exclude_sources) cons } void Options::printUnused() const { - Options unused = getUnused(); + const Options unused = getUnused(); // Two cases: single value, or a section. If it's a single value, // we can check it directly. If it's a section, we can see if it has @@ -1076,7 +1076,7 @@ void checkForUnusedOptions() { void checkForUnusedOptions(const Options& options, const std::string& data_dir, const std::string& option_file) { - Options unused = options.getUnused(); + const Options unused = options.getUnused(); if (not unused.getChildren().empty()) { // Construct a string with all the fuzzy matches for each unused option From bde607ed2e921d8016401959d3356d18c981b942 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:09:14 +0000 Subject: [PATCH 197/412] Replace `endl` with `\n` --- include/bout/options.hxx | 8 ++++---- src/sys/options.cxx | 14 +++++++------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index c214048ccf..74d2a59318 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -494,7 +494,7 @@ public: // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return val; } @@ -513,7 +513,7 @@ public: value_used = true; // Mark the option as used output_info << _("\tOption ") << full_name << " = " << def << " (" << DEFAULT_SOURCE - << ")" << std::endl; + << ")\n"; return def; } T val = as(def); @@ -546,7 +546,7 @@ public: *this = def; output_info << _("\tOption ") << full_name << " = " << def.full_name << " (" - << DEFAULT_SOURCE << ")" << std::endl; + << DEFAULT_SOURCE << ")\n"; } else { // Check if this was previously set as a default option if (bout::utils::variantEqualTo(attributes.at("source"), DEFAULT_SOURCE)) { @@ -570,7 +570,7 @@ public: if (is_section) { // Option not found output_info << _("\tOption ") << full_name << " = " << def << " (" << DEFAULT_SOURCE - << ")" << std::endl; + << ")\n"; return def; } T val = as(def); diff --git a/src/sys/options.cxx b/src/sys/options.cxx index f1fbc3f12b..205c4b4029 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -332,7 +332,7 @@ std::string Options::as(const std::string& UNUSED(similar_to)) cons // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } @@ -401,7 +401,7 @@ int Options::as(const int& UNUSED(similar_to)) const { // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } @@ -436,7 +436,7 @@ BoutReal Options::as(const BoutReal& UNUSED(similar_to)) const { // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } @@ -476,7 +476,7 @@ bool Options::as(const bool& UNUSED(similar_to)) const { // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } @@ -735,7 +735,7 @@ Array Options::as>(const Array& similar_to) // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } @@ -762,7 +762,7 @@ Matrix Options::as>(const Matrix& similar_t // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } @@ -789,7 +789,7 @@ Tensor Options::as>(const Tensor& similar_t // Specify the source of the setting output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; } - output_info << endl; + output_info << '\n'; return result; } From 1e19b2e0d752316dc57d8abdf97aeaa161971313 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:35:51 +0000 Subject: [PATCH 198/412] Add helper function for print `Options` "key = value" with source --- src/sys/options.cxx | 92 +++++++++++++++++---------------------------- 1 file changed, 34 insertions(+), 58 deletions(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 205c4b4029..5157cde151 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -316,27 +316,6 @@ void Options::assign<>(Tensor val, std::string source) { _set_no_check(std::move(val), std::move(source)); } -template <> -std::string Options::as(const std::string& UNUSED(similar_to)) const { - if (is_section) { - throw BoutException(_("Option {:s} has no value"), full_name); - } - - // Mark this option as used - value_used = true; - - std::string result = bout::utils::variantToString(value); - - output_info << _("\tOption ") << full_name << " = " << result; - if (attributes.count("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; - - return result; -} - namespace { /// Use FieldFactory to evaluate expression double parseExpression(const Options::ValueType& value, const Options* options, @@ -356,8 +335,36 @@ double parseExpression(const Options::ValueType& value, const Options* options, full_name, bout::utils::variantToString(value), error.what()); } } + +/// Helper function to print `key = value` with optional source +template +void printNameValueSourceLine(const Options& option, const T& value) { + output_info.write(_("\tOption {} = {}"), option.str(), value); + if (option.hasAttribute("source")) { + // Specify the source of the setting + output_info.write(" ({})", + bout::utils::variantToString(option.attributes.at("source"))); + } + output_info.write("\n"); +} } // namespace +template <> +std::string Options::as(const std::string& UNUSED(similar_to)) const { + if (is_section) { + throw BoutException(_("Option {:s} has no value"), full_name); + } + + // Mark this option as used + value_used = true; + + std::string result = bout::utils::variantToString(value); + + printNameValueSourceLine(*this, result); + + return result; +} + template <> int Options::as(const int& UNUSED(similar_to)) const { if (is_section) { @@ -396,12 +403,7 @@ int Options::as(const int& UNUSED(similar_to)) const { value_used = true; - output_info << _("\tOption ") << full_name << " = " << result; - if (attributes.count("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; + printNameValueSourceLine(*this, result); return result; } @@ -431,12 +433,7 @@ BoutReal Options::as(const BoutReal& UNUSED(similar_to)) const { // Mark this option as used value_used = true; - output_info << _("\tOption ") << full_name << " = " << result; - if (attributes.count("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; + printNameValueSourceLine(*this, result); return result; } @@ -470,13 +467,7 @@ bool Options::as(const bool& UNUSED(similar_to)) const { value_used = true; - output_info << _("\tOption ") << full_name << " = " << toString(result); - - if (attributes.count("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; + printNameValueSourceLine(*this, toString(result)); return result; } @@ -730,12 +721,7 @@ Array Options::as>(const Array& similar_to) // Mark this option as used value_used = true; - output_info << _("\tOption ") << full_name << " = Array"; - if (hasAttribute("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; + printNameValueSourceLine(*this, "Array"); return result; } @@ -757,12 +743,7 @@ Matrix Options::as>(const Matrix& similar_t // Mark this option as used value_used = true; - output_info << _("\tOption ") << full_name << " = Matrix"; - if (hasAttribute("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; + printNameValueSourceLine(*this, "Matrix"); return result; } @@ -784,12 +765,7 @@ Tensor Options::as>(const Tensor& similar_t // Mark this option as used value_used = true; - output_info << _("\tOption ") << full_name << " = Tensor"; - if (hasAttribute("source")) { - // Specify the source of the setting - output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")"; - } - output_info << '\n'; + printNameValueSourceLine(*this, "Tensor"); return result; } From 949ab0da891a0127b23297e0b34cc67c6435fc36 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:49:20 +0000 Subject: [PATCH 199/412] Add default move ctor/assignment and dtors to `Matrix/Tensor` --- include/bout/utils.hxx | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 3e02b74c39..84ed7aed31 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -205,6 +205,8 @@ public: using size_type = int; Matrix() = default; + Matrix(Matrix&&) = default; + Matrix& operator=(Matrix&&) = default; Matrix(size_type n1, size_type n2) : n1(n1), n2(n2) { ASSERT2(n1 >= 0); ASSERT2(n2 >= 0); @@ -215,6 +217,7 @@ public: // Prevent copy on write for Matrix data.ensureUnique(); } + ~Matrix() = default; /// Reallocate the Matrix to shape \p new_size_1 by \p new_size_2 /// @@ -299,6 +302,8 @@ public: using size_type = int; Tensor() = default; + Tensor(Tensor&&) = default; + Tensor& operator=(Tensor&&) = default; Tensor(size_type n1, size_type n2, size_type n3) : n1(n1), n2(n2), n3(n3) { ASSERT2(n1 >= 0); ASSERT2(n2 >= 0); @@ -310,6 +315,7 @@ public: // Prevent copy on write for Tensor data.ensureUnique(); } + ~Tensor() = default; /// Reallocate the Tensor with shape \p new_size_1 by \p new_size_2 by \p new_size_3 /// From 4d7d309197881a85c4d40ba49dc6aa5a29d6e50d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:50:29 +0000 Subject: [PATCH 200/412] Pass char-literal to `std::string::find` instead of string literal --- include/bout/options.hxx | 2 +- src/sys/options.cxx | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 74d2a59318..1816bfd0ab 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -701,7 +701,7 @@ public: /// Print just the name of this object without parent sections std::string name() const { - auto pos = full_name.rfind(":"); + auto pos = full_name.rfind(':'); if (pos == std::string::npos) { // No parent section or sections return full_name; diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 5157cde151..eb2e86bb2a 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -127,7 +127,7 @@ Options& Options::operator[](const std::string& name) { } // If name is compound, e.g. "section:subsection", then split the name - auto subsection_split = name.find(":"); + auto subsection_split = name.find(':'); if (subsection_split != std::string::npos) { return (*this)[name.substr(0, subsection_split)][name.substr(subsection_split + 1)]; } @@ -166,7 +166,7 @@ const Options& Options::operator[](const std::string& name) const { } // If name is compound, e.g. "section:subsection", then split the name - auto subsection_split = name.find(":"); + auto subsection_split = name.find(':'); if (subsection_split != std::string::npos) { return (*this)[name.substr(0, subsection_split)][name.substr(subsection_split + 1)]; } From 5e1ae531348d104db5c480826d013dafb1a17be9 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:51:25 +0000 Subject: [PATCH 201/412] Don't use `else` after `return` --- include/bout/options.hxx | 3 +-- src/sys/options.cxx | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 1816bfd0ab..3a11eaf199 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -705,9 +705,8 @@ public: if (pos == std::string::npos) { // No parent section or sections return full_name; - } else { - return full_name.substr(pos + 1); } + return full_name.substr(pos + 1); } /// Return a new Options instance which contains all the values diff --git a/src/sys/options.cxx b/src/sys/options.cxx index eb2e86bb2a..3ead805df2 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -276,9 +276,8 @@ bool Options::isSection(const std::string& name) const { auto it = children.find(name); if (it == children.end()) { return false; - } else { - return it->second.isSection(); } + return it->second.isSection(); } template <> From a1e5163536282f293f37896c0934e265abb4fdf6 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:56:23 +0000 Subject: [PATCH 202/412] Rename some short identifiers --- include/bout/options.hxx | 36 ++++++++++++++++++------------------ src/sys/options.cxx | 28 ++++++++++++++-------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 3a11eaf199..1f5e62ea33 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -381,9 +381,9 @@ public: /// Note: Specialised versions for types stored in ValueType template void assign(T val, std::string source = "") { - std::stringstream ss; - ss << val; - _set(ss.str(), std::move(source), false); + std::stringstream as_str; + as_str << val; + _set(as_str.str(), std::move(source), false); } /// Force to a value @@ -461,20 +461,20 @@ public: // If the variant is a string then we may be able to parse it if (bout::utils::holds_alternative(value)) { - std::stringstream ss(bout::utils::get(value)); - ss >> val; + std::stringstream as_str(bout::utils::get(value)); + as_str >> val; // Check if the parse failed - if (ss.fail()) { + if (as_str.fail()) { throw BoutException("Option {:s} could not be parsed ('{:s}')", full_name, bout::utils::variantToString(value)); } // Check if there are characters remaining std::string remainder; - std::getline(ss, remainder); - for (const char& ch : remainder) { - if (!std::isspace(static_cast(ch))) { + std::getline(as_str, remainder); + for (const unsigned char chr : remainder) { + if (!std::isspace(chr)) { // Meaningful character not parsed throw BoutException("Option {:s} could not be parsed", full_name); } @@ -656,8 +656,8 @@ public: // Setting options template - void forceSet(const std::string& key, T t, const std::string& source = "") { - (*this)[key].force(t, source); + void forceSet(const std::string& key, T val, const std::string& source = "") { + (*this)[key].force(val, source); } /*! @@ -669,11 +669,11 @@ public: if (!is_section) { return false; } - auto it = children.find(key); - if (it == children.end()) { + auto child = children.find(key); + if (child == children.end()) { return false; } - return it->second.isSet(); + return child->second.isSet(); } /// Get options, passing in a reference to a variable @@ -835,8 +835,8 @@ private: /// Tests if two values are similar. template - bool similar(T a, T b) const { - return a == b; + bool similar(T lhs, T rhs) const { + return lhs == rhs; } }; @@ -878,8 +878,8 @@ void Options::assign<>(Tensor val, std::string source); /// Specialised similar comparison methods template <> -inline bool Options::similar(BoutReal a, BoutReal b) const { - return fabs(a - b) < 1e-10; +inline bool Options::similar(BoutReal lhs, BoutReal rhs) const { + return fabs(lhs - rhs) < 1e-10; } /// Specialised as routines diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 3ead805df2..ff473599e0 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -133,9 +133,9 @@ Options& Options::operator[](const std::string& name) { } // Find and return if already exists - auto it = children.find(name); - if (it != children.end()) { - return it->second; + auto child = children.find(name); + if (child != children.end()) { + return child->second; } // Doesn't exist yet, so add @@ -172,13 +172,13 @@ const Options& Options::operator[](const std::string& name) const { } // Find and return if already exists - auto it = children.find(name); - if (it == children.end()) { + auto child = children.find(name); + if (child == children.end()) { // Doesn't exist throw BoutException(_("Option {:s}:{:s} does not exist"), full_name, name); } - return it->second; + return child->second; } std::multiset @@ -273,11 +273,11 @@ bool Options::isSection(const std::string& name) const { } // Is there a child section? - auto it = children.find(name); - if (it == children.end()) { + const auto child = children.find(name); + if (child == children.end()) { return false; } - return it->second.isSection(); + return child->second.isSection(); } template <> @@ -874,9 +874,9 @@ void Options::cleanCache() { FieldFactory::get()->cleanCache(); } std::map Options::subsections() const { std::map sections; - for (const auto& it : children) { - if (it.second.is_section) { - sections[it.first] = &it.second; + for (const auto& child : children) { + if (child.second.is_section) { + sections[child.first] = &child.second; } } return sections; @@ -907,8 +907,8 @@ fmt::format_parse_context::iterator bout::details::OptionsFormatterBase::parse(fmt::format_parse_context& ctx) { const auto* closing_brace = std::find(ctx.begin(), ctx.end(), '}'); - std::for_each(ctx.begin(), closing_brace, [&](auto it) { - switch (it) { + std::for_each(ctx.begin(), closing_brace, [&](auto ctx_opt) { + switch (ctx_opt) { case 'd': docstrings = true; break; From 5b40cb2fa7b3a43ff7a47e7c686bdd14e14b1062 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:57:19 +0000 Subject: [PATCH 203/412] Use `std::string::empty` instead of comparing to empty object --- src/sys/options.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index ff473599e0..411e365669 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -267,7 +267,7 @@ bool Options::isSet() const { } bool Options::isSection(const std::string& name) const { - if (name == "") { + if (name.empty()) { // Test this object return is_section; } From 4c3b1e8ed1469f5a0a655cff4067c70e0a3ade13 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 14:58:59 +0000 Subject: [PATCH 204/412] Avoid unnecessary copy --- src/sys/options.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 411e365669..208a66fee6 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -1006,7 +1006,7 @@ bout::details::OptionsFormatterBase::format(const Options& options, // Only print section headers if the section has a name and it has // non-section children - const auto children = options.getChildren(); + const auto& children = options.getChildren(); const bool has_child_values = std::any_of(children.begin(), children.end(), [](const auto& child) { return child.second.isValue(); }); From f63501af1098266fc706691354c32b5711030c29 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 15:03:11 +0000 Subject: [PATCH 205/412] Handle self-assignment for `Options` --- src/sys/options.cxx | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 208a66fee6..dca5180d19 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -229,6 +229,10 @@ Options::fuzzyFind(const std::string& name, std::string::size_type distance) con } Options& Options::operator=(const Options& other) { + if (this == &other) { + return *this; + } + // Note: Here can't do copy-and-swap because pointers to parents are stored value = other.value; From 5e4595d2c43162a0d4ca85ed45e254805a4630a8 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 15:16:50 +0000 Subject: [PATCH 206/412] Simplify implementation of `Options::root()` singleton --- include/bout/options.hxx | 2 -- src/sys/options.cxx | 15 +++------------ 2 files changed, 3 insertions(+), 14 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 1f5e62ea33..546830af3c 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -782,8 +782,6 @@ private: /// The source label given to default values static const std::string DEFAULT_SOURCE; - static Options* root_instance; ///< Only instance of the root section - Options* parent_instance{nullptr}; std::string full_name; // full path name for logging only diff --git a/src/sys/options.cxx b/src/sys/options.cxx index dca5180d19..d10ebee76b 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -39,22 +39,13 @@ std::string Options::getDefaultSource() { return DEFAULT_SOURCE; } /// having been used constexpr auto conditionally_used_attribute = "conditionally used"; -Options* Options::root_instance{nullptr}; - Options& Options::root() { - if (root_instance == nullptr) { - // Create the singleton - root_instance = new Options(); - } - return *root_instance; + static Options root_instance; + return root_instance; } void Options::cleanup() { - if (root_instance == nullptr) { - return; - } - delete root_instance; - root_instance = nullptr; + root() = Options{}; } Options::Options(const Options& other) From e77b6af5df8e361f939c90af4e45a8e610e68bb8 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 16:18:36 +0000 Subject: [PATCH 207/412] Initialise some local variables --- src/sys/options.cxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index d10ebee76b..4836b250f8 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -365,14 +365,14 @@ int Options::as(const int& UNUSED(similar_to)) const { throw BoutException(_("Option {:s} has no value"), full_name); } - int result; + int result = 0; if (bout::utils::holds_alternative(value)) { result = bout::utils::get(value); } else { // Cases which get a BoutReal then check if close to an integer - BoutReal rval; + BoutReal rval = BoutNaN; if (bout::utils::holds_alternative(value)) { rval = bout::utils::get(value); @@ -408,7 +408,7 @@ BoutReal Options::as(const BoutReal& UNUSED(similar_to)) const { throw BoutException(_("Option {:s} has no value"), full_name); } - BoutReal result; + BoutReal result = BoutNaN; if (bout::utils::holds_alternative(value)) { result = static_cast(bout::utils::get(value)); @@ -438,7 +438,7 @@ bool Options::as(const bool& UNUSED(similar_to)) const { throw BoutException(_("Option {:s} has no value"), full_name); } - bool result; + bool result = false; if (bout::utils::holds_alternative(value)) { result = bout::utils::get(value); From eb4a31df14513f0d47c2eff72ebbc62e2837e4a8 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 16:41:20 +0000 Subject: [PATCH 208/412] Silence clang-tidy warning about macro use in options header --- include/bout/options.hxx | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 546830af3c..8619d9329a 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -968,6 +968,8 @@ private: template <> struct fmt::formatter : public bout::details::OptionsFormatterBase {}; +// NOLINTBEGIN(cppcoreguidelines-macro-usage) + /// Define for reading options which passes the variable name #define OPTION(options, var, def) pointer(options)->get(#var, var, def) @@ -1028,4 +1030,6 @@ struct fmt::formatter : public bout::details::OptionsFormatterBase {}; __LINE__) = Options::root()[name].overrideDefault(value); \ } +// NOLINTEND(cppcoreguidelines-macro-usage) + #endif // __OPTIONS_H__ From 1f16f7c41bc280f3bd4ad759c753d031476389fe Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 16:43:38 +0000 Subject: [PATCH 209/412] Move value to avoid unnecessary copy --- include/bout/options.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 8619d9329a..aab392cade 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -858,7 +858,7 @@ inline void Options::assign<>(std::string val, std::string source) { // Note: const char* version needed to avoid conversion to bool template <> inline void Options::assign<>(const char* val, std::string source) { - _set(std::string(val), source, false); + _set(std::string(val), std::move(source), false); } // Note: Field assignments don't check for previous assignment (always force) template <> From d285662b7e0cdef436387447982afcb467452f1e Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 19 Jan 2024 17:25:57 +0000 Subject: [PATCH 210/412] Implement move ctor/assignment for `Options` --- include/bout/options.hxx | 34 +++++++++++++++------------------- src/sys/options.cxx | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 50 insertions(+), 19 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index aab392cade..7da50c1151 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -181,9 +181,20 @@ public: /// Example: { {"key1", 42}, {"key2", field} } Options(std::initializer_list> values); - /// Copy constructor Options(const Options& other); + /// Copy assignment + /// + /// This replaces the value, attributes and all children + /// + /// Note that if only the value is desired, then that can be copied using + /// the value member directly e.g. option2.value = option1.value; + /// + Options& operator=(const Options& other); + + Options(Options&& other) noexcept; + Options& operator=(Options&& other) noexcept; + ~Options() = default; /// Get a reference to the only root instance @@ -209,14 +220,11 @@ public: public: using Base = bout::utils::variant; - /// Constructor AttributeType() = default; - /// Copy constructor AttributeType(const AttributeType& other) = default; - /// Move constructor - AttributeType(AttributeType&& other) : Base(std::move(other)) {} - - /// Destructor + AttributeType(AttributeType&& other) = default; + AttributeType& operator=(const AttributeType& other) = default; + AttributeType& operator=(AttributeType&& other) = default; ~AttributeType() = default; /// Assignment operator, including move assignment @@ -228,9 +236,6 @@ public: return *this; } - /// Copy assignment operator - AttributeType& operator=(const AttributeType& other) = default; - /// Initialise with a value /// This enables AttributeTypes to be constructed using initializer lists template @@ -361,15 +366,6 @@ public: return inputvalue; } - /// Copy assignment - /// - /// This replaces the value, attributes and all children - /// - /// Note that if only the value is desired, then that can be copied using - /// the value member directly e.g. option2.value = option1.value; - /// - Options& operator=(const Options& other); - /// Assign a value to the option. /// This will throw an exception if already has a value /// diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 4836b250f8..122ba8f4e5 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -61,6 +61,19 @@ Options::Options(const Options& other) } } +Options::Options(Options&& other) noexcept + : value(std::move(other.value)), attributes(std::move(other.attributes)), + parent_instance(other.parent_instance), full_name(std::move(other.full_name)), + is_section(other.is_section), children(std::move(other.children)), + value_used(other.value_used) { + + // Ensure that this is the parent of all children, + // otherwise will point to the original Options instance + for (auto& child : children) { + child.second.parent_instance = this; + } +} + template <> Options::Options(const char* value) { assign(value); @@ -247,6 +260,28 @@ Options& Options::operator=(const Options& other) { return *this; } +Options& Options::operator=(Options&& other) noexcept { + if (this == &other) { + return *this; + } + + // Note: Here can't do copy-and-swap because pointers to parents are stored + + value = std::move(other.value); + attributes = std::move(other.attributes); + full_name = std::move(other.full_name); + is_section = other.is_section; + children = std::move(other.children); + value_used = other.value_used; + + // Ensure that this is the parent of all children, + // otherwise will point to the original Options instance + for (auto& child : children) { + child.second.parent_instance = this; + } + return *this; +} + bool Options::isSet() const { // Only values can be set/unset if (is_section) { From 263a1562389780816359905f28980c106e8b7faa Mon Sep 17 00:00:00 2001 From: ZedThree Date: Fri, 19 Jan 2024 17:43:19 +0000 Subject: [PATCH 211/412] Apply clang-format changes --- src/sys/options.cxx | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 122ba8f4e5..a165188f79 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -44,9 +44,7 @@ Options& Options::root() { return root_instance; } -void Options::cleanup() { - root() = Options{}; -} +void Options::cleanup() { root() = Options{}; } Options::Options(const Options& other) : value(other.value), attributes(other.attributes), @@ -62,10 +60,10 @@ Options::Options(const Options& other) } Options::Options(Options&& other) noexcept - : value(std::move(other.value)), attributes(std::move(other.attributes)), - parent_instance(other.parent_instance), full_name(std::move(other.full_name)), - is_section(other.is_section), children(std::move(other.children)), - value_used(other.value_used) { + : value(std::move(other.value)), attributes(std::move(other.attributes)), + parent_instance(other.parent_instance), full_name(std::move(other.full_name)), + is_section(other.is_section), children(std::move(other.children)), + value_used(other.value_used) { // Ensure that this is the parent of all children, // otherwise will point to the original Options instance From 998bd0a77ed84fb2bc6751bc0a63c4bff3695994 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 22 Jan 2024 09:17:22 +0000 Subject: [PATCH 212/412] Make move ctors `noexcept` Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- include/bout/utils.hxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 84ed7aed31..c735c5cfc5 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -205,8 +205,8 @@ public: using size_type = int; Matrix() = default; - Matrix(Matrix&&) = default; - Matrix& operator=(Matrix&&) = default; + Matrix(Matrix&&) noexcept = default; + Matrix& operator=(Matrix&&) noexcept = default; Matrix(size_type n1, size_type n2) : n1(n1), n2(n2) { ASSERT2(n1 >= 0); ASSERT2(n2 >= 0); @@ -302,8 +302,8 @@ public: using size_type = int; Tensor() = default; - Tensor(Tensor&&) = default; - Tensor& operator=(Tensor&&) = default; + Tensor(Tensor&&) noexcept = default; + Tensor& operator=(Tensor&&) noexcept = default; Tensor(size_type n1, size_type n2, size_type n3) : n1(n1), n2(n2), n3(n3) { ASSERT2(n1 >= 0); ASSERT2(n2 >= 0); From 329b7138187131ac9a0541e05a0011689c644312 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Mon, 22 Jan 2024 09:17:57 +0000 Subject: [PATCH 213/412] Apply clang-format changes --- include/bout/utils.hxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index c735c5cfc5..b26b23e4c0 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -205,8 +205,8 @@ public: using size_type = int; Matrix() = default; - Matrix(Matrix&&) noexcept = default; - Matrix& operator=(Matrix&&) noexcept = default; + Matrix(Matrix&&) noexcept = default; + Matrix& operator=(Matrix&&) noexcept = default; Matrix(size_type n1, size_type n2) : n1(n1), n2(n2) { ASSERT2(n1 >= 0); ASSERT2(n2 >= 0); @@ -302,8 +302,8 @@ public: using size_type = int; Tensor() = default; - Tensor(Tensor&&) noexcept = default; - Tensor& operator=(Tensor&&) noexcept = default; + Tensor(Tensor&&) noexcept = default; + Tensor& operator=(Tensor&&) noexcept = default; Tensor(size_type n1, size_type n2, size_type n3) : n1(n1), n2(n2), n3(n3) { ASSERT2(n1 >= 0); ASSERT2(n2 >= 0); From 2d15e2c1c28f2e1e46b51029740eb674024c9fd4 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 22 Jan 2024 15:13:08 +0000 Subject: [PATCH 214/412] Remove unused bundled `post_bout` library --- tools/pylib/post_bout/ListDict.py | 61 - tools/pylib/post_bout/__init__.py | 95 -- tools/pylib/post_bout/basic_info.py | 421 ------ tools/pylib/post_bout/grate2.py | 52 - tools/pylib/post_bout/pb_corral.py | 540 -------- tools/pylib/post_bout/pb_draw.py | 1692 ------------------------- tools/pylib/post_bout/pb_nonlinear.py | 99 -- tools/pylib/post_bout/pb_present.py | 213 ---- tools/pylib/post_bout/read_cxx.py | 139 -- tools/pylib/post_bout/read_inp.py | 433 ------- tools/pylib/post_bout/rms.py | 55 - 11 files changed, 3800 deletions(-) delete mode 100644 tools/pylib/post_bout/ListDict.py delete mode 100644 tools/pylib/post_bout/__init__.py delete mode 100644 tools/pylib/post_bout/basic_info.py delete mode 100644 tools/pylib/post_bout/grate2.py delete mode 100644 tools/pylib/post_bout/pb_corral.py delete mode 100644 tools/pylib/post_bout/pb_draw.py delete mode 100644 tools/pylib/post_bout/pb_nonlinear.py delete mode 100644 tools/pylib/post_bout/pb_present.py delete mode 100644 tools/pylib/post_bout/read_cxx.py delete mode 100644 tools/pylib/post_bout/read_inp.py delete mode 100644 tools/pylib/post_bout/rms.py diff --git a/tools/pylib/post_bout/ListDict.py b/tools/pylib/post_bout/ListDict.py deleted file mode 100644 index f500825651..0000000000 --- a/tools/pylib/post_bout/ListDict.py +++ /dev/null @@ -1,61 +0,0 @@ -from __future__ import print_function -import sys -import os - -try: - boutpath = os.environ["BOUT_TOP"] - pylibpath = boutpath + "/pylib" - pbpath = pylibpath + "/post_bout" - boutdatapath = pylibpath + "/boutdata" - boututilpath = pylibpath + "/boututils" - - allpath = [boutpath, pylibpath, pbpath, boutdatapath, boututilpath] - [sys.path.append(elem) for elem in allpath] -except: - print("meh") - -import numpy as np - - -def ListDictKey(input, key): - # given a key and a list of dictionaries this method returns an ordered - # list of requested key values - output = [] - for x in input: - try: - # print x[key] - output.append(x[key]) - except: - print("Key not found") - return 1 - - return output - - -def ListDictFilt(input, key, valuelist): - # given a key,value pair and a list of dictionaries this - # method returns an ordered list of dictionaries where (dict(key)==value) = True - # http://stackoverflow.com/questions/5762643/how-to-filter-list-of-dictionaries-with-matching-values-for-a-given-key - try: - x = copyf(input, key, valuelist) - return x - except: - return [] - - -def copyf(dictlist, key, valuelist): - return [dictio for dictio in dictlist if dictio[key] in valuelist] - - -# def subset(obj): -# #def __init__(self,alldb,key,valuelist,model=False): -# selection = ListDictFilt(obj.mode_db,obj.key,valuelist) -# if len(selection) !=0: -# LinRes.__init__(obj,selection) -# self.skey = key -# if model==True: -# self.model() -# else: -# LinRes.__init__(self,alldb) -# if model==True: -# self.model() diff --git a/tools/pylib/post_bout/__init__.py b/tools/pylib/post_bout/__init__.py deleted file mode 100644 index 069ae3e85b..0000000000 --- a/tools/pylib/post_bout/__init__.py +++ /dev/null @@ -1,95 +0,0 @@ -from __future__ import print_function -from __future__ import absolute_import - -################################################## -# BOUT++ data package -# -# Routines for examining simulation results for BOUT++ -# -################################################## - -print("Loading BOUT++ post processing routines") - -# Load routines from separate files -import sys -import os - -try: - boutpath = os.environ["BOUT_TOP"] - pylibpath = boutpath + "/tools/pylib" - boutdatapath = pylibpath + "/boutdata" - boututilpath = pylibpath + "/boututils" - allpath = [boutpath, pylibpath, boutdatapath, boututilpath] - [sys.path.append(elem) for elem in allpath] - print(sys.path) - - # sys.path.append('/home/cryosphere/BOUT/tools/pylib') - # sys.path.append('/home/cryosphere/BOUT/tools/pylib/boutdata') - # sys.path.append('/home/cryosphere/BOUT/tools/pylib/boututils') - - print("in post_bout/__init__.py") - - import matplotlib - - matplotlib.use("pdf") # savemovie must be called as a diff. sesssion - - import gobject - import numpy as np -except ImportError: - print("can't find the modules I need, you fail") - sys.exit() # no point in going on - - -# import some bout specific modules -try: - import boutdata - import boututils -except: - print("can't find bout related modules, you fail") - -# import some home-brewed modules - - -# create some aliases - - -try: - from read_grid import read_grid -except: - print("Sorry, no read_grid") - -try: - from .read_inp import parse_inp, read_inp, read_log, metadata -except: - print("Sorry no parse_inp") - -try: - from .read_cxx import read_cxx, get_evolved_cxx, no_comment_cxx -except: - print("Sorry no read_cxx") - -try: - from post_bout import save, read -except: - print("Sorry, no show") - -try: - from .basic_info import basic_info, fft_info -except: - print("Sorry, no basic_info") - -try: - from .pb_corral import corral, LinRes, subset -except: - print("No corral") - -try: - from . import ListDict -except: - print("No ListDict") - -try: - # from rotate_mp import rotate - from rotate2 import rotate -except: - print("No rotate") diff --git a/tools/pylib/post_bout/basic_info.py b/tools/pylib/post_bout/basic_info.py deleted file mode 100644 index 563bfe6e98..0000000000 --- a/tools/pylib/post_bout/basic_info.py +++ /dev/null @@ -1,421 +0,0 @@ -from __future__ import print_function -from __future__ import division -from builtins import zip -from builtins import range -from past.utils import old_div - -# basic_info return some statistical averages and harmonic info -import numpy as np -import math - - -def basic_info(data, meta, rescale=True, rotate=False, user_peak=0, nonlinear=None): - print("in basic_info") - # from . import read_grid,parse_inp,read_inp,show - - dims = data.shape - ndims = len(dims) - - mxg = meta["MXG"]["v"] - - if ndims == 4: - nt, nx, ny, nz = data.shape - print(nt, nx, ny) - else: - print("something with dimesions") - - dc = ( - data.mean(1).mean(1).mean(1) - ) # there MUST be a way to indicate all axis at once - amp = abs(data).max(1).max(1).max(1) - dt = meta["dt"]["v"] - - if rescale: - amp_o = amp - dc - fourDamp = np.repeat(amp_o, nx * ny * nz) - fourDamp = fourDamp.reshape(nt, nx, ny, nz) - dc_n = old_div(dc, amp_o) - data_n = old_div(data, fourDamp) - - print(data.shape) - dfdt = np.gradient(data)[0] - dfdt = abs(dfdt).max(1).max(1).max(1) - - ave = {"amp": amp, "dc": dc, "amp_o": amp_o, "dfdt": dfdt} - - else: - print("no rescaling") - ave = {"amp": amp, "dc": dc} - - if nonlinear is not None: # add nonlinear part if user provides - nl = abs(nonlinear[:, mxg : -1.0 * mxg, :, :]).max(1).max(1).max(1) - nl_norm = (old_div(nl, dfdt)) * dt - - ave["nl"] = nl - ave["nl_norm"] = nl_norm - - if rotate: - print("rotate stuff") - # will need to provide some grid geometry to do this one - else: - print("or not") - - # let's identify the dominant modes, for now at every [t,x] slice - # if the data set is too large we can average over x - peaks_db = fft_info( - data, user_peak, meta=meta - ) # Nt X Nx X (# of loc. max) list of dict - - # print peaks[0]['gamma'] - return peaks_db, ave - - -def fft_info( - data, - user_peak, - dimension=[3, 4], - rescale=False, - wavelet=False, - show=False, - meta=0, - edgefix=False, -): - import numpy as np - import math - - print("in fft_inf0") - - dims = data.shape - ndims = len(dims) - - if ndims == 4: - nt, nx, ny, nz = data.shape - print(data.shape) - else: - print("something with dimesions") - - # data2 = data - # if edgefix: - # data2 = np.zeros((nt,nx,ny+1,nz+1)) - - # for t in range(nt): - # for x in range(nx): - # temp = np.append(data[t,x,:,:],[data[t,x,0,:]],0) - # data2[t,x,:,:] = np.append(temp, - # np.transpose([temp[:,0]]),1) - - # dt, k labels for the revelant dimensions - - dt = meta["dt"]["v"] - dz = meta["dz"] - # IC = meta['IC'] - ky_max = old_div(ny, 2) - kz_max = old_div(nz, 2) - amp = abs(data).max(2).max(2) # nt x nx - - print("dt: ", dt) - - # print data[0,2,:,:] - - IC = amp[0, :].max() # intial condition, set - print(IC) - - fft_data = np.fft.fft2(data)[ - :, :, 0:ky_max, 0:kz_max - ] # by default the last 2 dimensions - - power = fft_data.conj() * fft_data - # print power[0].max(), (IC*(ky_max)*(kz_max))**2 - - cross_pow = old_div((fft_data * (np.roll(fft_data, 1, axis=0)).conj()), (ny * nz)) - - if rescale: - fft_data_n = np.fft.fft2(data_n)[:, :, 0:ky_max, 0:kz_max] - pow_n = np.sqrt((fft_data_n.conj() * fft_data_n).real) - - peaks = [[[] for i in range(nx)] for j in range(nt)] # a list of dictionaries - peaks_db = [] - - peak_hist = [[0 for i in range(kz_max)] for j in range(ky_max)] # a 2d bin array - - # for now using a lame 2x loop method - - if user_peak != 0: - for mem in user_peak: - print(mem) - peak_hist[int(mem[0])][int(mem[1])] = abs( - power.mean(0).mean(0)[int(mem[0]), int(mem[1])] - ) - - # floor = ((IC*(kz_max*ky_max))**2)/10000 - - else: - for t in range(nt): - for x in range(nx): - peaks[t][x] = local_maxima( - power[t, x, :, :], 0, floor=(IC * (kz_max * ky_max)) ** 2 - ) - for p in peaks[t][ - x - ]: # looping over each returned peakset at some fixed t,x pair - peak_hist[p["y_i"]][ - p["z_i"] - ] += 1 # average across t and x, at least exclude pad - floor = 0 - - # this array is usefull for determining what the dominant modes are - # but we want to retain the option of observing how the amplitude - # of any give harmonic varies in space - - peak_hist = np.array(peak_hist) - - # let's find the top N overall powerfull harmnonics - net_peak = local_maxima(peak_hist, user_peak, bug=False) - - print("net_peak: ", net_peak, user_peak != 0) - # dom_mode = [{'amp':[],'amp_n':[],'phase':[],'freq':[],'gamma':[]} for x in net_peak] - dom_mode_db = [] - - Bp = meta["Bpxy"]["v"][:, old_div(ny, 2)] - B = meta["Bxy"]["v"][:, old_div(ny, 2)] - Bt = meta["Btxy"]["v"][:, old_div(ny, 2)] - - rho_s = meta["rho_s"]["v"] - - L_z = old_div(meta["L_z"], rho_s) - # L_z = - L_y = meta["lpar"] # already normalized earlier in read_inp.py - L_norm = old_div(meta["lbNorm"], rho_s) - - hthe0_n = 1e2 * meta["hthe0"]["v"] / rho_s # no x dep - hthe0_n_x = old_div(L_y, (2 * np.pi)) # no x dep - - print("L_z,Ly: ", L_z, L_y) - - # if user provides the harmo nic info overide the found peaks - - # thi is where all the good stuff is picked up - - # look at each mode annd pull out some usefull linear measures - for i, p in enumerate(net_peak): - # print i,p['y_i'],p['z_i'],fft_data.shape,fft_data[:,:,p['y_i'],p['z_i']].shape - - amp = ( - old_div(np.sqrt(power[:, :, p["y_i"], p["z_i"]]), (kz_max * ky_max)) - ).real - - # print (np.angle(fft_data[:,:,p['y_i'],p['z_i']],deg=False)).real - - phase = -np.array( - np.gradient( - np.squeeze(np.angle(fft_data[:, :, p["y_i"], p["z_i"]], deg=False)) - )[0].real - ) # nt x nx - - gamma_instant = np.array(np.gradient(np.log(np.squeeze(amp)))[0]) - - # loop over radaii - phasenew = [] - gammanew = [] - from scipy.interpolate import interp2d, interp1d - from scipy import interp - - gamma_t = np.transpose(gamma_instant) - for i, phase_r in enumerate(np.transpose(phase)): - gamma_r = gamma_t[i] - jumps = np.where(abs(phase_r) > old_div(np.pi, 32)) - # print jumps - if len(jumps[0]) != 0: - all_pts = np.array(list(range(0, nt))) - good_pts = (np.where(abs(phase_r) < old_div(np.pi, 3)))[0] - # print good_pts,good_pts - # f = interp1d(good_pts,phase_r[good_pts],fill_value=.001) - # print max(all_pts), max(good_pts) - # phasenew.append(f(all_pts)) - try: - phase_r = interp(all_pts, good_pts, phase_r[good_pts]) - gamma_r = interp(all_pts, good_pts, gamma_r[good_pts]) - except: - "no phase smoothing" - phasenew.append(phase_r) - gammanew.append(gamma_r) - - phase = old_div(np.transpose(phasenew), dt) - - gamma_i = old_div(np.transpose(gammanew), dt) - - amp_n = ( - old_div(np.sqrt(power[:, :, p["y_i"], p["z_i"]]), (kz_max * ky_max * amp)) - ).real - # amp_n = dom_mode[i]['amp_n'] #nt x nx - - # let just look over the nx range - # lnamp = np.log(amp[nt/2:,2:-2]) - try: - lnamp = np.log(amp[old_div(nt, 2) :, :]) - except: - print("some log(0) stuff in basic_info") - - t = dt * np.array(list(range(nt))) # dt matters obviouslyww - r = np.polyfit(t[old_div(nt, 2) :], lnamp, 1, full=True) - - gamma_est = r[0][0] # nx - f0 = np.exp(r[0][1]) # nx - res = r[1] - pad = [0, 0] - # gamma_est = np.concatenate([pad,gamma_est,pad]) - # f0 = np.concatenate([pad,f0,pad]) - # res = np.concatenate([pad,res,pad]) - - # sig = res/np.sqrt((x['nt']-2)) - sig = np.sqrt(old_div(res, (nt - 2))) - # sig0 = sig*np.sqrt(1/(x['nt'])+ ) # who cares - sig1 = sig * np.sqrt(old_div(1.0, (nt * t.var()))) - nt = np.array(nt) - print("shapes ", nt.shape, nt, lnamp.shape, res.shape, gamma_est) - # print r - res = 1 - old_div(res, (nt * lnamp.var(0))) # nx - res[0:2] = 0 - res[-2:] = 0 - - gamma = [gamma_est, sig1, f0, res] - - # gamma_est2 = np.gradient(amp)[0]/(amp[:,:]*dt) - # gamma_w = np.gradient(gamma_est2)[0] - - # gamma_i = np.abs(gamma_w).argmin(0) #index of the minimum for any given run - # for j in range(nx): - # gamma_w[0:max([gamma_i[j],nt/3]),j] = np.average(gamma_w)*100000.0 - - freq = np.array( - weighted_avg_and_std(phase[-10:, :], weights=np.ones(phase[-10:, :].shape)) - ) - - # gamma = weighted_avg_and_std( - # gamma_est2[-5:,:],weights=np.ones(gamma_est2[-5:,:].shape)) - - k = [ - [p["y_i"], p["z_i"]], - [2 * math.pi * float(p["y_i"]) / L_y, 2 * math.pi * p["z_i"] / L_z], - ] - # L_y is normalized - - # simple k def, works in drift-instability fine - # k = [[p['y_i'],p['z_i']], - # [(B/Bp)**-1*2*math.pi*float(p['y_i'])/(L_y),(B/Bp)*2*math.pi*p['z_i']/L_z]] - - # k_r = [[p['y_i'],p['z_i']], - # [(Bp/B)*2*math.pi*float(p['y_i'])/(L_y), - # (B/Bp)*2*math.pi*p['z_i']/L_z]] - - k_r = [ - [p["y_i"], p["z_i"]], - [ - 2 * math.pi * float(p["y_i"]) / (L_y), - (old_div(B, Bp)) * 2 * math.pi * p["z_i"] / L_z - + (old_div(Bt, B)) * 2 * math.pi * float(p["y_i"]) / (L_y), - ], - ] - - # revised - # k_r = [[p['y_i'],p['z_i']], - # [2*math.pi*float(p['y_i'])/(L_y), - # (Bp/B)*2*math.pi*p['z_i']/L_z - # - (Bt/Bp)*2*math.pi*float(p['y_i'])/(L_y)]] - # revised - - # what I think is the most general one, works in drift-instability again - # seems to work for Bz only helimak, now trying Bp = Bt - # k = [[p['y_i'],p['z_i']], - # [((Bp/B)*float(p['y_i'])/(hthe0_n)) + - # 2*np.pi*p['z_i']*np.sqrt(1-(Bp/B)**2)/L_z, - # 2*math.pi*p['z_i']/L_norm - - # float(p['y_i'])*np.sqrt(1-(Bp/B)**2)/(hthe0_n)]] - # k = [[p['y_i'],p['z_i']], - # [((Bp/B)*float(p['y_i'])/(hthe0_n)), - # 2*math.pi*p['z_i']/L_norm]] - # BOTH SEEM TO PRODOCE SAME RESULTS - - # k = [[p['y_i'],p['z_i']], - # [(float(p['y_i'])/(hthe0_n_x)), - # 2*math.pi*float(p['z_i'])/L_norm]] - - dom_mode_db.append( - { - "modeid": i, - "k": k[1], - "gamma": gamma, - "freq": freq, - "amp": amp, - "amp_n": amp_n, - "phase": phase, - "mn": k[0], - "nt": nt, - "k_r": k_r[1], - "gamma_i": gamma_i, - } - ) - - return dom_mode_db - - -# return a 2d array fof boolean values, a very simple boolian filter -def local_maxima(array2d, user_peak, index=False, count=4, floor=0, bug=False): - from operator import itemgetter, attrgetter - - if user_peak == 0: - where = ( - (array2d >= np.roll(array2d, 1, 0)) - & (array2d >= np.roll(array2d, -1, 0)) - & (array2d >= np.roll(array2d, 0, 1)) - & (array2d >= np.roll(array2d, 0, -1)) - & (array2d >= old_div(array2d.max(), 5.0)) - & (array2d > floor * np.ones(array2d.shape)) - & (array2d >= array2d.mean()) - ) - else: # some simpler filter if user indicated some modes - where = array2d > floor - - # ignore the lesser local maxima, throw out anything with a ZERO - if bug == True: - print(array2d, array2d[where.nonzero()], where.nonzero()[0]) - - peaks = list(zip(where.nonzero()[0], where.nonzero()[1], array2d[where.nonzero()])) - - peaks = sorted(peaks, key=itemgetter(2), reverse=True) - - if len(peaks) > count and user_peak == 0: - peaks = peaks[0:count] - - keys = ["y_i", "z_i", "amp"] - - peaks = [dict(list(zip(keys, peaks[x]))) for x in range(len(peaks))] - - return peaks - # return np.array(peak_dic) - - -def weighted_avg_and_std(values, weights): - """ - Returns the weighted average and standard deviation. - - values, weights -- Numpy ndarrays with the same shape. - """ - - if len(values.shape) == 2: - average = np.average(values, 0) # , weights=weights) - variance = old_div( - ( - np.inner( - weights.transpose(), ((values - average) ** 2).transpose() - ).diagonal() - ), - weights.sum(0), - ) - else: - average = np.average(values, weights=weights) - variance = old_div( - np.dot(weights, (values - average) ** 2), weights.sum() - ) # Fast and numerically precise - - return [average, variance] diff --git a/tools/pylib/post_bout/grate2.py b/tools/pylib/post_bout/grate2.py deleted file mode 100644 index 5157863cc2..0000000000 --- a/tools/pylib/post_bout/grate2.py +++ /dev/null @@ -1,52 +0,0 @@ -from __future__ import print_function -from builtins import range - -### -# compute average growth rate bout variable f and plane y -# prints value in plane y and total average -# optional tind excludes initial 'tind' time steps -# Note it masks the values != Inf -### -import numpy as np -from boutdata.collect import collect -from boututils.moment_xyzt import moment_xyzt - - -def avgrate(p, y=None, tind=None): - if tind is None: - tind = 0 - - rmsp_f = moment_xyzt(p, "RMS").rms - - ni = np.shape(rmsp_f)[1] - nj = np.shape(rmsp_f)[2] - - growth = np.zeros((ni, nj)) - - with np.errstate(divide="ignore"): - for i in range(ni): - for j in range(nj): - growth[i, j] = np.gradient(np.log(rmsp_f[tind::, i, j]))[-1] - - d = np.ma.masked_array(growth, np.isnan(growth)) - - # masked arrays - # http://stackoverflow.com/questions/5480694/numpy-calculate-averages-with-nans-removed - - print("Total average growth rate= ", np.mean(np.ma.masked_array(d, np.isinf(d)))) - if y is not None: - print( - "Growth rate in plane", - y, - "= ", - np.mean(np.ma.masked_array(growth[:, y], np.isnan(growth[:, y]))), - ) - - -# test -if __name__ == "__main__": - path = "/Users/brey/BOUT/bout/examples/elm-pb/data" - - data = collect("P", path=path) - - avgrate(data, 32) diff --git a/tools/pylib/post_bout/pb_corral.py b/tools/pylib/post_bout/pb_corral.py deleted file mode 100644 index df9a9b00b6..0000000000 --- a/tools/pylib/post_bout/pb_corral.py +++ /dev/null @@ -1,540 +0,0 @@ -# note - these commands are only run by default in interactive mode -from __future__ import print_function -from __future__ import absolute_import -from __future__ import division -from builtins import filter -from builtins import range -from past.utils import old_div -from builtins import object -import os -import sys - -try: - boutpath = os.environ["BOUT_TOP"] - pylibpath = boutpath + "tools/pylib" - pbpath = pylibpath + "/post_bout" - boutdatapath = pylibpath + "/boutdata" - boututilpath = pylibpath + "/boututils" - - allpath = [boutpath, pylibpath, pbpath, boutdatapath, boututilpath] - [sys.path.append(elem) for elem in allpath] - -except: - print("unable to append needed .py files") - -sys.path.append("/usr/local/pylib") - -import post_bout as post_bout -from .ListDict import ListDictKey, ListDictFilt -from .read_inp import parse_inp, read_inp, read_log -from .basic_info import weighted_avg_and_std -from .read_cxx import read_cxx, findlowpass - - -import os -import numpy as np -import pickle -import subprocess - - -def corral( - cached=True, refresh=False, debug=False, IConly=1, logname="status.log", skew=False -): - print("in corral") - log = read_log(logname=logname) - # done = log['done'] - runs = log["runs"] # a list of all directories, we need this, - # only need 'runs' if the simulation is done - - current = log["current"] # always return the last data_dir - - print(log) - print("current:", current) - - if refresh == True: - for i, path in enumerate(runs): - print(i, path) - a = post_bout.save(path=path, IConly=IConly) # re post-process a run - - elif ( - cached == False - ): # if all the ind. simulation pkl files are in place skip this part - a = post_bout.save(path=current) # save to current dir - # here is really where you shoudl write to status.log - # write_log('status.log', - cached = True - - # if done: - - all_ave = [] - all_modes = [] - print("last_one: ") - for i, val in enumerate(runs): - print(val) - mode_db, ave_db = post_bout.read(path=val) - # alldata.append(array) - all_modes.append(mode_db) - all_ave.append(ave_db) - - # build the end database - - # remove the read in pickle - - # return alldb - def islist(input): - return isinstance(input, list) - - all_modes = list(filter(islist, all_modes)) - # all_ave = filter(islist,all_ave) - - # alldb = sum(alldb,[]) - # alldata = np.array(alldata) - all_modes = sum(all_modes, []) - - nt = [] - for mode in all_modes: - nt.append(len(mode["amp"])) - nt = [max(nt)] - - nt = nt[0] - t = list(range(nt)) - i = 0 - - if debug: - return all_modes, all_ave - else: - return LinRes(all_modes) - - -class LinRes(object): - def __init__(self, all_modes): - self.mode_db = all_modes - self.db = all_modes - # self.ave_db = all_ave - - alldb = self.db - # self.modekeys = data[0]['fields']['Ni']['modes'][0].keys() - # print len(alldb) - - self.meta = np.array(ListDictKey(self.db, "meta"))[0] - - self.keys = list((self.mode_db)[0].keys()) - # self.avekeys = data[0]['fields']['Ni']['ave'].keys() - - # self.nrun = len(alldb) #number of runs - - self.path = np.array(ListDictKey(self.db, "path")) - self.cxx = [] - self.maxN = [] - - self.ave = np.array(ListDictKey(alldb, "ave")) - - # [self.cxx.append(read_cxx(path=elem,boutcxx='2fluid.cxx.ref')) for elem in self.path] - # [self.maxN.append(findlowpass(elem)) for elem in self.cxx] - [ - self.cxx.append(read_cxx(path=elem, boutcxx="physics_code.cxx.ref")) - for elem in self.path - ] - - self.maxZ = np.array(ListDictKey(alldb, "maxZ")) - self.maxN = self.maxZ - # self.maxN = findlowpass(self.cxx) #low pass filt from .cxx - - self.nx = np.array(ListDictKey(alldb, "nx"))[0] - self.ny = np.array(ListDictKey(alldb, "ny"))[0] - self.nz = np.array(ListDictKey(alldb, "nz"))[0] - - # self.nt = int(data[0]['meta']['NOUT']['v']+1) - self.Rxy = np.array(ListDictKey(alldb, "Rxy")) - self.Rxynorm = np.array(ListDictKey(alldb, "Rxynorm")) - self.nt = np.array(ListDictKey(alldb, "nt")) - - self.dt = np.array(ListDictKey(alldb, "dt")) - self.nfields = np.array(ListDictKey(alldb, "nfields")) - - self.field = np.array(ListDictKey(alldb, "field")) - - self.k = np.array(ListDictKey(alldb, "k")) - self.k_r = np.array(ListDictKey(alldb, "k_r")) - - self.mn = np.array(ListDictKey(alldb, "mn")) - - # return ListDictKey(alldb,'phase') - - # self.phase = np.array(ListDictKey(alldb,'phase')) - self.phase = ListDictKey(alldb, "phase") - - # self.amp= np.array(ListDictKey(alldb,'amp')) - # self.amp_n=np.array(ListDictKey(alldb,'amp_n')) - # self.dc= [] - # self.freq = np.array(ListDictKey(alldb,'k')) - # self.gamma = np.array(ListDictKey(alldb,'gamma')) - - self.amp = ListDictKey(alldb, "amp") - self.amp_n = ListDictKey(alldb, "amp_n") - self.dc = [] - # self.freq = np.array(ListDictKey(alldb,'k')) - self.gamma = np.array(ListDictKey(alldb, "gamma")) - self.gamma_i = np.array(ListDictKey(alldb, "gamma_i")) - - self.freq = np.array(ListDictKey(alldb, "freq")) - - self.IC = np.array(ListDictKey(alldb, "IC")) - self.dz = np.array(ListDictKey(alldb, "dz")) - self.meta["dz"] = np.array(list(set(self.dz).union())) - - self.nmodes = self.dz.size - - self.MN = np.array(ListDictKey(alldb, "MN")) - # self.MN = np.float32(self.mn) - # self.MN[:,1] = self.mn[:,1]/self.dz - self.nrun = len(set(self.path).union()) - self.L = np.array(ListDictKey(alldb, "L")) - # self.C_s = - self.modeid = np.array(ListDictKey(alldb, "modeid")) - - self.trans = np.array(ListDictKey(alldb, "transform")) - - if np.any(self.trans): - self.phase_r = ListDictKey(alldb, "phase_r") - self.gamma_r = np.array(ListDictKey(alldb, "gamma_r")) - self.amp_r = ListDictKey(alldb, "amp_r") - self.freq_r = np.array(ListDictKey(alldb, "freq_r")) - - # try: - # self.model(haswak=False) # - # except: - # self.M = 0 - - # try: - try: # analytic model based on simple matrix - self.models = [] - # self.models.append(_model(self)) #create a list to contain models - self.models.append( - _model(self, haswak=True, name="haswak") - ) # another model - # self.models.append(_model(self,haswak=True,name='haswak_0',m=0)) - # for Ln in range(10): - # Lval = 10**((.2*Ln -1)/10) - # #Lval = 10**(Ln-1) - # #Lval = - # print Lval - # self.models.append(_model(self,varL=True,name='varL'+str(Lval),Lval=Lval,haswak=True)) - - except: - self.M = 0 - - try: # analytic models based on user defined complex omega - self.ref = [] - self.ref.append(_ref(self)) - # self.ref.append(_ref(self,haswak=False,name='drift')) - # demand a complex omega to compare - # self.ref.append(_ref(self,haswas=True,name='haswak')) - except: - self.ref = 0 - - # self.models.append(_model(self,haswak2=True,name='haswak2')) - - # except: - # print 'FAIL' - - def _amp(self, tind, xind): - # first select modes that actually have valid (tind,xind) - # indecies - # s = subset(self.db,'modeid',modelist) - return np.array([self.amp[i][tind, xind] for i in range(self.nmodes)]) - - # def model(self,field='Ni',plot=False,haswak=False): - - # #enrich the object - # allk = self.k_r[:,1,self.nx/2] #one location for now - # allkpar = self.k_r[:,0,self.nx/2] #one location for now - - # self.M = [] - # self.eigsys = [] - # self.gammaA = [] - # self.omegaA = [] - # self.eigvec = [] - # self.gammamax = [] - # self.omegamax = [] - - # #allk = np.arange(0.1,100.0,.1) - # #allk= np.sort(list(set(allk).union())) - - # for i,k in enumerate(allk): - # #print i - # #M =np.matrix(np.random.rand(3,3),dtype=complex) - # M = np.zeros([3,3],dtype=complex) - # M[0,0] = 0 - # M[0,1] = k/(self.L[i,self.nx/2,self.ny/2]) - # M[1,0] = (2*np.pi/self.meta['lpar'][self.nx/2])**2 * self.meta['sig_par'][0]*complex(0,k**-2) - # M[1,1]= -(2*np.pi/self.meta['lpar'][self.nx/2])**2 * self.meta['sig_par'][0]*complex(0,k**-2) - - # if haswak: - # M[0,0] = M[0,0] + M[1,1]*complex(0,k**2) - # M[0,1] = M[0,1] + M[1,0]*complex(0,k**2) - - # #if rho_conv: - - # #M[1,0] = (allkpar[i])**2 * self.meta['sig_par'][0]*complex(0,k**-2) - # #M[1,1]= -(allkpar[i])**2 * self.meta['sig_par'][0]*complex(0,k**-2) - - # eigsys= np.linalg.eig(M) - # gamma = (eigsys)[0].imag - # omega =(eigsys)[0].real - # eigvec = eigsys[1] - - # self.M.append(M) - # self.eigsys.append(eigsys) - # self.gammaA.append(gamma) - # self.gammamax.append(max(gamma)) - # where = ((gamma == gamma.max()) & (omega != 0)) - # self.omegamax.append(omega[where[0]]) - # self.eigvec.append(eigvec) - # self.omegaA.append(omega) - - class __model__(object): - def __init__(self): - self.M = 0 - - -class subset(LinRes): - def __init__(self, alldb, key, valuelist, model=False): - selection = ListDictFilt(alldb, key, valuelist) - if len(selection) != 0: - LinRes.__init__(self, selection) - self.skey = key - if model == True: - self.model() - else: - LinRes.__init__(self, alldb) - if model == True: - self.model() - - -# class subset(originClass): -# def __init__(self,alldb,key,valuelist,model=False): -# selection = ListDictFilt(alldb,key,valuelist) -# if len(selection) !=0: -# originClass.__init__(self,selection,input_obj.ave_db) -# self.skey = key -# if model==True: -# self.model() -# else: -# origin.__init__(self,alldb) -# if model==True: -# self.model() - -# not sure if this is the best way . . . - - -# class subset(object): -# def __init__(self,input_obj,key,valuelist,model=False): -# selection = ListDictFilt(input_obj.mode_db,key,valuelist) -# if len(selection) !=0: -# import copy -# self = copy.copy(input_obj) -# self.__init__(selection,input_obj.ave_db) -# self.skey = key -# if model==True: -# self.model() -# else: -# self = input_obj -# if model==True: -# self.model() - - -class _ref(object): # NOT a derived obj, just takes one as a var - def __init__(self, input_obj, name="haswak", haswak=True): - allk = input_obj.k_r[:, 1, old_div(input_obj.nx, 2)] # one location for now - allkpar = input_obj.k_r[:, 0, old_div(input_obj.nx, 2)] # one location for now - self.name = name - - self.gamma = [] - self.omega = [] - self.soln = {} - self.soln["gamma"] = [] - self.soln["freq"] = [] - - for i, k in enumerate(allk): - omega_star = old_div( - -(k), - (input_obj.L[i, old_div(input_obj.nx, 2), old_div(input_obj.ny, 2)]), - ) - - nu = ( - 2 * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)] - ) ** 2 * input_obj.meta["sig_par"][0] - - if haswak: - omega = old_div(-omega_star, (1 + (k) ** 2)) - gamma = old_div(((k**2) * omega_star**2), (nu * (1 + k**2) ** 3)) - else: - # omega = -np.sqrt(nu*omega_star)/(np.sqrt(2)*k) + nu**(3/2)/(8*np.sqrt(2*omega_star)*k**3) - # gamma = np.sqrt(nu*omega_star)/(np.sqrt(2)*k) - nu/(2* k**2) + nu**(3/2)/(8*np.sqrt(2*omega_star)*k**3) - omega = -omega_star + old_div((2 * k**4 * omega_star**3), nu**2) - gamma = old_div((k * omega_star) ** 2, nu) - ( - 5 * (k**6 * omega_star * 4 / nu**3) - ) - self.gamma.append(gamma) - self.omega.append(omega) - - self.soln["freq"] = np.transpose(np.array(self.omega)) - self.soln["gamma"] = np.transpose(np.array(self.gamma)) - - -class _model(object): # NOT a derived class,but one that takes a class as input - def __init__( - self, - input_obj, - name="drift", - haswak=False, - rho_conv=False, - haswak2=False, - varL=False, - Lval=1.0, - m=1, - ): - allk = input_obj.k_r[:, 1, old_div(input_obj.nx, 2)] # one location for now - allkpar = input_obj.k_r[:, 0, old_div(input_obj.nx, 2)] # one location for now - - # numerical value to compare against - - numgam = input_obj.gamma[:, 0, old_div(input_obj.nx, 2)] - numfreq = input_obj.freq[:, 0, old_div(input_obj.nx, 2)] - self.name = name - - self.M = [] - self.eigsys = [] - self.gammaA = [] - self.omegaA = [] - self.eigvec = [] - self.gammamax = [] - self.omegamax = [] - self.k = [] - self.m = m - - self.soln = {} - self.soln["freq"] = [] - self.soln["gamma"] = [] - self.soln["gammamax"] = [] - self.soln["freqmax"] = [] - - self.chi = {} - self.chi["freq"] = [] - self.chi["gamma"] = [] - - for i, k in enumerate(allk): - # print i - # M =np.matrix(np.random.rand(3,3),dtype=complex) - M = np.zeros([4, 4], dtype=complex) - M[0, 0] = 0 - # k = k/np.sqrt(10) - # L = (input_obj.L)*np.sqrt(10) - - if k == 0: - k = 1e-5 - - # print k {n,phi,v,ajpar} - M[0, 1] = old_div( - k, (input_obj.L[i, old_div(input_obj.nx, 2), old_div(input_obj.ny, 2)]) - ) - M[1, 0] = ( - (2 * m * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)]) ** 2 - * input_obj.meta["sig_par"][0] - * complex(0, (k) ** -2) - ) - M[1, 1] = ( - -( - (2 * m * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)]) - ** 2 - ) - * input_obj.meta["sig_par"][0] - * complex(0, (k) ** -2) - ) - - # parallel dynamics - # M[2,2] = k/(input_obj.L[i,input_obj.nx/2,input_obj.ny/2]) - # M[2,0] = -(2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2]) - # M[0,2] = -(2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2]) - - # M[1,0] = (2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2])**2 * input_obj.meta['sig_par'][0] - # M[1,1]= -(2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2])**2 * input_obj.meta['sig_par'][0] - - # ajpar dynamics - effectively parallel electron dynamics instead of - - if haswak: - M[0, 0] = ( - -( - ( - 2 - * m - * np.pi - / input_obj.meta["lpar"][old_div(input_obj.nx, 2)] - ) - ** 2 - ) - * input_obj.meta["sig_par"][0] - * complex(0, 1) - ) - M[0, 1] = ( - 2 * m * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)] - ) ** 2 * input_obj.meta["sig_par"][0] * complex(0, 1) + M[0, 1] - - if varL: - M[0, 1] = Lval * M[0, 1] - - if rho_conv: # not used - M[1, 0] = ( - (allkpar[i]) ** 2 - * input_obj.meta["sig_par"][0] - * complex(0, (k) ** -2) - ) - M[1, 1] = ( - -((allkpar[i]) ** 2) - * input_obj.meta["sig_par"][0] - * complex(0, (k) ** -2) - ) - - eigsys = np.linalg.eig(M) - gamma = (eigsys)[0].imag - omega = (eigsys)[0].real - eigvec = eigsys[1] - self.k.append(k) - - self.M.append(M) - self.eigsys.append(eigsys) - - self.gammaA.append(gamma) - self.soln["gamma"].append(gamma) - - self.gammamax.append(max(gamma)) - self.soln["gammamax"].append(max(gamma)) - - where = (gamma == gamma.max()) & (omega != 0) - # if len(where) > 1: - # where = where[0] - self.omegamax.append(omega[where]) - self.soln["freqmax"].append(omega[where]) - - # print k,gamma,where,M,omega - chigam = old_div(((numgam - max(gamma)) ** 2), max(gamma)) - chifreq = old_div(((numfreq - omega[where]) ** 2), omega[where]) - - self.eigvec.append(eigvec) - self.omegaA.append(omega) - self.soln["freq"].append(omega) - - self.chi["freq"].append(chifreq[i]) - - self.chi["gamma"].append(chigam[i]) - - self.dim = M.shape[0] - self.soln["freq"] = np.transpose(np.array(self.soln["freq"])) - self.soln["gamma"] = np.transpose(np.array(self.soln["gamma"])) - self.chi["freq"] = np.transpose(np.array(self.chi["freq"])) - self.chi["gamma"] = np.transpose(np.array(self.chi["gamma"])) - - # self.soln = {} - # self.soln['freq'] = self.omegaA - # self.soln['gamma'] = self.gammaA diff --git a/tools/pylib/post_bout/pb_draw.py b/tools/pylib/post_bout/pb_draw.py deleted file mode 100644 index 272aab9c35..0000000000 --- a/tools/pylib/post_bout/pb_draw.py +++ /dev/null @@ -1,1692 +0,0 @@ -from __future__ import print_function -from __future__ import absolute_import -from __future__ import division -from builtins import str -from builtins import range -from past.utils import old_div - -# some standard analytic stuff to plot, if appending just overplot gam or omeg -from .pb_corral import LinRes -from .ListDict import ListDictKey, ListDictFilt -import numpy as np - -import matplotlib.pyplot as plt -from matplotlib import cm -import matplotlib.artist as artist -import matplotlib.ticker as ticker -import matplotlib.pyplot as plt -import matplotlib.patches as patches -from matplotlib.figure import Figure -from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas -from matplotlib.backends.backend_pdf import PdfPages - -from reportlab.platypus import * -from reportlab.lib.styles import getSampleStyleSheet -from reportlab.rl_config import defaultPageSize -from reportlab.lib.units import inch -from reportlab.graphics.charts.linecharts import HorizontalLineChart -from reportlab.graphics.shapes import Drawing -from reportlab.graphics.charts.lineplots import LinePlot -from reportlab.graphics.widgets.markers import makeMarker -from reportlab.lib import colors - -from replab_x_vs_y import RL_Plot -from matplotlib.ticker import ScalarFormatter, FormatStrFormatter, MultipleLocator - - -class LinResDraw(LinRes): - def __init__(self, alldb): - LinRes.__init__(self, alldb) - - def plottheory( - self, pp, m=1, canvas=None, comp="gamma", field="Ni", allroots=False - ): - if len(self.models) == 0: - try: - self.models = [] - self.models.append(_model(self)) # create a list to contain models - self.models.append( - _model(self, haswak=True, name="haswak") - ) # another model - except: - return 0 - - s = subset(self.db, "field", [field]) - - modelist = [] - - [modelist.append([m, n + 1]) for n in range(min(s.maxN) - 1)] - - s = subset(s.db, "mn", modelist) - - allk = s.k[:, 1, old_div(s.nx, 2)] - ki = np.argsort(allk) - - ownpage = False - if canvas is None: - ownpage = True - - if ownpage: # if not an overplot - fig1 = plt.figure() - canvas = fig1.add_subplot(1, 1, 1) - - label = "gamma analytic" - - # if comp=='gamma': - # y = np.array(s.gammamax)[ki] - # else: - # y = np.array(s.omegamax)[ki] - - for m in s.models: - print(m.name) - - for i, m in enumerate(s.models): - print(m.name, comp, m.soln[comp].shape) - - if allroots: - for elem in m.soln[comp]: - # y = [] - # elem has 2 or more elements - y = (np.array(elem)[ki]).flatten() # n values - # y = y.astype('float') - print(y.shape) - canvas.plot( - (allk[ki]).flatten(), y, ",", label=label, c=cm.jet(0.2 * i) - ) - try: - ymax = (np.array(m.soln[comp + "max"])[ki]).flatten() - # ymax = (np.array(m.gammamax)[ki]).flatten() - ymax = ymax.astype("float") - print(comp, " ymax:", ymax) - canvas.plot( - (allk[ki]).flatten(), ymax, "-", label=label, c=cm.jet(0.2 * i) - ) - # if comp=='gamma': - # y = (np.array(m.gammamax)[ki]).flatten() - - # else: - # y = (np.array(m.omegamax)[ki]).flatten() - - # print m.name, ':' ,y.astype('float') - - except: - print("fail to add theory curve") - - canvas.annotate(m.name, (allk[ki[0]], 1.1 * ymax[0]), fontsize=8) - canvas.annotate(m.name, (1.1 * allk[ki[-1]], 1.1 * ymax[-1]), fontsize=8) - - try: - for i, m in enumerate(s.ref): - if not allroots: - y = (np.array(m.soln[comp])[ki]).flatten() - y = y.astype("float") - canvas.plot( - (allk[ki]).flatten(), - y, - "--", - label=label, - c=cm.jet(0.2 * i), - ) - except: - print("no reference curve") - - if ownpage: # set scales if this is its own plot - # canvas.set_yscale('symlog',linthreshy=1e-13) - # canvas.set_xscale('log') - - canvas.axis("tight") - canvas.set_xscale("log") - canvas.set_yscale("symlog") - fig1.savefig(pp, format="pdf") - plt.close(fig1) - else: # if not plot its probably plotted iwth sim data, print chi somewhere - for i, m in enumerate(s.models): - textstr = r"$\chi^2$" + "$=%.2f$" % (m.chi[comp].sum()) - print(textstr) - # textstr = '$\L=%.2f$'%(m.chi[comp].sum()) - props = dict(boxstyle="square", facecolor="white", alpha=0.3) - textbox = canvas.text( - 0.1, - 0.1, - textstr, - transform=canvas.transAxes, - fontsize=10, - verticalalignment="top", - bbox=props, - ) - - def plotomega( - self, - pp, - canvas=None, - field="Ni", - yscale="linear", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - comp="gamma", - pltlegend="both", - overplot=False, - gridON=True, - trans=False, - infobox=True, - ): - colors = [ - "b.", - "r.", - "k.", - "c.", - "g.", - "y.", - "m.", - "b.", - "r.", - "k.", - "c.", - "g.", - "y.", - "m.", - ] - colordash = [ - "b", - "r", - "k", - "c", - "g", - "y", - "m", - "b", - "r", - "k", - "c", - "g", - "y", - "m", - ] - - if canvas is None: - ownpage = True - else: - ownpage = False - - if ownpage: - fig1 = plt.figure() - fig1.subplots_adjust(bottom=0.12) - fig1.subplots_adjust(top=0.80) - fig1.subplots_adjust(right=0.83) - fig1.subplots_adjust(left=0.17) - canvas = fig1.add_subplot(1, 1, 1) - clonex = canvas.twinx() - # if trans: - # cloney = canvas.twiny() - - dzhandles = [] - parhandles = [] - parlabels = [] - dzlabels = [] - - m_shift = 1 - for q in np.array(list(range(1))) + m_shift: - s = subset(self.db, "field", [field]) # pick field - maxZ = min(s.maxN) - modelist = [] - [modelist.append([q, p + 1]) for p in range(maxZ - 1)] - print(modelist) - print(q, "in plotgamma") - - s = subset(s.db, "mn", modelist) - - xrange = old_div(s.nx, 2) - 2 - - xrange = [old_div(s.nx, 2), old_div(s.nx, 2) + xrange] - - y = np.array(ListDictKey(s.db, comp)) - - # y = s.gamma #nmodes x 2 x nx ndarray - k = s.k ##nmodes x 2 x nx ndarray k_zeta - - kfactor = np.mean( - old_div(s.k_r[:, 1, old_div(s.nx, 2)], s.k[:, 1, old_div(s.nx, 2)]) - ) # good enough for now - - print( - k[:, 1, old_div(s.nx, 2)].shape, - y[:, 0, old_div(s.nx, 2)].shape, - len(colors), - ownpage, - ) # ,k[:,1,s.nx/2],y[:,0,s.nx/2] - - parhandles.append( - canvas.errorbar( - np.squeeze(k[:, 1, old_div(s.nx, 2)]), - np.squeeze(y[:, 0, old_div(s.nx, 2)]), - yerr=np.squeeze(y[:, 1, old_div(s.nx, 2)]), - fmt=colors[q], - ) - ) - - parlabels.append("m " + str(q)) - - # loop over dz sets and connect with dotted line . . . - jj = 0 - - ymin_data = np.max(np.array(ListDictKey(s.db, comp))) - ymax_data = 0 # for bookeeping - - for p in list(set(s.path).union()): - print(p, "in plotomega") - - sub_s = subset(s.db, "path", [p]) - j = sub_s.dz[0] - # print sub_s.amp.shape - s_i = np.argsort(sub_s.mn[:, 1]) # sort by 'local' m, global m is ok also - # print s_i, sub_s.mn, sub_s.nx, jj - y = np.array(ListDictKey(sub_s.db, comp)) - y_alt = 2.0 * np.array(ListDictKey(sub_s.db, comp)) - - k = sub_s.k ## - if q == m_shift: # fix the parallel mode - dzhandles.append( - canvas.plot( - k[s_i, 1, old_div(sub_s.nx, 2)], - y[s_i, 0, old_div(sub_s.nx, 2)], - color=colordash[jj], - alpha=0.5, - ) - ) - # clonex.plot(k[s_i,1,sub_s.nx/2], - # y_alt[s_i,0,sub_s.nx/2],color=colordash[jj],alpha=.5) - # if np.any(sub_s.trans) and trans: - # comp_r = comp+'_r' - # k_r = sub_s.k_r - # y2 = np.array(ListDictKey(sub_s.db,comp_r)) - # cloney.plot(k[s_i,1,sub_s.nx/2], - # y2[s_i,0,sub_s.nx/2],'k.',ms = 3) - - ymin_data = np.min([np.min(y[s_i, 0, old_div(sub_s.nx, 2)]), ymin_data]) - ymax_data = np.max([np.max(y[s_i, 0, old_div(sub_s.nx, 2)]), ymax_data]) - - print("dzhandle color", jj) - # dzlabels.append("DZ: "+ str(2*j)+r'$\pi$') - dzlabels.append(j) - - if yscale == "log": - factor = 10 - else: - factor = 2 - print("annotating") - canvas.annotate( - str(j), - ( - k[s_i[0], 1, old_div(sub_s.nx, 2)], - y[s_i[0], 0, old_div(sub_s.nx, 2)], - ), - fontsize=8, - ) - p = canvas.axvspan( - k[s_i[0], 1, old_div(sub_s.nx, 2)], - k[s_i[-1], 1, old_div(sub_s.nx, 2)], - facecolor=colordash[jj], - alpha=0.01, - ) - print("done annotating") - else: - canvas.plot( - k[s_i, 1, old_div(sub_s.nx, 2)], - y[s_i, 0, old_div(sub_s.nx, 2)], - color=colordash[jj], - alpha=0.3, - ) - - jj = jj + 1 - - dzhandles = np.array(dzhandles).flatten() - dzlabels = np.array(dzlabels).flatten() - - dzlabels = list(set(dzlabels).union()) - - dz_i = np.argsort(dzlabels) - - dzhandles = dzhandles[dz_i] - dzlabels_cp = np.array(dzlabels)[dz_i] - - print(type(dzlabels), np.size(dzlabels)) - for i in range(np.size(dzlabels)): - dzlabels[i] = "DZ: " + str(dzlabels_cp[i]) # +r"$\pi$" - - parlabels = np.array(parlabels).flatten() - - # if pltlegend =='both': # - - print("legends") - - # l1 = legend(parhandles,parlabels,loc = 3,prop={'size':6}) - # l2 = legend(dzhandles,dzlabels,loc = 1,prop={'size':6}) - # plt.gca().add_artist(l1) - - # else: - # legend(dzhandles,dzlabels,loc=3,prop={'size':6}) - if overplot == True: - try: - self.plottheory(pp, canvas=canvas, comp=comp, field=field) - # self.plottheory(pp,comp=comp) - except: - print("no theory plot") - if infobox: - textstr = "$\L_{\parallel}=%.2f$\n$\L_{\partial_r n}=%.2f$\n$B=%.2f$" % ( - s.meta["lpar"][old_div(s.nx, 2)], - s.meta["L"][old_div(s.nx, 2), old_div(s.ny, 2)], - s.meta["Bpxy"]["v"][old_div(s.nx, 2), old_div(s.ny, 2)], - ) - props = dict(boxstyle="square", facecolor="white", alpha=0.3) - textbox = canvas.text( - 0.82, - 0.95, - textstr, - transform=canvas.transAxes, - fontsize=10, - verticalalignment="top", - bbox=props, - ) - # leg = canvas.legend(handles,labels,ncol=2,loc='best',prop={'size':4},fancybox=True) - # textbox.get_frame().set_alpha(0.3) - # matplotlib.patches.Rectangle - # p = patches.Rectangle((0, 0), 1, 1, fc="r") - # p = str('L_par') - # leg = canvas.legend([p], ["Red Rectangle"],loc='best',prop={'size':4}) - # leg.get_frame().set_alpha(0.3) - - # cloney.set_xlim(xmin,xmax) - try: - canvas.set_yscale(yscale) - canvas.set_xscale(xscale) - - if yscale == "symlog": - canvas.set_yscale(yscale, linthreshy=1e-13) - if xscale == "symlog": - canvas.set_xscale(xscale, linthreshy=1e-13) - - if gridON: - canvas.grid() - except: - try: - canvas.set_yscale("symlog") - except: - print("scaling failed completely") - - # print '[xmin, xmax, ymin, ymax]: ',[xmin, xmax, ymin, ymax] - - clonex.set_yscale(yscale) # must be called before limits are set - - try: - if yscale == "linear": - formatter = ticker.ScalarFormatter() - formatter.set_powerlimits((-2, 2)) # force scientific notation - canvas.yaxis.set_major_formatter(formatter) - clonex.yaxis.set_major_formatter(formatter) - # canvas.useOffset=False - except: - print("fail 1") - [xmin, xmax, ymin, ymax] = canvas.axis() - - if yscale == "symlog": - clonex.set_yscale(yscale, linthreshy=1e-9) - if xscale == "symlog": - clonex.set_xscale(xscale, linthreshy=1e-9) - # if np.any(s.trans) and trans: - [xmin1, xmax1, ymin1, ymax1] = canvas.axis() - if trans: - try: - cloney = canvas.twiny() - # cloney.set_yscale(yscale) - cloney.set_xscale(xscale) - [xmin1, xmax1, ymin2, ymax2] = canvas.axis() - - if xscale == "symlog": - cloney.set_xscale(xscale, linthreshy=1e-9) - if yscale == "symlog": - cloney.set_yscale(yscale, linthreshy=1e-9) - if yscale == "linear": - cloney.yaxis.set_major_formatter(formatter) - except: - print("fail trans") - # cloney.useOffset=False - - # if xscale =='symlog' and trans: - # cloney.set_yscale(yscale,linthreshy=1e-9) - # cloney.set_xscale(xscale,linthreshy=1e-9) - - Ln_drive_scale = s.meta["w_Ln"][0] ** -1 - # Ln_drive_scale = 2.1e3 - clonex.set_ylim(Ln_drive_scale * ymin, Ln_drive_scale * ymax) - - try: - if trans: - # k_factor = #scales from k_zeta to k_perp - cloney.set_xlim(kfactor * xmin, kfactor * xmax) - # if np.any(sub_s.trans) and trans: - # comp_r = comp+'_r' - # y2 = np.array(ListDictKey(sub_s.db,comp_r)) - # #canvas.plot(k[s_i,1,sub_s.nx/2], - # # y2[s_i,0,sub_s.nx/2],'k.',ms = 3) - - # cloney.plot(k_r[s_i,1,sub_s.nx/2], - # y2[s_i,0,sub_s.nx/2],'k.',ms = 3) - # print 'np.sum(np.abs(y-y2)): ',np.sum(np.abs(y-y2)),comp_r - # kfactor =1.0 - # cloney.set_xlim(xmin,xmax) - cloney.set_ylim( - ymin, ymax - ) # because cloney shares the yaxis with canvas it may overide them, this fixes that - cloney.set_xlabel(r"$k_{\perp} \rho_{ci}$", fontsize=18) - except: - print("moar fail") - # clonex.set_xscale(xscale) - - # except: - # #canvas.set_xscale('symlog', linthreshx=0.1) - # print 'extra axis FAIL' - - # if yscale == 'linear': - # canvas.yaxis.set_major_locator(ticker.LinearLocator(numticks=8)) - - # minorLocator = MultipleLocator(.005) - # canvas.yaxis.set_minor_locator(minorLocator) - # spawn another y label - - # clone = canvas.twinx() - # s2 = np.sin(2*np.pi*t) - # ax2.plot(x, s2, 'r.') - - # ion_acoust_str = r"$\frac{c_s}{L_{\partial_r n}}}$" - - if comp == "gamma": - canvas.set_ylabel( - r"$\frac{\gamma}{\omega_{ci}}$", fontsize=18, rotation="horizontal" - ) - clonex.set_ylabel( - r"$\frac{\gamma}{\frac{c_s}{L_n}}$", - color="k", - fontsize=18, - rotation="horizontal", - ) - if comp == "freq": - canvas.set_ylabel( - r"$\frac{\omega}{\omega_{ci}}$", fontsize=18, rotation="horizontal" - ) - clonex.set_ylabel( - r"$\frac{\omega}{\frac{c_s}{L_n}}$", - color="k", - fontsize=18, - rotation="horizontal", - ) - - if comp == "amp": - canvas.set_ylabel(r"$A_k$", fontsize=18, rotation="horizontal") - clonex.set_ylabel( - r"$\frac{A_k}{A_{max}}$", color="k", fontsize=18, rotation="horizontal" - ) - - canvas.set_xlabel(r"$k_{\zeta} \rho_{ci}$", fontsize=18) - - title = comp + " computed from " + field - # canvas.set_title(title,fontsize=14) - fig1.suptitle(title, fontsize=14) - - if ownpage: - try: - fig1.savefig(pp, format="pdf") - except: - print("pyplt doesnt like you") - plt.close(fig1) - - def plotfreq( - self, pp, field="Ni", clip=0, xaxis="t", xscale="linear", yscale="linear" - ): - # colors = ['b','g','r','c','m','y','k','b','g','r','c','m','y','k'] - colors = [ - "b.", - "g.", - "r.", - "c.", - "m.", - "y.", - "k.", - "b.", - "g.", - "r.", - "c.", - "m.", - "y", - "k", - ] - plt.figure() - - # s = subset(self.db,'field',[field]) #pick field - - for q in range(4): - s = subset(self.db, "field", [field]) # pick field across all dz sets - modelist = [] - [modelist.append([q + 1, p + 1]) for p in range(5)] - print(q, "in plotgamma") - s = subset(s.db, "mn", modelist) - - gamma = s.freq # nmodes x 2 x nx ndarray - k = s.k ##nmodes x 2 x nx ndarray - - plt.errorbar( - k[:, 1, old_div(s.nx, 2)], - gamma[:, 0, old_div(s.nx, 2)], - yerr=gamma[:, 1, old_div(s.nx, 2)], - fmt=colors[q], - ) - plt.plot( - k[:, 1, old_div(s.nx, 2)], - gamma[:, 0, old_div(s.nx, 2)], - "k:", - alpha=0.3, - ) - - # loop over dz sets and connect with dotted line . . . - for j in list(set(s.dz).union()): - # print j,len(s.mn) - sub_s = subset(s.db, "dz", [j]) - gamma = sub_s.gamma - k = sub_s.k ## - plt.plot( - k[:, 1, old_div(sub_s.nx, 2)], - gamma[:, 0, old_div(sub_s.nx, 2)], - "k:", - alpha=0.1, - ) - - try: - plt.yscale(yscale) - except: - print("yscale fail") - - try: - plt.xscale(yscale) - except: - plt.xscale("symlog") - plt.xlabel(r"$k \rho_{ci}$", fontsize=14) - plt.ylabel(r"$\frac{\omega}{\omega_{ci}}$", fontsize=14) - # plt.title(r'$\frac{\omega}\{\omega_{ci}}$ '+ 'computed from'+field+ 'field',fontsize=10) - - plt.savefig(pp, format="pdf") - plt.close() - - def plotgamma( - self, - pp, - field="Ni", - yscale="symlog", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - comp="gamma", - overplot=False, - trans=True, - ): - self.plotomega( - pp, - field=field, - yscale=yscale, - clip=clip, - xaxis=xaxis, - xscale=xscale, - xrange=xrange, - comp=comp, - overplot=overplot, - trans=trans, - ) - - def plotfreq2( - self, - pp, - field="Ni", - yscale="symlog", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - comp="freq", - overplot=False, - trans=True, - ): - self.plotomega( - pp, - field=field, - yscale=yscale, - clip=clip, - xaxis=xaxis, - xscale=xscale, - xrange=xrange, - comp=comp, - overplot=overplot, - trans=trans, - ) - - def plotvsK( - self, - pp, - rootfig=None, - field="Ni", - yscale="log", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - comp="amp", - pltlegend="both", - overplot=False, - gridON=True, - trans=False, - infobox=True, - m=1, - t=[0], - file=None, - save=True, - ): - colors = [ - "b.", - "r.", - "k.", - "c.", - "g.", - "y.", - "m.", - "b.", - "r.", - "k.", - "c.", - "g.", - "y.", - "m.", - ] - colordash = [ - "b", - "r", - "k", - "c", - "g", - "y", - "m", - "b", - "r", - "k", - "c", - "g", - "y", - "m", - ] - - if rootfig is None: - ownpage = True - else: - ownpage = False - - if ownpage: - fig1 = plt.figure() - fig1.subplots_adjust(bottom=0.12) - fig1.subplots_adjust(top=0.80) - fig1.subplots_adjust(right=0.83) - fig1.subplots_adjust(left=0.17) - canvas = fig1.add_subplot(1, 1, 1) - clonex = canvas.twinx() - # if trans: - # cloney = canvas.twiny() - else: - canvas = rootfig.add_subplot(1, 1, 1) - - dzhandles = [] - parhandles = [] - parlabels = [] - dzlabels = [] - - # pick the modes - m_shift = m - for q in np.array(list(range(1))) + m_shift: - s = subset(self.db, "field", [field]) # pick field - maxZ = min(s.maxN) - modelist = [] - [modelist.append([q, p + 1]) for p in range(maxZ - 1)] - # print q,'in plotgamma' - s = subset(s.db, "mn", modelist) - - # set x-range - xrange = old_div(s.nx, 2) - 2 - xrange = [old_div(s.nx, 2), old_div(s.nx, 2) + xrange] - - # pull up the data - y = np.array(ListDictKey(s.db, comp)) - print("y.shape", y.shape) - - # in case multiple timesteps are indicated - all_y = [] - all_yerr = [] - if comp == "amp": - for elem in t: - all_y.append(np.squeeze(y[:, elem, :])) - all_yerr.append(np.squeeze(0 * y[:, elem, :])) - ynorm = np.max(all_y) - # all_y = np.array(np.squeeze(all_y)) - # all_yerr = np.array(np.squeeze(all_yerr)) - - else: - all_y.append(np.squeeze(y[:, 0, :])) - all_yerr.append(np.squeeze(y[:, 1, :])) - ynorm = s.meta["w_Ln"][0] - - k = s.k ##nmodes x 2 x nx ndarray k_zeta - - kfactor = np.mean( - old_div(s.k_r[:, 1, old_div(s.nx, 2)], s.k[:, 1, old_div(s.nx, 2)]) - ) # good enough for now - - for elem in range(np.size(t)): - # print 'printing line' , elem - errorline = parhandles.append( - canvas.errorbar( - k[:, 1, old_div(s.nx, 2)], - all_y[elem][:, old_div(s.nx, 2)], - yerr=all_yerr[elem][:, old_div(s.nx, 2)], - fmt=colors[q], - ) - ) - - parlabels.append("m " + str(q)) - - # loop over dz sets and connect with dotted line . . . - jj = 0 # will reference dz color - - ymin_data = np.max(np.array(ListDictKey(s.db, comp))) - ymax_data = 0 # for bookeeping - - for p in list(set(s.path).union()): - sub_s = subset(s.db, "path", [p]) - j = sub_s.dz[0] - # print sub_s.amp.shape - s_i = np.argsort(sub_s.mn[:, 1]) # sort by 'local' m, global m is ok also - # print s_i, sub_s.mn, sub_s.nx, jj - y = np.array(ListDictKey(sub_s.db, comp)) - y_alt = 2.0 * np.array(ListDictKey(sub_s.db, comp)) - all_y = [] - all_yerr = [] - if comp == "amp": - for elem in t: - all_y.append(np.squeeze(y[:, elem, :])) - all_yerr.append(np.squeeze(0 * y[:, elem, :])) - else: - all_y.append(np.squeeze(y[:, 0, :])) - all_yerr.append(np.squeeze(y[:, 1, :])) - - k = sub_s.k ## - - for elem in range(np.size(t)): - if q == m_shift: # fix the parallel mode - dzhandles.append( - canvas.plot( - k[s_i, 1, old_div(sub_s.nx, 2)], - all_y[elem][s_i, old_div(sub_s.nx, 2)], - color=colordash[jj], - alpha=0.5, - ) - ) - - ymin_data = np.min( - [np.min(y[s_i, old_div(sub_s.nx, 2)]), ymin_data] - ) - ymax_data = np.max( - [np.max(y[s_i, old_div(sub_s.nx, 2)]), ymax_data] - ) - - dzlabels.append(j) - - if yscale == "log": - factor = 10 - else: - factor = 2 - # print 'annotating' - canvas.annotate( - str(j), - ( - k[s_i[0], 1, old_div(sub_s.nx, 2)], - y[elem][s_i[0], old_div(sub_s.nx, 2)], - ), - fontsize=8, - ) - # p = canvas.axvspan(k[s_i[0],1,sub_s.nx/2], k[s_i[-1],1,sub_s.nx/2], - # facecolor=colordash[jj], alpha=0.01) - print("done annotating") - else: - canvas.plot( - k[s_i, 1, old_div(sub_s.nx, 2)], - y[elem][s_i, old_div(sub_s.nx, 2)], - color=colordash[jj], - alpha=0.3, - ) - - jj = jj + 1 - - dzhandles = np.array(dzhandles).flatten() - dzlabels = np.array(dzlabels).flatten() - - dzlabels = list(set(dzlabels).union()) - - dz_i = np.argsort(dzlabels) - - dzhandles = dzhandles[dz_i] - dzlabels_cp = np.array(dzlabels)[dz_i] - - # print type(dzlabels), np.size(dzlabels) - for i in range(np.size(dzlabels)): - dzlabels[i] = "DZ: " + str(dzlabels_cp[i]) # +r"$\pi$" - - parlabels = np.array(parlabels).flatten() - - if overplot == True: - try: - self.plottheory(pp, canvas=canvas, comp=comp, field=field) - # self.plottheory(pp,comp=comp) - except: - print("no theory plot") - if infobox: - textstr = "$\L_{\parallel}=%.2f$\n$\L_{\partial_r n}=%.2f$\n$B=%.2f$" % ( - s.meta["lpar"][old_div(s.nx, 2)], - s.meta["L"][old_div(s.nx, 2), old_div(s.ny, 2)], - s.meta["Bpxy"]["v"][old_div(s.nx, 2), old_div(s.ny, 2)], - ) - props = dict(boxstyle="square", facecolor="white", alpha=0.3) - textbox = canvas.text( - 0.82, - 0.95, - textstr, - transform=canvas.transAxes, - fontsize=10, - verticalalignment="top", - bbox=props, - ) - # leg = canvas.legend(handles,labels,ncol=2,loc='best',prop={'size':4},fancybox=True) - - # cloney.set_xlim(xmin,xmax) - try: - canvas.set_yscale(yscale) - canvas.set_xscale(xscale) - - if yscale == "symlog": - canvas.set_yscale(yscale, linthreshy=1e-13) - if xscale == "symlog": - canvas.set_xscale(xscale, linthreshy=1e-13) - - if gridON: - canvas.grid() - except: - try: - canvas.set_yscale("symlog") - except: - print("scaling failed completely") - - ################################################################## - - if ownpage and rootfig is None: - clonex.set_yscale(yscale) # must be called before limits are set - - try: - if yscale == "linear": - formatter = ticker.ScalarFormatter() - formatter.set_powerlimits((-2, 2)) # force scientific notation - canvas.yaxis.set_major_formatter(formatter) - clonex.yaxis.set_major_formatter(formatter) - # canvas.useOffset=False - except: - print("fail 1") - [xmin, xmax, ymin, ymax] = canvas.axis() - - if yscale == "symlog": - clonex.set_yscale(yscale, linthreshy=1e-9) - if xscale == "symlog": - clonex.set_xscale(xscale, linthreshy=1e-9) - # if np.any(s.trans) and trans: - [xmin1, xmax1, ymin1, ymax1] = canvas.axis() - if trans: - try: - cloney = canvas.twiny() - # cloney.set_yscale(yscale) - cloney.set_xscale(xscale) - [xmin1, xmax1, ymin2, ymax2] = canvas.axis() - - if xscale == "symlog": - cloney.set_xscale(xscale, linthreshy=1e-9) - if yscale == "symlog": - cloney.set_yscale(yscale, linthreshy=1e-9) - if yscale == "linear": - cloney.yaxis.set_major_formatter(formatter) - except: - print("fail trans") - - Ln_drive_scale = s.meta["w_Ln"][0] ** -1 - # Ln_drive_scale = 2.1e3 - # clonex.set_ylim(Ln_drive_scale*ymin, Ln_drive_scale*ymax) - clonex.set_ylim(ynorm**-1 * ymin, ynorm**-1 * ymax) - - try: - if trans: - # k_factor = #scales from k_zeta to k_perp - cloney.set_xlim(kfactor * xmin, kfactor * xmax) - - cloney.set_ylim( - ymin, ymax - ) # because cloney shares the yaxis with canvas it may overide them, this fixes that - cloney.set_xlabel(r"$k_{\perp} \rho_{ci}$", fontsize=18) - except: - print("moar fail") - # clonex.set_xscale(xscale) - - # ion_acoust_str = r"$\frac{c_s}{L_{\partial_r n}}}$" - - if comp == "gamma": - canvas.set_ylabel( - r"$\frac{\gamma}{\omega_{ci}}$", fontsize=18, rotation="horizontal" - ) - clonex.set_ylabel( - r"$\frac{\gamma}{\frac{c_s}{L_n}}$", - color="k", - fontsize=18, - rotation="horizontal", - ) - if comp == "freq": - canvas.set_ylabel( - r"$\frac{\omega}{\omega_{ci}}$", fontsize=18, rotation="horizontal" - ) - clonex.set_ylabel( - r"$\frac{\omega}{\frac{c_s}{L_n}}$", - color="k", - fontsize=18, - rotation="horizontal", - ) - - if comp == "amp": - canvas.set_ylabel(r"$A_k$", fontsize=18, rotation="horizontal") - clonex.set_ylabel( - r"$\frac{A_k}{A_{max}}$", - color="k", - fontsize=18, - rotation="horizontal", - ) - - canvas.set_xlabel(r"$k_{\zeta} \rho_{ci}$", fontsize=18) - - title = comp + " computed from " + field - # canvas.set_title(title,fontsize=14) - fig1.suptitle(title, fontsize=14) - - if not ownpage: - print("probably for a movie") - fig1 = rootfig - # canvasjunk = fig1.add_subplot(1,1,1) - # canvasjunk = canvas - - if save: - if file is None: - try: - fig1.savefig(pp, format="pdf") - except: - print("pyplt doesnt like you") - else: - try: - fig1.savefig(file, dpi=200) - except: - print("no movie for you ;(") - - if ownpage: - # fig1.close() - plt.close(fig1) - - def plotmodes( - self, - pp, - field="Ni", - comp="amp", - math="1", - ylim=1, - yscale="symlog", - clip=False, - xaxis="t", - xscale="linear", - xrange=1, - debug=False, - yaxis=r"$\frac{Ni}{Ni_0}$", - linestyle="-", - summary=True, - ): - Nplots = self.nrun - - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] - styles = ["^", "s"] - - fig1 = plt.figure() - - fig2 = plt.figure() - - Modes = subset(self.db, "field", [field]) # pick field - - adj = fig2.subplots_adjust(hspace=0.4, wspace=0.4) - fig2.suptitle("Dominant mode " + comp + " for " + field) - props = dict(alpha=0.8, edgecolors="none") - - allcurves = fig1.add_subplot(1, 1, 1) - fig1.suptitle("Dominant mode behavior for " + field) - - modenames = [] - k = 0 - - for j in list(set(Modes.path).union()): # - s = subset(Modes.db, "path", [j]) # pick run - dz = s.dz[0] - xr = list( - range( - old_div(s.nx, 2) - old_div(xrange, 2), - old_div(s.nx, 2) + old_div(xrange, 2) + 1, - ) - ) - data = np.array( - ListDictKey(s.db, comp) - ) # pick component should be ok for a fixed dz key - - data = data # + 1e-32 #hacky way to deal with buggy scaling - ax = fig2.add_subplot(round(old_div(Nplots, 3.0) + 1.0), 3, k + 1) - - ax.grid(True, linestyle="-", color=".75") - handles = [] - # modenames.append(str(j)) - - # find the "biggest" mode for this dz - d = data[:, s.nt[0] - 1, :] # nmode X nx array - # d = s.gamma[:,2,:] - where = d == np.nanmax(d) - z = where.nonzero() # mode index and n index - imax = z[0][0] - # xi_max = z[1][0] - xi_max = old_div(s.nx, 2) - - if debug and yscale == "log": - gamma = np.array(ListDictKey(s.db, "gamma")) # nmodes x 2 x nx - - for i in range(s.nmodes): - if math == "gamma": - out = old_div(np.gradient(data[i, :, xr])[1], data[i, :, xr]) - else: - out = data[i, 2:, xi_max] # skip the first 2 points - - if xaxis == "t": - # print 'out.size', out.size, out.shape - x = np.array(list(range(out.size))) - # plt.plot(x,out.flatten(),c=colors[k]) - label = str(s.mn[i]) - # handles.append(ax.plot(x,out.flatten(), - # c=cm.jet(1.*k),label = label)) - ax.plot( - x, out.flatten(), c=cm.jet(0.2 * i), label=label, linestyle="-" - ) - - else: - x = np.array(ListDictKey(s.db, xaxis))[i, :, xr] - # x #an N? by nx array - print(x[:, 1], out[:, 0]) - plt.scatter(x[:, 1], out[:, 0]) # ,c=colors[k]) - ax.scatter( - x[:, 1], out[:, 0] - ) # ,c=colors[k])#,alpha = (1 +i)/s.nmodes) - - # detect error (bar data - print("error bars:", x, out) - - # ax.legend(handles,labels,loc='best',prop={'size':6}) - - formatter = ticker.ScalarFormatter() - formatter.set_powerlimits((0, 0)) - ax.xaxis.set_major_formatter(formatter) - # ax.axis('tight') - if yscale == "linear": - ax.yaxis.set_major_formatter(formatter) - if yscale == "symlog": - ax.set_yscale("symlog", linthreshy=1e-13) - else: - try: - ax.set_yscale(yscale) - except: - print("may get weird axis") - ax.set_yscale("symlog") - # if comp=='phase' or yscale=='linear': - # ax.set_xscale('symlog',linthreshx=1.0) - - ax.set_xscale(xscale) - - ax.axis("tight") - artist.setp(ax.axes.get_xticklabels(), fontsize=6) - artist.setp(ax.axes.get_yticklabels(), fontsize=8) - # artist.setp(ax.axes.get_yscale(), fontsize=8) - ax.set_title(str(dz), fontsize=10) - ax.set_xlabel(xaxis) - handles, labels = ax.get_legend_handles_labels() - leg = ax.legend( - handles, labels, ncol=2, loc="best", prop={"size": 4}, fancybox=True - ) - leg.get_frame().set_alpha(0.3) - # x = s.Rxy[imax,:,s.ny/2] - - t0 = 2 - if clip == True: - t0 = round(old_div(s.nt[0], 3)) - y = np.squeeze(data[imax, t0:, xi_max]) - x = np.array(list(range(y.size))) - - print(imax, xi_max) - - label = ( - str([round(elem, 3) for elem in s.MN[imax]]) - + str(s.mn[imax]) - + " at x= " - + str(xi_max) - + " ," - + str( - round( - old_div(s.gamma[imax, 2, xi_max], s.gamma[imax, 0, xi_max]), 3 - ) - ) - + "% " - + str(round(s.gamma[imax, 0, xi_max], 4)) - ) - - short_label = str(dz) - print(short_label, x.shape, y.shape) - allcurves.plot(x, y, ".", c=cm.jet(1.0 * k / len(x)), label=label) - # print len(x), k*len(x)/(Nplots+2),s.nrun - allcurves.annotate( - short_label, - (x[k * len(x) / (Nplots + 1)], y[k * len(x) / (Nplots + 1)]), - fontsize=8, - ) - - # modenames.append(str([round(elem,3) for elem in s.MN[imax]]) - # +str(s.mn[imax])+' at x= '+str(xi_max)+' ,'+str(s.gamma[imax,2,xi_max])) - - if debug and yscale == "log": - gam = gamma[imax, 0, xi_max] - f0 = gamma[imax, 1, xi_max] - allcurves.plot(x, f0 * np.exp(gam * s.dt[imax] * x), "k:") - - k += 1 - - # if ylim: - # allcurves.set_ylim(data[,xi_max].min(),5*data[:,xi_max].max()) - - fig2.savefig(pp, format="pdf") - - handles, labels = allcurves.get_legend_handles_labels() - allcurves.legend(handles, labels, loc="best", prop={"size": 6}) - # allcurves.legend(modenames,loc='best',prop={'size':6}) - allcurves.set_title( - field + " " + comp + ", all runs, " + yscale + " yscale", fontsize=10 - ) - allcurves.set_ylabel(yaxis) - allcurves.set_xlabel(xaxis) - - if yscale == "linear": - allcurves.yaxis.set_major_formatter(formatter) - else: - try: - allcurves.set_yscale(yscale) - except: - print("may get weird axis scaling") - if yscale == "log": - allcurves.axis("tight") - # allcurves.set_ylim(data.min(),data.max()) - # allcurves.set_yscale(yscale,nonposy='mask') - - # plt.xscale(xscale) - - # plt.legend(modenames,loc='best') - if summary: - fig1.savefig(pp, format="pdf") - plt.close(fig1) - - plt.close(fig2) - - # except: - # print "Sorry you fail" - - def plotradeigen( - self, pp, field="Ni", comp="amp", yscale="linear", xscale="linear" - ): - Nplots = self.nrun - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] - fig1 = plt.figure() - - fig2 = plt.figure() - adj = fig2.subplots_adjust(hspace=0.4, wspace=0.4) - - # canvas = FigureCanvas(fig) - - Modes = subset(self.db, "field", [field]) - - k = 0 - fig2.suptitle("Dominant mode behavior for " + field) - props = dict(alpha=0.8, edgecolors="none") - - allcurves = fig1.add_subplot(1, 1, 1) - fig1.suptitle("Dominant mode behavior for " + field) - - modeleg = [] - - for p in list(set(Modes.path).union()): - print(p) - s = subset(Modes.db, "path", [p]) # pick run - # data = np.array(ListDictKey(s.db,comp)) #pick component - j = s.dz[0] - ax = fig2.add_subplot(round(old_div(Nplots, 3.0) + 1.0), 3, k + 1) - ax.grid(True, linestyle="-", color=".75") - data = np.array(ListDictKey(s.db, comp)) # pick component - handles = [] - - # find the "biggest" mode for this dz - d = data[:, s.nt[0] - 1, :] # nmode X nx array - where = d == d.max() - z = where.nonzero() # mode index and n index - imax = z[0][0] - modeleg.append( - str([round(elem, 3) for elem in s.MN[imax]]) + str(s.mn[imax]) - ) - - # str(s.k[:,1,:][z]) - - for i in range(s.nmodes): - # out = mode[mode.ny/2,:] - # print i,s.Rxynorm.shape,s.ny - x = np.squeeze(s.Rxynorm[i, :, old_div(s.ny, 2)]) - y = data[i, s.nt[0] - 1, :] - - handles.append(ax.plot(x, y, c=cm.jet(1.0 * k / len(x)))) - - formatter = ticker.ScalarFormatter() - formatter.set_powerlimits((0, 0)) - ax.xaxis.set_major_formatter(formatter) - - if yscale == "linear": - ax.yaxis.set_major_formatter(formatter) - else: - ax.set_yscale(yscale) - - artist.setp(ax.axes.get_xticklabels(), fontsize=6) - artist.setp(ax.axes.get_yticklabels(), fontsize=8) - # artist.setp(ax.axes.get_yscale(), fontsize=8) - ax.set_title(str(j), fontsize=10) - - x = np.squeeze(s.Rxynorm[imax, :, old_div(s.ny, 2)]) - y = data[imax, s.nt[0] - 1, :] - # allcurves.plot(x,y,c= colors[k]) - allcurves.plot(x, y, c=cm.jet(0.1 * k / len(x))) - print(k) - k = k + 1 - - fig2.savefig(pp, format="pdf") - if yscale == "linear": - allcurves.yaxis.set_major_formatter(formatter) - else: - allcurves.set_yscale(yscale) - try: - allcurves.set_xscale(xscale) - except: - allcurves.set_xscale("symlog") - - # allcurves.xaxis.set_major_formatter(ticker.NullFormatter()) - allcurves.legend(modeleg, loc="best", prop={"size": 6}) - allcurves.set_xlabel(r"$\frac{x}{\rho_{ci}}$") - allcurves.set_ylabel(r"$\frac{Ni}{Ni_0}$") - fig1.savefig(pp, format="pdf") - plt.close(fig1) - plt.close(fig2) - - def plotmodes2( - self, - pp, - field="Ni", - comp="amp", - math="1", - ylim=1, - yscale="symlog", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - debug=False, - ): - Nplots = self.nrun - Modes = subset(self.db, "field", [field]) # pick field - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] - - fig = Figure() - plt.figure() - - canvas = FigureCanvas(fig) - k = 0 - nrow = round(old_div(Nplots, 3.0) + 1.0) - ncol = 3 - # nrow = round(Nplots/3.0 + 1.0) - # ncol = round(Nplots/3.0 + 1.0) - f, axarr = plt.subplots(int(nrow), int(ncol)) - - for p in list(set(Modes.path).union()): # - s = subset(Modes.db, "path", [p]) # pick run - j = s.dz[0] - xr = list( - range( - old_div(s.nx, 2) - old_div(xrange, 2), - old_div(s.nx, 2) + old_div(xrange, 2) + 1, - ) - ) - data = np.array(ListDictKey(s.db, comp)) # pick component - # ax =fig.add_subplot(round(Nplots/3.0 + 1.0),3,k+1) - - for i in range(s.nmodes): - out = data[i, :, xr] - - print(j, i) - if xaxis == "t": - x = list(range(out.size)) - # plt.scatter(x,out.flatten(),c=colors[k]) - plt.scatter(x, out.flatten(), c=cm.jet(1.0 * k / len(x))) - # axarr[j%(ncol),j/ncol].scatter(x,out.flatten(),c=colors[k])#,alpha = (1 +i)/s.nmodes) - axarr[old_div(j, ncol), j % (ncol)].scatter( - x, out.flatten(), c=cm.jet(1.0 * k / len(x)) - ) # - - else: - x = np.array(ListDictKey(s.db, xaxis))[i, :, xr] - # x #an N? by nx array - print(x[:, 1], out[:, 0]) - plt.scatter(x[:, 1], out[:, 0]) # ,c=colors[k]) - axarr[j % (col), old_div(j, col)].scatter( - x[:, 1], out[:, 0] - ) # ,c=colors[k])#,alpha = (1 +i)/s.nmodes) - - # detect error (bar data - print("error bars:", x, out) - - axarr[old_div(j, ncol), j % (ncol)].set_yscale(yscale) - axarr[old_div(j, ncol), j % (ncol)].set_xscale(xscale) - axarr[old_div(j, ncol), j % (ncol)].set_title(str(j), fontsize=10) - axarr[old_div(j, ncol), j % (ncol)].set_xlabel(xaxis) - - plt.setp([a.get_xticklabels() for a in axarr[0, :]], visible=False) - plt.setp([a.get_yticklabels() for a in axarr[:, ncol - 1]], visible=False) - - if ylim: - axarr[j % (ncol), old_div(j, ncol)].set_ylim(data.min(), 5 * data.max()) - k += 1 - - plt.title(field + " " + comp + ", all runs, " + yscale + " yscale", fontsize=10) - plt.xlabel(xaxis) - if ylim: - plt.ylim(data.min(), 10 * data.max()) - - plt.yscale(yscale, nonposy="mask") - plt.xscale(xscale) - - fig.savefig(pp, format="pdf") - plt.savefig(pp, format="pdf") - - plt.close() - - return 0 - - def plotMacroDep( - self, - pp, - field="Ni", - yscale="symlog", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - ): - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] - plt.figure() - - def savemovie( - self, field="Ni", yscale="log", xscale="log", moviename="spectrum.avi" - ): - print("Making movie animation.mpg - this make take a while") - files = [] - - for t in range(self.nt[0] - 3): - print(t) - filename = str("%03d" % (t + 1) + ".png") - self.plotvsK( - "dont need pp", - yscale="log", - t=[1, t + 2], - xscale="log", - overplot=False, - comp="amp", - trans=True, - file=filename, - ) - files.append(filename) - - command = ( - "mencoder", - "mf://*.png", - "-mf", - "type=png:w=800:h=600:fps=10", - "-ovc", - "lavc", - "-lavcopts", - "vcodec=mpeg4", - "-oac", - "copy", - "-o", - moviename, - ) - - import subprocess, os - - subprocess.check_call(command) - os.system("rm *png") - - def printmeta(self, pp, filename="output2.pdf", debug=False): - import os - from pyPdf import PdfFileWriter, PdfFileReader - - PAGE_HEIGHT = defaultPageSize[1] - styles = getSampleStyleSheet() - Title = "BOUT++ Results" - Author = "Dmitry Meyerson" - URL = "" - email = "dmitry.meyerson@gmail.com" - Abstract = """This document highlights some results from BOUT++ simulation""" - Elements = [] - HeaderStyle = styles["Heading1"] - ParaStyle = styles["Normal"] - PreStyle = styles["Code"] - - def header( - txt, style=HeaderStyle, klass=Paragraph, sep=0.3 - ): # return styled text with a space - s = Spacer(0.2 * inch, sep * inch) - para = klass(txt, style) - sect = [s, para] - result = KeepTogether(sect) - return result - - def p(txt): # wrapper for header - return header(txt, style=ParaStyle, sep=0.1) - - def pre(txt): # return styled text with a space - s = Spacer(0.1 * inch, 0.1 * inch) - p = Preformatted(txt, PreStyle) - precomps = [s, p] - result = KeepTogether(precomps) - return result - - def graphout(name, datain, xaxis=None): - if xaxis is None: - xaxis = list(range(datain.size)) - if xlabel is None: - xlabel = "" - if ylabel is None: - ylabel = "" - - drawing = Drawing(400, 200) - # data = [ - # ((1,1), (2,2), (2.5,1), (3,3), (4,5)), - # ((1,2), (2,3), (2.5,2), (3.5,5), (4,6)) - # ] - dataview = [tuple([(xaxis[i], datain[i]) for i in range(datain.size)])] - lp = LinePlot() - lp.x = 50 - lp.y = 50 - lp.height = 125 - lp.width = 300 - lp.data = dataview - lp.xValueAxis.xLabelFormat = "{mmm} {yy}" - lp.lineLabels.fontSize = 6 - lp.lineLabels.boxStrokeWidth = 0.5 - lp.lineLabels.visible = 1 - lp.lineLabels.boxAnchor = "c" - # lp.joinedLines = 1 - # lp.lines[0].symbol = makeMarker('FilledCircle') - # lp.lines[1].symbol = makeMarker('Circle') - # lp.lineLabelFormat = '%2.0f' - # lp.strokeColor = colors.black - # lp.xValueAxis.valueMin = min(xaxis) - # lp.xValueAxis.valueMax = max(xaxis) - # lp.xValueAxis.valueSteps = xaxis - # lp.xValueAxis.labelTextFormat = '%2.1f' - # lp.yValueAxis.valueMin = min(datain) - # lp.yValueAxis.valueMax = max(datain) - # lp.yValueAxis.valueSteps = [1, 2, 3, 5, 6] - drawing.add(lp) - return drawing - - def go(): - doc = SimpleDocTemplate("meta.pdf") - doc.build(Elements) - - mytitle = header(Title) - myname = header(Author, sep=0.1, style=ParaStyle) - mysite = header(URL, sep=0.1, style=ParaStyle) - mymail = header(email, sep=0.1, style=ParaStyle) - abstract_title = header("ABSTRACT") - myabstract = p(Abstract) - head_info = [mytitle, myname, mysite, mymail, abstract_title, myabstract] - Elements.extend(head_info) - - meta_title = header("metadata", sep=0) - metasection = [] - metasection.append(meta_title) - - for i, elem in enumerate(self.meta): - # if type(self.meta[elem]) != type(np.array([])): - - print(elem, type(self.meta[elem])) - - if type(self.meta[elem]) == type({}): - print("{}") - data = np.array(self.meta[elem]["v"]) - unit_label = str(self.meta[elem]["u"]) - else: - data = np.array(self.meta[elem]) - unit_label = "" - - xaxis = np.squeeze(self.meta["Rxy"]["v"][:, old_div(self.ny, 2)]) - - if data.shape == (self.nx, self.ny): - datastr = np.squeeze(data[:, old_div(self.ny, 2)]) - # metasection.append(graphout('stuff',datastr,xaxis=xaxis)) - # metasection.append(RL_Plot(datastr,xaxis)) - - metasection.append(RL_Plot(datastr, xaxis, linelabel=str(elem))) - # metasection.append(RL_Plot(datastr,xaxis,xlabel='xlabel')) - elif data.shape == self.nx: - datastr = data - # metasection.append(graphout('stuff',datastr,xaxis=xaxis)) - # metasection.append(RL_Plot(datastr,xaxis,linelabel=str(elem))) - elif data.shape == (1,): - data = data[0] - metasection.append( - header( - str(elem) + ": " + str(data) + " " + unit_label, - sep=0.1, - style=ParaStyle, - ) - ) - else: - print(elem, data, data.shape) - metasection.append( - header( - str(elem) + ": " + str(data) + " " + unit_label, - sep=0.1, - style=ParaStyle, - ) - ) - - src = KeepTogether(metasection) - Elements.append(src) - - cxxtitle = header("Equations in CXX") - cxxsection = [] - # print self.cxx - cxxsection.append(header(self.cxx[0], sep=0.1, style=ParaStyle)) - cxxsrc = KeepTogether(cxxsection) - - Elements.append(cxxsrc) - # for i,elem in enumerate(self.cxx): - # if type(self.meta[elem])== type({}): - # print elem #np.array(self.meta[elem]['v']).shape() - # if np.array(self.meta[elem]['v']).shape == (self.nx,self.ny): - # datastr = str(self.meta[elem]['v'][:,self.ny/2]) - # metasection.append(graphout('stuff', - # self.meta[elem]['v'][:,self.ny/2])) - # else: - # datastr = str(self.meta[elem]['v']) - # metasection.append(header(str(elem)+': '+datastr - # + ' '+ str(self.meta[elem]['u']), - # sep=0.1, style=ParaStyle)) - - if debug: - return Elements - go() - - output = PdfFileWriter() - metapdf = PdfFileReader(file("meta.pdf", "rb")) - mainpdf = PdfFileReader(file("output.pdf", "rb")) - - for i in range(0, metapdf.getNumPages()): - output.addPage(metapdf.getPage(i)) - - for i in range(0, mainpdf.getNumPages()): - output.addPage(mainpdf.getPage(i)) - - outputFile = filename - outputStream = file(outputFile, "wb") - output.write(outputStream) - outputStream.close() - print("Consolidation complete.") - - -class subset(LinResDraw): - def __init__(self, alldb, key, valuelist, model=False): - selection = ListDictFilt(alldb, key, valuelist) - if len(selection) != 0: - LinRes.__init__(self, selection) - self.skey = key - if model == True: - self.model() - else: - LinRes.__init__(self, alldb) - if model == True: - self.model() diff --git a/tools/pylib/post_bout/pb_nonlinear.py b/tools/pylib/post_bout/pb_nonlinear.py deleted file mode 100644 index 3fb726d4f8..0000000000 --- a/tools/pylib/post_bout/pb_nonlinear.py +++ /dev/null @@ -1,99 +0,0 @@ -from __future__ import absolute_import -from __future__ import division -from builtins import range -from past.utils import old_div - -# some function to plot nonlinear stuff -from .pb_corral import LinRes -from .ListDict import ListDictKey, ListDictFilt -import numpy as np - -import matplotlib.pyplot as plt -from matplotlib import cm -import matplotlib.artist as artist -import matplotlib.ticker as ticker -import matplotlib.pyplot as plt -import matplotlib.patches as patches -from matplotlib.figure import Figure -from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas -from matplotlib.backends.backend_pdf import PdfPages - -from reportlab.platypus import * -from reportlab.lib.styles import getSampleStyleSheet -from reportlab.rl_config import defaultPageSize -from reportlab.lib.units import inch -from reportlab.graphics.charts.linecharts import HorizontalLineChart -from reportlab.graphics.shapes import Drawing -from reportlab.graphics.charts.lineplots import LinePlot -from reportlab.graphics.widgets.markers import makeMarker -from reportlab.lib import colors - -from replab_x_vs_y import RL_Plot -from matplotlib.ticker import ScalarFormatter, FormatStrFormatter, MultipleLocator - - -class NLinResDraw(LinRes): - def __init__(self, alldb): - LinRes.__init__(self, alldb) - - def plotnlrhs( - self, - pp, - field="Ni", - yscale="linear", - clip=0, - xaxis="t", - xscale="linear", - xrange=1, - ): - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] - - Modes = subset(self.db, "field", [field]) # pick field - comp = "ave" - - fig1 = plt.figure() - adj = fig1.subplots_adjust(hspace=0.4, wspace=0.4) - fig1.suptitle("Nonlinear contribution for " + field) - props = dict(alpha=0.8, edgecolors="none") - Nplots = self.nrun - - k = 0 - for j in list(set(Modes.path).union()): - s = subset(Modes.db, "path", [j]) # pick a run folder - many modes - dz = s.dz[0] - data = s.ave[0]["nl"] - x = np.array(list(range(data.size))) - - ax = fig1.add_subplot(round(old_div(Nplots, 2.0) + 1.0), 2, k + 1) - ax.set_ylabel(r"$\frac{ddt_N}{ddt}$", fontsize=12, rotation="horizontal") - k += 1 - ax.grid(True, linestyle="-", color=".75") - try: - ax.set_yscale(yscale, linthreshy=1e-13) - except: - ax.set_yscale("linear") - i = 1 - ax.plot(x, data.flatten(), c=cm.jet(0.2 * i), linestyle="-") - - # data = np.array(ListDictKey(s.db,comp)) #pick component should be ok for a fixed dz key - - # we are not interested in looping over all modes - - fig1.savefig(pp, format="pdf") - plt.close(fig1) - - # return 0 - - -class subset(NLinResDraw): - def __init__(self, alldb, key, valuelist, model=False): - selection = ListDictFilt(alldb, key, valuelist) - if len(selection) != 0: - LinRes.__init__(self, selection) - self.skey = key - if model == True: - self.model() - else: - LinRes.__init__(self, alldb) - if model == True: - self.model() diff --git a/tools/pylib/post_bout/pb_present.py b/tools/pylib/post_bout/pb_present.py deleted file mode 100644 index 64fcaf1ec6..0000000000 --- a/tools/pylib/post_bout/pb_present.py +++ /dev/null @@ -1,213 +0,0 @@ -from __future__ import print_function -from __future__ import absolute_import -from builtins import str -from builtins import range -from .pb_draw import LinResDraw, subset -from .pb_corral import LinRes -from .pb_nonlinear import NLinResDraw -from pb_transport import Transport - -import numpy as np -import matplotlib.pyplot as plt - -import matplotlib.pyplot as plt -from matplotlib.figure import Figure -from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas -from matplotlib.backends.backend_pdf import PdfPages -import matplotlib.artist as artist -import matplotlib.ticker as ticker - -# from matplotlib.ticker import FuncFormatter -# from matplotlib.ticker import ScalarFormatter - -from reportlab.platypus import * -from reportlab.lib.styles import getSampleStyleSheet -from reportlab.rl_config import defaultPageSize -from reportlab.lib.units import inch -from reportlab.graphics.charts.linecharts import HorizontalLineChart -from reportlab.graphics.shapes import Drawing -from reportlab.graphics.charts.lineplots import LinePlot -from reportlab.graphics.widgets.markers import makeMarker -from reportlab.lib import colors - -from replab_x_vs_y import RL_Plot - -# for movie making -from multiprocessing import Queue, Pool -import multiprocessing -import subprocess - -# uses LinResDraw to make a pdf - - -class LinResPresent(LinResDraw, NLinResDraw, Transport): - def __init__(self, alldb): - LinResDraw.__init__(self, alldb) - NLinResDraw.__init__(self, alldb) - Transport.__init__(self, alldb) - - def show( - self, - filter=True, - quick=False, - pdfname="output2.pdf", - debug=False, - spectrum_movie=False, - ): - colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"] - pp = PdfPages("output.pdf") - - # start by removing modes above the maxN threshold - modelist = [] - [ - modelist.append(list(self.modeid[p])) - for p in range(self.nmodes) - if self.mn[p][1] <= self.maxN[p] - ] - - s = subset(self.db, "modeid", modelist) - - try: - # fig = Figure(figsize=(6,6)) - # fig = plt.figure() - dz0 = list(set(s.dz).union())[0] - ss = subset(s.db, "dz", [dz0]) - - # show initial condition and the first step after - s.plotvsK( - pp, - yscale="log", - xscale="log", - t=[0, 1, -1], - overplot=False, - comp="amp", - trans=True, - ) - - if spectrum_movie: - ss.savemovie() - - except: - print("no scatter") - # 2D true NM spectrum with color code and boxes around spectral res regions log scale - - plt.figure() - i = 0 - for j in list( - set(s.dz).union() - ): # looping over runs, over unique 'dz' key values - ss = subset(s.db, "dz", [j]) # subset where dz = j - plt.scatter(ss.MN[:, 1], ss.MN[:, 0], c=colors[i]) - plt.annotate(str(j), (ss.MN[0, 1], ss.MN[0, 0])) - i += 1 - - plt.title(" Ni spectrum at t=0, all x") - plt.ylabel("M -parallel") - plt.xlabel("N - axisymmteric") - plt.xscale("log") - plt.grid(True, linestyle="-", color=".75") - - try: - plt.savefig(pp, format="pdf") - except: - print("FAILED TO save 1st part") - - plt.close() - - # for elem in self.meta['evolved']['v']: - # s.plotnl(pp - - if self.meta["nonlinear"]["v"] == "true": - self.plotnlrhs(pp) - - if self.meta["transport"] == "true": - self.plotnlrms(pp) - - for elem in self.meta["evolved"]: - s.plotmodes( - pp, - yscale="symlog", - comp="phase", - linestyle=".", - field=elem, - summary=False, - ) - s.plotmodes(pp, yscale="symlog", field=elem, summary=False) - print(elem) - try: - s.plotmodes( - pp, yscale="symlog", field=elem, comp="gamma_i", summary=False - ) - except: - print("gamma_i plot for " + elem + " failed") - - # s.plotmodes(pp,yscale='symlog',summary=False) - - modelist = [] - # maxZ = - # [modelist.append([1,p+1]) for p in range(maxZ-1)] - [ - modelist.append(list(self.modeid[p])) - for p in range(self.nmodes) - if self.mn[p][1] <= self.maxN[p] - ] - ss = subset(s.db, "mn", modelist) - - if debug: # just a few problematic slides - fig1 = plt.figure() - pp_bug = PdfPages("debug.pdf") - # ss.plotmodes(pp_bug,yscale='symlog',comp='phase',summary=False) - s.plotfreq2(pp_bug, xscale="log", yscale="symlog", overplot=True) - ss.plotgamma(pp_bug, xscale="log", yscale="symlog", overplot=True) - ss.plottheory(pp_bug) - ss.plottheory(pp_bug, comp="freq") - fig1.savefig(pp_bug, format="pdf") - pp_bug.close() - pp.close() - return 0 - - dir(ss) - ss.plotmodes(pp, yscale="log", debug=True, summary=False) - ss.plotmodes(pp, yscale="symlog", comp="phase", summary=False) - ss.plotmodes(pp, yscale="symlog", comp="phase", field="rho", summary=False) - print(dir(ss)) - - # ss.plotmodes(pp,yscale='log',comp='phase',clip=True) - - # ss.plotfreq2(pp,xscale='log',yscale='linear',overplot=False) - for elem in self.meta["evolved"]: - ss.plotfreq2( - pp, xscale="log", yscale="symlog", field=elem, overplot=True, trans=True - ) - - # ss.plotfreq2(pp,xscale='log',yscale='symlog',field='rho',overplot=True) - - if quick == True: - pp.close() - s.printmeta(pp) - - # plt.savefig(pp, format='pdf') - return 0 - - all_fields = list(set(s.field).union()) - - s.plotgamma(pp, xscale="log", yscale="linear", overplot=True, trans=True) - - s.plotgamma(pp, yscale="symlog", xscale="log", overplot=True) - s.plotgamma(pp, yscale="symlog", xscale="log", field="rho", overplot=True) - - try: - s.plotfreq2(pp, xscale="log", yscale="linear", overplot=True) - # s.plotfreq2(pp,xscale='log',yscale='symlog',overplot=False) - s.plotfreq2(pp, xscale="log", yscale="symlog", field="rho", overplot=True) - - # s.plotfreq2(pp,xscale='log',yscale='linear') - except: - print("something terrible") - - s.plotradeigen(pp, yscale="linear") - # s.plotradeigen(pp,field ='Vi',yscale='linear') - s.plotradeigen(pp, field="rho", yscale="log") - - pp.close() - s.printmeta(pp, filename=pdfname) # append a metadata header diff --git a/tools/pylib/post_bout/read_cxx.py b/tools/pylib/post_bout/read_cxx.py deleted file mode 100644 index eda88aac5b..0000000000 --- a/tools/pylib/post_bout/read_cxx.py +++ /dev/null @@ -1,139 +0,0 @@ -from builtins import range -from read_grid import read_grid -from ordereddict import OrderedDict -import numpy as np -import string -import re - - -def findlowpass(cxxstring): - ##p1="lowPass\(.*\)" - p1 = "lowPass\(.*\,(.*)\)" - maxN = np.array(re.findall(p1, cxxstring)) - # print substrings - - # p2=("[0-9]") - - # maxN = np.array([re.findall(p2,elem) for elem in substrings]).flatten() - - if maxN.size == 0: - return 100 - else: - output = int(min(maxN)) - if output == 0: - return 20 - else: - return output - - -def no_comment_cxx(path=".", boutcxx="physics_code.cxx.ref"): - # print 'no_comment' - boutcxx = path + "/" + boutcxx - # boutcxx = open(boutcxx,'r').readlines() - f = open(boutcxx, "r") - boutcxx = f.read() - f.close() - - start = string.find(boutcxx, "/*") - end = string.find(boutcxx, "*/") + 2 - - s = boutcxx[0:start] - for i in range(string.count(boutcxx, "/*")): - start = string.find(boutcxx, "/*", end) - s = s + boutcxx[end + 1 : start - 1] - - end = string.find(boutcxx, "*/", end) + 2 - - s = s + boutcxx[end + 1 :] - - # pattern = "\n \s* \(//)* .* \n" #pattern for a section start [All],[Ni], etc - pattern = "\n+.*;" # everythin - pattern = re.compile(pattern) - result = re.findall(pattern, s) - - # print result - - nocomment = [] - for elem in result: - # print elem - elem = elem.lstrip() - stop = elem.find("//") - # print start,stop - - if stop > 0: - nocomment.append(elem[0:stop]) - elif stop == -1: - nocomment.append(elem) - - # result = pattern.match(val) - # start = string.find(z,'\n //') - # end =string.find(boutcxx,'*/')+2 - # print nocomment - - return nocomment - - -def get_evolved_cxx(cxxfile=None): - if cxxfile is None: - cxxfile = no_comment_cxx() - - # s = cxxfile - # section_0 = string.find(s,'int physics_run(BoutReal t)') - # section_1 = string.find(s,'return',section_0) - # s = s[section_0:section_1] - temp = [] - - for x in cxxfile: - i = x.find("bout_solve(") - # print i,x - if i != -1: - comma_i = x[i::].find('"') - comma_j = x[i::].rfind('"') - # print x[i+comma_i:i+comma_j+1] - temp.append(x[i + comma_i + 1 : i + comma_j]) - - evolved = [] - [evolved.append(x) for x in set(temp)] - return np.array(evolved) - - -def read_cxx(path=".", boutcxx="physics_code.cxx.ref", evolved=""): - # print path, boutcxx - boutcxx = path + "/" + boutcxx - # boutcxx = open(boutcxx,'r').readlines() - f = open(boutcxx, "r") - boutcxx = f.read() - f.close() - - # start by stripping out all comments - # look at the 1st character of all list elements - # for now use a gross loop, vectorize later - - start = string.find(boutcxx, "/*") - end = string.find(boutcxx, "*/") + 2 - - s = boutcxx[0:start] - for i in range(string.count(boutcxx, "/*")): - start = string.find(boutcxx, "/*", end) - s = s + boutcxx[end + 1 : start - 1] - - end = string.find(boutcxx, "*/", end) + 2 - - s = s + boutcxx[end + 1 :] - - section_0 = string.find(s, "int physics_run(BoutReal t)") - section_1 = string.find(s, "return", section_0) - s = s[section_0:section_1] - - tmp = open("./read_cxx.tmp", "w") - tmp.write(s) - tmp.close() - tmp = open("./read_cxx.tmp", "r") - - cxxlist = "" - - for line in tmp: - if line[0] != "//" and line.isspace() == False: - cxxlist = cxxlist + line.split("//")[0] - - return cxxlist diff --git a/tools/pylib/post_bout/read_inp.py b/tools/pylib/post_bout/read_inp.py deleted file mode 100644 index 87de7ddf3a..0000000000 --- a/tools/pylib/post_bout/read_inp.py +++ /dev/null @@ -1,433 +0,0 @@ -from __future__ import print_function -from __future__ import absolute_import -from __future__ import division -from builtins import str -from past.utils import old_div -from builtins import object -from read_grid import read_grid -from ordereddict import OrderedDict -import numpy as np -from boututils.file_import import file_import -from .read_cxx import * - - -def read_inp(path="", boutinp="BOUT.inp"): - boutfile = path + "/" + boutinp - boutinp = open(boutfile, "r").readlines() - - # start by stripping out all comments - # look at the 1st character of all list elements - # for now use a gross loop, vectorize later - boutlist = [] - - for i, val in enumerate(boutinp): - if val[0] != "#" and val.isspace() == False: - boutlist.append(val.split("#")[0]) - - return boutlist - - -def parse_inp(boutlist): - import re - from ordereddict import OrderedDict - - if not boutlist: - return 0 - - # boutdic={} unordered standard dict - boutdic = OrderedDict() - - # regex is messy see http://docs.python.org/howto/regex.html#regex-howto - pattern = "\[\S*\]" # pattern for a section start [All],[Ni], etc - - pattern = re.compile(pattern) - - boutdic["[main]"] = {} - current = "[main]" - - for i, val in enumerate(boutlist): - # print i,val - result = pattern.match(val) - # while the current value is not a new section name add everything to the current section - - if result is None: - # print val - key, value = val.split("=") - value = value.replace('"', "") - # print current, key,value - - boutdic[current][key.strip()] = value.strip() - else: - boutdic[result.group()] = {} - current = result.group() - - return boutdic - - -def read_log(path=".", logname="status.log"): - print("in read_log") - import re - from ordereddict import OrderedDict - - # logfile = path+'/'+logname - logfile = logname - print(logfile) - logcase = open(logfile, "r").readlines() - - # start by stripping out all comments - # look at the 1st character of all list elements - # for now use a gross loop, vectorize later - loglist = [] - - for i, val in enumerate(logcase): - if val[0] != "#" and val.isspace() == False: - loglist.append(val.split("#")[0]) - - if not loglist: - return 0 - - logdict = OrderedDict() - logdict["runs"] = [] - # print len(loglist) - print(loglist) - # print loglist[len(loglist)-1] == 'last one\n' - - # last = loglist.pop().rstrip() - - # logdict['done'] = last == 'done' - - logdict["current"] = loglist.pop().rstrip() - for i, val in enumerate(loglist): - print(val) - logdict["runs"].append(val.rstrip()) - - logdict["runs"].append(logdict["current"]) - - # print logdict - return logdict - - -def metadata(inpfile="BOUT.inp", path=".", v=False): - filepath = path + "/" + inpfile - print(filepath) - inp = read_inp(path=path, boutinp=inpfile) - inp = parse_inp(inp) # inp file - print(path) - outinfo = file_import(path + "/BOUT.dmp.0.nc") # output data - - try: - print(path) - cxxinfo = no_comment_cxx(path=path, boutcxx="physics_code.cxx.ref") - # evolved = get_evolved_cxx(cxxinfo) - fieldkeys = get_evolved_cxx(cxxinfo) - fieldkeys = ["[" + elem + "]" for elem in fieldkeys] - except: - print("cant find the cxx file") - - # gridoptions = {'grid':grid,'mesh':mesh} - if "[mesh]" in list(inp.keys()): - # IC = outinfo - IC = read_grid(path + "/BOUT.dmp.0.nc") # output data again - elif "grid" in inp["[main]"]: - gridname = inp["[main]"]["grid"] - try: - IC = read_grid(gridname) # have to be an ansoulte file path for now - print("IC: ", type(IC)) - # print IC.variables - # print gridname - except: - # print gridname - print("Fail to load the grid file") - # print IC - - # print gridname - # print len(IC) - # print IC - - evolved = [] - collected = [] - ICscale = [] - - # fieldkeys = ['[Ni]','[Te]','[Ti]','[Vi]','[rho]', - # '[Ajpar]','[Apar]','[vEBx]','[vEBy]','[vEBz]', - # '[jpar]','[phi]'] - - # construct fieldkeys from cxx info - # fieldkeys = ['['+x+']' for x in evolved] - # fieldkeys = evolved - - # just look ahead and see what 3D fields have been output - available = np.array([str(x) for x in outinfo]) - a = np.array([(len(outinfo[x].shape) == 4) for x in available]) - available = available[a] - - defaultIC = float(inp["[All]"].get("scale", 0.0)) - - # print inp.keys() - - # figure out which fields are evolved - print(fieldkeys) - - for section in list(inp.keys()): # loop over section keys - print("section: ", section) - if section in fieldkeys: # pick the relevant sections - print(section) - # print inp[section].get('evolve','True') - # rint (inp[section].get('evolve','True')).lower().strip() - if ( - inp[section].get("evolve", "True").lower().strip() == "true" - ): # and section[1:-1] in available : - print("ok reading") - evolved.append(section.strip("[]")) - ICscale.append(float(inp[section].get("scale", defaultIC))) - - if inp[section].get("collect", "False").lower().strip() == "true": - collected.append(section.strip("[]")) - - try: - if inp["[physics]"].get("transport", "False").lower().strip() == "true": - vEBstr = ["vEBx", "vEBy", "vEBz", "vEBrms"] - [collected.append(item) for item in vEBstr] - except: - print("no [physics] key") - - meta = OrderedDict() - - class ValUnit(object): - def __init__(self, value=0, units=""): - self.u = units - self.v = value - - def todict(self): - return {"u": self.u, "v": self.v} - - # def decode_valunit(d): - - def ToFloat(metaString): - try: - return float(metaString) - except ValueError: - return metaString - - # meta['evolved'] = ValUnit(evolved,'') - meta["evolved"] = evolved - meta["collected"] = collected - meta["IC"] = np.array(ICscale) - d = {} - - print("evolved: ", evolved) - - # read meta data from .inp file, this is whre most metadata get written - for section in list(inp.keys()): - if ("evolve" not in inp[section]) and ( - "first" not in inp[section] - ): # hacky way to exclude some less relevant metadata - for elem in list(inp[section].keys()): - meta[elem] = ValUnit(ToFloat(inp[section][elem])) - d[elem] = np.array(ToFloat(inp[section][elem])) - - # read in some values from the grid(IC) and scale them as needed - norms = { - "Ni0": ValUnit(1.0e14, "cm^-3"), - "bmag": ValUnit(1.0e4, "gauss"), - "Ni_x": ValUnit(1.0e14, "cm^-3"), - "Te_x": ValUnit(1.0, "eV"), - "Ti_x": ValUnit(1.0, "eV"), - "Rxy": ValUnit(1, "m"), - "Bxy": ValUnit(1.0e4, "gauss"), - "Bpxy": ValUnit(1.0e4, "gauss"), - "Btxy": ValUnit(1.0e4, "gauss"), - "Zxy": ValUnit(1, "m"), - "dlthe": ValUnit(1, "m"), - "dx": ValUnit(1, "m"), - "hthe0": ValUnit(1, "m"), - } - - availkeys = np.array([str(x) for x in outinfo]) - tmp1 = np.array([x for x in availkeys]) - # b = np.array([x if x not in available for x in a]) - tmp2 = np.array([x for x in tmp1 if x not in available]) - static_fields = np.array([x for x in tmp2 if x in list(norms.keys())]) - # static_fields = tmp2 - - # print availkeys - # print meta.keys() - # print IC.variables.keys() - # print tmp1 - # print tmp2 - - for elem in static_fields: - print("elem: ", elem) - meta[elem] = ValUnit(IC.variables[elem][:] * norms[elem].v, norms[elem].u) - d[elem] = np.array(IC.variables[elem][:] * norms[elem].v) - - for elem in IC.variables: - if elem not in meta: - if elem in list(norms.keys()): - meta[elem] = ValUnit( - IC.variables[elem][:] * norms[elem].v, norms[elem].u - ) - d[elem] = np.array(IC.variables[elem][:] * norms[elem].v) - else: - meta[elem] = IC.variables[elem][:] - d[elem] = IC.variables[elem][:] - - # print d.keys() - - # if case some values are missing - default = { - "bmag": 1, - "Ni_x": 1, - "NOUT": 100, - "TIMESTEP": 1, - "MZ": 32, - "AA": 1, - "Zeff": ValUnit(1, ""), - "ZZ": 1, - "zlowpass": 0.0, - "transport": False, - } - diff = set(default.keys()).difference(set(d.keys())) - - for elem in diff: - # print 'diff: ',elem - meta[elem] = default[elem] - d[elem] = np.array(default[elem]) - - # print meta.keys() - # print d.keys() - - # print meta['zlowpass'] - - if meta["zlowpass"] != 0: - print(meta["MZ"].v, meta["zlowpass"].v) - meta["maxZ"] = int(np.floor(meta["MZ"].v * meta["zlowpass"].v)) - else: - meta["maxZ"] = 5 - - # meta['nx'] = nx - # meta['ny']= ny - meta["dt"] = meta["TIMESTEP"] - - # nx,ny = d['Rxy'].shape - - # print meta['AA'].v - - meta["rho_s"] = ValUnit( - 1.02e2 * np.sqrt(d["AA"] * d["Te_x"]) / (d["ZZ"] * d["bmag"]), "cm" - ) # ion gyrorad at T_e, in cm - meta["rho_i"] = ValUnit( - 1.02e2 * np.sqrt(d["AA"] * d["Ti_x"]) / (d["ZZ"] * d["bmag"]), "cm" - ) - meta["rho_e"] = ValUnit(2.38 * np.sqrt(d["Te_x"]) / (d["bmag"]), "cm") - - meta["fmei"] = ValUnit(1.0 / 1836.2 / d["AA"]) - - meta["lambda_ei"] = 24.0 - np.log(old_div(np.sqrt(d["Ni_x"]), d["Te_x"])) - meta["lambda_ii"] = 23.0 - np.log( - d["ZZ"] ** 3 * np.sqrt(2.0 * d["Ni_x"]) / (d["Ti_x"] ** 1.5) - ) # - - meta["wci"] = 1.0 * 9.58e3 * d["ZZ"] * d["bmag"] / d["AA"] # ion gyrofrteq - meta["wpi"] = ( - 1.32e3 * d["ZZ"] * np.sqrt(old_div(d["Ni_x"], d["AA"])) - ) # ion plasma freq - - meta["wce"] = 1.78e7 * d["bmag"] # electron gyrofreq - meta["wpe"] = 5.64e4 * np.sqrt(d["Ni_x"]) # electron plasma freq - - meta["v_the"] = 4.19e7 * np.sqrt(d["Te_x"]) # cm/s - meta["v_thi"] = 9.79e5 * np.sqrt(old_div(d["Ti_x"], d["AA"])) # cm/s - meta["c_s"] = 9.79e5 * np.sqrt(5.0 / 3.0 * d["ZZ"] * d["Te_x"] / d["AA"]) # - meta["v_A"] = 2.18e11 * np.sqrt(old_div(1.0, (d["AA"] * d["Ni_x"]))) - - meta["nueix"] = 2.91e-6 * d["Ni_x"] * meta["lambda_ei"] / d["Te_x"] ** 1.5 # - meta["nuiix"] = ( - 4.78e-8 - * d["ZZ"] ** 4.0 - * d["Ni_x"] - * meta["lambda_ii"] - / d["Ti_x"] ** 1.5 - / np.sqrt(d["AA"]) - ) # - meta["nu_hat"] = meta["Zeff"].v * meta["nueix"] / meta["wci"] - - meta["L_d"] = 7.43e2 * np.sqrt(old_div(d["Te_x"], d["Ni_x"])) - meta["L_i_inrt"] = ( - 2.28e7 * np.sqrt(old_div(d["AA"], d["Ni_x"])) / d["ZZ"] - ) # ion inertial length in cm - meta["L_e_inrt"] = 5.31e5 * np.sqrt(d["Ni_x"]) # elec inertial length in cm - - meta["Ve_x"] = 4.19e7 * d["Te_x"] - - meta["R0"] = old_div((d["Rxy"].max() + d["Rxy"].min()), 2.0) - - print(d["Rxy"].mean(1)) - print(d["ZMAX"]) - print(d["ZMIN"]) - meta["L_z"] = ( - 1e2 * 2 * np.pi * d["Rxy"].mean(1) * (d["ZMAX"] - d["ZMIN"]) - ) # in cm toroidal range - meta["dz"] = d["ZMAX"] - d["ZMIN"] - - # meta['lbNorm']=meta['L_z']*(d['Bpxy']/d['Bxy']).mean(1) #-binormal coord range [cm] - meta["lbNorm"] = meta["L_z"] * (old_div(d["Bxy"], d["Bpxy"])).mean(1) - - # meta['zPerp']=np.array(meta['lbNorm']).mean*np.array(range(d['MZ']))/(d['MZ']-1) - # let's calculate some profile properties - dx = np.gradient(d["Rxy"])[0] - meta["L"] = ( - 1.0 - * 1e2 - * dx - * (meta["Ni0"].v) - / np.gradient(meta["Ni0"].v)[0] - / meta["rho_s"].v - ) - - meta["w_Ln"] = old_div( - meta["c_s"], (np.min(abs(meta["L"])) * meta["wci"] * meta["rho_s"].v) - ) # normed to wci - - AA = meta["AA"].v - ZZ = d["ZZ"] - Te_x = d["Te_x"] - Ti_x = d["Ti_x"] - fmei = meta["fmei"].v - - meta["lpar"] = ( - 1e2 * ((old_div(d["Bxy"], d["Bpxy"])) * d["dlthe"]).sum(1) / meta["rho_s"].v - ) # -[normed], average over flux surfaces, parallel length - - # yes dlthe is always the vertical displacement - # dlthe = (hthe0*2 pi)/nz - # meta['lpar']=1e2*(d['Bxy']/d['Bpxy']).mean(1)*d['dlthe'].mean(1) #function of x - meta["sig_par"] = old_div(1.0, (fmei * 0.51 * meta["nu_hat"])) - # meta['heat_nue'] = ((2*np.pi/meta['lpar'])**2)/(fmei*meta['nu_hat']) - # kz_e = kz_i*(rho_e/rho_i) - # kz_s = kz_i*(rho_s/rho_i) - # kz_i = (TWOPI/L_z)*(indgen((*current_str).fft.nz+1))*rho_i - - # knorm = (TWOPI/lbNorm)*(indgen((*current_str).fft.nz+1))*rho_s - - # for now just translate - for elem in meta: - if type(meta[elem]).__name__ == "ValUnit": - meta[elem] = {"u": meta[elem].u, "v": meta[elem].v} - - print("meta: ", type(meta)) - return meta - - # meta['DZ'] =inp['[main]']['ZMAX']#-b['[main]']['ZMIN'] - # AA = inp['[2fluid]']['AA'] - # Ni0 = IC.variables['Ni0'][:]*1.e14 - # bmag = IC.variables['bmag'][:]*1.e4 #to cgs - # Ni_x = IC.variables['Ni_x'][:]*1.e14 # cm^-3 - # Te_x - - # rho_s = 1.02e2*sqrt(AA.v*Te_x.v)/ZZ.v/bmag.v - # rho_i - # rho_e - - -# for i,val in enumerate(boutlist): diff --git a/tools/pylib/post_bout/rms.py b/tools/pylib/post_bout/rms.py deleted file mode 100644 index 6a9bdb1929..0000000000 --- a/tools/pylib/post_bout/rms.py +++ /dev/null @@ -1,55 +0,0 @@ -from __future__ import division -from builtins import range -from past.utils import old_div - -### -# rms(f) : compute growth rate vs. time based on rms of bout variable f for all grid points -# plot_rms (x,y): plots the graph growth_rate vs. time for grid point x,y -### - - -import numpy as np -from pylab import plot, show, xlabel, ylabel, tight_layout -from boutdata.collect import collect - - -def rms(f): - nt = f.shape[0] - - ns = f.shape[1] - ne = f.shape[2] - nz = f.shape[3] - - ar = np.zeros([nz]) - - rms = np.zeros([nt, ns, ne]) - - for i in range(nt): - for j in range(ns): - for k in range(ne): - ar = f[i, j, k, :] - valav = np.sum(ar) - tot = np.sum(old_div(np.power(ar - valav, 2), nz)) - rms[i, j, k] = np.sqrt(tot) - return rms - - -def plot_rms(x, y): - s = plot(np.gradient(np.log(rmsp[:, x, y]))) - ylabel("$\gamma / \omega_A$", fontsize=25) - xlabel("Time$(\\tau_A)$", fontsize=25) - tight_layout() - return s - - -# test -if __name__ == "__main__": - path = "../../../examples/elm-pb/data" - - data = collect("P", path=path) - - rmsp = rms(data) - - plot_rms(34, 32) - tight_layout() - show() From 0a2c86634aea2f9b60e8ba5abf14f67a6710943f Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 25 Jan 2024 16:54:03 +0000 Subject: [PATCH 215/412] Remove unused `format.hxx` header Previously used for annotating `printf` like functions, since replaced with `fmt` formatting --- CMakeLists.txt | 1 - include/bout/boutexception.hxx | 2 -- include/bout/format.hxx | 16 ---------------- include/bout/msg_stack.hxx | 1 - include/bout/optionsreader.hxx | 1 - include/bout/output.hxx | 1 - include/bout/sys/expressionparser.hxx | 1 - 7 files changed, 23 deletions(-) delete mode 100644 include/bout/format.hxx diff --git a/CMakeLists.txt b/CMakeLists.txt index 88b31e8553..483672fb67 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -115,7 +115,6 @@ set(BOUT_SOURCES ./include/bout/field_factory.hxx ./include/bout/fieldgroup.hxx ./include/bout/fieldperp.hxx - ./include/bout/format.hxx ./include/bout/fv_ops.hxx ./include/bout/generic_factory.hxx ./include/bout/globalfield.hxx diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx index 5b8a421692..243b819961 100644 --- a/include/bout/boutexception.hxx +++ b/include/bout/boutexception.hxx @@ -10,8 +10,6 @@ class BoutException; #include #include -#include "bout/format.hxx" - #include "fmt/core.h" /// Throw BoutRhsFail with \p message if any one process has non-zero diff --git a/include/bout/format.hxx b/include/bout/format.hxx deleted file mode 100644 index 846303a3fd..0000000000 --- a/include/bout/format.hxx +++ /dev/null @@ -1,16 +0,0 @@ -#ifndef __BOUT_FORMAT_H__ -#define __BOUT_FORMAT_H__ - -/// Tell GCC that a function has a printf-style like argument -/// The first argument is the position of format string, and the -/// second is the position of the first variadic argument -/// Note that it seems to start counting from 1, and also counts a -/// *this pointer, as the first argument, so often 2 would be the -/// first argument. -#if defined(__GNUC__) -#define BOUT_FORMAT_ARGS(i, j) __attribute__((format(printf, i, j))) -#else -#define BOUT_FORMAT_ARGS(i, j) -#endif - -#endif //__BOUT_FORMAT_H__ diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx index cc19a7b9f6..2a9afc65cb 100644 --- a/include/bout/msg_stack.hxx +++ b/include/bout/msg_stack.hxx @@ -31,7 +31,6 @@ class MsgStack; #include "bout/build_config.hxx" -#include "bout/format.hxx" #include "bout/unused.hxx" #include "fmt/core.h" diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx index 428c7a8c8f..32c302a3f7 100644 --- a/include/bout/optionsreader.hxx +++ b/include/bout/optionsreader.hxx @@ -34,7 +34,6 @@ class OptionsReader; #ifndef __OPTIONSREADER_H__ #define __OPTIONSREADER_H__ -#include "bout/format.hxx" #include "bout/options.hxx" #include "fmt/core.h" diff --git a/include/bout/output.hxx b/include/bout/output.hxx index ef09aa7ee5..ccecd5681a 100644 --- a/include/bout/output.hxx +++ b/include/bout/output.hxx @@ -37,7 +37,6 @@ class Output; #include "bout/assert.hxx" #include "bout/boutexception.hxx" -#include "bout/format.hxx" #include "bout/sys/gettext.hxx" // for gettext _() macro #include "bout/unused.hxx" diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx index a22b41e499..660ad20ab3 100644 --- a/include/bout/sys/expressionparser.hxx +++ b/include/bout/sys/expressionparser.hxx @@ -27,7 +27,6 @@ #ifndef EXPRESSION_PARSER_H #define EXPRESSION_PARSER_H -#include "bout/format.hxx" #include "bout/unused.hxx" #include "fmt/core.h" From aca26793f47d84a249f498ecfacd8a76ec668867 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 25 Jan 2024 17:06:43 +0000 Subject: [PATCH 216/412] Replace `MAYBE_UNUSED` macro with C++17 `[[maybe_unused]]` --- include/bout/field.hxx | 2 +- include/bout/interpolation_xz.hxx | 2 +- include/bout/interpolation_z.hxx | 2 +- include/bout/invert_laplace.hxx | 4 ++-- include/bout/mesh.hxx | 2 +- include/bout/monitor.hxx | 4 ++-- include/bout/output.hxx | 2 +- include/bout/paralleltransform.hxx | 2 +- include/bout/solver.hxx | 2 +- include/bout/sundials_backports.hxx | 14 +++++------ include/bout/unused.hxx | 20 ---------------- src/bout++.cxx | 5 ++-- src/invert/fft_fftw.cxx | 24 +++++++++---------- .../laplace/impls/multigrid/multigrid_alg.cxx | 2 +- src/invert/laplace/invert_laplace.cxx | 7 +++--- src/mesh/coordinates.cxx | 8 +++---- src/mesh/data/gridfromfile.cxx | 16 ++++++------- src/mesh/difops.cxx | 4 ++-- src/mesh/index_derivs.cxx | 2 +- src/mesh/parallel/fci.hxx | 2 +- src/solver/impls/arkode/arkode.cxx | 2 +- src/solver/impls/cvode/cvode.cxx | 3 ++- src/solver/impls/ida/ida.cxx | 2 +- src/solver/impls/petsc/petsc.cxx | 13 +++++----- src/solver/impls/slepc/slepc.cxx | 2 +- src/solver/solver.cxx | 2 +- src/sys/derivs.cxx | 18 +++++++------- src/sys/hyprelib.cxx | 4 ++-- src/sys/options.cxx | 2 +- src/sys/options/options_netcdf.cxx | 6 ++--- tests/MMS/time/time.cxx | 8 +++---- tests/unit/sys/test_options.cxx | 16 ++++++------- tests/unit/test_extras.hxx | 24 +++++++++---------- 33 files changed, 104 insertions(+), 124 deletions(-) diff --git a/include/bout/field.hxx b/include/bout/field.hxx index 9a425942c1..a4f4f52803 100644 --- a/include/bout/field.hxx +++ b/include/bout/field.hxx @@ -370,7 +370,7 @@ inline bool isUniform(const T& f, bool allpe = false, /// @param[in] allpe Check over all processors /// @param[in] region The region to assume is uniform template > -inline BoutReal getUniform(const T& f, MAYBE_UNUSED(bool allpe) = false, +inline BoutReal getUniform(const T& f, [[maybe_unused]] bool allpe = false, const std::string& region = "RGN_ALL") { #if CHECK > 1 if (not isUniform(f, allpe, region)) { diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 89524f8056..3f8e37d3fd 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -276,7 +276,7 @@ public: ReturnType create(Options* options = nullptr, Mesh* mesh = nullptr) const { return Factory::create(getType(options), mesh); } - ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const { + ReturnType create(const std::string& type, [[maybe_unused]] Options* options) const { return Factory::create(type, nullptr); } diff --git a/include/bout/interpolation_z.hxx b/include/bout/interpolation_z.hxx index 596b2634fb..b11d7ff5b6 100644 --- a/include/bout/interpolation_z.hxx +++ b/include/bout/interpolation_z.hxx @@ -82,7 +82,7 @@ public: Region region_in = {}) const { return Factory::create(getType(nullptr), y_offset, mesh, region_in); } - ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const { + ReturnType create(const std::string& type, [[maybe_unused]] Options* options) const { return Factory::create(type, 0, nullptr, Region{}); } diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index c4ae5efdf8..78417b9fce 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -275,8 +275,8 @@ public: /// performance information, with optional name for the time /// dimension void outputVars(Options& output_options) const { outputVars(output_options, "t"); } - virtual void outputVars(MAYBE_UNUSED(Options& output_options), - MAYBE_UNUSED(const std::string& time_dimension)) const {} + virtual void outputVars([[maybe_unused]] Options& output_options, + [[maybe_unused]] const std::string& time_dimension) const {} /// Register performance monitor with \p solver, prefix output with /// `Options` section name diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index cec1486ac9..8f73552ea5 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -135,7 +135,7 @@ public: /// Add output variables to \p output_options /// These are used for post-processing - virtual void outputVars(MAYBE_UNUSED(Options& output_options)) {} + virtual void outputVars([[maybe_unused]] Options& output_options) {} // Get routines to request data from mesh file diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx index eb86c01554..5bc4fc7e12 100644 --- a/include/bout/monitor.hxx +++ b/include/bout/monitor.hxx @@ -50,8 +50,8 @@ public: /// Callback function for when a clean shutdown is initiated virtual void cleanup(){}; - virtual void outputVars(MAYBE_UNUSED(Options& options), - MAYBE_UNUSED(const std::string& time_dimension)) {} + virtual void outputVars([[maybe_unused]] Options& options, + [[maybe_unused]] const std::string& time_dimension) {} protected: /// Get the currently set timestep for this monitor diff --git a/include/bout/output.hxx b/include/bout/output.hxx index ef09aa7ee5..4e3a812d89 100644 --- a/include/bout/output.hxx +++ b/include/bout/output.hxx @@ -144,7 +144,7 @@ public: void print([[maybe_unused]] const std::string& message) override{}; void enable() override{}; void disable() override{}; - void enable(MAYBE_UNUSED(bool enable)){}; + void enable([[maybe_unused]] bool enable){}; bool isEnabled() override { return false; } }; diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx index bb00dcbd45..4a7e4989c8 100644 --- a/include/bout/paralleltransform.hxx +++ b/include/bout/paralleltransform.hxx @@ -83,7 +83,7 @@ public: } /// Output variables used by a ParallelTransform instance to \p output_options - virtual void outputVars(MAYBE_UNUSED(Options& output_options)) {} + virtual void outputVars([[maybe_unused]] Options& output_options) {} /// If \p twist_shift_enabled is true, does a `Field3D` with Y direction \p ytype /// require a twist-shift at branch cuts on closed field lines? diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index f795808f6a..d110d7ff17 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -269,7 +269,7 @@ public: virtual void constraint(Vector3D& v, Vector3D& C_v, std::string name); /// Set a maximum internal timestep (only for explicit schemes) - virtual void setMaxTimestep(MAYBE_UNUSED(BoutReal dt)) {} + virtual void setMaxTimestep([[maybe_unused]] BoutReal dt) {} /// Return the current internal timestep virtual BoutReal getCurrentTimestep() { return 0.0; } diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index c5e0f3ab15..c4f4aa59ef 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -27,19 +27,19 @@ #if SUNDIALS_VERSION_MAJOR < 3 using SUNLinearSolver = int*; -inline void SUNLinSolFree(MAYBE_UNUSED(SUNLinearSolver solver)) {} +inline void SUNLinSolFree([[maybe_unused]] SUNLinearSolver solver) {} using sunindextype = long int; #endif #if SUNDIALS_VERSION_MAJOR < 4 using SUNNonlinearSolver = int*; -inline void SUNNonlinSolFree(MAYBE_UNUSED(SUNNonlinearSolver solver)) {} +inline void SUNNonlinSolFree([[maybe_unused]] SUNNonlinearSolver solver) {} #endif #if SUNDIALS_VERSION_MAJOR < 6 namespace sundials { struct Context { - Context(void* comm MAYBE_UNUSED()) {} + Context(void* comm [[maybe_unused]]) {} }; } // namespace sundials @@ -51,13 +51,13 @@ constexpr auto SUN_PREC_NONE = PREC_NONE; inline N_Vector N_VNew_Parallel(MPI_Comm comm, sunindextype local_length, sunindextype global_length, - MAYBE_UNUSED(SUNContext sunctx)) { + [[maybe_unused]] SUNContext sunctx) { return N_VNew_Parallel(comm, local_length, global_length); } #if SUNDIALS_VERSION_MAJOR >= 3 inline SUNLinearSolver SUNLinSol_SPGMR(N_Vector y, int pretype, int maxl, - MAYBE_UNUSED(SUNContext sunctx)) { + [[maybe_unused]] SUNContext sunctx) { #if SUNDIALS_VERSION_MAJOR == 3 return SUNSPGMR(y, pretype, maxl); #else @@ -66,12 +66,12 @@ inline SUNLinearSolver SUNLinSol_SPGMR(N_Vector y, int pretype, int maxl, } #if SUNDIALS_VERSION_MAJOR >= 4 inline SUNNonlinearSolver SUNNonlinSol_FixedPoint(N_Vector y, int m, - MAYBE_UNUSED(SUNContext sunctx)) { + [[maybe_unused]] SUNContext sunctx) { return SUNNonlinSol_FixedPoint(y, m); } inline SUNNonlinearSolver SUNNonlinSol_Newton(N_Vector y, - MAYBE_UNUSED(SUNContext sunctx)) { + [[maybe_unused]] SUNContext sunctx) { return SUNNonlinSol_Newton(y); } #endif // SUNDIALS_VERSION_MAJOR >= 4 diff --git a/include/bout/unused.hxx b/include/bout/unused.hxx index 6e7a46c7c0..74fd3c2f98 100644 --- a/include/bout/unused.hxx +++ b/include/bout/unused.hxx @@ -37,24 +37,4 @@ #define UNUSED(x) x #endif -/// Mark a function parameter as possibly unused in the function body -/// -/// Unlike `UNUSED`, this has to go around the type as well: -/// -/// MAYBE_UNUSED(int foo); -#ifdef __has_cpp_attribute -#if __has_cpp_attribute(maybe_unused) -#define MAYBE_UNUSED(x) [[maybe_unused]] x -#endif -#endif -#ifndef MAYBE_UNUSED -#if defined(__GNUC__) -#define MAYBE_UNUSED(x) [[gnu::unused]] x -#elif defined(_MSC_VER) -#define MAYBE_UNUSED(x) __pragma(warning(suppress : 4100)) x -#else -#define MAYBE_UNUSED(x) x -#endif -#endif - #endif //__UNUSED_H__ diff --git a/src/bout++.cxx b/src/bout++.cxx index 1dc93dc76d..481a928bec 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -190,8 +190,7 @@ int BoutInitialise(int& argc, char**& argv) { // but it's possible that only happens in BoutFinalise, which is // too late for that check. const auto datadir = Options::root()["datadir"].withDefault(DEFAULT_DIR); - MAYBE_UNUSED() - const auto optionfile = + [[maybe_unused]] const auto optionfile = Options::root()["optionfile"].withDefault(args.opt_file); const auto settingsfile = Options::root()["settingsfile"].withDefault(args.set_file); @@ -837,7 +836,7 @@ BoutMonitor::BoutMonitor(BoutReal timestep, Options& options) .doc(_("Name of file whose existence triggers a stop")) .withDefault("BOUT.stop"))) {} -int BoutMonitor::call(Solver* solver, BoutReal t, MAYBE_UNUSED(int iter), int NOUT) { +int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int NOUT) { TRACE("BoutMonitor::call({:e}, {:d}, {:d})", t, iter, NOUT); // Increment Solver's iteration counter, and set the global `iteration` diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx index f158fa3d7a..514396c828 100644 --- a/src/invert/fft_fftw.cxx +++ b/src/invert/fft_fftw.cxx @@ -106,8 +106,8 @@ void fft_init(bool fft_measure) { #if !BOUT_USE_OPENMP // Serial code -void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), - MAYBE_UNUSED(dcomplex* out)) { +void rfft([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length, + [[maybe_unused]] dcomplex* out) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else @@ -170,8 +170,8 @@ void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), #endif } -void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length), - MAYBE_UNUSED(BoutReal* out)) { +void irfft([[maybe_unused]] const dcomplex* in, [[maybe_unused]] int length, + [[maybe_unused]] BoutReal* out) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else @@ -233,8 +233,8 @@ void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length), } #else // Parallel thread-safe version of rfft and irfft -void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), - MAYBE_UNUSED(dcomplex* out)) { +void rfft([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length, + [[maybe_unused]] dcomplex* out) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else @@ -312,8 +312,8 @@ void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), #endif } -void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length), - MAYBE_UNUSED(BoutReal* out)) { +void irfft([[maybe_unused]] const dcomplex* in, [[maybe_unused]] int length, + [[maybe_unused]] BoutReal* out) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else @@ -388,8 +388,8 @@ void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length), #endif // Discrete sine transforms (B Shanahan) -void DST(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), - MAYBE_UNUSED(dcomplex* out)) { +void DST([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length, + [[maybe_unused]] dcomplex* out) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else @@ -446,8 +446,8 @@ void DST(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length), #endif } -void DST_rev(MAYBE_UNUSED(dcomplex* in), MAYBE_UNUSED(int length), - MAYBE_UNUSED(BoutReal* out)) { +void DST_rev([[maybe_unused]] dcomplex* in, [[maybe_unused]] int length, + [[maybe_unused]] BoutReal* out) { #if !BOUT_HAS_FFTW throw BoutException("This instance of BOUT++ has been compiled without fftw support."); #else diff --git a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx index 0043c95d18..88556e02ad 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx @@ -704,7 +704,7 @@ void MultigridAlg::communications(BoutReal* x, int level) { MPI_Status status[4]; int stag, rtag; - MAYBE_UNUSED(int ierr); + [[maybe_unused]] int ierr; if (zNP > 1) { MPI_Request requests[] = {MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL, diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index dc3d1a3c3f..eb2b15aef2 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -782,9 +782,10 @@ void Laplacian::savePerformance(Solver& solver, const std::string& name) { solver.addMonitor(&monitor, Solver::BACK); } -int Laplacian::LaplacianMonitor::call(MAYBE_UNUSED(Solver* solver), - MAYBE_UNUSED(BoutReal time), MAYBE_UNUSED(int iter), - MAYBE_UNUSED(int nout)) { +int Laplacian::LaplacianMonitor::call([[maybe_unused]] Solver* solver, + [[maybe_unused]] BoutReal time, + [[maybe_unused]] int iter, + [[maybe_unused]] int nout) { // Nothing to do, values are always calculated return 0; } diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx index 25d623aad8..5ec0bb79e1 100644 --- a/src/mesh/coordinates.cxx +++ b/src/mesh/coordinates.cxx @@ -1528,7 +1528,7 @@ Field3D Coordinates::DDZ(const Field3D& f, CELL_LOC outloc, const std::string& m // Parallel gradient Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var, - MAYBE_UNUSED(CELL_LOC outloc), + [[maybe_unused]] CELL_LOC outloc, const std::string& UNUSED(method)) { TRACE("Coordinates::Grad_par( Field2D )"); ASSERT1(location == outloc @@ -1550,7 +1550,7 @@ Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc, // vparallel times the parallel derivative along unperturbed B-field Coordinates::FieldMetric Coordinates::Vpar_Grad_par(const Field2D& v, const Field2D& f, - MAYBE_UNUSED(CELL_LOC outloc), + [[maybe_unused]] CELL_LOC outloc, const std::string& UNUSED(method)) { ASSERT1(location == outloc || (outloc == CELL_DEFAULT && location == f.getLocation())); @@ -1829,8 +1829,8 @@ Field3D Coordinates::Laplace(const Field3D& f, CELL_LOC outloc, // Full perpendicular Laplacian, in form of inverse of Laplacian operator in LaplaceXY // solver -Field2D Coordinates::Laplace_perpXY(MAYBE_UNUSED(const Field2D& A), - MAYBE_UNUSED(const Field2D& f)) { +Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A, + [[maybe_unused]] const Field2D& f) { TRACE("Coordinates::Laplace_perpXY( Field2D )"); #if not(BOUT_USE_METRIC_3D) Field2D result; diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index aa66b145c7..41147ba76c 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -134,10 +134,10 @@ bool GridFile::get(Mesh* m, Field3D& var, const std::string& name, BoutReal def, namespace { /// Visitor that returns the shape of its argument struct GetDimensions { - std::vector operator()(MAYBE_UNUSED(bool value)) { return {1}; } - std::vector operator()(MAYBE_UNUSED(int value)) { return {1}; } - std::vector operator()(MAYBE_UNUSED(BoutReal value)) { return {1}; } - std::vector operator()(MAYBE_UNUSED(const std::string& value)) { return {1}; } + std::vector operator()([[maybe_unused]] bool value) { return {1}; } + std::vector operator()([[maybe_unused]] int value) { return {1}; } + std::vector operator()([[maybe_unused]] BoutReal value) { return {1}; } + std::vector operator()([[maybe_unused]] const std::string& value) { return {1}; } std::vector operator()(const Array& array) { return {array.size()}; } std::vector operator()(const Matrix& array) { const auto shape = array.shape(); @@ -471,10 +471,10 @@ void GridFile::readField(Mesh* m, const std::string& name, int UNUSED(ys), int U } } -bool GridFile::get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector& var), - MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len), - MAYBE_UNUSED(int offset), - MAYBE_UNUSED(GridDataSource::Direction dir)) { +bool GridFile::get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector& var, + [[maybe_unused]] const std::string& name, [[maybe_unused]] int len, + [[maybe_unused]] int offset, + [[maybe_unused]] GridDataSource::Direction dir) { TRACE("GridFile::get(vector)"); return false; diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx index 9b7665ad30..f252abe0ea 100644 --- a/src/mesh/difops.cxx +++ b/src/mesh/difops.cxx @@ -645,7 +645,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, } ASSERT1(outloc == g.getLocation()); - MAYBE_UNUSED(Mesh * mesh) = f.getMesh(); + [[maybe_unused]] Mesh* mesh = f.getMesh(); Field3D result{emptyFrom(f).setLocation(outloc)}; @@ -862,7 +862,7 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method, } Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, - CELL_LOC outloc, MAYBE_UNUSED(Solver* solver)) { + CELL_LOC outloc, [[maybe_unused]] Solver* solver) { TRACE("Field3D, Field3D"); ASSERT1_FIELDS_COMPATIBLE(f, g); diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx index 769315ca68..f8b660cf70 100644 --- a/src/mesh/index_derivs.cxx +++ b/src/mesh/index_derivs.cxx @@ -59,7 +59,7 @@ STAGGER Mesh::getStagger(const CELL_LOC inloc, const CELL_LOC outloc, } } -STAGGER Mesh::getStagger(const CELL_LOC vloc, MAYBE_UNUSED(const CELL_LOC inloc), +STAGGER Mesh::getStagger(const CELL_LOC vloc, [[maybe_unused]] const CELL_LOC inloc, const CELL_LOC outloc, const CELL_LOC allowedStaggerLoc) const { TRACE("Mesh::getStagger -- four arguments"); ASSERT1(inloc == outloc); diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 6d7c3d14e2..a749c084cc 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -127,7 +127,7 @@ public: bool canToFromFieldAligned() const override { return false; } bool requiresTwistShift(bool UNUSED(twist_shift_enabled), - MAYBE_UNUSED(YDirectionType ytype)) override { + [[maybe_unused]] YDirectionType ytype) override { // No Field3Ds require twist-shift, because they cannot be field-aligned ASSERT1(ytype == YDirectionType::Standard); diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 13e0dd817e..9691f2f7da 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -161,7 +161,7 @@ constexpr auto& ARKStepSetUserData = ARKodeSetUserData; #if SUNDIALS_VERSION_MAJOR < 6 void* ARKStepCreate(ARKRhsFn fe, ARKRhsFn fi, BoutReal t0, N_Vector y0, - MAYBE_UNUSED(SUNContext context)) { + [[maybe_unused]] SUNContext context) { return ARKStepCreate(fe, fi, t0, y0); } #endif diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 70eb3b8841..f35ae680d5 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -112,7 +112,8 @@ constexpr auto CV_NEWTON = 0; #endif #if SUNDIALS_VERSION_MAJOR >= 3 -void* CVodeCreate(int lmm, MAYBE_UNUSED(int iter), MAYBE_UNUSED(SUNContext context)) { +void* CVodeCreate(int lmm, [[maybe_unused]] int iter, + [[maybe_unused]] SUNContext context) { #if SUNDIALS_VERSION_MAJOR == 3 return CVodeCreate(lmm, iter); #elif SUNDIALS_VERSION_MAJOR == 4 || SUNDIALS_VERSION_MAJOR == 5 diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index b008ebf903..189a103bbe 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -85,7 +85,7 @@ constexpr auto& ida_pre_shim = ida_pre; #endif #if SUNDIALS_VERSION_MAJOR < 6 -void* IDACreate(MAYBE_UNUSED(SUNContext)) { return IDACreate(); } +void* IDACreate([[maybe_unused]] SUNContext) { return IDACreate(); } #endif IdaSolver::IdaSolver(Options* opts) diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx index 9270848998..7a2b2cf3de 100644 --- a/src/solver/impls/petsc/petsc.cxx +++ b/src/solver/impls/petsc/petsc.cxx @@ -749,10 +749,10 @@ PetscErrorCode solver_rhsjacobian(TS UNUSED(ts), BoutReal UNUSED(t), Vec UNUSED( PetscFunctionReturn(0); } #else -PetscErrorCode solver_rhsjacobian(MAYBE_UNUSED(TS ts), MAYBE_UNUSED(BoutReal t), - MAYBE_UNUSED(Vec globalin), Mat* J, Mat* Jpre, - MAYBE_UNUSED(MatStructure* str), - MAYBE_UNUSED(void* f_data)) { +PetscErrorCode solver_rhsjacobian([[maybe_unused]] TS ts, [[maybe_unused]] BoutReal t, + [[maybe_unused]] Vec globalin, Mat* J, Mat* Jpre, + [[maybe_unused]] MatStructure* str, + [[maybe_unused]] void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; @@ -797,8 +797,9 @@ PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, Vec UNUSED(glob } #else PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, - MAYBE_UNUSED(Vec globalindot), MAYBE_UNUSED(PetscReal a), - Mat* J, Mat* Jpre, MatStructure* str, void* f_data) { + [[maybe_unused]] Vec globalindot, + [[maybe_unused]] PetscReal a, Mat* J, Mat* Jpre, + MatStructure* str, void* f_data) { PetscErrorCode ierr; PetscFunctionBegin; diff --git a/src/solver/impls/slepc/slepc.cxx b/src/solver/impls/slepc/slepc.cxx index f90afe717e..8cbb002d11 100644 --- a/src/solver/impls/slepc/slepc.cxx +++ b/src/solver/impls/slepc/slepc.cxx @@ -572,7 +572,7 @@ void SlepcSolver::monitor(PetscInt its, PetscInt nconv, PetscScalar eigr[], static int nConvPrev = 0; // Disable floating-point exceptions for the duration of this function - MAYBE_UNUSED(QuietFPE quiet_fpe{}); + [[maybe_unused]] QuietFPE quiet_fpe{}; // No output until after first iteration if (its < 1) { diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx index 9dd31f011e..45b2e6a2bb 100644 --- a/src/solver/solver.cxx +++ b/src/solver/solver.cxx @@ -1498,7 +1498,7 @@ void Solver::post_rhs(BoutReal UNUSED(t)) { } // Make sure 3D fields are at the correct cell location, etc. - for (MAYBE_UNUSED(const auto& f) : f3d) { + for ([[maybe_unused]] const auto& f : f3d) { ASSERT1_FIELDS_COMPATIBLE(*f.var, *f.F_var); } diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx index 7f629cfbb5..ee9bcbcc2c 100644 --- a/src/sys/derivs.cxx +++ b/src/sys/derivs.cxx @@ -331,8 +331,8 @@ Field3D D2DXDY(const Field3D& f, CELL_LOC outloc, const std::string& method, } Coordinates::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc, - MAYBE_UNUSED(const std::string& method), - MAYBE_UNUSED(const std::string& region)) { + [[maybe_unused]] const std::string& method, + [[maybe_unused]] const std::string& region) { #if BOUT_USE_METRIC_3D Field3D tmp{f}; return D2DXDZ(tmp, outloc, method, region); @@ -356,8 +356,8 @@ Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc, const std::string& method, } Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc, - MAYBE_UNUSED(const std::string& method), - MAYBE_UNUSED(const std::string& region)) { + [[maybe_unused]] const std::string& method, + [[maybe_unused]] const std::string& region) { #if BOUT_USE_METRIC_3D Field3D tmp{f}; return D2DYDZ(tmp, outloc, method, region); @@ -369,8 +369,8 @@ Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc, #endif } -Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc, MAYBE_UNUSED(const std::string& method), - const std::string& region) { +Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc, + [[maybe_unused]] const std::string& method, const std::string& region) { // If staggering in z, take y-derivative at f's location. const auto y_location = (outloc == CELL_ZLOW or f.getLocation() == CELL_ZLOW) ? CELL_DEFAULT : outloc; @@ -426,9 +426,9 @@ Coordinates::FieldMetric VDDZ(const Field2D& v, const Field2D& f, CELL_LOC outlo } // Note that this is zero because no compression is included -Coordinates::FieldMetric VDDZ(MAYBE_UNUSED(const Field3D& v), const Field2D& f, - CELL_LOC outloc, MAYBE_UNUSED(const std::string& method), - MAYBE_UNUSED(const std::string& region)) { +Coordinates::FieldMetric VDDZ([[maybe_unused]] const Field3D& v, const Field2D& f, + CELL_LOC outloc, [[maybe_unused]] const std::string& method, + [[maybe_unused]] const std::string& region) { #if BOUT_USE_METRIC_3D Field3D tmp{f}; return bout::derivatives::index::VDDZ(v, tmp, outloc, method, region) diff --git a/src/sys/hyprelib.cxx b/src/sys/hyprelib.cxx index e833162726..691e53230f 100644 --- a/src/sys/hyprelib.cxx +++ b/src/sys/hyprelib.cxx @@ -39,7 +39,7 @@ HypreLib::HypreLib() { } } -HypreLib::HypreLib(MAYBE_UNUSED() const HypreLib& other) noexcept { +HypreLib::HypreLib([[maybe_unused]] const HypreLib& other) noexcept { BOUT_OMP(critical(HypreLib)) { // No need to initialise Hypre, because it must already be initialised @@ -47,7 +47,7 @@ HypreLib::HypreLib(MAYBE_UNUSED() const HypreLib& other) noexcept { } } -HypreLib::HypreLib(MAYBE_UNUSED() HypreLib&& other) noexcept { +HypreLib::HypreLib([[maybe_unused]] HypreLib&& other) noexcept { BOUT_OMP(critical(HypreLib)) { // No need to initialise Hypre, because it must already be initialised diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 45cacd4acc..34ecf87683 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -683,7 +683,7 @@ struct ConvertContainer { Container operator()(const Container& value) { return value; } template - Container operator()(MAYBE_UNUSED(const Other& value)) { + Container operator()([[maybe_unused]] const Other& value) { throw BoutException(error_message); } diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx index eda2b0bfbd..65fbca14c0 100644 --- a/src/sys/options/options_netcdf.cxx +++ b/src/sys/options/options_netcdf.cxx @@ -196,8 +196,7 @@ NcType NcTypeVisitor::operator()(const double& UNUSED(t)) { } template <> -MAYBE_UNUSED() -NcType NcTypeVisitor::operator()(const float& UNUSED(t)) { +[[maybe_unused]] NcType NcTypeVisitor::operator()(const float& UNUSED(t)) { return ncFloat; } @@ -403,8 +402,7 @@ void NcPutAttVisitor::operator()(const double& value) { var.putAtt(name, ncDouble, value); } template <> -MAYBE_UNUSED() -void NcPutAttVisitor::operator()(const float& value) { +[[maybe_unused]] void NcPutAttVisitor::operator()(const float& value) { var.putAtt(name, ncFloat, value); } template <> diff --git a/tests/MMS/time/time.cxx b/tests/MMS/time/time.cxx index 346662a8e3..97f376a31a 100644 --- a/tests/MMS/time/time.cxx +++ b/tests/MMS/time/time.cxx @@ -10,7 +10,7 @@ class TimeTest : public PhysicsModel { public: - int init(MAYBE_UNUSED(bool restart)) { + int init([[maybe_unused]] bool restart) { solver->add(f, "f"); // Solve a single 3D field setSplitOperator(); @@ -18,16 +18,16 @@ class TimeTest : public PhysicsModel { return 0; } - int rhs(MAYBE_UNUSED(BoutReal time)) { + int rhs([[maybe_unused]] BoutReal time) { ddt(f) = f; return 0; } - int convective(MAYBE_UNUSED(BoutReal time)) { + int convective([[maybe_unused]] BoutReal time) { ddt(f) = 0.5 * f; return 0; } - int diffusive(MAYBE_UNUSED(BoutReal time)) { + int diffusive([[maybe_unused]] BoutReal time) { ddt(f) = 0.5 * f; return 0; } diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index 40458757ec..1f0ae92ed2 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -326,7 +326,7 @@ TEST_F(OptionsTest, ValueUsed) { Options options; options["key1"] = 1; EXPECT_FALSE(options["key1"].valueUsed()); - MAYBE_UNUSED(const int value) = options["key1"]; + [[maybe_unused]] const int value = options["key1"]; EXPECT_TRUE(options["key1"].valueUsed()); } @@ -1245,17 +1245,17 @@ TEST_F(OptionsTest, GetUnused) { // This shouldn't count as unused option["section2"]["value5"].attributes["source"] = "Output"; - MAYBE_UNUSED(auto value1) = option["section1"]["value1"].as(); - MAYBE_UNUSED(auto value3) = option["section2"]["subsection1"]["value3"].as(); + [[maybe_unused]] auto value1 = option["section1"]["value1"].as(); + [[maybe_unused]] auto value3 = option["section2"]["subsection1"]["value3"].as(); Options expected_unused{{"section1", {{"value2", "hello"}}}, {"section2", {{"subsection1", {{"value4", 3.2}}}}}}; EXPECT_EQ(option.getUnused(), expected_unused); - MAYBE_UNUSED(auto value2) = option["section1"]["value2"].as(); - MAYBE_UNUSED(auto value4) = option["section2"]["subsection1"]["value4"].as(); - MAYBE_UNUSED(auto value5) = option["section2"]["value5"].as(); + [[maybe_unused]] auto value2 = option["section1"]["value2"].as(); + [[maybe_unused]] auto value4 = option["section2"]["subsection1"]["value4"].as(); + [[maybe_unused]] auto value5 = option["section2"]["value5"].as(); Options expected_empty{}; @@ -1333,8 +1333,8 @@ TEST_F(OptionsTest, CheckForUnusedOptions) { // This shouldn't count as unused option["section2"]["value5"].attributes["source"] = "Output"; - MAYBE_UNUSED(auto value1) = option["section1"]["value1"].as(); - MAYBE_UNUSED(auto value3) = option["section2"]["subsection1"]["value3"].as(); + [[maybe_unused]] auto value1 = option["section1"]["value1"].as(); + [[maybe_unused]] auto value3 = option["section2"]["subsection1"]["value3"].as(); EXPECT_THROW(bout::checkForUnusedOptions(option, "data", "BOUT.inp"), BoutException); } diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index f0868ddf49..845ea4f255 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -51,13 +51,13 @@ inline std::ostream& operator<<(std::ostream& out, const SpecificInd& index) } /// Helpers to get the type of a Field as a string -auto inline getFieldType(MAYBE_UNUSED(const Field2D& field)) -> std::string { +auto inline getFieldType([[maybe_unused]] const Field2D& field) -> std::string { return "Field2D"; } -auto inline getFieldType(MAYBE_UNUSED(const Field3D& field)) -> std::string { +auto inline getFieldType([[maybe_unused]] const Field3D& field) -> std::string { return "Field3D"; } -auto inline getFieldType(MAYBE_UNUSED(const FieldPerp& field)) -> std::string { +auto inline getFieldType([[maybe_unused]] const FieldPerp& field) -> std::string { return "FieldPerp"; } @@ -339,7 +339,7 @@ public: bool hasVar(const std::string& UNUSED(name)) override { return false; } - bool get(MAYBE_UNUSED(Mesh* m), std::string& sval, const std::string& name, + bool get([[maybe_unused]] Mesh* m, std::string& sval, const std::string& name, const std::string& def = "") override { if (values[name].isSet()) { sval = values[name].as(); @@ -348,7 +348,7 @@ public: sval = def; return false; } - bool get(MAYBE_UNUSED(Mesh* m), int& ival, const std::string& name, + bool get([[maybe_unused]] Mesh* m, int& ival, const std::string& name, int def = 0) override { if (values[name].isSet()) { ival = values[name].as(); @@ -357,7 +357,7 @@ public: ival = def; return false; } - bool get(MAYBE_UNUSED(Mesh* m), BoutReal& rval, const std::string& name, + bool get([[maybe_unused]] Mesh* m, BoutReal& rval, const std::string& name, BoutReal def = 0.0) override { if (values[name].isSet()) { rval = values[name].as(); @@ -394,15 +394,15 @@ public: return false; } - bool get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector& var), - MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len), - MAYBE_UNUSED(int def) = 0, Direction = GridDataSource::X) override { + bool get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector& var, + [[maybe_unused]] const std::string& name, [[maybe_unused]] int len, + [[maybe_unused]] int def = 0, Direction = GridDataSource::X) override { throw BoutException("Not Implemented"); return false; } - bool get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector& var), - MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len), - MAYBE_UNUSED(int def) = 0, + bool get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector& var, + [[maybe_unused]] const std::string& name, [[maybe_unused]] int len, + [[maybe_unused]] int def = 0, Direction UNUSED(dir) = GridDataSource::X) override { throw BoutException("Not Implemented"); return false; From e329eb60d2713694f2eab2c35bf3786ad1804bc3 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 25 Jan 2024 17:39:00 +0000 Subject: [PATCH 217/412] Use C++17's `inline` variable feature to remove some code We no longer need separate declarations of static/constexpr variables, as C++17 now handles this better. Note that `static constexpr` members imply `inline`, while namespace scope `constexpr` implies `static` but not `inline` --- include/bout/generic_factory.hxx | 8 -------- include/bout/revision.hxx.in | 6 ++---- include/bout/version.hxx.in | 14 ++++++-------- src/invert/laplace/invert_laplace.cxx | 4 ---- src/invert/laplacexz/laplacexz.cxx | 5 ----- src/invert/parderiv/invert_parderiv.cxx | 4 ---- src/invert/pardiv/invert_pardiv.cxx | 4 ---- src/mesh/interpolation/hermite_spline_z.cxx | 7 ------- src/mesh/interpolation_xz.cxx | 8 -------- src/mesh/mesh.cxx | 5 ----- src/solver/impls/rkgeneric/rkscheme.cxx | 5 ----- src/solver/solver.cxx | 5 ----- tests/unit/include/bout/test_generic_factory.cxx | 9 --------- 13 files changed, 8 insertions(+), 76 deletions(-) diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx index f7a0692af8..9493ef77f1 100644 --- a/include/bout/generic_factory.hxx +++ b/include/bout/generic_factory.hxx @@ -48,14 +48,6 @@ /// RegisterInFactory register("derived_type"); /// auto foo = MyFactory::getInstance().create("derived_type"); /// -/// In a .cxx file the static members should be declared: -/// -/// constexpr decltype(MyFactory::type_name) MyFactory::type_name; -/// constexpr decltype(MyFactory::section_name) MyFactory::section_name; -/// constexpr decltype(MyFactory::option_name) MyFactory::option_name; -/// constexpr decltype(MyFactory::default_type) MyFactory::default_type; -/// -/// /// @tparam BaseType The base class that this factory creates /// @tparam DerivedFactory The derived factory inheriting from this class /// @tparam TypeCreator The function signature for creating a new BaseType diff --git a/include/bout/revision.hxx.in b/include/bout/revision.hxx.in index f0e3abdb8b..393e8cc34f 100644 --- a/include/bout/revision.hxx.in +++ b/include/bout/revision.hxx.in @@ -7,18 +7,16 @@ #ifndef BOUT_REVISION_H #define BOUT_REVISION_H -// TODO: Make these all `inline` when we upgrade to C++17 - namespace bout { namespace version { /// The git commit hash #ifndef BOUT_REVISION -constexpr auto revision = "@BOUT_REVISION@"; +inline constexpr auto revision = "@BOUT_REVISION@"; #else // Stringify value passed at compile time #define BUILDFLAG1_(x) #x #define BUILDFLAG(x) BUILDFLAG1_(x) -constexpr auto revision = BUILDFLAG(BOUT_REVISION); +inline constexpr auto revision = BUILDFLAG(BOUT_REVISION); #undef BUILDFLAG1 #undef BUILDFLAG #endif diff --git a/include/bout/version.hxx.in b/include/bout/version.hxx.in index 06a32808af..3eaf40dbd7 100644 --- a/include/bout/version.hxx.in +++ b/include/bout/version.hxx.in @@ -5,22 +5,20 @@ #ifndef BOUT_VERSION_H #define BOUT_VERSION_H -// TODO: Make these all `inline` when we upgrade to C++17 - namespace bout { namespace version { /// The full version number -constexpr auto full = "@BOUT_VERSION@"; +inline constexpr auto full = "@BOUT_VERSION@"; /// The major version number -constexpr int major = @BOUT_VERSION_MAJOR@; +inline constexpr int major = @BOUT_VERSION_MAJOR@; /// The minor version number -constexpr int minor = @BOUT_VERSION_MINOR@; +inline constexpr int minor = @BOUT_VERSION_MINOR@; /// The patch version number -constexpr int patch = @BOUT_VERSION_PATCH@; +inline constexpr int patch = @BOUT_VERSION_PATCH@; /// The version pre-release identifier -constexpr auto prerelease = "@BOUT_VERSION_TAG@"; +inline constexpr auto prerelease = "@BOUT_VERSION_TAG@"; /// The full version number as a double -constexpr double as_double = @BOUT_VERSION_MAJOR@.@BOUT_VERSION_MINOR@@BOUT_VERSION_PATCH@; +inline constexpr double as_double = @BOUT_VERSION_MAJOR@.@BOUT_VERSION_MINOR@@BOUT_VERSION_PATCH@; } // namespace version } // namespace bout diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index dc3d1a3c3f..f234309f47 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -805,7 +805,3 @@ void laplace_tridag_coefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcom const Field2D* ccoef, const Field2D* d, CELL_LOC loc) { Laplacian::defaultInstance()->tridagCoefs(jx, jy, jz, a, b, c, ccoef, d, loc); } -constexpr decltype(LaplaceFactory::type_name) LaplaceFactory::type_name; -constexpr decltype(LaplaceFactory::section_name) LaplaceFactory::section_name; -constexpr decltype(LaplaceFactory::option_name) LaplaceFactory::option_name; -constexpr decltype(LaplaceFactory::default_type) LaplaceFactory::default_type; diff --git a/src/invert/laplacexz/laplacexz.cxx b/src/invert/laplacexz/laplacexz.cxx index a2b99280e6..d064f62104 100644 --- a/src/invert/laplacexz/laplacexz.cxx +++ b/src/invert/laplacexz/laplacexz.cxx @@ -5,8 +5,3 @@ // DO NOT REMOVE: ensures linker keeps all symbols in this TU void LaplaceXZFactory::ensureRegistered() {} - -constexpr decltype(LaplaceXZFactory::type_name) LaplaceXZFactory::type_name; -constexpr decltype(LaplaceXZFactory::section_name) LaplaceXZFactory::section_name; -constexpr decltype(LaplaceXZFactory::option_name) LaplaceXZFactory::option_name; -constexpr decltype(LaplaceXZFactory::default_type) LaplaceXZFactory::default_type; diff --git a/src/invert/parderiv/invert_parderiv.cxx b/src/invert/parderiv/invert_parderiv.cxx index bc8ad8669f..e14c0ee1d2 100644 --- a/src/invert/parderiv/invert_parderiv.cxx +++ b/src/invert/parderiv/invert_parderiv.cxx @@ -39,7 +39,3 @@ const Field2D InvertPar::solve(const Field2D& f) { // DO NOT REMOVE: ensures linker keeps all symbols in this TU void InvertParFactory::ensureRegistered() {} -constexpr decltype(InvertParFactory::type_name) InvertParFactory::type_name; -constexpr decltype(InvertParFactory::section_name) InvertParFactory::section_name; -constexpr decltype(InvertParFactory::option_name) InvertParFactory::option_name; -constexpr decltype(InvertParFactory::default_type) InvertParFactory::default_type; diff --git a/src/invert/pardiv/invert_pardiv.cxx b/src/invert/pardiv/invert_pardiv.cxx index d05b594aa1..30e421edd8 100644 --- a/src/invert/pardiv/invert_pardiv.cxx +++ b/src/invert/pardiv/invert_pardiv.cxx @@ -39,7 +39,3 @@ Field2D InvertParDiv::solve(const Field2D& f) { // DO NOT REMOVE: ensures linker keeps all symbols in this TU void InvertParDivFactory::ensureRegistered() {} -constexpr decltype(InvertParDivFactory::type_name) InvertParDivFactory::type_name; -constexpr decltype(InvertParDivFactory::section_name) InvertParDivFactory::section_name; -constexpr decltype(InvertParDivFactory::option_name) InvertParDivFactory::option_name; -constexpr decltype(InvertParDivFactory::default_type) InvertParDivFactory::default_type; diff --git a/src/mesh/interpolation/hermite_spline_z.cxx b/src/mesh/interpolation/hermite_spline_z.cxx index 921094af73..c4c44cb7b4 100644 --- a/src/mesh/interpolation/hermite_spline_z.cxx +++ b/src/mesh/interpolation/hermite_spline_z.cxx @@ -192,10 +192,3 @@ void ZInterpolationFactory::ensureRegistered() {} namespace { RegisterZInterpolation registerzinterphermitespline{"hermitespline"}; } // namespace - -constexpr decltype(ZInterpolationFactory::type_name) ZInterpolationFactory::type_name; -constexpr decltype(ZInterpolationFactory::section_name) - ZInterpolationFactory::section_name; -constexpr decltype(ZInterpolationFactory::option_name) ZInterpolationFactory::option_name; -constexpr decltype(ZInterpolationFactory::default_type) - ZInterpolationFactory::default_type; diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx index 11dbdc215d..f7f0b457f2 100644 --- a/src/mesh/interpolation_xz.cxx +++ b/src/mesh/interpolation_xz.cxx @@ -93,11 +93,3 @@ RegisterXZInterpolation registerinterpmonotonichermite RegisterXZInterpolation registerinterplagrange4pt{"lagrange4pt"}; RegisterXZInterpolation registerinterpbilinear{"bilinear"}; } // namespace - -constexpr decltype(XZInterpolationFactory::type_name) XZInterpolationFactory::type_name; -constexpr decltype(XZInterpolationFactory::section_name) - XZInterpolationFactory::section_name; -constexpr decltype(XZInterpolationFactory::option_name) - XZInterpolationFactory::option_name; -constexpr decltype(XZInterpolationFactory::default_type) - XZInterpolationFactory::default_type; diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 7f3c5195b4..0f6315a987 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -756,11 +756,6 @@ void Mesh::recalculateStaggeredCoordinates() { } } -constexpr decltype(MeshFactory::type_name) MeshFactory::type_name; -constexpr decltype(MeshFactory::section_name) MeshFactory::section_name; -constexpr decltype(MeshFactory::option_name) MeshFactory::option_name; -constexpr decltype(MeshFactory::default_type) MeshFactory::default_type; - std::optional Mesh::getCommonRegion(std::optional lhs, std::optional rhs) { if (!lhs.has_value()) { diff --git a/src/solver/impls/rkgeneric/rkscheme.cxx b/src/solver/impls/rkgeneric/rkscheme.cxx index 740adec909..25de364533 100644 --- a/src/solver/impls/rkgeneric/rkscheme.cxx +++ b/src/solver/impls/rkgeneric/rkscheme.cxx @@ -308,8 +308,3 @@ void RKScheme::zeroSteps() { } } } - -constexpr decltype(RKSchemeFactory::type_name) RKSchemeFactory::type_name; -constexpr decltype(RKSchemeFactory::section_name) RKSchemeFactory::section_name; -constexpr decltype(RKSchemeFactory::option_name) RKSchemeFactory::option_name; -constexpr decltype(RKSchemeFactory::default_type) RKSchemeFactory::default_type; diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx index 9dd31f011e..d88f753f44 100644 --- a/src/solver/solver.cxx +++ b/src/solver/solver.cxx @@ -1571,8 +1571,3 @@ void Solver::calculate_mms_error(BoutReal t) { *(f.MMS_err) = *(f.var) - solution; } } - -constexpr decltype(SolverFactory::type_name) SolverFactory::type_name; -constexpr decltype(SolverFactory::section_name) SolverFactory::section_name; -constexpr decltype(SolverFactory::option_name) SolverFactory::option_name; -constexpr decltype(SolverFactory::default_type) SolverFactory::default_type; diff --git a/tests/unit/include/bout/test_generic_factory.cxx b/tests/unit/include/bout/test_generic_factory.cxx index 9368356151..f8a1e20bfa 100644 --- a/tests/unit/include/bout/test_generic_factory.cxx +++ b/tests/unit/include/bout/test_generic_factory.cxx @@ -37,10 +37,6 @@ class BaseFactory : public Factory { static constexpr auto option_name = "type"; static constexpr auto default_type = "base"; }; -constexpr decltype(BaseFactory::type_name) BaseFactory::type_name; -constexpr decltype(BaseFactory::section_name) BaseFactory::section_name; -constexpr decltype(BaseFactory::option_name) BaseFactory::option_name; -constexpr decltype(BaseFactory::default_type) BaseFactory::default_type; BaseFactory::RegisterInFactory registerme("base"); BaseFactory::RegisterInFactory registerme1("derived1"); @@ -76,11 +72,6 @@ class ComplicatedFactory static constexpr auto default_type = "basecomplicated"; }; -constexpr decltype(ComplicatedFactory::type_name) ComplicatedFactory::type_name; -constexpr decltype(ComplicatedFactory::section_name) ComplicatedFactory::section_name; -constexpr decltype(ComplicatedFactory::option_name) ComplicatedFactory::option_name; -constexpr decltype(ComplicatedFactory::default_type) ComplicatedFactory::default_type; - namespace { ComplicatedFactory::RegisterInFactory registerme3("basecomplicated"); ComplicatedFactory::RegisterInFactory From 7e0ccad9c8fb15f3b1328ba8a671116d26bc1416 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 25 Jan 2024 17:47:20 +0000 Subject: [PATCH 218/412] Remove disgusting hack to placate linker --- CMakeLists.txt | 1 - include/bout/generic_factory.hxx | 6 ------ include/bout/interpolation_xz.hxx | 2 -- include/bout/interpolation_z.hxx | 2 -- include/bout/invert/laplacexz.hxx | 2 -- include/bout/invert_parderiv.hxx | 1 - include/bout/invert_pardiv.hxx | 1 - src/invert/laplacexz/laplacexz.cxx | 7 ------- src/invert/parderiv/invert_parderiv.cxx | 3 --- src/invert/pardiv/invert_pardiv.cxx | 3 --- src/mesh/interpolation/hermite_spline_z.cxx | 2 -- src/mesh/interpolation_xz.cxx | 2 -- 12 files changed, 32 deletions(-) delete mode 100644 src/invert/laplacexz/laplacexz.cxx diff --git a/CMakeLists.txt b/CMakeLists.txt index 88b31e8553..7e2eb0777d 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -245,7 +245,6 @@ set(BOUT_SOURCES ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx - ./src/invert/laplacexz/laplacexz.cxx ./src/invert/parderiv/impls/cyclic/cyclic.cxx ./src/invert/parderiv/impls/cyclic/cyclic.hxx ./src/invert/parderiv/invert_parderiv.cxx diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx index 9493ef77f1..e5186d9331 100644 --- a/include/bout/generic_factory.hxx +++ b/include/bout/generic_factory.hxx @@ -68,11 +68,6 @@ protected: Factory() = default; - /// Disgusting hack to defeat linker throwing out the registration - /// symbols. If necessary, override this and put the (empty) - /// implementation in the same TU as the registration symbols - static void ensureRegistered() {} - /// Return either \p options or the section from root Options* optionsOrDefaultSection(Options* options) const { if (options == nullptr) { @@ -87,7 +82,6 @@ public: /// Get the singleton instance static DerivedFactory& getInstance() { static DerivedFactory instance{}; - DerivedFactory::ensureRegistered(); return instance; } diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 89524f8056..84df698c74 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -279,8 +279,6 @@ public: ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const { return Factory::create(type, nullptr); } - - static void ensureRegistered(); }; template diff --git a/include/bout/interpolation_z.hxx b/include/bout/interpolation_z.hxx index 596b2634fb..1506bd9bf2 100644 --- a/include/bout/interpolation_z.hxx +++ b/include/bout/interpolation_z.hxx @@ -85,8 +85,6 @@ public: ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const { return Factory::create(type, 0, nullptr, Region{}); } - - static void ensureRegistered(); }; template diff --git a/include/bout/invert/laplacexz.hxx b/include/bout/invert/laplacexz.hxx index 1b1ebef832..21baaecd1d 100644 --- a/include/bout/invert/laplacexz.hxx +++ b/include/bout/invert/laplacexz.hxx @@ -54,8 +54,6 @@ public: ReturnType create(const std::string& type, Options* options) const { return Factory::create(type, nullptr, options, CELL_CENTRE); } - - static void ensureRegistered(); }; template diff --git a/include/bout/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx index 5a83a7f4e8..a8917c76fc 100644 --- a/include/bout/invert_parderiv.hxx +++ b/include/bout/invert_parderiv.hxx @@ -57,7 +57,6 @@ public: ReturnType create(const std::string& type, Options* options) const { return Factory::create(type, options, CELL_CENTRE, nullptr); } - static void ensureRegistered(); }; template diff --git a/include/bout/invert_pardiv.hxx b/include/bout/invert_pardiv.hxx index 23ea59e943..fa3ce37cdd 100644 --- a/include/bout/invert_pardiv.hxx +++ b/include/bout/invert_pardiv.hxx @@ -57,7 +57,6 @@ public: ReturnType create(const std::string& type, Options* options) const { return Factory::create(type, options, CELL_CENTRE, nullptr); } - static void ensureRegistered(); }; template diff --git a/src/invert/laplacexz/laplacexz.cxx b/src/invert/laplacexz/laplacexz.cxx deleted file mode 100644 index d064f62104..0000000000 --- a/src/invert/laplacexz/laplacexz.cxx +++ /dev/null @@ -1,7 +0,0 @@ -#include "impls/cyclic/laplacexz-cyclic.hxx" -#include "impls/petsc/laplacexz-petsc.hxx" - -#include - -// DO NOT REMOVE: ensures linker keeps all symbols in this TU -void LaplaceXZFactory::ensureRegistered() {} diff --git a/src/invert/parderiv/invert_parderiv.cxx b/src/invert/parderiv/invert_parderiv.cxx index e14c0ee1d2..d1ef9ba9e8 100644 --- a/src/invert/parderiv/invert_parderiv.cxx +++ b/src/invert/parderiv/invert_parderiv.cxx @@ -36,6 +36,3 @@ const Field2D InvertPar::solve(const Field2D& f) { var = solve(var); return DC(var); } - -// DO NOT REMOVE: ensures linker keeps all symbols in this TU -void InvertParFactory::ensureRegistered() {} diff --git a/src/invert/pardiv/invert_pardiv.cxx b/src/invert/pardiv/invert_pardiv.cxx index 30e421edd8..0fc995ab32 100644 --- a/src/invert/pardiv/invert_pardiv.cxx +++ b/src/invert/pardiv/invert_pardiv.cxx @@ -36,6 +36,3 @@ Field2D InvertParDiv::solve(const Field2D& f) { var = solve(var); return DC(var); } - -// DO NOT REMOVE: ensures linker keeps all symbols in this TU -void InvertParDivFactory::ensureRegistered() {} diff --git a/src/mesh/interpolation/hermite_spline_z.cxx b/src/mesh/interpolation/hermite_spline_z.cxx index c4c44cb7b4..305000799c 100644 --- a/src/mesh/interpolation/hermite_spline_z.cxx +++ b/src/mesh/interpolation/hermite_spline_z.cxx @@ -187,8 +187,6 @@ Field3D ZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_z, return interpolate(f, region_str); } -void ZInterpolationFactory::ensureRegistered() {} - namespace { RegisterZInterpolation registerzinterphermitespline{"hermitespline"}; } // namespace diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx index f7f0b457f2..d459d5ccef 100644 --- a/src/mesh/interpolation_xz.cxx +++ b/src/mesh/interpolation_xz.cxx @@ -84,8 +84,6 @@ const Field3D interpolate(const Field2D& f, const Field3D& delta_x) { return result; } -void XZInterpolationFactory::ensureRegistered() {} - namespace { RegisterXZInterpolation registerinterphermitespline{"hermitespline"}; RegisterXZInterpolation registerinterpmonotonichermitespline{ From 02cecc99ceca4ab072346b57c05c8d379dff465b Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 25 Jan 2024 10:12:10 -0800 Subject: [PATCH 219/412] Apply suggestions from code review Adds some `override` keywords Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- tests/MMS/time/time.cxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/MMS/time/time.cxx b/tests/MMS/time/time.cxx index 97f376a31a..17e1f547ab 100644 --- a/tests/MMS/time/time.cxx +++ b/tests/MMS/time/time.cxx @@ -10,7 +10,7 @@ class TimeTest : public PhysicsModel { public: - int init([[maybe_unused]] bool restart) { + int init([[maybe_unused]] bool restart) override { solver->add(f, "f"); // Solve a single 3D field setSplitOperator(); @@ -18,7 +18,7 @@ class TimeTest : public PhysicsModel { return 0; } - int rhs([[maybe_unused]] BoutReal time) { + int rhs([[maybe_unused]] BoutReal time) override { ddt(f) = f; return 0; } From a1fceb507e7d1ad3f80d7347e034e14208fe499d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 09:18:04 +0000 Subject: [PATCH 220/412] Revert "Remove disgusting hack to placate linker" This reverts commit 7e0ccad9c8fb15f3b1328ba8a671116d26bc1416. This is still required for static linking --- CMakeLists.txt | 1 + include/bout/generic_factory.hxx | 6 ++++++ include/bout/interpolation_xz.hxx | 2 ++ include/bout/interpolation_z.hxx | 2 ++ include/bout/invert/laplacexz.hxx | 2 ++ include/bout/invert_parderiv.hxx | 1 + include/bout/invert_pardiv.hxx | 1 + src/invert/laplacexz/laplacexz.cxx | 7 +++++++ src/invert/parderiv/invert_parderiv.cxx | 3 +++ src/invert/pardiv/invert_pardiv.cxx | 3 +++ src/mesh/interpolation/hermite_spline_z.cxx | 2 ++ src/mesh/interpolation_xz.cxx | 2 ++ 12 files changed, 32 insertions(+) create mode 100644 src/invert/laplacexz/laplacexz.cxx diff --git a/CMakeLists.txt b/CMakeLists.txt index 7e2eb0777d..88b31e8553 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -245,6 +245,7 @@ set(BOUT_SOURCES ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx + ./src/invert/laplacexz/laplacexz.cxx ./src/invert/parderiv/impls/cyclic/cyclic.cxx ./src/invert/parderiv/impls/cyclic/cyclic.hxx ./src/invert/parderiv/invert_parderiv.cxx diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx index e5186d9331..9493ef77f1 100644 --- a/include/bout/generic_factory.hxx +++ b/include/bout/generic_factory.hxx @@ -68,6 +68,11 @@ protected: Factory() = default; + /// Disgusting hack to defeat linker throwing out the registration + /// symbols. If necessary, override this and put the (empty) + /// implementation in the same TU as the registration symbols + static void ensureRegistered() {} + /// Return either \p options or the section from root Options* optionsOrDefaultSection(Options* options) const { if (options == nullptr) { @@ -82,6 +87,7 @@ public: /// Get the singleton instance static DerivedFactory& getInstance() { static DerivedFactory instance{}; + DerivedFactory::ensureRegistered(); return instance; } diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 84df698c74..89524f8056 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -279,6 +279,8 @@ public: ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const { return Factory::create(type, nullptr); } + + static void ensureRegistered(); }; template diff --git a/include/bout/interpolation_z.hxx b/include/bout/interpolation_z.hxx index 1506bd9bf2..596b2634fb 100644 --- a/include/bout/interpolation_z.hxx +++ b/include/bout/interpolation_z.hxx @@ -85,6 +85,8 @@ public: ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const { return Factory::create(type, 0, nullptr, Region{}); } + + static void ensureRegistered(); }; template diff --git a/include/bout/invert/laplacexz.hxx b/include/bout/invert/laplacexz.hxx index 21baaecd1d..1b1ebef832 100644 --- a/include/bout/invert/laplacexz.hxx +++ b/include/bout/invert/laplacexz.hxx @@ -54,6 +54,8 @@ public: ReturnType create(const std::string& type, Options* options) const { return Factory::create(type, nullptr, options, CELL_CENTRE); } + + static void ensureRegistered(); }; template diff --git a/include/bout/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx index a8917c76fc..5a83a7f4e8 100644 --- a/include/bout/invert_parderiv.hxx +++ b/include/bout/invert_parderiv.hxx @@ -57,6 +57,7 @@ public: ReturnType create(const std::string& type, Options* options) const { return Factory::create(type, options, CELL_CENTRE, nullptr); } + static void ensureRegistered(); }; template diff --git a/include/bout/invert_pardiv.hxx b/include/bout/invert_pardiv.hxx index fa3ce37cdd..23ea59e943 100644 --- a/include/bout/invert_pardiv.hxx +++ b/include/bout/invert_pardiv.hxx @@ -57,6 +57,7 @@ public: ReturnType create(const std::string& type, Options* options) const { return Factory::create(type, options, CELL_CENTRE, nullptr); } + static void ensureRegistered(); }; template diff --git a/src/invert/laplacexz/laplacexz.cxx b/src/invert/laplacexz/laplacexz.cxx new file mode 100644 index 0000000000..d064f62104 --- /dev/null +++ b/src/invert/laplacexz/laplacexz.cxx @@ -0,0 +1,7 @@ +#include "impls/cyclic/laplacexz-cyclic.hxx" +#include "impls/petsc/laplacexz-petsc.hxx" + +#include + +// DO NOT REMOVE: ensures linker keeps all symbols in this TU +void LaplaceXZFactory::ensureRegistered() {} diff --git a/src/invert/parderiv/invert_parderiv.cxx b/src/invert/parderiv/invert_parderiv.cxx index d1ef9ba9e8..e14c0ee1d2 100644 --- a/src/invert/parderiv/invert_parderiv.cxx +++ b/src/invert/parderiv/invert_parderiv.cxx @@ -36,3 +36,6 @@ const Field2D InvertPar::solve(const Field2D& f) { var = solve(var); return DC(var); } + +// DO NOT REMOVE: ensures linker keeps all symbols in this TU +void InvertParFactory::ensureRegistered() {} diff --git a/src/invert/pardiv/invert_pardiv.cxx b/src/invert/pardiv/invert_pardiv.cxx index 0fc995ab32..30e421edd8 100644 --- a/src/invert/pardiv/invert_pardiv.cxx +++ b/src/invert/pardiv/invert_pardiv.cxx @@ -36,3 +36,6 @@ Field2D InvertParDiv::solve(const Field2D& f) { var = solve(var); return DC(var); } + +// DO NOT REMOVE: ensures linker keeps all symbols in this TU +void InvertParDivFactory::ensureRegistered() {} diff --git a/src/mesh/interpolation/hermite_spline_z.cxx b/src/mesh/interpolation/hermite_spline_z.cxx index 305000799c..c4c44cb7b4 100644 --- a/src/mesh/interpolation/hermite_spline_z.cxx +++ b/src/mesh/interpolation/hermite_spline_z.cxx @@ -187,6 +187,8 @@ Field3D ZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_z, return interpolate(f, region_str); } +void ZInterpolationFactory::ensureRegistered() {} + namespace { RegisterZInterpolation registerzinterphermitespline{"hermitespline"}; } // namespace diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx index d459d5ccef..f7f0b457f2 100644 --- a/src/mesh/interpolation_xz.cxx +++ b/src/mesh/interpolation_xz.cxx @@ -84,6 +84,8 @@ const Field3D interpolate(const Field2D& f, const Field3D& delta_x) { return result; } +void XZInterpolationFactory::ensureRegistered() {} + namespace { RegisterXZInterpolation registerinterphermitespline{"hermitespline"}; RegisterXZInterpolation registerinterpmonotonichermitespline{ From d3beaa2fc759a9c1f983820634ff82e78e5c5159 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 09:34:47 +0000 Subject: [PATCH 221/412] Remove some more redundant constexpr definitions --- include/bout/index_derivs.hxx | 7 ------- src/mesh/index_derivs.cxx | 3 --- src/solver/impls/imex-bdf2/imex-bdf2.cxx | 3 --- tests/unit/field/test_vector2d.cxx | 4 ---- tests/unit/test_extras.cxx | 5 ----- 5 files changed, 22 deletions(-) diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx index 8cb5c88aff..456f98f8c2 100644 --- a/include/bout/index_derivs.hxx +++ b/include/bout/index_derivs.hxx @@ -124,13 +124,6 @@ public: BoutReal apply(const stencil& v, const stencil& f) const { return func(v, f); } }; -// Redundant definitions because C++ -// Not necessary in C++17 -template -constexpr FF DerivativeType::func; -template -constexpr metaData DerivativeType::meta; - ///////////////////////////////////////////////////////////////////////////////// /// Following code is for dealing with registering a method/methods for all /// template combinations, in conjunction with the template_combinations code. diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx index 769315ca68..a89b8eb6aa 100644 --- a/src/mesh/index_derivs.cxx +++ b/src/mesh/index_derivs.cxx @@ -485,7 +485,6 @@ class FFTDerivativeType { } static constexpr metaData meta{"FFT", 0, DERIV::Standard}; }; -constexpr metaData FFTDerivativeType::meta; class FFT2ndDerivativeType { public: @@ -544,7 +543,6 @@ class FFT2ndDerivativeType { } static constexpr metaData meta{"FFT", 0, DERIV::StandardSecond}; }; -constexpr metaData FFT2ndDerivativeType::meta; produceCombinations, Set, Set>, @@ -574,7 +572,6 @@ class SplitFluxDerivativeType { } static constexpr metaData meta{"SPLIT", 2, DERIV::Flux}; }; -constexpr metaData SplitFluxDerivativeType::meta; produceCombinations< Set -// Need to provide a redundant declaration because C++ -constexpr int FakeMeshFixture::nx; -constexpr int FakeMeshFixture::ny; -constexpr int FakeMeshFixture::nz; - ::testing::AssertionResult IsSubString(const std::string& str, const std::string& substring) { if (str.find(substring) != std::string::npos) { From 85ff636216ba2e203d9370d07ea065f770d4511d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 10:33:05 +0000 Subject: [PATCH 222/412] Remove `Options::OptionValue` nested class The only use of this class (the `Options::values` view, returning a newly constructed `std::map`) was removed a few years ago, so this is no longer needed --- include/bout/options.hxx | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index bf1704100f..97b4e41f3c 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -731,21 +731,6 @@ public: /// clean the cache of parsed options static void cleanCache(); - /*! - * Class used to store values, together with - * information about their origin and usage - */ - struct OptionValue { - std::string value; - std::string source; // Source of the setting - mutable bool used = false; // Set to true when used - - /// This constructor needed for map::emplace - /// Can be removed in C++17 with map::insert and brace initialisation - OptionValue(std::string value, std::string source, bool used) - : value(std::move(value)), source(std::move(source)), used(used) {} - }; - /// Read-only access to internal options and sections /// to allow iteration over the tree std::map subsections() const; From fd8b0e6b99238f688e8008919b887f57374adb5c Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 10:44:05 +0000 Subject: [PATCH 223/412] Replace template dispatch with `if constexpr` --- tests/unit/field/test_field_factory.cxx | 27 +++++-------------------- 1 file changed, 5 insertions(+), 22 deletions(-) diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx index c0d17915a4..af819400e4 100644 --- a/tests/unit/field/test_field_factory.cxx +++ b/tests/unit/field/test_field_factory.cxx @@ -37,32 +37,15 @@ class FieldFactoryCreationTest : public FakeMeshFixture { FieldFactory factory; - // We can't just decide which FieldFactory::create?D function to - // call with - // - // if (bout::utils::is_Field3D::value) { - // return factory.create3D(...); - // } else { - // return factory.create2D(...); - // } - // - // as this is *runtime* so the compiler still needs to evaluate both - // branches -- until C++17 when we can use `if constexpr ...` - template - T createDispatch(std::true_type, Args&&... args) { - return factory.create3D(std::forward(args)...); - } - - template - T createDispatch(std::false_type, Args&&... args) { - return factory.create2D(std::forward(args)...); - } - // Generic way of calling either FieldFactory::create2D or // FieldFactory::create3D template T create(Args&&... args) { - return createDispatch(bout::utils::is_Field3D{}, std::forward(args)...); + if constexpr (bout::utils::is_Field3D{}) { + return factory.create3D(std::forward(args)...); + } else { + return factory.create2D(std::forward(args)...); + } } }; From d3a2001d3fbc6ebfcaca19411ac924d48955b32d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 11:00:50 +0000 Subject: [PATCH 224/412] Replace `std::get` with actual type in tests --- tests/unit/include/test_derivs.cxx | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/tests/unit/include/test_derivs.cxx b/tests/unit/include/test_derivs.cxx index 5e62ec51ce..e91339be24 100644 --- a/tests/unit/include/test_derivs.cxx +++ b/tests/unit/include/test_derivs.cxx @@ -70,8 +70,7 @@ class DerivativesTest const BoutReal box_length{TWOPI / grid_size}; // Set all the variables for this direction - // In C++14 this can be the more explicit std::get() - switch (std::get<0>(GetParam())) { + switch (std::get(GetParam())) { case DIRECTION::X: nx = grid_size; dir = &Index::x; @@ -113,8 +112,7 @@ class DerivativesTest velocity = makeField([&](Index& UNUSED(i)) { return 2.0; }, mesh); // Get the expected result for this order of derivative - // Again, could be nicer in C++17 with std::get(GetParam()) - switch (std::get<1>(GetParam())) { + switch (std::get(GetParam())) { case DERIV::Standard: expected = makeField( [&](Index& i) { return std::cos((i.*dir)() * box_length) * box_length; }, mesh); @@ -191,7 +189,7 @@ auto getMethodsForDirection(DERIV derivative_order, DIRECTION direction) auto methodDirectionTupleToString( const ::testing::TestParamInfo>& param) -> std::string { - return std::get<2>(param.param); + return std::get(param.param); } // Instantiate the test for X, Y, Z for first derivatives @@ -278,8 +276,8 @@ INSTANTIATE_TEST_SUITE_P(FluxZ, DerivativesTestAdvection, // single test, just instantiate it for each direction/order combination TEST_P(DerivativesTest, Sanity) { auto derivative = DerivativeStore::getInstance().getStandardDerivative( - std::get<2>(GetParam()), std::get<0>(GetParam()), STAGGER::None, - std::get<1>(GetParam())); + std::get(GetParam()), std::get(GetParam()), STAGGER::None, + std::get(GetParam())); Field3D result{mesh}; result.allocate(); @@ -292,8 +290,8 @@ TEST_P(DerivativesTest, Sanity) { // single test, just instantiate it for each direction/order combination TEST_P(DerivativesTestAdvection, Sanity) { auto derivative = DerivativeStore::getInstance().getFlowDerivative( - std::get<2>(GetParam()), std::get<0>(GetParam()), STAGGER::None, - std::get<1>(GetParam())); + std::get(GetParam()), std::get(GetParam()), STAGGER::None, + std::get(GetParam())); Field3D result{mesh}; result.allocate(); @@ -327,7 +325,7 @@ INSTANTIATE_TEST_SUITE_P(FirstZ, FirstDerivativesInterfaceTest, TEST_P(FirstDerivativesInterfaceTest, Sanity) { Field3D result; - switch (std::get<0>(GetParam())) { + switch (std::get(GetParam())) { case DIRECTION::X: result = bout::derivatives::index::DDX(input); break; @@ -363,7 +361,7 @@ INSTANTIATE_TEST_SUITE_P(Z, SecondDerivativesInterfaceTest, TEST_P(SecondDerivativesInterfaceTest, Sanity) { Field3D result; - switch (std::get<0>(GetParam())) { + switch (std::get(GetParam())) { case DIRECTION::X: result = bout::derivatives::index::D2DX2(input); break; @@ -399,7 +397,7 @@ INSTANTIATE_TEST_SUITE_P(Z, FourthDerivativesInterfaceTest, TEST_P(FourthDerivativesInterfaceTest, Sanity) { Field3D result; - switch (std::get<0>(GetParam())) { + switch (std::get(GetParam())) { case DIRECTION::X: result = bout::derivatives::index::D4DX4(input); break; @@ -437,7 +435,7 @@ INSTANTIATE_TEST_SUITE_P(Z, UpwindDerivativesInterfaceTest, TEST_P(UpwindDerivativesInterfaceTest, Sanity) { Field3D result; - switch (std::get<0>(GetParam())) { + switch (std::get(GetParam())) { case DIRECTION::X: result = bout::derivatives::index::VDDX(velocity, input); break; @@ -475,7 +473,7 @@ INSTANTIATE_TEST_SUITE_P(Z, FluxDerivativesInterfaceTest, TEST_P(FluxDerivativesInterfaceTest, Sanity) { Field3D result; - switch (std::get<0>(GetParam())) { + switch (std::get(GetParam())) { case DIRECTION::X: result = bout::derivatives::index::FDDX(velocity, input); break; From 11564ed9042d9357711f48e112be038b0157012f Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 11:01:19 +0000 Subject: [PATCH 225/412] Use `std::invoke` rather than pointer-to-member-function syntax --- tests/unit/include/test_derivs.cxx | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/tests/unit/include/test_derivs.cxx b/tests/unit/include/test_derivs.cxx index e91339be24..a6b8e43ef0 100644 --- a/tests/unit/include/test_derivs.cxx +++ b/tests/unit/include/test_derivs.cxx @@ -102,11 +102,10 @@ class DerivativesTest mesh->createDefaultRegions(); + using std::invoke; // Make the input and expected output fields - // Weird `(i.*dir)()` syntax here in order to call the direction method - // C++17 makes this nicer with std::invoke input = makeField( - [&](Index& i) { return std::sin((i.*dir)() * box_length); }, mesh); + [&](Index& i) { return std::sin(invoke(dir, i) * box_length); }, mesh); // Make the velocity field velocity = makeField([&](Index& UNUSED(i)) { return 2.0; }, mesh); @@ -115,19 +114,20 @@ class DerivativesTest switch (std::get(GetParam())) { case DERIV::Standard: expected = makeField( - [&](Index& i) { return std::cos((i.*dir)() * box_length) * box_length; }, mesh); + [&](Index& i) { return std::cos(invoke(dir, i) * box_length) * box_length; }, + mesh); break; case DERIV::StandardSecond: expected = makeField( [&](Index& i) { - return -std::sin((i.*dir)() * box_length) * pow(box_length, 2); + return -std::sin(invoke(dir, i) * box_length) * pow(box_length, 2); }, mesh); break; case DERIV::StandardFourth: expected = makeField( [&](Index& i) { - return std::sin((i.*dir)() * box_length) * pow(box_length, 4); + return std::sin(invoke(dir, i) * box_length) * pow(box_length, 4); }, mesh); break; @@ -136,7 +136,9 @@ class DerivativesTest case DERIV::Upwind: case DERIV::Flux: expected = makeField( - [&](Index& i) { return 2.0 * std::cos((i.*dir)() * box_length) * box_length; }, + [&](Index& i) { + return 2.0 * std::cos(invoke(dir, i) * box_length) * box_length; + }, mesh); break; default: From aa8d5fe50d799a2bb872c87affef6db08e46d739 Mon Sep 17 00:00:00 2001 From: Giorgis Georgakoudis Date: Thu, 1 Feb 2024 06:22:27 -0800 Subject: [PATCH 226/412] Update CUDA standard to cxx17, add CI build test --- .github/workflows/tests.yml | 27 +++++++++++++++++++++++++++ cmake/SetupBOUTThirdParty.cmake | 5 +++-- 2 files changed, 30 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c449beb4ca..42965e75e8 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -240,3 +240,30 @@ jobs: shell: bash env: TRAVIS_BUILD_DIR: ${{ github.workspace }} + CUDA: + timeout-minutes: 60 + runs-on: ubuntu-latest + container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest + + steps: + - uses: actions/checkout@v4 + with: + submodules: true + - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04 + run: | + . /spack/share/spack/setup-env.sh + spack env activate -p /spack-env + git config --global --add safe.directory $GITHUB_WORKSPACE + rm -rf build + cmake -S $GITHUB_WORKSPACE -B build \ + -DCMAKE_C_COMPILER=gcc \ + -DCMAKE_CXX_COMPILER=g++ \ + -DBOUT_ENABLE_RAJA=on \ + -DBOUT_ENABLE_UMPIRE=on \ + -DBOUT_ENABLE_CUDA=on \ + -DCMAKE_CUDA_ARCHITECTURES=80 \ + -DCUDA_ARCH=compute_80,code=sm_80 \ + -DBOUT_ENABLE_WARNINGS=off \ + -DBOUT_USE_SYSTEM_FMT=on + cd build + make -j 4 diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index e1d6f00cb4..ef0fd438d4 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -19,9 +19,10 @@ if (BOUT_HAS_CUDA) set(BOUT_SOURCES_CXX ${BOUT_SOURCES}) list(FILTER BOUT_SOURCES_CXX INCLUDE REGEX ".*\.cxx") - set_source_files_properties(${BOUT_SOURCES_CXX} PROPERTIES LANGUAGE CUDA ) + # NOTE: CUDA inherits the CXX standard setting from the top-level + # compile features, set for the bout++ target. + set_source_files_properties(${BOUT_SOURCES_CXX} PROPERTIES LANGUAGE CUDA) find_package(CUDAToolkit) - set_target_properties(bout++ PROPERTIES CUDA_STANDARD 14) set_target_properties(bout++ PROPERTIES CUDA_SEPARABLE_COMPILATION ON) set_target_properties(bout++ PROPERTIES POSITION_INDEPENDENT_CODE ON) set_target_properties(bout++ PROPERTIES LINKER_LANGUAGE CUDA) From 71718850a2b1a74d47868484a5e988498f03c4f0 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 2 Feb 2024 19:29:20 -0800 Subject: [PATCH 227/412] Read local part of global 3D fields If the size of the array matches the global array, read the piece of the array that is used on the local processor. --- src/sys/options.cxx | 5 +++ src/sys/options/options_adios.cxx | 54 +++++++++++++++++++++---------- 2 files changed, 42 insertions(+), 17 deletions(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 14d9e47d91..ffe14a4f11 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -558,6 +558,11 @@ Field3D Options::as(const Field3D& similar_to) const { // If dimension sizes not the same, may be able // to select a region from it using Mesh e.g. if this // is from the input grid file. + const auto [tx, ty, tz] = tensor.shape(); + throw BoutException("Size mismatch for option {:s}: Tensor ({}, {}, {}) cannot be " + "converted to Field3D ({}, {}, {})", + full_name, tx, ty, tz, localmesh->LocalNx, localmesh->LocalNy, + localmesh->LocalNz); } throw BoutException(_("Value for option {:s} cannot be converted to a Field3D"), diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index e93a1fea94..d29e1a657c 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -42,6 +42,8 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& std::vector data; adios2::Variable variable = io.InquireVariable(name); + using bout::globals::mesh; + if (variable.ShapeID() == adios2::ShapeID::GlobalValue) { T value; reader.Get(variable, &value, adios2::Mode::Sync); @@ -93,6 +95,41 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& return Options(value); } case 3: { + if ((static_cast(dims[0]) == mesh->GlobalNx) + and (static_cast(dims[1]) == mesh->GlobalNy) + and (static_cast(dims[2]) == mesh->GlobalNz)) { + // Global array. Read just this processor's part of it + + Tensor value(mesh->LocalNx, mesh->LocalNy, mesh->LocalNz); + + // Offset of this processor's data into the global array + adios2::Dims start = {static_cast(mesh->MapGlobalX), + static_cast(mesh->MapGlobalY), + static_cast(mesh->MapGlobalZ)}; + + // The size of the mapped region + adios2::Dims count = {static_cast(mesh->MapCountX), + static_cast(mesh->MapCountY), + static_cast(mesh->MapCountZ)}; + + // Where the actual data starts in data pointer (to exclude ghost cells) + adios2::Dims memStart = {static_cast(mesh->MapLocalX), + static_cast(mesh->MapLocalY), + static_cast(mesh->MapLocalZ)}; + + // The actual size of data pointer in memory (including ghost cells) + adios2::Dims memCount = {static_cast(mesh->LocalNx), + static_cast(mesh->LocalNy), + static_cast(mesh->LocalNz)}; + + variableD.SetSelection({start, count}); + variableD.SetMemorySelection({memStart, memCount}); + BoutReal* data = value.begin(); + reader.Get(variableD, data, adios2::Mode::Sync); + return Options(value); + } + // Doesn't match global array size. + // Read the entire array, in case it can be handled later Tensor value(static_cast(dims[0]), static_cast(dims[1]), static_cast(dims[2])); BoutReal* data = value.begin(); @@ -289,11 +326,6 @@ void ADIOSPutVarVisitor::operator()(const Field2D& value) { static_cast(value.getNy())}; adios2::Variable var = stream.GetArrayVariable(varname, shape); - /* std::cout << "PutVar Field2D rank " << BoutComm::rank() << " var = " << varname - << " shape = " << shape[0] << "x" << shape[1] << " count = " << count[0] - << "x" << count[1] << " Nx*Ny = " << value.getNx() << "x" << value.getNy() - << " memStart = " << memStart[0] << "x" << memStart[1] - << " memCount = " << memCount[0] << "x" << memCount[1] << std::endl;*/ var.SetSelection({start, count}); var.SetMemorySelection({memStart, memCount}); stream.engine.Put(var, &value(0, 0)); @@ -331,13 +363,6 @@ void ADIOSPutVarVisitor::operator()(const Field3D& value) { static_cast(value.getNz())}; adios2::Variable var = stream.GetArrayVariable(varname, shape); - /*std::cout << "PutVar Field3D rank " << BoutComm::rank() << " var = " << varname - << " shape = " << shape[0] << "x" << shape[1] << "x" << shape[2] - << " count = " << count[0] << "x" << count[1] << "x" << count[2] - << " Nx*Ny = " << value.getNx() << "x" << value.getNy() << "x" - << value.getNz() << " memStart = " << memStart[0] << "x" << memStart[1] << "x" - << memStart[2] << " memCount = " << memCount[0] << "x" << memCount[1] << "x" - << memCount[2] << std::endl;*/ var.SetSelection({start, count}); var.SetMemorySelection({memStart, memCount}); stream.engine.Put(var, &value(0, 0, 0)); @@ -370,11 +395,6 @@ void ADIOSPutVarVisitor::operator()(const FieldPerp& value) { static_cast(value.getNz())}; adios2::Variable var = stream.GetArrayVariable(varname, shape); - /* std::cout << "PutVar FieldPerp rank " << BoutComm::rank() << " var = " << varname - << " shape = " << shape[0] << "x" << shape[1] << " count = " << count[0] - << "x" << count[1] << " Nx*Ny = " << value.getNx() << "x" << value.getNy() - << " memStart = " << memStart[0] << "x" << memStart[1] - << " memCount = " << memCount[0] << "x" << memCount[1] << std::endl; */ var.SetSelection({start, count}); var.SetMemorySelection({memStart, memCount}); stream.engine.Put(var, &value(0, 0)); From 006852a9582707b975bca8983e0dc2d13c355e83 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 2 Feb 2024 20:17:09 -0800 Subject: [PATCH 228/412] ADIOS: Read Field2D and FieldPerp fields Potentially ambiguous, as it uses the size of the global array to determine whether it is a Field2D or FieldPerp. --- src/sys/options/options_adios.cxx | 63 +++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index d29e1a657c..b313d7bc79 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -89,6 +89,69 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& return Options(value); } case 2: { + // This could be a Field2D (XY) or FieldPerp (XZ) + // Here we look for array sizes, but if Y and Z dimensions are the same size + // then it's ambiguous. This method also depends on the global Mesh object. + // Some possibilities: + // - Add an attribute to specify field type or dimension labels + // - Load all the data, and select a region when converting to a Field in Options + // - Add a lazy loading type to Options, and load data when needed + if ((static_cast(dims[0]) == mesh->GlobalNx) + and (static_cast(dims[1]) == mesh->GlobalNy)) { + // Probably a Field2D + + // Read just the local piece of the array + Matrix value(mesh->LocalNx, mesh->LocalNy); + + // Offset of this processor's data into the global array + adios2::Dims start = {static_cast(mesh->MapGlobalX), + static_cast(mesh->MapGlobalY)}; + + // The size of the mapped region + adios2::Dims count = {static_cast(mesh->MapCountX), + static_cast(mesh->MapCountY)}; + + // Where the actual data starts in data pointer (to exclude ghost cells) + adios2::Dims memStart = {static_cast(mesh->MapLocalX), + static_cast(mesh->MapLocalY)}; + + // The actual size of data pointer in memory (including ghost cells) + adios2::Dims memCount = {static_cast(mesh->LocalNx), + static_cast(mesh->LocalNy)}; + variableD.SetSelection({start, count}); + variableD.SetMemorySelection({memStart, memCount}); + BoutReal* data = value.begin(); + reader.Get(variableD, data, adios2::Mode::Sync); + return Options(value); + } + if ((static_cast(dims[0]) == mesh->GlobalNx) + and (static_cast(dims[2]) == mesh->GlobalNz)) { + // Probably a FieldPerp + + // Read just the local piece of the array + Matrix value(mesh->LocalNx, mesh->LocalNz); + + // Offset of this processor's data into the global array + adios2::Dims start = {static_cast(mesh->MapGlobalX), + static_cast(mesh->MapGlobalZ)}; + + // The size of the mapped region + adios2::Dims count = {static_cast(mesh->MapCountX), + static_cast(mesh->MapCountZ)}; + + // Where the actual data starts in data pointer (to exclude ghost cells) + adios2::Dims memStart = {static_cast(mesh->MapLocalX), + static_cast(mesh->MapLocalZ)}; + + // The actual size of data pointer in memory (including ghost cells) + adios2::Dims memCount = {static_cast(mesh->LocalNx), + static_cast(mesh->LocalNz)}; + variableD.SetSelection({start, count}); + variableD.SetMemorySelection({memStart, memCount}); + BoutReal* data = value.begin(); + reader.Get(variableD, data, adios2::Mode::Sync); + return Options(value); + } Matrix value(static_cast(dims[0]), static_cast(dims[1])); BoutReal* data = value.begin(); reader.Get(variableD, data, adios2::Mode::Sync); From aece5f4e6733d7374fee20cdb3f4d8a924280f66 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 6 Feb 2024 19:07:14 -0800 Subject: [PATCH 229/412] Options: Delete copy constructor and copy assignment Accidentally copying Options leads to unexpected bugs where changes (e.g documentation) changes a copy rather than the original. Usually what is intended is a reference, but the author omits an `&`. Copy assignment is also ambiguous: Is it the value, the attributes, or the children that should be copied? Now if a copy is really intended, there is a `.copy()` method (thanks Rust!) --- include/bout/options.hxx | 57 +++++++++++++++++++++++++++------- src/mesh/data/gridfromfile.cxx | 14 ++++----- src/sys/options.cxx | 56 ++++++++++----------------------- 3 files changed, 68 insertions(+), 59 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index c45149cbdd..b0eded7e29 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -12,9 +12,9 @@ * options and allows access to all sub-sections * ************************************************************************** -* Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu +* Copyright 2010-2024 BOUT++ contributors * -* Contact: Ben Dudson, bd512@york.ac.uk +* Contact: Ben Dudson, dudson2@llnl.gov * * This file is part of BOUT++. * @@ -36,8 +36,8 @@ class Options; #pragma once -#ifndef __OPTIONS_H__ -#define __OPTIONS_H__ +#ifndef OPTIONS_H +#define OPTIONS_H #include "bout/bout_types.hxx" #include "bout/field2d.hxx" @@ -155,6 +155,30 @@ class Options; * This is used to represent all the options passed to BOUT++ either in a file or on the * command line. * + * Copying options + * --------------- + * + * The copy constructor and copy assignment operator are deleted, so + * this is a compile-time error: + * + * Options options2 = options1["value"]; + * + * This is because it's ambiguous what is meant, and because accidental copies + * were a frequent source of hard-to-understand bugs. Usually a reference is + * intended, rather than a copy: + * + * Options& ref = options1["value"]; + * + * so that changes to `ref` or its children are reflected in `options1`. + * If the intent is to copy the value of the option, then just copy that: + * + * option2.value = options1["value"].value; + * + * If a full deep copy of the option, its attributes and children + * (recursively) is really desired, then use the `copy()` method: + * + * Options options2 = options1["value"].copy(); + * */ class Options { public: @@ -181,16 +205,25 @@ public: /// Example: { {"key1", 42}, {"key2", field} } Options(std::initializer_list> values); - Options(const Options& other); + /// Options must be explicitly copied + /// + /// Option option2 = option1.copy(); + /// + Options(const Options& other) = delete; - /// Copy assignment + /// Copy assignment must be explicit + /// + /// Option option2 = option1.copy(); /// - /// This replaces the value, attributes and all children + /// Note that the value can be copied using: /// - /// Note that if only the value is desired, then that can be copied using - /// the value member directly e.g. option2.value = option1.value; + /// option2.value = option1.value; /// - Options& operator=(const Options& other); + Options& operator=(const Options& other) = delete; + + /// Make a deep copy of this Options, + /// recursively copying children. + Options copy() const; Options(Options&& other) noexcept; Options& operator=(Options&& other) noexcept; @@ -539,7 +572,7 @@ public: if (is_section) { // Option not found - *this = def; + this->value = def.value; output_info << _("\tOption ") << full_name << " = " << def.full_name << " (" << DEFAULT_SOURCE << ")\n"; @@ -1013,4 +1046,4 @@ struct fmt::formatter : public bout::details::OptionsFormatterBase {}; // NOLINTEND(cppcoreguidelines-macro-usage) -#endif // __OPTIONS_H__ +#endif // OPTIONS_H diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index 41147ba76c..9e2e9e72ca 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -172,7 +172,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, return false; } - Options option = data[name]; + Options& option = data[name]; // Global (x, y, z) dimensions of field const std::vector size = bout::utils::visit(GetDimensions{}, option.value); @@ -499,8 +499,7 @@ bool GridFile::get(Mesh* UNUSED(m), std::vector& var, const std::strin bool GridFile::hasXBoundaryGuards(Mesh* m) { // Global (x,y) dimensions of some field // a grid file should always contain "dx" - Options option = data["dx"]; - const std::vector size = bout::utils::visit(GetDimensions{}, option.value); + const std::vector size = bout::utils::visit(GetDimensions{}, data["dx"].value); if (size.empty()) { // handle case where "dx" is not present - non-standard grid file @@ -535,8 +534,7 @@ bool GridFile::readgrid_3dvar_fft(Mesh* m, const std::string& name, int yread, i } /// Check the size of the data - Options option = data[name]; - const std::vector size = bout::utils::visit(GetDimensions{}, option.value); + const std::vector size = bout::utils::visit(GetDimensions{}, data[name].value); if (size.size() != 3) { output_warn.write("\tWARNING: Number of dimensions of {:s} incorrect\n", name); @@ -622,7 +620,7 @@ bool GridFile::readgrid_3dvar_real(const std::string& name, int yread, int ydest return false; } - Options option = data[name]; + Options& option = data[name]; /// Check the size of the data const std::vector size = bout::utils::visit(GetDimensions{}, option.value); @@ -665,7 +663,7 @@ bool GridFile::readgrid_perpvar_fft(Mesh* m, const std::string& name, int xread, } /// Check the size of the data - Options option = data[name]; + Options& option = data[name]; const std::vector size = bout::utils::visit(GetDimensions{}, option.value); if (size.size() != 2) { @@ -748,7 +746,7 @@ bool GridFile::readgrid_perpvar_real(const std::string& name, int xread, int xde } /// Check the size of the data - Options option = data[name]; + Options& option = data[name]; const std::vector size = bout::utils::visit(GetDimensions{}, option.value); if (size.size() != 2) { diff --git a/src/sys/options.cxx b/src/sys/options.cxx index ffe14a4f11..6dc7979b6c 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -46,17 +46,23 @@ Options& Options::root() { void Options::cleanup() { root() = Options{}; } -Options::Options(const Options& other) - : value(other.value), attributes(other.attributes), - parent_instance(other.parent_instance), full_name(other.full_name), - is_section(other.is_section), children(other.children), - value_used(other.value_used) { +Options Options::copy() const { + Options result; - // Ensure that this is the parent of all children, - // otherwise will point to the original Options instance - for (auto& child : children) { - child.second.parent_instance = this; + result.value = value; + result.attributes = attributes; + result.parent_instance = parent_instance; + result.full_name = full_name; + result.is_section = is_section; + result.value_used = value_used; + + // Recursively copy children + for (const auto& child : children) { + // Note: The child's parent_instance pointer will be updated when + // result is moved. + result.children.emplace(child.first, child.second.copy()); } + return result; } Options::Options(Options&& other) noexcept @@ -103,7 +109,7 @@ Options::Options(std::initializer_list> values) }; for (const auto& value : values) { - (*this)[value.first] = value.second; + (*this)[value.first] = value.second.copy(); // value.second was constructed from the "bare" `Options(T)` so // doesn't have `full_name` set. This clobbers // `(*this)[value.first].full_name` in the copy constructor, so we @@ -230,34 +236,6 @@ Options::fuzzyFind(const std::string& name, std::string::size_type distance) con return matches; } -Options& Options::operator=(const Options& other) { - if (this == &other) { - return *this; - } - - // Note: Here can't do copy-and-swap because pointers to parents are stored - - value = other.value; - - // Assigning the attributes. - // The simple assignment operator fails to compile with Apple Clang 12 - // attributes = other.attributes; - attributes.clear(); - attributes.insert(other.attributes.begin(), other.attributes.end()); - - full_name = other.full_name; - is_section = other.is_section; - children = other.children; - value_used = other.value_used; - - // Ensure that this is the parent of all children, - // otherwise will point to the original Options instance - for (auto& child : children) { - child.second.parent_instance = this; - } - return *this; -} - Options& Options::operator=(Options&& other) noexcept { if (this == &other) { return *this; @@ -833,7 +811,7 @@ Options Options::getUnused(const std::vector& exclude_sources) cons // Copy this object, and then we're going to chuck out everything // that has been used. This turns out to be easier than copying just // the unused options into an empty instance - Options unused = *this; + Options unused = this->copy(); if (unused.isValue()) { // If this is from an excluded source, count it as being used From 377836a57ba2a0a391eb933cb1e91de4a73eac20 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 6 Feb 2024 20:19:39 -0800 Subject: [PATCH 230/412] Arkode solver: Remove accidental Options copy Should be a reference. Caught because copy constructor is deleted. --- src/solver/impls/arkode/arkode.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 9691f2f7da..aabe2ae050 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -357,7 +357,7 @@ int ArkodeSolver::init() { f2dtols.reserve(f2d.size()); std::transform(begin(f2d), end(f2d), std::back_inserter(f2dtols), [abstol = abstol](const VarStr& f2) { - auto f2_options = Options::root()[f2.name]; + auto& f2_options = Options::root()[f2.name]; const auto wrong_name = f2_options.isSet("abstol"); if (wrong_name) { output_warn << "WARNING: Option 'abstol' for field " << f2.name From 08a764f661c9fc5ad407b2a72e4f104d4f106c2f Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 6 Feb 2024 21:06:40 -0800 Subject: [PATCH 231/412] CVode solver: Options accidental copy --- src/solver/impls/cvode/cvode.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index f35ae680d5..3e53f783e0 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -290,7 +290,7 @@ int CvodeSolver::init() { f2dtols.reserve(f2d.size()); std::transform(begin(f2d), end(f2d), std::back_inserter(f2dtols), [this](const VarStr& f2) { - auto f2_options = Options::root()[f2.name]; + auto& f2_options = Options::root()[f2.name]; const auto wrong_name = f2_options.isSet("abstol"); if (wrong_name) { output_warn << "WARNING: Option 'abstol' for field " << f2.name From d70c605d732d9c6aca32085a726f26cc482ce642 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 6 Feb 2024 21:20:33 -0800 Subject: [PATCH 232/412] Unit test FakeGridDataSource: explicit Options copy --- tests/unit/test_extras.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 845ea4f255..6f78e99fd3 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -332,7 +332,7 @@ class FakeGridDataSource : public GridDataSource { public: FakeGridDataSource() {} /// Constructor setting values which can be fetched from this source - FakeGridDataSource(Options& values) : values(values) {} + FakeGridDataSource(const Options& values) : values(values.copy()) {} /// Take an rvalue (e.g. initializer list), convert to lvalue and delegate constructor FakeGridDataSource(Options&& values) : FakeGridDataSource(values) {} From fbc64c6312fc06084e16a15a61ea6efe98ebaf43 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 7 Feb 2024 13:42:10 +0000 Subject: [PATCH 233/412] Apply black changes --- tests/MMS/diffusion2/runtest | 2 +- tools/tokamak_grids/all/grid2bout.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest index d915018d8d..6039c6faa6 100755 --- a/tests/MMS/diffusion2/runtest +++ b/tests/MMS/diffusion2/runtest @@ -27,7 +27,7 @@ build_and_log("MMS diffusion test") inputs = [ ("X", ["mesh:nx"]), ("Y", ["mesh:ny"]), - ("Z", ["MZ"]) # , + ("Z", ["MZ"]), # , # ("XYZ", ["mesh:nx", "mesh:ny", "MZ"]) ] diff --git a/tools/tokamak_grids/all/grid2bout.py b/tools/tokamak_grids/all/grid2bout.py index da62a37aeb..6520e8f116 100644 --- a/tools/tokamak_grids/all/grid2bout.py +++ b/tools/tokamak_grids/all/grid2bout.py @@ -3,6 +3,7 @@ """ + from __future__ import print_function from numpy import max From e3a864f156e0ce9eda35549216b69ba5f0b01df3 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 7 Feb 2024 13:43:53 +0000 Subject: [PATCH 234/412] Apply black changes --- tests/MMS/diffusion2/runtest | 2 +- tools/tokamak_grids/all/grid2bout.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest index d915018d8d..6039c6faa6 100755 --- a/tests/MMS/diffusion2/runtest +++ b/tests/MMS/diffusion2/runtest @@ -27,7 +27,7 @@ build_and_log("MMS diffusion test") inputs = [ ("X", ["mesh:nx"]), ("Y", ["mesh:ny"]), - ("Z", ["MZ"]) # , + ("Z", ["MZ"]), # , # ("XYZ", ["mesh:nx", "mesh:ny", "MZ"]) ] diff --git a/tools/tokamak_grids/all/grid2bout.py b/tools/tokamak_grids/all/grid2bout.py index da62a37aeb..6520e8f116 100644 --- a/tools/tokamak_grids/all/grid2bout.py +++ b/tools/tokamak_grids/all/grid2bout.py @@ -3,6 +3,7 @@ """ + from __future__ import print_function from numpy import max From 182c21b4a2d02fe9b58cc6088f3cf0a3ae3291ee Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 7 Feb 2024 21:14:47 -0800 Subject: [PATCH 235/412] Options: Add CopyableOptions for initializer_list construction C++ initializer_lists don't play nicely with uncopyable types https://blog.knatten.org/2018/10/05/why-you-cant-list-initialize-containers-of-non-copyable-types/ List initialization of Options now constructs nested initializer lists of `Options::CopyableOptions`, then walks this tree to move data into Options. This simplifies some of the logic, since we're now traversing the tree of Options starting from the root. --- include/bout/options.hxx | 48 ++++++++++++++++++++++++++++++++----- include/bout/options_io.hxx | 2 +- src/sys/options.cxx | 37 ---------------------------- 3 files changed, 43 insertions(+), 44 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index b0eded7e29..5edc75e910 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -199,11 +199,52 @@ public: assign(value); } + /// The type used to store values + using ValueType = + bout::utils::variant, Matrix, Tensor>; + + /// A tree representation with leaves containing ValueType. + /// Used to construct Options from initializer lists. + /// + /// Note: Either there are children OR value is assigned + struct CopyableOptions { + template + CopyableOptions(T value) : value(std::move(value)) {} + + CopyableOptions(std::initializer_list> children) : children(std::move(children)) {} + ValueType value; + std::initializer_list> children; + }; + + /// Type of initializer_list that can be used to create Options + /// This is a workaround for initializer_lists not being movable. + using InitializerList = std::initializer_list>; + /// Construct with a nested initializer list /// This allows Options trees to be constructed, using a mix of types. /// /// Example: { {"key1", 42}, {"key2", field} } - Options(std::initializer_list> values); + /// + /// Note: Options doesn't have a copy constructor, and initializer lists + /// don't play nicely with uncopyable types. Instead, we create + /// a tree of CopyableOptions and then move. + Options(InitializerList values, + Options* parent_instance = nullptr, const std::string& full_name = "") + : parent_instance(parent_instance), full_name(std::move(full_name)), is_section(true) { + for (const auto& value_it : values) { + std::string child_name = fmt::format("{}:{}", full_name, value_it.first); + if (value_it.second.children.size() != 0) { + // A section, so construct with an initializer_list + children.emplace(value_it.first, + Options(std::move(value_it.second.children), this, std::move(child_name))); + } else { + // A value + auto pair_it = children.emplace(value_it.first, Options(this, std::move(child_name))); + pair_it.first->second.value = std::move(value_it.second.value); + } + } + } /// Options must be explicitly copied /// @@ -236,11 +277,6 @@ public: /// Free all memory static void cleanup(); - /// The type used to store values - using ValueType = - bout::utils::variant, Matrix, Tensor>; - /// The type used to store attributes /// Extends the variant class so that cast operator can be implemented /// and assignment operator overloaded diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 65c3cb7dd1..199722d32d 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -98,7 +98,7 @@ public: /// {"append", false} /// }); static std::unique_ptr - create(std::initializer_list> config_list) { + create(Options::InitializerList config_list) { Options config(config_list); // Construct an Options to pass by reference return create(config); } diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 6dc7979b6c..8475835468 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -21,7 +21,6 @@ #include #include -#include #include #include #include @@ -83,42 +82,6 @@ Options::Options(const char* value) { assign(value); } -Options::Options(std::initializer_list> values) { - // Yes, this looks bad, but bear with me... The _only_ way to - // construct a nested initializer_list is inside-out, from the - // bottom of the tree structure. Unfortunately, this is very much - // not how you would want to construct the tree of options, as we - // don't have the parent section's name as we construct each - // child. Therefore, when we _do_ construct the parent, we'll need - // to recursively step down the tree, prepending the parent's name - // to each child. Rather than have a private member to do that, we - // use a lambda. And to make that lambda recursive, we need to have - // a nested lambda. - auto append_section_name = [](auto& children, const std::string& section_name) { - auto append_impl = [](auto& children, const std::string& section_name, - auto& append_ref) mutable -> void { - for (auto& child : children) { - child.second.full_name = - fmt::format("{}:{}", section_name, child.second.full_name); - if (child.second.is_section) { - append_ref(child.second.children, section_name, append_ref); - } - } - }; - append_impl(children, section_name, append_impl); - }; - - for (const auto& value : values) { - (*this)[value.first] = value.second.copy(); - // value.second was constructed from the "bare" `Options(T)` so - // doesn't have `full_name` set. This clobbers - // `(*this)[value.first].full_name` in the copy constructor, so we - // need to explicitly set it again - (*this)[value.first].full_name = value.first; - append_section_name((*this)[value.first].children, value.first); - } -} - Options& Options::operator[](const std::string& name) { TRACE("Options::operator[]"); From 058faeef6c80c04c4596a88a258d205298f251d7 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 7 Feb 2024 22:47:08 -0800 Subject: [PATCH 236/412] Unit tests compiling Tests that use copy constructor changed to test copy method. Unit tests compile but failing. Probably initializer_list construction issue. --- tests/unit/src/test_bout++.cxx | 2 +- tests/unit/sys/test_options.cxx | 26 +++++++++++++------------- tests/unit/sys/test_optionsreader.cxx | 8 ++++---- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/tests/unit/src/test_bout++.cxx b/tests/unit/src/test_bout++.cxx index e5d5419dfc..6f22ad76aa 100644 --- a/tests/unit/src/test_bout++.cxx +++ b/tests/unit/src/test_bout++.cxx @@ -378,7 +378,7 @@ TEST(BoutInitialiseFunctions, SetRunStartInfo) { bout::experimental::setRunStartInfo(options); - auto run_section = options["run"]; + auto& run_section = options["run"]; ASSERT_TRUE(run_section.isSection()); EXPECT_TRUE(run_section.isSet("version")); diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx index 1f0ae92ed2..dbb687880d 100644 --- a/tests/unit/sys/test_options.cxx +++ b/tests/unit/sys/test_options.cxx @@ -602,23 +602,23 @@ TEST_F(OptionsTest, OptionsMacroConstReference) { EXPECT_EQ(val, 42); } -/// Copy constructor copies value +/// Copy method copies value TEST_F(OptionsTest, CopyOption) { Options option1; option1 = 42; - Options option2(option1); + Options option2(option1.copy()); EXPECT_EQ(option2.as(), 42); } -/// Copy constructor makes independent copy +/// Copy method makes independent copy TEST_F(OptionsTest, CopyOptionDistinct) { Options option1; option1 = 42; - Options option2(option1); + Options option2(option1.copy()); option1.force(23); @@ -632,7 +632,7 @@ TEST_F(OptionsTest, CopySection) { option1["key"] = 42; // option1 now a section - Options option2(option1); + Options option2(option1.copy()); EXPECT_EQ(option2["key"].as(), 42); } @@ -643,7 +643,7 @@ TEST_F(OptionsTest, CopySectionParent) { option1["key"] = 42; - Options option2(option1); + Options option2(option1.copy()); EXPECT_TRUE(&option2["key"].parent() == &option2); } @@ -653,7 +653,7 @@ TEST_F(OptionsTest, AssignOption) { option1 = 42; - option2 = option1; + option2 = option1.copy(); EXPECT_EQ(option2.as(), 42); } @@ -663,7 +663,7 @@ TEST_F(OptionsTest, AssignSection) { option1["key"] = 42; - option2 = option1; + option2 = option1.copy(); EXPECT_EQ(option2["key"].as(), 42); EXPECT_TRUE(option2["key"].isValue()); @@ -675,7 +675,7 @@ TEST_F(OptionsTest, AssignSectionReplace) { option1["key"] = 42; option2["key"] = 23; - option2 = option1; + option2 = option1.copy(); EXPECT_EQ(option2["key"].as(), 42); } @@ -685,7 +685,7 @@ TEST_F(OptionsTest, AssignSectionParent) { option1["key"] = 42; - option2 = option1; + option2 = option1.copy(); EXPECT_TRUE(&option2["key"].parent() == &option2); } @@ -695,7 +695,7 @@ TEST_F(OptionsTest, AssignSubSection) { option1["key1"] = 42; - option2["key2"] = option1; + option2["key2"] = option1.copy(); EXPECT_EQ(option2["key2"]["key1"].as(), 42); } @@ -705,7 +705,7 @@ TEST_F(OptionsTest, AssignSubSectionParent) { option1["key1"] = 42; - option2["key2"] = option1; + option2["key2"] = option1.copy(); EXPECT_EQ(&option2["key2"].parent(), &option2); EXPECT_EQ(&option2["key2"]["key1"].parent(), &option2["key2"]); @@ -1042,7 +1042,7 @@ TEST_F(OptionsTest, DocStringNotCopied) { Options option; option = 32; - Options option2 = option; + Options option2 = option.copy(); int value = option2.doc("test value"); diff --git a/tests/unit/sys/test_optionsreader.cxx b/tests/unit/sys/test_optionsreader.cxx index 3bb71bb510..c5f8d20dcf 100644 --- a/tests/unit/sys/test_optionsreader.cxx +++ b/tests/unit/sys/test_optionsreader.cxx @@ -352,7 +352,7 @@ test6 = h2`+`:on`e-`more # Escape sequences in the middle OptionsReader reader; reader.read(Options::getRoot(), filename); - auto options = Options::root()["tests"]; + auto& options = Options::root()["tests"]; EXPECT_EQ(options["test1"].as(), 3); EXPECT_EQ(options["test2"].as(), 15); @@ -398,7 +398,7 @@ twopi = 2 * π # Unicode symbol defined for pi OptionsReader reader; reader.read(Options::getRoot(), filename); - auto options = Options::root()["tests"]; + auto& options = Options::root()["tests"]; EXPECT_EQ(options["結果"].as(), 8); EXPECT_DOUBLE_EQ(options["value"].as(), 1.3 * (1 + 3)); @@ -425,7 +425,7 @@ value = [a = 1, OptionsReader reader; reader.read(Options::getRoot(), filename.c_str()); - auto options = Options::root(); + auto& options = Options::root(); EXPECT_EQ(options["result"].as(), 6); EXPECT_EQ(options["value"].as(), 5); @@ -452,7 +452,7 @@ value = [a = 1, OptionsReader reader; reader.read(Options::getRoot(), filename.c_str()); - auto options = Options::root(); + auto& options = Options::root(); EXPECT_EQ(options["result"].as(), 6); EXPECT_EQ(options["value"].as(), 5); From e2a5473480197a5002aa903ce8b71e41f18caf89 Mon Sep 17 00:00:00 2001 From: bendudson Date: Thu, 8 Feb 2024 06:49:14 +0000 Subject: [PATCH 237/412] Apply clang-format changes --- include/bout/options.hxx | 18 +++++++++++------- include/bout/options_io.hxx | 3 +-- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 5edc75e910..94cfc68116 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -212,7 +212,9 @@ public: template CopyableOptions(T value) : value(std::move(value)) {} - CopyableOptions(std::initializer_list> children) : children(std::move(children)) {} + CopyableOptions( + std::initializer_list> children) + : children(std::move(children)) {} ValueType value; std::initializer_list> children; }; @@ -229,18 +231,20 @@ public: /// Note: Options doesn't have a copy constructor, and initializer lists /// don't play nicely with uncopyable types. Instead, we create /// a tree of CopyableOptions and then move. - Options(InitializerList values, - Options* parent_instance = nullptr, const std::string& full_name = "") - : parent_instance(parent_instance), full_name(std::move(full_name)), is_section(true) { + Options(InitializerList values, Options* parent_instance = nullptr, + const std::string& full_name = "") + : parent_instance(parent_instance), full_name(std::move(full_name)), + is_section(true) { for (const auto& value_it : values) { std::string child_name = fmt::format("{}:{}", full_name, value_it.first); if (value_it.second.children.size() != 0) { // A section, so construct with an initializer_list - children.emplace(value_it.first, - Options(std::move(value_it.second.children), this, std::move(child_name))); + children.emplace(value_it.first, Options(std::move(value_it.second.children), + this, std::move(child_name))); } else { // A value - auto pair_it = children.emplace(value_it.first, Options(this, std::move(child_name))); + auto pair_it = + children.emplace(value_it.first, Options(this, std::move(child_name))); pair_it.first->second.value = std::move(value_it.second.value); } } diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 199722d32d..4c70159514 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -97,8 +97,7 @@ public: /// {"type", "netcdf"}, /// {"append", false} /// }); - static std::unique_ptr - create(Options::InitializerList config_list) { + static std::unique_ptr create(Options::InitializerList config_list) { Options config(config_list); // Construct an Options to pass by reference return create(config); } From 83d51bf26d588bd2d158de53aebe0c2b41883652 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 8 Feb 2024 10:43:57 -0800 Subject: [PATCH 238/412] Options: Fix initialization_list construction When setting a value, the `is_section` member should be `false`, and the "source" attribute must be set. --- include/bout/options.hxx | 24 ++++-------------------- src/sys/options.cxx | 27 +++++++++++++++++++++++---- 2 files changed, 27 insertions(+), 24 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 94cfc68116..7330afdbcb 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -214,7 +214,7 @@ public: CopyableOptions( std::initializer_list> children) - : children(std::move(children)) {} + : children(children) {} ValueType value; std::initializer_list> children; }; @@ -232,23 +232,7 @@ public: /// don't play nicely with uncopyable types. Instead, we create /// a tree of CopyableOptions and then move. Options(InitializerList values, Options* parent_instance = nullptr, - const std::string& full_name = "") - : parent_instance(parent_instance), full_name(std::move(full_name)), - is_section(true) { - for (const auto& value_it : values) { - std::string child_name = fmt::format("{}:{}", full_name, value_it.first); - if (value_it.second.children.size() != 0) { - // A section, so construct with an initializer_list - children.emplace(value_it.first, Options(std::move(value_it.second.children), - this, std::move(child_name))); - } else { - // A value - auto pair_it = - children.emplace(value_it.first, Options(this, std::move(child_name))); - pair_it.first->second.value = std::move(value_it.second.value); - } - } - } + std::string section_name = ""); /// Options must be explicitly copied /// @@ -611,8 +595,8 @@ public: ASSERT0(def.isValue()); if (is_section) { - // Option not found - this->value = def.value; + // Option not found. Copy the value from the default. + this->_set_no_check(def.value, DEFAULT_SOURCE); output_info << _("\tOption ") << full_name << " = " << def.full_name << " (" << DEFAULT_SOURCE << ")\n"; diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 8475835468..8618667035 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -56,10 +56,10 @@ Options Options::copy() const { result.value_used = value_used; // Recursively copy children - for (const auto& child : children) { - // Note: The child's parent_instance pointer will be updated when - // result is moved. - result.children.emplace(child.first, child.second.copy()); + for (const auto& child_it : children) { + auto pair_it = result.children.emplace(child_it.first, child_it.second.copy()); + Options& child = pair_it.first->second; + child.parent_instance = &result; } return result; } @@ -82,6 +82,25 @@ Options::Options(const char* value) { assign(value); } +Options::Options(InitializerList values, Options* parent_instance, std::string section_name) + : parent_instance(parent_instance), full_name(std::move(section_name)), + is_section(true) { + for (const auto& value_it : values) { + std::string child_name = full_name.empty() ? value_it.first : fmt::format("{}:{}", full_name, value_it.first); + if (value_it.second.children.size() != 0) { + // A section, so construct with an initializer_list + children.emplace(value_it.first, Options(value_it.second.children, + this, std::move(child_name))); + } else { + // A value + auto pair_it = + children.emplace(value_it.first, Options(this, std::move(child_name))); + Options& child = pair_it.first->second; + child._set_no_check(value_it.second.value, ""); + } + } +} + Options& Options::operator[](const std::string& name) { TRACE("Options::operator[]"); From 8a95feca54e7baf31d4a1936ac2d565032d70c17 Mon Sep 17 00:00:00 2001 From: bendudson Date: Thu, 8 Feb 2024 18:45:23 +0000 Subject: [PATCH 239/412] Apply clang-format changes --- src/sys/options.cxx | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 8618667035..49a81cfa88 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -82,19 +82,22 @@ Options::Options(const char* value) { assign(value); } -Options::Options(InitializerList values, Options* parent_instance, std::string section_name) - : parent_instance(parent_instance), full_name(std::move(section_name)), - is_section(true) { +Options::Options(InitializerList values, Options* parent_instance, + std::string section_name) + : parent_instance(parent_instance), full_name(std::move(section_name)), + is_section(true) { for (const auto& value_it : values) { - std::string child_name = full_name.empty() ? value_it.first : fmt::format("{}:{}", full_name, value_it.first); + std::string child_name = full_name.empty() + ? value_it.first + : fmt::format("{}:{}", full_name, value_it.first); if (value_it.second.children.size() != 0) { // A section, so construct with an initializer_list - children.emplace(value_it.first, Options(value_it.second.children, - this, std::move(child_name))); + children.emplace(value_it.first, + Options(value_it.second.children, this, std::move(child_name))); } else { // A value auto pair_it = - children.emplace(value_it.first, Options(this, std::move(child_name))); + children.emplace(value_it.first, Options(this, std::move(child_name))); Options& child = pair_it.first->second; child._set_no_check(value_it.second.value, ""); } From de2b29383a871002c2bb0c993dcc15b5cbea57de Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 14:49:30 +0000 Subject: [PATCH 240/412] Tests: Replace use of `std::tmpnam` This generates link-time warning about it being dangerous. Replaced instead with wrapper around `std::filesystem::temp_directory_path` --- tests/unit/sys/test_options_netcdf.cxx | 10 +++---- tests/unit/sys/test_optionsreader.cxx | 31 +++++++++---------- tests/unit/sys/test_output.cxx | 16 +++++----- tests/unit/test_tmpfiles.hxx | 41 ++++++++++++++++++++++++++ 4 files changed, 66 insertions(+), 32 deletions(-) create mode 100644 tests/unit/test_tmpfiles.hxx diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx index 5869cf4932..38c80ca58c 100644 --- a/tests/unit/sys/test_options_netcdf.cxx +++ b/tests/unit/sys/test_options_netcdf.cxx @@ -7,13 +7,14 @@ #include "gtest/gtest.h" #include "test_extras.hxx" +#include "test_tmpfiles.hxx" #include "bout/field3d.hxx" #include "bout/mesh.hxx" #include "bout/options_io.hxx" using bout::OptionsIO; -#include +#include /// Global mesh namespace bout { @@ -25,11 +26,8 @@ extern Mesh* mesh; // Reuse the "standard" fixture for FakeMesh class OptionsNetCDFTest : public FakeMeshFixture { public: - OptionsNetCDFTest() : FakeMeshFixture() {} - ~OptionsNetCDFTest() override { std::remove(filename.c_str()); } - // A temporary filename - std::string filename{std::tmpnam(nullptr)}; + bout::testing::TempFile filename; WithQuietOutput quiet{output_info}; }; @@ -265,7 +263,7 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) { options["thing2"] = 3.0; options["thing2"].attributes["time_dimension"] = "t"; - OptionsIO::create({{"type", "netcdf"}, {"file", filename}, {"append", true}}) + OptionsIO::create({{"type", "netcdf"}, {"file", filename.string()}, {"append", true}}) ->write(options); } diff --git a/tests/unit/sys/test_optionsreader.cxx b/tests/unit/sys/test_optionsreader.cxx index 3bb71bb510..74283a7c42 100644 --- a/tests/unit/sys/test_optionsreader.cxx +++ b/tests/unit/sys/test_optionsreader.cxx @@ -1,4 +1,5 @@ #include "test_extras.hxx" +#include "test_tmpfiles.hxx" #include "bout/optionsreader.hxx" #include "gtest/gtest.h" @@ -6,7 +7,6 @@ #include "bout/output.hxx" #include "bout/utils.hxx" -#include #include #include #include @@ -28,8 +28,6 @@ class OptionsReaderTest : public ::testing::Test { // Make sure options singleton is clean Options::cleanup(); - - std::remove(filename.c_str()); } // Write cout to buffer instead of stdout @@ -39,7 +37,7 @@ class OptionsReaderTest : public ::testing::Test { WithQuietOutput quiet{output_info}; // A temporary filename - std::string filename{std::tmpnam(nullptr)}; + bout::testing::TempFile filename; }; TEST_F(OptionsReaderTest, BadFilename) { @@ -196,7 +194,7 @@ bool_key = false OptionsReader reader; Options* options = Options::getRoot(); - reader.read(options, filename); + reader.read(options, filename.string()); ASSERT_TRUE(options->isSet("flag")); @@ -236,7 +234,7 @@ bool_key = false TEST_F(OptionsReaderTest, ReadBadFile) { OptionsReader reader; Options* options = Options::getRoot(); - EXPECT_THROW(reader.read(options, filename), BoutException); + EXPECT_THROW(reader.read(options, filename.string()), BoutException); } TEST_F(OptionsReaderTest, ReadBadFileSectionIncomplete) { @@ -251,7 +249,7 @@ int_key = 34 OptionsReader reader; Options* options = Options::getRoot(); - EXPECT_THROW(reader.read(options, filename), BoutException); + EXPECT_THROW(reader.read(options, filename.string()), BoutException); }; TEST_F(OptionsReaderTest, ReadBadFileSectionEmptyName) { @@ -266,7 +264,7 @@ int_key = 34 OptionsReader reader; Options* options = Options::getRoot(); - EXPECT_THROW(reader.read(options, filename), BoutException); + EXPECT_THROW(reader.read(options, filename.string()), BoutException); }; TEST_F(OptionsReaderTest, WriteFile) { @@ -280,7 +278,7 @@ TEST_F(OptionsReaderTest, WriteFile) { Options* subsection2 = section1->getSection("subsection2"); subsection2->set("string_key", "BOUT++", "test"); - reader.write(options, filename); + reader.write(options, filename.string()); std::ifstream test_file(filename); std::stringstream test_buffer; @@ -297,7 +295,8 @@ TEST_F(OptionsReaderTest, WriteFile) { } TEST_F(OptionsReaderTest, WriteBadFile) { - std::string filename1 = filename + std::tmpnam(nullptr); + std::string file_in_nonexistent_dir = + bout::testing::test_directory() / "dir_that_doesnt_exist/some_filename"; OptionsReader reader; Options* options = Options::getRoot(); @@ -305,9 +304,7 @@ TEST_F(OptionsReaderTest, WriteBadFile) { Options* section1 = options->getSection("section1"); section1->set("int_key", 17, "test"); - EXPECT_THROW(reader.write(options, filename1), BoutException); - - std::remove(filename1.c_str()); + EXPECT_THROW(reader.write(options, file_in_nonexistent_dir), BoutException); } TEST_F(OptionsReaderTest, ReadEmptyString) { @@ -322,7 +319,7 @@ value = Options opt; OptionsReader reader; - reader.read(&opt, filename); + reader.read(&opt, filename.string()); std::string val = opt["value"]; EXPECT_TRUE(val.empty()); @@ -350,7 +347,7 @@ test6 = h2`+`:on`e-`more # Escape sequences in the middle test_file.close(); OptionsReader reader; - reader.read(Options::getRoot(), filename); + reader.read(Options::getRoot(), filename.string()); auto options = Options::root()["tests"]; @@ -376,7 +373,7 @@ some:value = 3 OptionsReader reader; - EXPECT_THROW(reader.read(Options::getRoot(), filename), BoutException); + EXPECT_THROW(reader.read(Options::getRoot(), filename.string()), BoutException); } TEST_F(OptionsReaderTest, ReadUnicodeNames) { @@ -396,7 +393,7 @@ twopi = 2 * π # Unicode symbol defined for pi test_file.close(); OptionsReader reader; - reader.read(Options::getRoot(), filename); + reader.read(Options::getRoot(), filename.string()); auto options = Options::root()["tests"]; diff --git a/tests/unit/sys/test_output.cxx b/tests/unit/sys/test_output.cxx index 661e7bb1af..1338d9ce13 100644 --- a/tests/unit/sys/test_output.cxx +++ b/tests/unit/sys/test_output.cxx @@ -1,9 +1,9 @@ +#include "test_tmpfiles.hxx" #include "bout/boutexception.hxx" #include "bout/output.hxx" #include "bout/output_bout_types.hxx" #include "gtest/gtest.h" -#include #include // stdout redirection code from https://stackoverflow.com/a/4043813/2043465 @@ -19,8 +19,6 @@ class OutputTest : public ::testing::Test { buffer.str(""); // When done redirect cout to its old self std::cout.rdbuf(sbuf); - - std::remove(filename.c_str()); } // Write cout to buffer instead of stdout @@ -28,7 +26,7 @@ class OutputTest : public ::testing::Test { // Save cout's buffer here std::streambuf* sbuf; // A temporary filename - std::string filename{std::tmpnam(nullptr)}; + bout::testing::TempFile filename; }; TEST_F(OutputTest, JustStdOutCpp) { @@ -56,7 +54,7 @@ TEST_F(OutputTest, OpenFile) { std::string test_output = "To stdout and file\n"; - local_output.open(filename); + local_output.open(filename.string()); local_output << test_output; std::ifstream test_file(filename); @@ -73,7 +71,7 @@ TEST_F(OutputTest, JustPrint) { std::string test_output = "To stdout only\n"; - local_output.open(filename); + local_output.open(filename.string()); local_output.print(test_output); std::ifstream test_file(filename); @@ -92,7 +90,7 @@ TEST_F(OutputTest, DisableEnableStdout) { std::string file_and_stdout = "To stdout and file\n"; // Open temporary file and close stdout - local_output.open(filename); + local_output.open(filename.string()); local_output.disable(); local_output << file_only; @@ -219,7 +217,7 @@ TEST_F(OutputTest, ConditionalJustPrint) { std::string test_output = "To stdout only\n"; - local_output.open(filename); + local_output.open(filename.string()); local_output.print(test_output); std::ifstream test_file(filename); @@ -288,7 +286,7 @@ TEST_F(OutputTest, DummyJustPrint) { std::string test_output = "To stdout only\n"; - dummy.open(filename); + dummy.open(filename.string()); dummy.print(test_output); std::ifstream test_file(filename); diff --git a/tests/unit/test_tmpfiles.hxx b/tests/unit/test_tmpfiles.hxx new file mode 100644 index 0000000000..35d7579df2 --- /dev/null +++ b/tests/unit/test_tmpfiles.hxx @@ -0,0 +1,41 @@ +#pragma once + +#include +#include +#include + +namespace bout::testing { + +/// Return a temporary directory that definitely exists +inline auto test_directory() { + auto test_dir = std::filesystem::temp_directory_path() / "bout_tests"; + create_directory(test_dir); + return test_dir; +} + +/// Create a uniquely named temporary file that is automatically cleaned up +class TempFile { + static int current_count() { + static int count{0}; + return count++; + } + + std::filesystem::path filename{test_directory() + / fmt::format("tempfile_{}", current_count())}; + +public: + TempFile() = default; + TempFile(const TempFile&) = delete; + TempFile(TempFile&&) = delete; + TempFile& operator=(const TempFile&) = delete; + TempFile& operator=(TempFile&&) = delete; + + ~TempFile() { std::filesystem::remove(filename); } + + // Enable conversions to std::string / const char* + operator std::string() const { return filename.string(); } + auto c_str() const { return filename.c_str(); } + auto string() const { return filename.string(); } +}; + +} // namespace bout::testing From 17d6f295fb2478f3fb40b70470b2869d40a312fc Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 14:53:41 +0000 Subject: [PATCH 241/412] Simplify small snippet with C++17 --- src/mesh/parallel/shiftedmetric.cxx | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx index c223b1abbc..84084d9cbb 100644 --- a/src/mesh/parallel/shiftedmetric.cxx +++ b/src/mesh/parallel/shiftedmetric.cxx @@ -264,11 +264,8 @@ ShiftedMetric::shiftZ(const Field3D& f, std::vector results{}; - for (auto& phase : phases) { - // In C++17 std::vector::emplace_back returns a reference, which - // would be very useful here! - results.emplace_back(&mesh); - auto& current_result = results.back(); + for (const auto& phase : phases) { + auto& current_result = results.emplace_back(&mesh); current_result.allocate(); current_result.setLocation(f.getLocation()); From 44f56495526bb84be2306746b7bbd2c7e3ab96e9 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 26 Jan 2024 14:55:40 +0000 Subject: [PATCH 242/412] Remove C++14 backfill for `std::uncaught_exceptions()` --- include/bout/msg_stack.hxx | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx index 993d8adb75..e8158c3200 100644 --- a/include/bout/msg_stack.hxx +++ b/include/bout/msg_stack.hxx @@ -130,20 +130,8 @@ GLOBAL MsgStack msg_stack; * constructor, and pops the message on destruction. */ class MsgStackItem { - /// Backfill for C++14: note this _wrong_ and only useful for our - /// purposes here, that is, telling us if there has been an uncaught - /// exception, which is why this is a private method - static int uncaught_exceptions() { -#if __cpp_lib_uncaught_exceptions >= 201411L - // C++17 version - return std::uncaught_exceptions(); -#else - // C++14 version - return static_cast(std::uncaught_exception()); -#endif - } // Number of uncaught exceptions when this instance was created - int exception_count = uncaught_exceptions(); + int exception_count = std::uncaught_exceptions(); public: // Not currently used anywhere @@ -161,7 +149,7 @@ public: line, file)) {} ~MsgStackItem() { // If an exception has occurred, don't pop the message - if (exception_count == uncaught_exceptions()) { + if (exception_count == std::uncaught_exceptions()) { msg_stack.pop(point); } } From 14a4a96dd9a08772e2b86c677a6a0f009c65580f Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 13:30:00 +0000 Subject: [PATCH 243/412] Delete helper class for pre-C++17 fold expressions --- include/bout/traits.hxx | 32 ++++---------------------------- 1 file changed, 4 insertions(+), 28 deletions(-) diff --git a/include/bout/traits.hxx b/include/bout/traits.hxx index ecfdec8a40..60f88bb392 100644 --- a/include/bout/traits.hxx +++ b/include/bout/traits.hxx @@ -12,26 +12,6 @@ class Options; namespace bout { namespace utils { -namespace details { -/// Helper class for fold expressions pre-C++17 -/// -/// Taken from "C++ Templates: The Complete Guide, Second Edition" -/// Addison-Wesley, 2017 -/// ISBN-13: 978-0-321-71412-1 -/// ISBN-10: 0-321-71412-1 -/// Copyright © 2017 by Addison-Wesley, David Vandevoorde, Nicolai -/// M. Josuttis, and Douglas Gregor. -constexpr bool and_all() { return true; } -template -constexpr bool and_all(T cond) { - return cond; -} -template -constexpr bool and_all(T cond, Ts... conds) { - return cond and and_all(conds...); -} -} // namespace details - /// If `T` is derived from `Field`, provides the member constant /// `value` equal to `true`. Otherwise `value is `false`. /// @@ -104,29 +84,25 @@ using is_Options = std::is_base_of; /// `Field2D` if `V` is `Field2D`, and `Field3D` if `V` is `Field3D`. template using EnableIfField = - typename std::enable_if::value...), - typename std::common_type::type>::type; + std::enable_if_t<(is_Field_v and ...), std::common_type_t>; /// Enable a function if all the Ts are subclasses of `Field2D`, and /// returns the common type template using EnableIfField2D = - typename std::enable_if::value...), - typename std::common_type::type>::type; + std::enable_if_t<(is_Field2D_v and ...), std::common_type_t>; /// Enable a function if all the Ts are subclasses of `Field3D`, and /// returns the common type template using EnableIfField3D = - typename std::enable_if::value...), - typename std::common_type::type>::type; + std::enable_if_t<(is_Field3D_v and ...), std::common_type_t>; /// Enable a function if all the Ts are subclasses of `FieldPerp`, and /// returns the common type template using EnableIfFieldPerp = - typename std::enable_if::value...), - typename std::common_type::type>::type; + std::enable_if_t<(is_FieldPerp_v and ...), std::common_type_t>; /// Enable a function if T is a subclass of Options template From a84faaa1f55055fce117cdfb15adcb25e9447b93 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 13:45:12 +0000 Subject: [PATCH 244/412] Add `is_Field*_v` inline constexpr variables --- include/bout/field.hxx | 12 +++++----- include/bout/globalindexer.hxx | 2 +- include/bout/hypre_interface.hxx | 4 ++-- include/bout/index_derivs_interface.hxx | 4 ++-- include/bout/interpolation.hxx | 2 +- include/bout/invertable_operator.hxx | 2 +- include/bout/petsc_interface.hxx | 4 ++-- include/bout/traits.hxx | 15 ++++++++++++ src/mesh/data/gridfromfile.cxx | 8 +++---- src/mesh/index_derivs.cxx | 14 +++++------ tests/unit/field/test_field_factory.cxx | 4 ++-- tests/unit/include/bout/test_traits.cxx | 32 ++++++++++++------------- 12 files changed, 58 insertions(+), 45 deletions(-) diff --git a/include/bout/field.hxx b/include/bout/field.hxx index a4f4f52803..c0693ec0fb 100644 --- a/include/bout/field.hxx +++ b/include/bout/field.hxx @@ -182,7 +182,7 @@ inline bool areFieldsCompatible(const Field& field1, const Field& field2) { /// copied and a data array that is allocated but not initialised. template inline T emptyFrom(const T& f) { - static_assert(bout::utils::is_Field::value, "emptyFrom only works on Fields"); + static_assert(bout::utils::is_Field_v, "emptyFrom only works on Fields"); return T(f.getMesh(), f.getLocation(), {f.getDirectionY(), f.getDirectionZ()}) .allocate(); } @@ -191,7 +191,7 @@ inline T emptyFrom(const T& f) { /// another field and a data array allocated and initialised to zero. template inline T zeroFrom(const T& f) { - static_assert(bout::utils::is_Field::value, "zeroFrom only works on Fields"); + static_assert(bout::utils::is_Field_v, "zeroFrom only works on Fields"); T result{emptyFrom(f)}; result = 0.; return result; @@ -201,7 +201,7 @@ inline T zeroFrom(const T& f) { /// another field and a data array allocated and filled with the given value. template inline T filledFrom(const T& f, BoutReal fill_value) { - static_assert(bout::utils::is_Field::value, "filledFrom only works on Fields"); + static_assert(bout::utils::is_Field_v, "filledFrom only works on Fields"); T result{emptyFrom(f)}; result = fill_value; return result; @@ -220,7 +220,7 @@ template < typename T, typename Function, typename = decltype(std::declval()(std::declval()))> inline T filledFrom(const T& f, Function func, std::string region_string = "RGN_ALL") { - static_assert(bout::utils::is_Field::value, "filledFrom only works on Fields"); + static_assert(bout::utils::is_Field_v, "filledFrom only works on Fields"); T result{emptyFrom(f)}; BOUT_FOR(i, result.getRegion(region_string)) { result[i] = func(i); } return result; @@ -289,14 +289,14 @@ inline void checkPositive(const T& f, const std::string& name = "field", /// Convert \p f to field-aligned space in \p region (default: whole domain) template inline T toFieldAligned(const T& f, const std::string& region = "RGN_ALL") { - static_assert(bout::utils::is_Field::value, "toFieldAligned only works on Fields"); + static_assert(bout::utils::is_Field_v, "toFieldAligned only works on Fields"); return f.getCoordinates()->getParallelTransform().toFieldAligned(f, region); } /// Convert \p f from field-aligned space in \p region (default: whole domain) template inline T fromFieldAligned(const T& f, const std::string& region = "RGN_ALL") { - static_assert(bout::utils::is_Field::value, "fromFieldAligned only works on Fields"); + static_assert(bout::utils::is_Field_v, "fromFieldAligned only works on Fields"); return f.getCoordinates()->getParallelTransform().fromFieldAligned(f, region); } diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index ab1c927832..9e8d72ba69 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -35,7 +35,7 @@ using InterpolationWeights = std::vector template class GlobalIndexer { public: - static_assert(bout::utils::is_Field::value, "GlobalIndexer only works with Fields"); + static_assert(bout::utils::is_Field_v, "GlobalIndexer only works with Fields"); using ind_type = typename T::ind_type; GlobalIndexer() = default; diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx index 2bbdfdae63..50a14767e0 100644 --- a/include/bout/hypre_interface.hxx +++ b/include/bout/hypre_interface.hxx @@ -73,7 +73,7 @@ class HypreVector { HypreLib hyprelib{}; public: - static_assert(bout::utils::is_Field::value, "HypreVector only works with Fields"); + static_assert(bout::utils::is_Field_v, "HypreVector only works with Fields"); using ind_type = typename T::ind_type; HypreVector() = default; @@ -338,7 +338,7 @@ class HypreMatrix { }; public: - static_assert(bout::utils::is_Field::value, "HypreMatrix only works with Fields"); + static_assert(bout::utils::is_Field_v, "HypreMatrix only works with Fields"); using ind_type = typename T::ind_type; HypreMatrix() = default; diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx index 1f6e8bfbe9..8f7e41a68e 100644 --- a/include/bout/index_derivs_interface.hxx +++ b/include/bout/index_derivs_interface.hxx @@ -48,7 +48,7 @@ T flowDerivative(const T& vel, const T& f, CELL_LOC outloc, const std::string& m AUTO_TRACE(); // Checks - static_assert(bout::utils::is_Field2D::value || bout::utils::is_Field3D::value, + static_assert(bout::utils::is_Field2D_v || bout::utils::is_Field3D_v, "flowDerivative only works on Field2D or Field3D input"); static_assert(derivType == DERIV::Upwind || derivType == DERIV::Flux, @@ -113,7 +113,7 @@ T standardDerivative(const T& f, CELL_LOC outloc, const std::string& method, AUTO_TRACE(); // Checks - static_assert(bout::utils::is_Field2D::value || bout::utils::is_Field3D::value, + static_assert(bout::utils::is_Field2D_v || bout::utils::is_Field3D_v, "standardDerivative only works on Field2D or Field3D input"); static_assert(derivType == DERIV::Standard || derivType == DERIV::StandardSecond diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx index 71fbd19e90..467d09cb42 100644 --- a/include/bout/interpolation.hxx +++ b/include/bout/interpolation.hxx @@ -56,7 +56,7 @@ inline BoutReal interp(const stencil& s) { template const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") { AUTO_TRACE(); - static_assert(bout::utils::is_Field2D::value || bout::utils::is_Field3D::value, + static_assert(bout::utils::is_Field2D_v || bout::utils::is_Field3D_v, "interp_to must be templated with one of Field2D or Field3D."); ASSERT1(loc != CELL_DEFAULT); // doesn't make sense to interplote to CELL_DEFAULT diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx index 7168324b75..91c79495ef 100644 --- a/include/bout/invertable_operator.hxx +++ b/include/bout/invertable_operator.hxx @@ -120,7 +120,7 @@ PetscErrorCode petscVecToField(Vec in, T& out) { template class InvertableOperator { static_assert( - bout::utils::is_Field::value, + bout::utils::is_Field_v, "InvertableOperator must be templated with one of FieldPerp, Field2D or Field3D"); public: diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 0698b2ec11..f9e4539826 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -75,7 +75,7 @@ inline MPI_Comm getComm([[maybe_unused]] const FieldPerp& field) { template class PetscVector { public: - static_assert(bout::utils::is_Field::value, "PetscVector only works with Fields"); + static_assert(bout::utils::is_Field_v, "PetscVector only works with Fields"); using ind_type = typename T::ind_type; struct VectorDeleter { @@ -250,7 +250,7 @@ void swap(PetscMatrix& first, PetscMatrix& second); template class PetscMatrix { public: - static_assert(bout::utils::is_Field::value, "PetscMatrix only works with Fields"); + static_assert(bout::utils::is_Field_v, "PetscMatrix only works with Fields"); using ind_type = typename T::ind_type; struct MatrixDeleter { diff --git a/include/bout/traits.hxx b/include/bout/traits.hxx index 60f88bb392..6ec5778ace 100644 --- a/include/bout/traits.hxx +++ b/include/bout/traits.hxx @@ -32,26 +32,41 @@ namespace utils { template using is_Field = std::is_base_of; +template +inline constexpr bool is_Field_v = std::is_base_of_v; + /// If `T` is derived from `Field2D`, provides the member constant /// `value` equal to `true`. Otherwise `value is `false`. template using is_Field2D = std::is_base_of; +template +inline constexpr bool is_Field2D_v = std::is_base_of_v; + /// If `T` is derived from `Field3D`, provides the member constant /// `value` equal to `true`. Otherwise `value is `false`. template using is_Field3D = std::is_base_of; +template +inline constexpr bool is_Field3D_v = std::is_base_of_v; + /// If `T` is derived from `FieldPerp`, provides the member constant /// `value` equal to `true`. Otherwise `value is `false`. template using is_FieldPerp = std::is_base_of; +template +inline constexpr bool is_FieldPerp_v = std::is_base_of_v; + /// If `T` is derived from `Options`, provides the member constant /// `value` equal to `true`. Otherwise `value is `false`. template using is_Options = std::is_base_of; +template +inline constexpr bool is_Options_v = std::is_base_of_v; + /// Enable a function if all the Ts are subclasses of `Field`, and /// returns the common type: i.e. `Field3D` if at least one argument /// is `Field3D`, otherwise `Field2D` if they are all `Field2D` diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index 41147ba76c..c2505b4839 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -157,7 +157,7 @@ template bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, CELL_LOC location) { static_assert( - bout::utils::is_Field::value, + bout::utils::is_Field_v, "templated GridFile::getField only works for Field2D, Field3D or FieldPerp"); Timer timer("io"); @@ -195,7 +195,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, } case 3: { // Check size if getting Field3D - if (bout::utils::is_Field2D::value or bout::utils::is_FieldPerp::value) { + if (bout::utils::is_Field2D_v or bout::utils::is_FieldPerp_v) { output_warn.write( "WARNING: Variable '{:s}' should be 2D, but has {:d} dimensions. Ignored\n", name, size.size()); @@ -272,7 +272,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, name, grid_xguards, mxg); } - if (not bout::utils::is_FieldPerp::value) { + if (not bout::utils::is_FieldPerp_v) { // Check if field dimensions are correct. y-direction if (grid_yguards > 0) { // including ghostpoints @@ -325,7 +325,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, } } - if (not bout::utils::is_FieldPerp::value) { + if (not bout::utils::is_FieldPerp_v) { ///If field does not include ghost points in y-direction -> ///Upper and lower Y boundaries copied from nearest point if (grid_yguards == 0) { diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx index d84f5ced37..9cccd6f7d7 100644 --- a/src/mesh/index_derivs.cxx +++ b/src/mesh/index_derivs.cxx @@ -426,10 +426,9 @@ class FFTDerivativeType { AUTO_TRACE(); ASSERT2(meta.derivType == DERIV::Standard) ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); - ASSERT2(direction == DIRECTION::Z); // Only in Z for now - ASSERT2(stagger == STAGGER::None); // Staggering not currently supported - ASSERT2( - bout::utils::is_Field3D::value); // Should never need to call this with Field2D + ASSERT2(direction == DIRECTION::Z); // Only in Z for now + ASSERT2(stagger == STAGGER::None); // Staggering not currently supported + ASSERT2(bout::utils::is_Field3D_v); // Should never need to call this with Field2D auto* theMesh = var.getMesh(); @@ -493,10 +492,9 @@ class FFT2ndDerivativeType { AUTO_TRACE(); ASSERT2(meta.derivType == DERIV::StandardSecond); ASSERT2(var.getMesh()->getNguard(direction) >= nGuards); - ASSERT2(direction == DIRECTION::Z); // Only in Z for now - ASSERT2(stagger == STAGGER::None); // Staggering not currently supported - ASSERT2( - bout::utils::is_Field3D::value); // Should never need to call this with Field2D + ASSERT2(direction == DIRECTION::Z); // Only in Z for now + ASSERT2(stagger == STAGGER::None); // Staggering not currently supported + ASSERT2(bout::utils::is_Field3D_v); // Should never need to call this with Field2D auto* theMesh = var.getMesh(); diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx index af819400e4..7bb8c680ad 100644 --- a/tests/unit/field/test_field_factory.cxx +++ b/tests/unit/field/test_field_factory.cxx @@ -41,7 +41,7 @@ class FieldFactoryCreationTest : public FakeMeshFixture { // FieldFactory::create3D template T create(Args&&... args) { - if constexpr (bout::utils::is_Field3D{}) { + if constexpr (bout::utils::is_Field3D_v) { return factory.create3D(std::forward(args)...); } else { return factory.create2D(std::forward(args)...); @@ -210,7 +210,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreateZStaggered) { auto expected = makeField( [](typename TypeParam::ind_type& index) -> BoutReal { auto offset = BoutReal{0.0}; - if (bout::utils::is_Field3D::value) { + if (bout::utils::is_Field3D_v) { offset = 0.5; } diff --git a/tests/unit/include/bout/test_traits.cxx b/tests/unit/include/bout/test_traits.cxx index 98f0c542ad..a6ff162722 100644 --- a/tests/unit/include/bout/test_traits.cxx +++ b/tests/unit/include/bout/test_traits.cxx @@ -10,34 +10,34 @@ TEST(BoutTraitsTest, IsField) { using namespace bout::utils; - static_assert(is_Field::value, "is_Field should be true"); - static_assert(is_Field::value, "is_Field should be true"); - static_assert(is_Field::value, "is_Field should be true"); - static_assert(is_Field::value, "is_Field should be true"); + static_assert(is_Field_v, "is_Field should be true"); + static_assert(is_Field_v, "is_Field should be true"); + static_assert(is_Field_v, "is_Field should be true"); + static_assert(is_Field_v, "is_Field should be true"); } TEST(BoutTraitsTest, IsField2D) { using namespace bout::utils; - static_assert(!is_Field2D::value, "is_Field2D should be false"); - static_assert(is_Field2D::value, "is_Field2D should be true"); - static_assert(!is_Field2D::value, "is_Field2D should be false"); - static_assert(!is_Field2D::value, "is_Field2D should be false"); + static_assert(!is_Field2D_v, "is_Field2D should be false"); + static_assert(is_Field2D_v, "is_Field2D should be true"); + static_assert(!is_Field2D_v, "is_Field2D should be false"); + static_assert(!is_Field2D_v, "is_Field2D should be false"); } TEST(BoutTraitsTest, IsField3D) { using namespace bout::utils; - static_assert(!is_Field3D::value, "is_Field3D should be false"); - static_assert(!is_Field3D::value, "is_Field3D should be false"); - static_assert(is_Field3D::value, "is_Field3D should be true"); - static_assert(!is_Field3D::value, "is_Field3D should be false"); + static_assert(!is_Field3D_v, "is_Field3D should be false"); + static_assert(!is_Field3D_v, "is_Field3D should be false"); + static_assert(is_Field3D_v, "is_Field3D should be true"); + static_assert(!is_Field3D_v, "is_Field3D should be false"); } TEST(BoutTraitsTest, IsFieldPerp) { using namespace bout::utils; - static_assert(!is_FieldPerp::value, "is_FieldPerp should be false"); - static_assert(!is_FieldPerp::value, "is_FieldPerp should be false"); - static_assert(!is_FieldPerp::value, "is_FieldPerp should be false"); - static_assert(is_FieldPerp::value, "is_FieldPerp should be true"); + static_assert(!is_FieldPerp_v, "is_FieldPerp should be false"); + static_assert(!is_FieldPerp_v, "is_FieldPerp should be false"); + static_assert(!is_FieldPerp_v, "is_FieldPerp should be false"); + static_assert(is_FieldPerp_v, "is_FieldPerp should be true"); } namespace { From 55abebdfdc158fc73f213dbee563fa31cd85a6bc Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 13:45:52 +0000 Subject: [PATCH 245/412] Use `std::is_*_v` inline constexpr variables instead of `::value` --- include/bout/globalindexer.hxx | 4 +- include/bout/hypre_interface.hxx | 17 ++++--- include/bout/interpolation.hxx | 4 +- include/bout/invertable_operator.hxx | 6 +-- include/bout/operatorstencil.hxx | 26 +++++------ include/bout/petsc_interface.hxx | 14 +++--- include/bout/physicsmodel.hxx | 4 +- include/bout/region.hxx | 8 ++-- include/bout/traits.hxx | 2 +- include/bout/utils.hxx | 2 +- tests/unit/field/test_fieldgroup.cxx | 4 +- .../include/bout/test_hypre_interface.cxx | 10 ++-- .../unit/include/bout/test_petsc_indexer.cxx | 25 +++++----- tests/unit/include/bout/test_petsc_matrix.cxx | 24 +++++----- tests/unit/include/bout/test_region.cxx | 21 +++------ tests/unit/include/bout/test_stencil.cxx | 18 ++++---- tests/unit/include/bout/test_traits.cxx | 46 +++++++++---------- tests/unit/sys/test_utils.cxx | 17 ++++--- 18 files changed, 118 insertions(+), 134 deletions(-) diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index 9e8d72ba69..f9253b23b8 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -72,7 +72,7 @@ public: regionInnerX = intersection(bndryCandidate, indices.getRegion("RGN_INNER_X")); regionOuterX = intersection(bndryCandidate, indices.getRegion("RGN_OUTER_X")); - if (std::is_same::value) { + if (std::is_same_v) { regionLowerY = Region({}); regionUpperY = Region({}); } else { @@ -86,7 +86,7 @@ public: int localSize = size(); MPI_Comm comm = - std::is_same::value ? fieldmesh->getXcomm() : BoutComm::get(); + std::is_same_v ? fieldmesh->getXcomm() : BoutComm::get(); fieldmesh->getMpi().MPI_Scan(&localSize, &globalEnd, 1, MPI_INT, MPI_SUM, comm); globalEnd--; int counter = globalStart = globalEnd - size() + 1; diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx index 50a14767e0..c26548e95e 100644 --- a/include/bout/hypre_interface.hxx +++ b/include/bout/hypre_interface.hxx @@ -138,7 +138,7 @@ public: : indexConverter(indConverter) { ASSERT1(indConverter->getMesh() == f.getMesh()); const MPI_Comm comm = - std::is_same::value ? f.getMesh()->getXcomm() : BoutComm::get(); + std::is_same_v ? f.getMesh()->getXcomm() : BoutComm::get(); HYPRE_BigInt jlower = indConverter->getGlobalStart(); HYPRE_BigInt jupper = jlower + indConverter->size() - 1; // inclusive end @@ -159,7 +159,7 @@ public: explicit HypreVector(IndexerPtr indConverter) : indexConverter(indConverter) { Mesh& mesh = *indConverter->getMesh(); const MPI_Comm comm = - std::is_same::value ? mesh.getXcomm() : BoutComm::get(); + std::is_same_v ? mesh.getXcomm() : BoutComm::get(); HYPRE_BigInt jlower = indConverter->getGlobalStart(); HYPRE_BigInt jupper = jlower + indConverter->size() - 1; // inclusive end @@ -380,7 +380,7 @@ public: : hypre_matrix(new HYPRE_IJMatrix, MatrixDeleter{}), index_converter(indConverter) { Mesh* mesh = indConverter->getMesh(); const MPI_Comm comm = - std::is_same::value ? mesh->getXcomm() : BoutComm::get(); + std::is_same_v ? mesh->getXcomm() : BoutComm::get(); parallel_transform = &mesh->getCoordinates()->getParallelTransform(); ilower = indConverter->getGlobalStart(); @@ -651,9 +651,8 @@ public: }(); const int ny = - std::is_same::value ? 1 : index_converter->getMesh()->LocalNy; - const int nz = - std::is_same::value ? 1 : index_converter->getMesh()->LocalNz; + std::is_same_v ? 1 : index_converter->getMesh()->LocalNy; + const int nz = std::is_same_v ? 1 : index_converter->getMesh()->LocalNz; std::transform( pw.begin(), pw.end(), std::back_inserter(positions), [this, ny, nz](ParallelTransform::PositionsAndWeights p) -> HYPRE_Int { @@ -714,7 +713,7 @@ public: HypreMatrix yup(int index = 0) { return ynext(index + 1); } HypreMatrix ydown(int index = 0) { return ynext(-index - 1); } HypreMatrix ynext(int dir) { - if (std::is_same::value and ((yoffset + dir) != 0)) { + if (std::is_same_v and ((yoffset + dir) != 0)) { throw BoutException("Can not get ynext for FieldPerp"); } HypreMatrix result; @@ -726,7 +725,7 @@ public: result.index_converter = index_converter; result.location = location; result.initialised = initialised; - result.yoffset = std::is_same::value ? 0 : yoffset + dir; + result.yoffset = std::is_same_v ? 0 : yoffset + dir; result.parallel_transform = parallel_transform; result.assembled = assembled; result.num_rows = num_rows; @@ -804,7 +803,7 @@ public: "values are: gmres, bicgstab, pcg") .withDefault(HYPRE_SOLVER_TYPE::bicgstab); - comm = std::is_same::value ? mesh.getXcomm() : BoutComm::get(); + comm = std::is_same_v ? mesh.getXcomm() : BoutComm::get(); auto print_level = options["hypre_print_level"] diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx index 467d09cb42..aa6b8358cb 100644 --- a/include/bout/interpolation.hxx +++ b/include/bout/interpolation.hxx @@ -121,12 +121,12 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL // We can't interpolate in y unless we're field-aligned // Field2D doesn't need to shift to/from field-aligned because it is axisymmetric, // so always set is_unaligned=false for Field2D. - const bool is_unaligned = std::is_same::value + const bool is_unaligned = std::is_same_v ? false : (var.getDirectionY() == YDirectionType::Standard); const T var_fa = is_unaligned ? toFieldAligned(var, "RGN_NOX") : var; - if (not std::is_base_of::value) { + if (not std::is_base_of_v) { // Field2D is axisymmetric, so YDirectionType::Standard and // YDirectionType::Aligned are equivalent, but trying to set // YDirectionType::Aligned explicitly is an error diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx index 91c79495ef..0de77d5d1d 100644 --- a/include/bout/invertable_operator.hxx +++ b/include/bout/invertable_operator.hxx @@ -197,7 +197,7 @@ public: } // Add the RGN_WITHBNDRIES region to the mesh. Requires RGN_NOBNDRY to be defined. - if (std::is_same::value) { + if (std::is_same_v) { if (not localmesh->hasRegion3D("RGN_WITHBNDRIES")) { // This avoids all guard cells and corners but includes boundaries // Note we probably don't want to include periodic boundaries as these @@ -242,7 +242,7 @@ public: localmesh->addRegion3D("RGN_WITHBNDRIES", nocorner3D); } - } else if (std::is_same::value) { + } else if (std::is_same_v) { if (not localmesh->hasRegion2D("RGN_WITHBNDRIES")) { // This avoids all guard cells and corners but includes boundaries Region nocorner2D = localmesh->getRegion2D("RGN_NOBNDRY"); @@ -280,7 +280,7 @@ public: localmesh->addRegion2D("RGN_WITHBNDRIES", nocorner2D); } - } else if (std::is_same::value) { + } else if (std::is_same_v) { if (not localmesh->hasRegionPerp("RGN_WITHBNDRIES")) { // This avoids all guard cells and corners but includes boundaries Region nocornerPerp = localmesh->getRegionPerp("RGN_NOBNDRY"); diff --git a/include/bout/operatorstencil.hxx b/include/bout/operatorstencil.hxx index c6a26c246f..1846dd059b 100644 --- a/include/bout/operatorstencil.hxx +++ b/include/bout/operatorstencil.hxx @@ -45,8 +45,8 @@ /// subtracted from them. template struct IndexOffset { - static_assert(std::is_same::value || std::is_same::value - || std::is_same::value, + static_assert(std::is_same_v || std::is_same_v + || std::is_same_v, "IndexOffset only works with SpecificInd types"); int dx = 0, dy = 0, dz = 0; @@ -133,8 +133,8 @@ using OffsetIndPerp = IndexOffset; template class OperatorStencil { public: - static_assert(std::is_same::value || std::is_same::value - || std::is_same::value, + static_assert(std::is_same_v || std::is_same_v + || std::is_same_v, "OperatorStencil only works with SpecificInd types"); using offset = IndexOffset; using stencil_part = std::vector; @@ -246,7 +246,7 @@ OperatorStencil squareStencil(Mesh* localmesh) { zero.xp(), zero.xm(), }; - if (!std::is_same::value) { + if (!std::is_same_v) { offsets.insert(zero.yp()); offsets.insert(zero.ym()); offsets.insert(zero.xp().yp()); @@ -254,7 +254,7 @@ OperatorStencil squareStencil(Mesh* localmesh) { offsets.insert(zero.xm().yp()); offsets.insert(zero.xm().ym()); } - if (!std::is_same::value) { + if (!std::is_same_v) { offsets.insert(zero.zp()); offsets.insert(zero.zm()); offsets.insert(zero.xp().zp()); @@ -262,7 +262,7 @@ OperatorStencil squareStencil(Mesh* localmesh) { offsets.insert(zero.xm().zp()); offsets.insert(zero.xm().zm()); } - if (std::is_same::value) { + if (std::is_same_v) { offsets.insert(zero.yp().zp()); offsets.insert(zero.yp().zm()); offsets.insert(zero.ym().zp()); @@ -272,9 +272,9 @@ OperatorStencil squareStencil(Mesh* localmesh) { stencil.add( [localmesh](T ind) -> bool { return (localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend - && (std::is_same::value + && (std::is_same_v || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend)) - && (std::is_same::value + && (std::is_same_v || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend))); }, offsetsVec); @@ -294,11 +294,11 @@ OperatorStencil starStencil(Mesh* localmesh) { zero.xp(), zero.xm(), }; - if (!std::is_same::value) { + if (!std::is_same_v) { offsets.insert(zero.yp()); offsets.insert(zero.ym()); } - if (!std::is_same::value) { + if (!std::is_same_v) { offsets.insert(zero.zp()); offsets.insert(zero.zm()); } @@ -306,9 +306,9 @@ OperatorStencil starStencil(Mesh* localmesh) { stencil.add( [localmesh](T ind) -> bool { return (localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend - && (std::is_same::value + && (std::is_same_v || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend)) - && (std::is_same::value + && (std::is_same_v || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend))); }, offsetsVec); diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index f9e4539826..0afcc8a30a 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -283,9 +283,8 @@ public: PetscMatrix(IndexerPtr indConverter, bool preallocate = true) : matrix(new Mat()), indexConverter(indConverter), pt(&indConverter->getMesh()->getCoordinates()->getParallelTransform()) { - MPI_Comm comm = std::is_same::value - ? indConverter->getMesh()->getXcomm() - : BoutComm::get(); + MPI_Comm comm = std::is_same_v ? indConverter->getMesh()->getXcomm() + : BoutComm::get(); const int size = indexConverter->size(); MatCreate(comm, matrix.get()); @@ -435,9 +434,8 @@ public: const auto pws = pt->getWeightsForYApproximation(index2.x(), index1.y(), index2.z(), yoffset); const int ny = - std::is_same::value ? 1 : indexConverter->getMesh()->LocalNy; - const int nz = - std::is_same::value ? 1 : indexConverter->getMesh()->LocalNz; + std::is_same_v ? 1 : indexConverter->getMesh()->LocalNy; + const int nz = std::is_same_v ? 1 : indexConverter->getMesh()->LocalNz; std::transform( pws.begin(), pws.end(), std::back_inserter(positions), @@ -501,7 +499,7 @@ public: PetscMatrix yup(int index = 0) { return ynext(index + 1); } PetscMatrix ydown(int index = 0) { return ynext(-index - 1); } PetscMatrix ynext(int dir) { - if (std::is_same::value && yoffset + dir != 0) { + if (std::is_same_v && yoffset + dir != 0) { throw BoutException("Can not get ynext for FieldPerp"); } PetscMatrix result; // Can't use copy constructor because don't @@ -509,7 +507,7 @@ public: result.matrix = matrix; result.indexConverter = indexConverter; result.pt = pt; - result.yoffset = std::is_same::value ? 0 : yoffset + dir; + result.yoffset = std::is_same_v ? 0 : yoffset + dir; result.initialised = initialised; return result; } diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index e0f046eb1f..049ed46e59 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -128,10 +128,10 @@ public: using jacobianfunc = int (PhysicsModel::*)(BoutReal t); template ::value>> + std::is_base_of_v>> using ModelPreconFunc = int (Model::*)(BoutReal t, BoutReal gamma, BoutReal delta); template ::value>> + std::is_base_of_v>> using ModelJacobianFunc = int (Model::*)(BoutReal t); PhysicsModel(); diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 13c4a137fa..3e10e04a25 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -482,8 +482,8 @@ template class Region { // Following prevents a Region being created with anything other // than Ind2D, Ind3D or IndPerp as template type - static_assert(std::is_base_of::value || std::is_base_of::value - || std::is_base_of::value, + static_assert(std::is_base_of_v || std::is_base_of_v + || std::is_base_of_v, "Region must be templated with one of IndPerp, Ind2D or Ind3D"); public: @@ -521,7 +521,7 @@ public: int nz, int maxregionblocksize = MAXREGIONBLOCKSIZE) : ny(ny), nz(nz) { #if CHECK > 1 - if (std::is_base_of::value) { + if (std::is_base_of_v) { if (nz != 1) { throw BoutException( "Trying to make Region with nz = {:d}, but expected nz = 1", nz); @@ -537,7 +537,7 @@ public: } } - if (std::is_base_of::value) { + if (std::is_base_of_v) { if (ny != 1) { throw BoutException( "Trying to make Region with ny = {:d}, but expected ny = 1", ny); diff --git a/include/bout/traits.hxx b/include/bout/traits.hxx index 6ec5778ace..15643064d3 100644 --- a/include/bout/traits.hxx +++ b/include/bout/traits.hxx @@ -121,7 +121,7 @@ using EnableIfFieldPerp = /// Enable a function if T is a subclass of Options template -using EnableIfOptions = std::enable_if_t::value>; +using EnableIfOptions = std::enable_if_t>; } // namespace utils } // namespace bout diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index b26b23e4c0..034657423a 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -106,7 +106,7 @@ struct function_traits; /// bout::utils::function_traits::arg<1>::type; /// // The following prints "true": /// std::cout << std::boolalpha -/// << std::is_same::value; +/// << std::is_same_v; /// /// Adapted from https://stackoverflow.com/a/9065203/2043465 template diff --git a/tests/unit/field/test_fieldgroup.cxx b/tests/unit/field/test_fieldgroup.cxx index bfb001fd2f..0374dfb894 100644 --- a/tests/unit/field/test_fieldgroup.cxx +++ b/tests/unit/field/test_fieldgroup.cxx @@ -283,9 +283,9 @@ TEST(FieldGroupTest, ConstIterator) { } TEST(FieldGroupTest, NotConstructableFromInt) { - EXPECT_FALSE((std::is_constructible::value)); + EXPECT_FALSE((std::is_constructible_v)); } TEST(FieldGroupTest, NotConstructableFromBoutReal) { - EXPECT_FALSE((std::is_constructible::value)); + EXPECT_FALSE((std::is_constructible_v)); } diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx index b7a7c2c50c..0518cacac0 100644 --- a/tests/unit/include/bout/test_hypre_interface.cxx +++ b/tests/unit/include/bout/test_hypre_interface.cxx @@ -185,7 +185,7 @@ class HypreMatrixTest : public FakeMeshFixture { indexA = ind_type((1 + field.getNy()) * field.getNz() + 1, field.getNy(), field.getNz()); - if (std::is_same::value) { + if (std::is_same_v) { indexB = indexA.zp(); iWD0 = indexB.zm(); @@ -389,7 +389,7 @@ TYPED_TEST(HypreMatrixTest, YUp) { HypreMatrix matrix(this->indexer); - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_THROW(matrix.yup(), BoutException); return; } @@ -398,7 +398,7 @@ TYPED_TEST(HypreMatrixTest, YUp) { MockTransform* transform = this->pt; const BoutReal value = 42.0; - if (std::is_same::value) { + if (std::is_same_v) { expected(this->indexA, this->indexB) = value; } else { EXPECT_CALL(*transform, getWeightsForYUpApproximation( @@ -422,7 +422,7 @@ TYPED_TEST(HypreMatrixTest, YDown) { HypreMatrix matrix(this->indexer); - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_THROW(matrix.yup(), BoutException); return; } @@ -431,7 +431,7 @@ TYPED_TEST(HypreMatrixTest, YDown) { MockTransform* transform = this->pt; const BoutReal value = 42.0; - if (std::is_same::value) { + if (std::is_same_v) { expected(this->indexB, this->indexA) = value; } else { EXPECT_CALL(*transform, getWeightsForYDownApproximation( diff --git a/tests/unit/include/bout/test_petsc_indexer.cxx b/tests/unit/include/bout/test_petsc_indexer.cxx index 40c29ddfbd..163913a1f7 100644 --- a/tests/unit/include/bout/test_petsc_indexer.cxx +++ b/tests/unit/include/bout/test_petsc_indexer.cxx @@ -39,11 +39,10 @@ class IndexerTest : public FakeMeshFixture { globalStarIndexer(bout::globals::mesh, starStencil(bout::globals::mesh)), globalDefaultIndexer(bout::globals::mesh), guardx(bout::globals::mesh->getNXPE()), - guardy(std::is_same::value ? 0 : bout::globals::mesh->getNYPE()), + guardy(std::is_same_v ? 0 : bout::globals::mesh->getNYPE()), nx(bout::globals::mesh->LocalNx - 2 * guardx), - ny(std::is_same::value ? 1 - : bout::globals::mesh->LocalNy - 2 * guardy), - nz(std::is_same::value ? 1 : bout::globals::mesh->LocalNz), + ny(std::is_same_v ? 1 : bout::globals::mesh->LocalNy - 2 * guardy), + nz(std::is_same_v ? 1 : bout::globals::mesh->LocalNz), mesh2(2, 2, 2) { mesh2.createDefaultRegions(); mesh2.setCoordinates(nullptr); @@ -108,7 +107,7 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { } // Check indices of Y guard cells are unique - if (!std::is_same::value) { + if (!std::is_same_v) { BOUT_FOR(i, f.getRegion("RGN_YGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); @@ -178,7 +177,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalSquareIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalSquareIndexer.getMesh()->xend); - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_GE(i.y(), this->globalSquareIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->globalSquareIndexer.getMesh()->yend); } @@ -188,7 +187,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalStarIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalStarIndexer.getMesh()->xend); - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_GE(i.y(), this->globalStarIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->globalStarIndexer.getMesh()->yend); } @@ -198,7 +197,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalDefaultIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalDefaultIndexer.getMesh()->xend); - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_GE(i.y(), this->globalDefaultIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->globalDefaultIndexer.getMesh()->yend); } @@ -208,7 +207,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->localIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->localIndexer.getMesh()->xend); - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_GE(i.y(), this->localIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->localIndexer.getMesh()->yend); } @@ -230,7 +229,7 @@ TYPED_TEST(IndexerTest, TestGetRegionBndry) { TYPED_TEST(IndexerTest, TestGetRegionLowerY) { Region rgn; - if (std::is_same::value) { + if (std::is_same_v) { rgn = this->globalSquareIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->globalStarIndexer.getRegionLowerY(); @@ -251,7 +250,7 @@ TYPED_TEST(IndexerTest, TestGetRegionLowerY) { TYPED_TEST(IndexerTest, TestGetRegionUpperY) { Region rgn; - if (std::is_same::value) { + if (std::is_same_v) { rgn = this->globalSquareIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->globalStarIndexer.getRegionUpperY(); @@ -306,8 +305,8 @@ TYPED_TEST(IndexerTest, TestSparsityPatternAvailable) { } TYPED_TEST(IndexerTest, TestGetNumDiagonal) { - const int squareStencilInteriorSize = std::is_same::value ? 19 : 9, - starStencilInteriorSize = std::is_same::value ? 7 : 5, + const int squareStencilInteriorSize = std::is_same_v ? 19 : 9, + starStencilInteriorSize = std::is_same_v ? 7 : 5, boundsSize = 1; int numBoundaryCells = 0; for (int i : this->globalSquareIndexer.getNumDiagonal()) { diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index 1fabd93a51..dc6e3fd3cd 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -57,7 +57,7 @@ class PetscMatrixTest : public FakeMeshFixture { stencil(squareStencil(bout::globals::mesh)), indexer(std::make_shared>(bout::globals::mesh, stencil)) { indexA = ind_type(field.getNy() * field.getNz() + 1, field.getNy(), field.getNz()); - if (std::is_same::value) { + if (std::is_same_v) { indexB = indexA.zp(); } else { indexB = indexA.yp(); @@ -65,7 +65,7 @@ class PetscMatrixTest : public FakeMeshFixture { iWU0 = indexB.xm(); iWU1 = indexB; iWU2 = indexB.xp(); - if (std::is_same::value) { + if (std::is_same_v) { iWD0 = indexB.zm(); iWD1 = indexB; iWD2 = indexB.zp(); @@ -269,13 +269,13 @@ TYPED_TEST(PetscMatrixTest, TestYUp) { PetscMatrix expected(this->indexer, false); MockTransform* transform = this->pt; SCOPED_TRACE("YUp"); - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_THROW(matrix.yup(), BoutException); } else { const BoutReal val = 3.141592; - if (std::is_same::value) { + if (std::is_same_v) { expected(this->indexA, this->indexB) = val; - } else if (std::is_same::value) { + } else if (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexB.x(), this->indexA.y(), this->indexB.z(), 1)) @@ -302,12 +302,12 @@ TYPED_TEST(PetscMatrixTest, TestYDown) { const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YDown"); - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_THROW(matrix.ydown(), BoutException); } else { - if (std::is_same::value) { + if (std::is_same_v) { expected(this->indexB, this->indexA) = val; - } else if (std::is_same::value) { + } else if (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexA.x(), this->indexB.y(), this->indexA.z(), -1)) @@ -351,10 +351,10 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextPos"); - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_THROW(matrix.ynext(1), BoutException); } else { - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexB.x(), this->indexA.y(), this->indexB.z(), 1)) @@ -380,10 +380,10 @@ TYPED_TEST(PetscMatrixTest, TestYNextNeg) { const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextNeg"); - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_THROW(matrix.ynext(-1), BoutException); } else { - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexA.x(), this->indexB.y(), this->indexA.z(), -1)) diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index fa46fed769..befcc07771 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -1119,36 +1119,27 @@ TEST_F(RegionTest, regionGetStatsEmpty) { } TEST(RegionIndexConversionTest, Ind3DtoInd2D) { - // This could just be: - // EXPECT_FALSE(std::is_convertible::value()); - // but requires C++14 - bool convert = std::is_convertible::value; - EXPECT_FALSE(convert); + EXPECT_FALSE((std::is_convertible_v)); } TEST(RegionIndexConversionTest, Ind2DtoInd3D) { - bool convert = std::is_convertible::value; - EXPECT_FALSE(convert); + EXPECT_FALSE((std::is_convertible_v)); } TEST(RegionIndexConversionTest, Ind2Dtoint) { - bool convert = std::is_convertible::value; - EXPECT_FALSE(convert); + EXPECT_FALSE((std::is_convertible_v)); } TEST(RegionIndexConversionTest, Ind3Dtoint) { - bool convert = std::is_convertible::value; - EXPECT_FALSE(convert); + EXPECT_FALSE((std::is_convertible_v)); } TEST(RegionIndexConversionTest, inttoInd2D) { - bool convert = std::is_convertible::value; - EXPECT_FALSE(convert); + EXPECT_FALSE((std::is_convertible_v)); } TEST(RegionIndexConversionTest, inttoInd3D) { - bool convert = std::is_convertible::value; - EXPECT_FALSE(convert); + EXPECT_FALSE((std::is_convertible_v)); } TEST(RegionIndex2DTest, MemberSize) { diff --git a/tests/unit/include/bout/test_stencil.cxx b/tests/unit/include/bout/test_stencil.cxx index 851abe957b..dc0c9c1fc9 100644 --- a/tests/unit/include/bout/test_stencil.cxx +++ b/tests/unit/include/bout/test_stencil.cxx @@ -11,8 +11,7 @@ template class IndexOffsetStructTests : public ::testing::Test { public: IndexOffsetStructTests() { - zero = T(0, std::is_same::value ? 1 : 5, - std::is_same::value ? 1 : 7); + zero = T(0, std::is_same_v ? 1 : 5, std::is_same_v ? 1 : 7); } IndexOffset noOffset; @@ -128,15 +127,15 @@ TYPED_TEST(IndexOffsetStructTests, AddToIndex) { offset4 = {2, 3, -2}; EXPECT_EQ(this->zero + offset1, this->zero.xp()); EXPECT_EQ(offset1 + this->zero, this->zero.xp()); - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_EQ(this->zero + offset2, this->zero.yp(2)); EXPECT_EQ(offset2 + this->zero, this->zero.yp(2)); } - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_EQ(this->zero + offset3, this->zero.zp(11)); EXPECT_EQ(offset3 + this->zero, this->zero.zp(11)); } - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_EQ(this->zero + offset4, this->zero.xp(2).yp(3).zm(2)); EXPECT_EQ(offset4 + this->zero, this->zero.xp(2).yp(3).zm(2)); } @@ -146,13 +145,13 @@ TYPED_TEST(IndexOffsetStructTests, SubtractFromIndex) { IndexOffset offset1 = {1, 0, 0}, offset2 = {0, 2, 0}, offset3 = {0, 0, 11}, offset4 = {2, 3, -2}; EXPECT_EQ(this->zero - offset1, this->zero.xm()); - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_EQ(this->zero - offset2, this->zero.ym(2)); } - if (!std::is_same::value) { + if (!std::is_same_v) { EXPECT_EQ(this->zero - offset3, this->zero.zm(11)); } - if (std::is_same::value) { + if (std::is_same_v) { EXPECT_EQ(this->zero - offset4, this->zero.zp(2).xm(2).ym(3)); } } @@ -162,8 +161,7 @@ class StencilUnitTests : public ::testing::Test { public: WithQuietOutput all{output}; StencilUnitTests() { - zero = T(0, std::is_same::value ? 1 : 5, - std::is_same::value ? 1 : 7); + zero = T(0, std::is_same_v ? 1 : 5, std::is_same_v ? 1 : 7); for (int i = 0; i < static_cast(sizes.size()); i++) { std::vector> part; for (int j = 0; j < sizes[i]; j++) { diff --git a/tests/unit/include/bout/test_traits.cxx b/tests/unit/include/bout/test_traits.cxx index a6ff162722..10becb1551 100644 --- a/tests/unit/include/bout/test_traits.cxx +++ b/tests/unit/include/bout/test_traits.cxx @@ -84,50 +84,50 @@ auto example_function(T, U) -> ResultType { TEST(BoutTraitsTest, EnableIfFieldOverloads) { using namespace bout::utils; - static_assert(std::is_same(), - std::declval()))>::value, + static_assert(std::is_same_v(), + std::declval()))>, "EnableIfField should enable function_overloads for two Fields"); static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should disable one overload of function_overloads.\n" "This static_assert should fail if the `function_overloads(T, BoutReal)` template\n" "is commented out"); static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should pick the correct version of specific_function_overloads"); static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should pick the correct version of specific_function_overloads"); static_assert( - std::is_same(), std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should pick the correct version of specific_function_overloads"); } TEST(BoutTraitsTest, EnableIfFieldReturnType) { using namespace bout::utils; static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should return Field2D for two Field2Ds"); static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should return Field3D for a Field2D and a Field3D"); static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should return Field3D for a Field2D and a Field3D"); static_assert( - std::is_same(), - std::declval()))>::value, + std::is_same_v(), + std::declval()))>, "EnableIfField should return Field3D for a Field3D and a Field3D"); } diff --git a/tests/unit/sys/test_utils.cxx b/tests/unit/sys/test_utils.cxx index 0826a742de..747257bafc 100644 --- a/tests/unit/sys/test_utils.cxx +++ b/tests/unit/sys/test_utils.cxx @@ -693,10 +693,10 @@ void function_template(T) {} TEST(FunctionTraitsTest, ResultType) { using bout::utils::function_traits; - static_assert(std::is_same::result_type, int>::value, + static_assert(std::is_same_v::result_type, int>, "Wrong result_type for function_traits of a typedef"); static_assert( - std::is_same::result_type, int>::value, + std::is_same_v::result_type, int>, "Wrong result_type for function_traits of a function pointer"); static_assert( std::is_same)>::result_type, @@ -719,9 +719,8 @@ TEST(FunctionTraitsTest, NumberOfArgs) { TEST(FunctionTraitsTest, FirstArg) { using bout::utils::function_traits; - static_assert( - std::is_same::arg<0>::type, char>::value, - "Wrong first argument type for function_traits of a typedef"); + static_assert(std::is_same_v::arg<0>::type, char>, + "Wrong first argument type for function_traits of a typedef"); static_assert(std::is_same::arg<0>::type, double>::value, "Wrong first argument type for function_traits of a function pointer"); @@ -730,10 +729,10 @@ TEST(FunctionTraitsTest, FirstArg) { int>::value, "Wrong first argument type for function_traits of a template function"); - static_assert(std::is_same::arg_t<0>, char>::value, + static_assert(std::is_same_v::arg_t<0>, char>, "Wrong first argument type for function_traits of a typedef using arg_t"); static_assert( - std::is_same::arg_t<0>, double>::value, + std::is_same_v::arg_t<0>, double>, "Wrong first argument type for function_traits of a function pointer using arg_t"); static_assert( std::is_same)>::arg_t<0>, @@ -743,10 +742,10 @@ TEST(FunctionTraitsTest, FirstArg) { TEST(FunctionTraitsTest, SecondArg) { using bout::utils::function_traits; - static_assert(std::is_same::arg<1>::type, int>::value, + static_assert(std::is_same_v::arg<1>::type, int>, "Wrong second argument type for function_traits of a typedef"); static_assert( - std::is_same::arg_t<1>, int>::value, + std::is_same_v::arg_t<1>, int>, "Wrong second argument type for function_traits of a typedef using arg_t"); } From d265442f309c6dcf45bbca2c5dd002a0576669f2 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 13:56:54 +0000 Subject: [PATCH 246/412] Use `if constexpr` with type-checking conditionals --- include/bout/globalindexer.hxx | 2 +- include/bout/interpolation.hxx | 2 +- include/bout/invertable_operator.hxx | 6 ++--- include/bout/operatorstencil.hxx | 10 ++++---- include/bout/region.hxx | 4 ++-- src/mesh/data/gridfromfile.cxx | 6 ++--- tests/unit/field/test_field_factory.cxx | 2 +- .../include/bout/test_hypre_interface.cxx | 10 ++++---- .../unit/include/bout/test_petsc_indexer.cxx | 14 +++++------ tests/unit/include/bout/test_petsc_matrix.cxx | 24 +++++++++---------- tests/unit/include/bout/test_stencil.cxx | 12 +++++----- 11 files changed, 46 insertions(+), 46 deletions(-) diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx index f9253b23b8..e756ead3b2 100644 --- a/include/bout/globalindexer.hxx +++ b/include/bout/globalindexer.hxx @@ -72,7 +72,7 @@ public: regionInnerX = intersection(bndryCandidate, indices.getRegion("RGN_INNER_X")); regionOuterX = intersection(bndryCandidate, indices.getRegion("RGN_OUTER_X")); - if (std::is_same_v) { + if constexpr (std::is_same_v) { regionLowerY = Region({}); regionUpperY = Region({}); } else { diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx index aa6b8358cb..aab3f61281 100644 --- a/include/bout/interpolation.hxx +++ b/include/bout/interpolation.hxx @@ -126,7 +126,7 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL : (var.getDirectionY() == YDirectionType::Standard); const T var_fa = is_unaligned ? toFieldAligned(var, "RGN_NOX") : var; - if (not std::is_base_of_v) { + if constexpr (not std::is_base_of_v) { // Field2D is axisymmetric, so YDirectionType::Standard and // YDirectionType::Aligned are equivalent, but trying to set // YDirectionType::Aligned explicitly is an error diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx index 0de77d5d1d..1940177bca 100644 --- a/include/bout/invertable_operator.hxx +++ b/include/bout/invertable_operator.hxx @@ -197,7 +197,7 @@ public: } // Add the RGN_WITHBNDRIES region to the mesh. Requires RGN_NOBNDRY to be defined. - if (std::is_same_v) { + if constexpr (std::is_same_v) { if (not localmesh->hasRegion3D("RGN_WITHBNDRIES")) { // This avoids all guard cells and corners but includes boundaries // Note we probably don't want to include periodic boundaries as these @@ -242,7 +242,7 @@ public: localmesh->addRegion3D("RGN_WITHBNDRIES", nocorner3D); } - } else if (std::is_same_v) { + } else if constexpr (std::is_same_v) { if (not localmesh->hasRegion2D("RGN_WITHBNDRIES")) { // This avoids all guard cells and corners but includes boundaries Region nocorner2D = localmesh->getRegion2D("RGN_NOBNDRY"); @@ -280,7 +280,7 @@ public: localmesh->addRegion2D("RGN_WITHBNDRIES", nocorner2D); } - } else if (std::is_same_v) { + } else if constexpr (std::is_same_v) { if (not localmesh->hasRegionPerp("RGN_WITHBNDRIES")) { // This avoids all guard cells and corners but includes boundaries Region nocornerPerp = localmesh->getRegionPerp("RGN_NOBNDRY"); diff --git a/include/bout/operatorstencil.hxx b/include/bout/operatorstencil.hxx index 1846dd059b..90ca73bc07 100644 --- a/include/bout/operatorstencil.hxx +++ b/include/bout/operatorstencil.hxx @@ -246,7 +246,7 @@ OperatorStencil squareStencil(Mesh* localmesh) { zero.xp(), zero.xm(), }; - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { offsets.insert(zero.yp()); offsets.insert(zero.ym()); offsets.insert(zero.xp().yp()); @@ -254,7 +254,7 @@ OperatorStencil squareStencil(Mesh* localmesh) { offsets.insert(zero.xm().yp()); offsets.insert(zero.xm().ym()); } - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { offsets.insert(zero.zp()); offsets.insert(zero.zm()); offsets.insert(zero.xp().zp()); @@ -262,7 +262,7 @@ OperatorStencil squareStencil(Mesh* localmesh) { offsets.insert(zero.xm().zp()); offsets.insert(zero.xm().zm()); } - if (std::is_same_v) { + if constexpr (std::is_same_v) { offsets.insert(zero.yp().zp()); offsets.insert(zero.yp().zm()); offsets.insert(zero.ym().zp()); @@ -294,11 +294,11 @@ OperatorStencil starStencil(Mesh* localmesh) { zero.xp(), zero.xm(), }; - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { offsets.insert(zero.yp()); offsets.insert(zero.ym()); } - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { offsets.insert(zero.zp()); offsets.insert(zero.zm()); } diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 3e10e04a25..5baf0454cd 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -521,7 +521,7 @@ public: int nz, int maxregionblocksize = MAXREGIONBLOCKSIZE) : ny(ny), nz(nz) { #if CHECK > 1 - if (std::is_base_of_v) { + if constexpr (std::is_base_of_v) { if (nz != 1) { throw BoutException( "Trying to make Region with nz = {:d}, but expected nz = 1", nz); @@ -537,7 +537,7 @@ public: } } - if (std::is_base_of_v) { + if constexpr (std::is_base_of_v) { if (ny != 1) { throw BoutException( "Trying to make Region with ny = {:d}, but expected ny = 1", ny); diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx index c2505b4839..5d871ac708 100644 --- a/src/mesh/data/gridfromfile.cxx +++ b/src/mesh/data/gridfromfile.cxx @@ -195,7 +195,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, } case 3: { // Check size if getting Field3D - if (bout::utils::is_Field2D_v or bout::utils::is_FieldPerp_v) { + if constexpr (bout::utils::is_Field2D_v or bout::utils::is_FieldPerp_v) { output_warn.write( "WARNING: Variable '{:s}' should be 2D, but has {:d} dimensions. Ignored\n", name, size.size()); @@ -272,7 +272,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, name, grid_xguards, mxg); } - if (not bout::utils::is_FieldPerp_v) { + if constexpr (not bout::utils::is_FieldPerp_v) { // Check if field dimensions are correct. y-direction if (grid_yguards > 0) { // including ghostpoints @@ -325,7 +325,7 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def, } } - if (not bout::utils::is_FieldPerp_v) { + if constexpr (not bout::utils::is_FieldPerp_v) { ///If field does not include ghost points in y-direction -> ///Upper and lower Y boundaries copied from nearest point if (grid_yguards == 0) { diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx index 7bb8c680ad..ca51b845b3 100644 --- a/tests/unit/field/test_field_factory.cxx +++ b/tests/unit/field/test_field_factory.cxx @@ -210,7 +210,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreateZStaggered) { auto expected = makeField( [](typename TypeParam::ind_type& index) -> BoutReal { auto offset = BoutReal{0.0}; - if (bout::utils::is_Field3D_v) { + if constexpr (bout::utils::is_Field3D_v) { offset = 0.5; } diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx index 0518cacac0..a56f061a6e 100644 --- a/tests/unit/include/bout/test_hypre_interface.cxx +++ b/tests/unit/include/bout/test_hypre_interface.cxx @@ -185,7 +185,7 @@ class HypreMatrixTest : public FakeMeshFixture { indexA = ind_type((1 + field.getNy()) * field.getNz() + 1, field.getNy(), field.getNz()); - if (std::is_same_v) { + if constexpr (std::is_same_v) { indexB = indexA.zp(); iWD0 = indexB.zm(); @@ -389,7 +389,7 @@ TYPED_TEST(HypreMatrixTest, YUp) { HypreMatrix matrix(this->indexer); - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_THROW(matrix.yup(), BoutException); return; } @@ -398,7 +398,7 @@ TYPED_TEST(HypreMatrixTest, YUp) { MockTransform* transform = this->pt; const BoutReal value = 42.0; - if (std::is_same_v) { + if constexpr (std::is_same_v) { expected(this->indexA, this->indexB) = value; } else { EXPECT_CALL(*transform, getWeightsForYUpApproximation( @@ -422,7 +422,7 @@ TYPED_TEST(HypreMatrixTest, YDown) { HypreMatrix matrix(this->indexer); - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_THROW(matrix.yup(), BoutException); return; } @@ -431,7 +431,7 @@ TYPED_TEST(HypreMatrixTest, YDown) { MockTransform* transform = this->pt; const BoutReal value = 42.0; - if (std::is_same_v) { + if constexpr (std::is_same_v) { expected(this->indexB, this->indexA) = value; } else { EXPECT_CALL(*transform, getWeightsForYDownApproximation( diff --git a/tests/unit/include/bout/test_petsc_indexer.cxx b/tests/unit/include/bout/test_petsc_indexer.cxx index 163913a1f7..082acafde6 100644 --- a/tests/unit/include/bout/test_petsc_indexer.cxx +++ b/tests/unit/include/bout/test_petsc_indexer.cxx @@ -107,7 +107,7 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { } // Check indices of Y guard cells are unique - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { BOUT_FOR(i, f.getRegion("RGN_YGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); @@ -177,7 +177,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalSquareIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalSquareIndexer.getMesh()->xend); - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_GE(i.y(), this->globalSquareIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->globalSquareIndexer.getMesh()->yend); } @@ -187,7 +187,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalStarIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalStarIndexer.getMesh()->xend); - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_GE(i.y(), this->globalStarIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->globalStarIndexer.getMesh()->yend); } @@ -197,7 +197,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->globalDefaultIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->globalDefaultIndexer.getMesh()->xend); - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_GE(i.y(), this->globalDefaultIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->globalDefaultIndexer.getMesh()->yend); } @@ -207,7 +207,7 @@ TYPED_TEST(IndexerTest, TestGetRegionNobndry) { BOUT_FOR(i, rgn) { EXPECT_GE(i.x(), this->localIndexer.getMesh()->xstart); EXPECT_LE(i.x(), this->localIndexer.getMesh()->xend); - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_GE(i.y(), this->localIndexer.getMesh()->ystart); EXPECT_LE(i.y(), this->localIndexer.getMesh()->yend); } @@ -229,7 +229,7 @@ TYPED_TEST(IndexerTest, TestGetRegionBndry) { TYPED_TEST(IndexerTest, TestGetRegionLowerY) { Region rgn; - if (std::is_same_v) { + if constexpr (std::is_same_v) { rgn = this->globalSquareIndexer.getRegionLowerY(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->globalStarIndexer.getRegionLowerY(); @@ -250,7 +250,7 @@ TYPED_TEST(IndexerTest, TestGetRegionLowerY) { TYPED_TEST(IndexerTest, TestGetRegionUpperY) { Region rgn; - if (std::is_same_v) { + if constexpr (std::is_same_v) { rgn = this->globalSquareIndexer.getRegionUpperY(); EXPECT_EQ(rgn.asUnique().size(), 0); rgn = this->globalStarIndexer.getRegionUpperY(); diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index dc6e3fd3cd..cc07145d8e 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -57,7 +57,7 @@ class PetscMatrixTest : public FakeMeshFixture { stencil(squareStencil(bout::globals::mesh)), indexer(std::make_shared>(bout::globals::mesh, stencil)) { indexA = ind_type(field.getNy() * field.getNz() + 1, field.getNy(), field.getNz()); - if (std::is_same_v) { + if constexpr (std::is_same_v) { indexB = indexA.zp(); } else { indexB = indexA.yp(); @@ -65,7 +65,7 @@ class PetscMatrixTest : public FakeMeshFixture { iWU0 = indexB.xm(); iWU1 = indexB; iWU2 = indexB.xp(); - if (std::is_same_v) { + if constexpr (std::is_same_v) { iWD0 = indexB.zm(); iWD1 = indexB; iWD2 = indexB.zp(); @@ -269,13 +269,13 @@ TYPED_TEST(PetscMatrixTest, TestYUp) { PetscMatrix expected(this->indexer, false); MockTransform* transform = this->pt; SCOPED_TRACE("YUp"); - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_THROW(matrix.yup(), BoutException); } else { const BoutReal val = 3.141592; - if (std::is_same_v) { + if constexpr (std::is_same_v) { expected(this->indexA, this->indexB) = val; - } else if (std::is_same_v) { + } else if constexpr (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexB.x(), this->indexA.y(), this->indexB.z(), 1)) @@ -302,12 +302,12 @@ TYPED_TEST(PetscMatrixTest, TestYDown) { const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YDown"); - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_THROW(matrix.ydown(), BoutException); } else { - if (std::is_same_v) { + if constexpr (std::is_same_v) { expected(this->indexB, this->indexA) = val; - } else if (std::is_same_v) { + } else if constexpr (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexA.x(), this->indexB.y(), this->indexA.z(), -1)) @@ -351,10 +351,10 @@ TYPED_TEST(PetscMatrixTest, TestYNextPos) { const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextPos"); - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_THROW(matrix.ynext(1), BoutException); } else { - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexB.x(), this->indexA.y(), this->indexB.z(), 1)) @@ -380,10 +380,10 @@ TYPED_TEST(PetscMatrixTest, TestYNextNeg) { const BoutReal val = 3.141592; MockTransform* transform = this->pt; SCOPED_TRACE("YNextNeg"); - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_THROW(matrix.ynext(-1), BoutException); } else { - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_CALL(*transform, getWeightsForYApproximation(this->indexA.x(), this->indexB.y(), this->indexA.z(), -1)) diff --git a/tests/unit/include/bout/test_stencil.cxx b/tests/unit/include/bout/test_stencil.cxx index dc0c9c1fc9..033a865154 100644 --- a/tests/unit/include/bout/test_stencil.cxx +++ b/tests/unit/include/bout/test_stencil.cxx @@ -127,15 +127,15 @@ TYPED_TEST(IndexOffsetStructTests, AddToIndex) { offset4 = {2, 3, -2}; EXPECT_EQ(this->zero + offset1, this->zero.xp()); EXPECT_EQ(offset1 + this->zero, this->zero.xp()); - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_EQ(this->zero + offset2, this->zero.yp(2)); EXPECT_EQ(offset2 + this->zero, this->zero.yp(2)); } - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_EQ(this->zero + offset3, this->zero.zp(11)); EXPECT_EQ(offset3 + this->zero, this->zero.zp(11)); } - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_EQ(this->zero + offset4, this->zero.xp(2).yp(3).zm(2)); EXPECT_EQ(offset4 + this->zero, this->zero.xp(2).yp(3).zm(2)); } @@ -145,13 +145,13 @@ TYPED_TEST(IndexOffsetStructTests, SubtractFromIndex) { IndexOffset offset1 = {1, 0, 0}, offset2 = {0, 2, 0}, offset3 = {0, 0, 11}, offset4 = {2, 3, -2}; EXPECT_EQ(this->zero - offset1, this->zero.xm()); - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_EQ(this->zero - offset2, this->zero.ym(2)); } - if (!std::is_same_v) { + if constexpr (!std::is_same_v) { EXPECT_EQ(this->zero - offset3, this->zero.zm(11)); } - if (std::is_same_v) { + if constexpr (std::is_same_v) { EXPECT_EQ(this->zero - offset4, this->zero.zp(2).xm(2).ym(3)); } } From afe76afccd3f1e66e9698504e1a7b871fd8771be Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 14:00:14 +0000 Subject: [PATCH 247/412] Tidy docstrings for `is_Field*_v` --- include/bout/traits.hxx | 28 +++++++++------------------- 1 file changed, 9 insertions(+), 19 deletions(-) diff --git a/include/bout/traits.hxx b/include/bout/traits.hxx index 15643064d3..4e03d6b526 100644 --- a/include/bout/traits.hxx +++ b/include/bout/traits.hxx @@ -12,58 +12,48 @@ class Options; namespace bout { namespace utils { -/// If `T` is derived from `Field`, provides the member constant -/// `value` equal to `true`. Otherwise `value is `false`. -/// -/// The following is C++14, but simplifies the use of `is_field`: -/// -/// template -/// constexpr bool is_field_v = is_field::value; +template +using is_Field = std::is_base_of; + +/// True if `T` is derived from `Field`, otherwise false /// /// Examples /// -------- /// /// template /// void print_field(const T& field) { -/// static_assert(bout::utils::is_field::value, +/// static_assert(bout::utils::is_Field_v, /// "print_field only works with Field2Ds, Field3Ds or FieldPerps") /// // implementation /// } -template -using is_Field = std::is_base_of; - template inline constexpr bool is_Field_v = std::is_base_of_v; -/// If `T` is derived from `Field2D`, provides the member constant -/// `value` equal to `true`. Otherwise `value is `false`. template using is_Field2D = std::is_base_of; +/// True if `T` is derived from `Field2D`, otherwise false template inline constexpr bool is_Field2D_v = std::is_base_of_v; -/// If `T` is derived from `Field3D`, provides the member constant -/// `value` equal to `true`. Otherwise `value is `false`. template using is_Field3D = std::is_base_of; +/// True if `T` is derived from `Field3D`, otherwise false template inline constexpr bool is_Field3D_v = std::is_base_of_v; -/// If `T` is derived from `FieldPerp`, provides the member constant -/// `value` equal to `true`. Otherwise `value is `false`. template using is_FieldPerp = std::is_base_of; +/// True if `T` is derived from `FieldPerp`, otherwise false template inline constexpr bool is_FieldPerp_v = std::is_base_of_v; -/// If `T` is derived from `Options`, provides the member constant -/// `value` equal to `true`. Otherwise `value is `false`. template using is_Options = std::is_base_of; +/// True if `T` is derived from `Options`, otherwise false template inline constexpr bool is_Options_v = std::is_base_of_v; From 9d51694d8d4c5cbea211c9ce5f2a4b01b78d35b5 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 14:06:38 +0000 Subject: [PATCH 248/412] Convert helper function to local lambda --- include/bout/solver.hxx | 10 ---------- src/solver/solver.cxx | 18 ++++++++++-------- 2 files changed, 10 insertions(+), 18 deletions(-) diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index d110d7ff17..896ce62965 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -399,16 +399,6 @@ protected: return in_vars != end(vars); } - /// Helper function for getLocalN: return the number of points to - /// evolve in \p f, plus the accumulator \p value - /// - /// If f.evolve_bndry, includes the boundary (NB: not guard!) points - /// - /// FIXME: This could be a lambda local to getLocalN with an `auto` - /// argument in C++14 - template - friend int local_N_sum(int value, const VarStr& f); - /// Vectors of variables to evolve std::vector> f2d; std::vector> f3d; diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx index 02e6ec6d04..1b7ec1fd74 100644 --- a/src/solver/solver.cxx +++ b/src/solver/solver.cxx @@ -973,12 +973,6 @@ int Solver::call_timestep_monitors(BoutReal simtime, BoutReal lastdt) { * Useful routines (protected) **************************************************************************/ -template -int local_N_sum(int value, const Solver::VarStr& f) { - const auto boundary_size = f.evolve_bndry ? size(f.var->getRegion("RGN_BNDRY")) : 0; - return value + boundary_size + size(f.var->getRegion("RGN_NOBNDRY")); -} - int Solver::getLocalN() { // Cache the value, so this is not repeatedly called. @@ -991,8 +985,16 @@ int Solver::getLocalN() { // Must be initialised ASSERT0(initialised); - const auto local_N_2D = std::accumulate(begin(f2d), end(f2d), 0, local_N_sum); - const auto local_N_3D = std::accumulate(begin(f3d), end(f3d), 0, local_N_sum); + // Return the number of points to evolve in f, plus the accumulator value. + // If f.evolve_bndry, includes the boundary (NB: not guard!) points + auto local_N_sum = [](int value, const auto& field) -> int { + const auto boundary_size = + field.evolve_bndry ? size(field.var->getRegion("RGN_BNDRY")) : 0; + return value + boundary_size + size(field.var->getRegion("RGN_NOBNDRY")); + }; + + const auto local_N_2D = std::accumulate(begin(f2d), end(f2d), 0, local_N_sum); + const auto local_N_3D = std::accumulate(begin(f3d), end(f3d), 0, local_N_sum); const auto local_N = local_N_2D + local_N_3D; cacheLocalN = local_N; From 6c7cd3e6bfca1452f9c43b27775cd3fd8ae6a089 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 14:06:52 +0000 Subject: [PATCH 249/412] Remove some out of date comments --- include/bout/region.hxx | 3 --- 1 file changed, 3 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 5baf0454cd..1cd36ccffe 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -649,7 +649,6 @@ public: auto currentIndices = getIndices(); // Lambda that returns true/false depending if the passed value is in maskIndices - // With C++14 T can be auto instead auto isInVector = [&](T val) { return std::binary_search(std::begin(maskIndices), std::end(maskIndices), val); }; @@ -673,7 +672,6 @@ public: auto currentIndices = getIndices(); // Lambda that returns true/false depending if the passed value is in maskIndices - // With C++14 T can be auto instead auto isInVector = [&](T val) { return mask[val]; }; // Erase elements of currentIndices that are in maskIndices @@ -699,7 +697,6 @@ public: auto currentIndices = getIndices(); // Lambda that returns true/false depending if the passed value is in otherIndices - // With C++14 T can be auto instead auto notInVector = [&](T val) { return !std::binary_search(std::begin(otherIndices), std::end(otherIndices), val); }; From 0920485732d33745ee8b30ffc6880236eef8a632 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 12 Feb 2024 14:16:01 +0000 Subject: [PATCH 250/412] Remove unnecessary `typename` in template --- include/bout/physicsmodel.hxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index 049ed46e59..ada97fc6fc 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -127,11 +127,11 @@ public: using preconfunc = int (PhysicsModel::*)(BoutReal t, BoutReal gamma, BoutReal delta); using jacobianfunc = int (PhysicsModel::*)(BoutReal t); - template >> + template >> using ModelPreconFunc = int (Model::*)(BoutReal t, BoutReal gamma, BoutReal delta); - template >> + template >> using ModelJacobianFunc = int (Model::*)(BoutReal t); PhysicsModel(); From a91b4aead0c6d54c17f3bafdcdf2b7b3ee5eb8a1 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Mon, 12 Feb 2024 14:28:16 +0000 Subject: [PATCH 251/412] Apply clang-format changes --- include/bout/operatorstencil.hxx | 38 ++++++++++++++++++-------------- include/bout/region.hxx | 7 +++--- 2 files changed, 26 insertions(+), 19 deletions(-) diff --git a/include/bout/operatorstencil.hxx b/include/bout/operatorstencil.hxx index 90ca73bc07..9a60f94ca7 100644 --- a/include/bout/operatorstencil.hxx +++ b/include/bout/operatorstencil.hxx @@ -45,9 +45,9 @@ /// subtracted from them. template struct IndexOffset { - static_assert(std::is_same_v || std::is_same_v - || std::is_same_v, - "IndexOffset only works with SpecificInd types"); + static_assert( + std::is_same_v || std::is_same_v || std::is_same_v, + "IndexOffset only works with SpecificInd types"); int dx = 0, dy = 0, dz = 0; const inline IndexOffset xp(int delta_x = 1) const { return {dx + delta_x, dy, dz}; } @@ -133,9 +133,9 @@ using OffsetIndPerp = IndexOffset; template class OperatorStencil { public: - static_assert(std::is_same_v || std::is_same_v - || std::is_same_v, - "OperatorStencil only works with SpecificInd types"); + static_assert( + std::is_same_v || std::is_same_v || std::is_same_v, + "OperatorStencil only works with SpecificInd types"); using offset = IndexOffset; using stencil_part = std::vector; using stencil_test = std::function; @@ -271,11 +271,14 @@ OperatorStencil squareStencil(Mesh* localmesh) { std::vector> offsetsVec(offsets.begin(), offsets.end()); stencil.add( [localmesh](T ind) -> bool { - return (localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend - && (std::is_same_v - || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend)) - && (std::is_same_v - || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend))); + return ( + localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend + && (std::is_same_v< + T, + IndPerp> || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend)) + && (std::is_same_v< + T, + Ind2D> || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend))); }, offsetsVec); stencil.add([](T UNUSED(ind)) -> bool { return true; }, {zero}); @@ -305,11 +308,14 @@ OperatorStencil starStencil(Mesh* localmesh) { std::vector> offsetsVec(offsets.begin(), offsets.end()); stencil.add( [localmesh](T ind) -> bool { - return (localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend - && (std::is_same_v - || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend)) - && (std::is_same_v - || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend))); + return ( + localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend + && (std::is_same_v< + T, + IndPerp> || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend)) + && (std::is_same_v< + T, + Ind2D> || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend))); }, offsetsVec); stencil.add([](T UNUSED(ind)) -> bool { return true; }, {zero}); diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 1cd36ccffe..cbaf0d0c31 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -482,9 +482,10 @@ template class Region { // Following prevents a Region being created with anything other // than Ind2D, Ind3D or IndPerp as template type - static_assert(std::is_base_of_v || std::is_base_of_v - || std::is_base_of_v, - "Region must be templated with one of IndPerp, Ind2D or Ind3D"); + static_assert( + std::is_base_of_v< + Ind2D, T> || std::is_base_of_v || std::is_base_of_v, + "Region must be templated with one of IndPerp, Ind2D or Ind3D"); public: using data_type = T; From f1a30a86712e8f291fe4041b015d7a5b574ef34b Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 14:41:11 +0000 Subject: [PATCH 252/412] CI: Delete default values from clang-tidy config --- .clang-tidy | 354 ---------------------------------------------------- 1 file changed, 354 deletions(-) diff --git a/.clang-tidy b/.clang-tidy index 48a434bc14..905a0b67a4 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -5,360 +5,6 @@ HeaderFilterRegex: '' AnalyzeTemporaryDtors: false FormatStyle: file CheckOptions: - - key: performance-unnecessary-copy-initialization.ExcludedContainerTypes - value: '' - - key: readability-suspicious-call-argument.PrefixSimilarAbove - value: '30' - - key: modernize-replace-auto-ptr.IncludeStyle - value: llvm - 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- key: cppcoreguidelines-narrowing-conversions.WarnOnEquivalentBitWidth - value: 'true' - - key: bugprone-misplaced-widening-cast.CheckImplicitCasts - value: 'false' - - key: cppcoreguidelines-non-private-member-variables-in-classes.IgnorePublicMemberVariables - value: 'false' - - key: modernize-loop-convert.MinConfidence - value: reasonable - - key: performance-unnecessary-value-param.AllowedTypes - value: '' - - key: readability-uniqueptr-delete-release.PreferResetCall - value: 'false' - - key: cppcoreguidelines-special-member-functions.AllowMissingMoveFunctionsWhenCopyIsDeleted - value: 'false' - - key: misc-definitions-in-headers.UseHeaderFileExtension - value: 'true' - - key: google-readability-namespace-comments.SpacesBeforeComments - value: '2' - - key: readability-function-cognitive-complexity.Threshold - value: '25' - - key: cppcoreguidelines-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic - value: 'true' - - key: readability-uppercase-literal-suffix.NewSuffixes - value: '' - - key: bugprone-suspicious-missing-comma.RatioThreshold - value: '0.200000' - - key: bugprone-argument-comment.IgnoreSingleArgument - value: '0' - - key: bugprone-narrowing-conversions.WarnOnEquivalentBitWidth - value: 'true' - - key: cppcoreguidelines-no-malloc.Allocations - value: '::malloc;::calloc' - - key: performance-faster-string-find.StringLikeClasses - value: '::std::basic_string;::std::basic_string_view' - - key: bugprone-sizeof-expression.WarnOnSizeOfIntegerExpression - value: 'false' - - key: bugprone-assert-side-effect.CheckFunctionCalls - value: 'false' - - key: bugprone-string-constructor.StringNames - value: '::std::basic_string;::std::basic_string_view' - - key: bugprone-narrowing-conversions.IgnoreConversionFromTypes - value: '' - - key: readability-function-size.BranchThreshold - value: '4294967295' - - key: bugprone-assert-side-effect.AssertMacros - value: assert,NSAssert,NSCAssert - - key: readability-function-size.StatementThreshold - value: '800' - - key: llvm-qualified-auto.AddConstToQualified - value: 'false' - - key: bugprone-signed-char-misuse.DiagnoseSignedUnsignedCharComparisons - value: 'true' - - key: readability-identifier-naming.IgnoreMainLikeFunctions - value: 'false' - - key: bugprone-exception-escape.IgnoredExceptions - value: '' - - key: readability-implicit-bool-conversion.AllowIntegerConditions - value: 'false' - - key: google-readability-function-size.StatementThreshold - value: '800' - - key: llvm-else-after-return.WarnOnConditionVariables - value: 'false' - - key: cppcoreguidelines-init-variables.MathHeader - value: '' - - key: bugprone-sizeof-expression.WarnOnSizeOfCompareToConstant - value: 'true' - - key: bugprone-reserved-identifier.AggressiveDependentMemberLookup - value: 'false' - - key: readability-suspicious-call-argument.DiceSimilarAbove - value: '70' - - key: readability-suspicious-call-argument.Dice - value: 'true' - - key: readability-suspicious-call-argument.Abbreviation - value: 'true' - - key: cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor - value: 'false' - - key: misc-throw-by-value-catch-by-reference.WarnOnLargeObjects - value: 'false' - - key: cppcoreguidelines-no-malloc.Deallocations - value: '::free' - - key: performance-inefficient-vector-operation.VectorLikeClasses - value: '::std::vector' - - key: bugprone-dangling-handle.HandleClasses - value: 'std::basic_string_view;std::experimental::basic_string_view' - - key: bugprone-implicit-widening-of-multiplication-result.IncludeStyle - value: llvm - - key: misc-unused-parameters.StrictMode - value: 'false' - - key: performance-unnecessary-value-param.IncludeStyle - value: llvm - - key: readability-suspicious-call-argument.JaroWinklerSimilarAbove - value: '85' - - key: readability-redundant-member-init.IgnoreBaseInCopyConstructors - value: 'false' - - key: llvm-else-after-return.WarnOnUnfixable - value: 'false' - - key: readability-simplify-subscript-expr.Types - value: '::std::basic_string;::std::basic_string_view;::std::vector;::std::array' - key: readability-identifier-length.IgnoredVariableNames value: '^n?[xyz]$' - key: readability-identifier-length.IgnoredParameterNames From 1d106aa3ce618ff1c6262ffb05a15225a4cea4f7 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 14:44:16 +0000 Subject: [PATCH 253/412] CI: Allow `f` as a parameter name --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index 905a0b67a4..cbbbf0b8c7 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -8,7 +8,7 @@ CheckOptions: - key: readability-identifier-length.IgnoredVariableNames value: '^n?[xyz]$' - key: readability-identifier-length.IgnoredParameterNames - value: '^[ijkxyz][01]?$' + value: '^[fijkxyz][01]?$' - key: readability-identifier-length.IgnoredLoopCounterNames value: '^[ijkxyz_]$' ... From 4dbc6825f89c84c5c67084556ae6c5a137c51d07 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 14:45:16 +0000 Subject: [PATCH 254/412] CI: Allow `d[xyz]` as a variable name --- .clang-tidy | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index cbbbf0b8c7..e2f2187c25 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -5,8 +5,10 @@ HeaderFilterRegex: '' AnalyzeTemporaryDtors: false FormatStyle: file CheckOptions: + + # Allow some common short names - key: readability-identifier-length.IgnoredVariableNames - value: '^n?[xyz]$' + value: '^[dn]?[xyz]$' - key: readability-identifier-length.IgnoredParameterNames value: '^[fijkxyz][01]?$' - key: readability-identifier-length.IgnoredLoopCounterNames From aa540d4c34e84d911aa12c0ed35c6bf801396035 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 14:53:21 +0000 Subject: [PATCH 255/412] CI: Ignore macros when trying to simplify boolean expressions --- .clang-tidy | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.clang-tidy b/.clang-tidy index e2f2187c25..a84f915f65 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -13,5 +13,10 @@ CheckOptions: value: '^[fijkxyz][01]?$' - key: readability-identifier-length.IgnoredLoopCounterNames value: '^[ijkxyz_]$' + + # Don't expand macros when simplifying boolean expressions, + # otherwise this breaks `ASSERT` macros! + - key: readability-simplify-boolean-expr.IgnoreMacros + value: 'true' ... From e92e3dc1b37dc909e0c8b918d9181d1727c8773d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 14:56:42 +0000 Subject: [PATCH 256/412] CI: Allow `i[xyz]` as parameter names --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index a84f915f65..cf8fd275d6 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -10,7 +10,7 @@ CheckOptions: - key: readability-identifier-length.IgnoredVariableNames value: '^[dn]?[xyz]$' - key: readability-identifier-length.IgnoredParameterNames - value: '^[fijkxyz][01]?$' + value: '^[fijkxyz][01xyz]?$' - key: readability-identifier-length.IgnoredLoopCounterNames value: '^[ijkxyz_]$' From 02591522bdd83e86611c9bba726329745b9515a7 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 14:58:15 +0000 Subject: [PATCH 257/412] CI: Disable check for "easily swappable parameters" --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index cf8fd275d6..7cd5b69b0f 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -1,5 +1,5 @@ --- -Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion' +Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' WarningsAsErrors: '' HeaderFilterRegex: '' AnalyzeTemporaryDtors: false From 01cec903ddce465177a87c9159015ccd0edbbb0d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 16:26:37 +0000 Subject: [PATCH 258/412] Fix a couple of warnings about array-decay-to-pointer Re-enable clang-tidy warning about same --- .clang-tidy | 2 +- include/bout/boutexception.hxx | 3 ++- include/bout/petsclib.hxx | 1 - src/sys/boutexception.cxx | 25 ++++++++++++------------- src/sys/petsclib.cxx | 12 ++++++++---- 5 files changed, 23 insertions(+), 20 deletions(-) diff --git a/.clang-tidy b/.clang-tidy index 7cd5b69b0f..48e4e39a68 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -1,5 +1,5 @@ --- -Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' +Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' WarningsAsErrors: '' HeaderFilterRegex: '' AnalyzeTemporaryDtors: false diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx index 243b819961..e041e56f74 100644 --- a/include/bout/boutexception.hxx +++ b/include/bout/boutexception.hxx @@ -6,6 +6,7 @@ class BoutException; #include "bout/build_config.hxx" +#include #include #include #include @@ -38,7 +39,7 @@ protected: std::string message; #if BOUT_USE_BACKTRACE static constexpr unsigned int TRACE_MAX = 128; - void* trace[TRACE_MAX]; + std::array trace{}; int trace_size; char** messages; #endif diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index dd3daa28aa..043dacb73f 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -125,7 +125,6 @@ public: private: static int count; ///< How many instances? - static char help[]; ///< Help string // Command-line arguments static int* pargc; diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx index 9b21303cae..3bc352771b 100644 --- a/src/sys/boutexception.cxx +++ b/src/sys/boutexception.cxx @@ -13,7 +13,9 @@ #include #endif +#include #include +#include #include @@ -74,18 +76,15 @@ std::string BoutException::getBacktrace() const { const auto syscom = fmt::format( FMT_STRING("addr2line {:p} -Cfpie {:.{}s} 2> /dev/null"), ptr, messages[i], p); // last parameter is the file name of the symbol - FILE* fp = popen(syscom.c_str(), "r"); - if (fp != nullptr) { - char out[1024]; - char* retstr; + FILE* file = popen(syscom.c_str(), "r"); + if (file != nullptr) { + std::array out{}; + char* retstr = nullptr; std::string buf; - do { - retstr = fgets(out, sizeof(out) - 1, fp); - if (retstr != nullptr) { - buf += retstr; - } - } while (retstr != nullptr); - int status = pclose(fp); + while ((retstr = fgets(out.data(), out.size() - 1, file)) != nullptr) { + buf += retstr; + } + int status = pclose(file); if (status == 0) { backtrace_message += buf; } @@ -100,7 +99,7 @@ std::string BoutException::getBacktrace() const { void BoutException::makeBacktrace() { #if BOUT_USE_BACKTRACE - trace_size = backtrace(trace, TRACE_MAX); - messages = backtrace_symbols(trace, trace_size); + trace_size = backtrace(trace.data(), TRACE_MAX); + messages = backtrace_symbols(trace.data(), trace_size); #endif } diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index b99c51320c..8b92d1abe0 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -1,4 +1,4 @@ -#include "bout/build_config.hxx" +#include "bout/build_defines.hxx" #if BOUT_HAS_PETSC @@ -12,12 +12,16 @@ // Define all the static member variables int PetscLib::count = 0; -char PetscLib::help[] = "BOUT++: Uses finite difference methods to solve plasma fluid " - "problems in curvilinear coordinates"; int* PetscLib::pargc = nullptr; char*** PetscLib::pargv = nullptr; PetscLogEvent PetscLib::USER_EVENT = 0; +namespace { +constexpr const char* PetscLibHelp = + "BOUT++: Uses finite difference methods to solve plasma fluid " + "problems in curvilinear coordinates"; +} + PetscLib::PetscLib(Options* opt) { BOUT_OMP(critical(PetscLib)) { @@ -31,7 +35,7 @@ PetscLib::PetscLib(Options* opt) { output << "Initialising PETSc\n"; PETSC_COMM_WORLD = BoutComm::getInstance()->getComm(); - PetscInitialize(pargc, pargv, nullptr, help); + PetscInitialize(pargc, pargv, nullptr, PetscLibHelp); PetscPopSignalHandler(); PetscLogEventRegister("Total BOUT++", 0, &USER_EVENT); From 485e8fec6150caecb4decee007228a66b60706d6 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 16:26:51 +0000 Subject: [PATCH 259/412] CI: Re-enable warning about varargs Ok now we're using fmt --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index 48e4e39a68..8dd259ec96 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -1,5 +1,5 @@ --- -Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' +Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' WarningsAsErrors: '' HeaderFilterRegex: '' AnalyzeTemporaryDtors: false From d08563b0f1a4a42dd77708ce53c8109e13d52db6 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 16:29:46 +0000 Subject: [PATCH 260/412] CI: Document why some checks are disabled --- .clang-tidy | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index 8dd259ec96..852939f63c 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -18,5 +18,25 @@ CheckOptions: # otherwise this breaks `ASSERT` macros! - key: readability-simplify-boolean-expr.IgnoreMacros value: 'true' -... +--- + +Disabled checks and reasons: + +These are all basically unavoidable in HPC numeric code: +-readability-magic-numbers +-cppcoreguidelines-avoid-magic-numbers +-cppcoreguidelines-pro-bounds-pointer-arithmetic +-readability-function-cognitive-complexity +-bugprone-easily-swappable-parameters + +This doesn't work very well: +-clang-analyzer-optin.mpi* + +This is a suggestion, and is perfectly fine: +-misc-no-recursion + +Expensive (and noisy, because we let exceptions escape from `main`): +-bugprone-exception-escape +TODO: This would be good to fix and re-enable: +-misc-non-private-member-variables-in-classes From fca7c4235e0cea3b96d730e1ce3f135c11ea6d19 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 16:58:58 +0000 Subject: [PATCH 261/412] CI: Re-enable a couple of accidentally disabled checks --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index 852939f63c..3be0af4917 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -1,5 +1,5 @@ --- -Checks: 'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' +Checks: 'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' WarningsAsErrors: '' HeaderFilterRegex: '' AnalyzeTemporaryDtors: false From 0c2d8f8205a8e825e1ba1e51b29369cc205316d8 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 17:00:28 +0000 Subject: [PATCH 262/412] Fix some other clang-tidy warnings arising from `BoutException` --- include/bout/boutexception.hxx | 13 ++++--------- src/sys/boutexception.cxx | 11 +++++++---- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx index e041e56f74..238c88654c 100644 --- a/include/bout/boutexception.hxx +++ b/include/bout/boutexception.hxx @@ -1,10 +1,7 @@ +#ifndef BOUT_EXCEPTION_H +#define BOUT_EXCEPTION_H -class BoutException; - -#ifndef __BOUT_EXCEPTION_H__ -#define __BOUT_EXCEPTION_H__ - -#include "bout/build_config.hxx" +#include "bout/build_defines.hxx" #include #include @@ -33,9 +30,7 @@ public: /// backtrace (if available) std::string getBacktrace() const; - const std::string header{"====== Exception thrown ======\n"}; - -protected: +private: std::string message; #if BOUT_USE_BACKTRACE static constexpr unsigned int TRACE_MAX = 128; diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx index 3bc352771b..8e69e35068 100644 --- a/src/sys/boutexception.cxx +++ b/src/sys/boutexception.cxx @@ -1,11 +1,9 @@ -#include "bout/build_config.hxx" +#include "bout/build_defines.hxx" #include #include #include -#include #include -#include #include #if BOUT_USE_BACKTRACE @@ -19,6 +17,10 @@ #include +namespace{ +const std::string header{"====== Exception thrown ======\n"}; +} + void BoutParallelThrowRhsFail(int status, const char* message) { int allstatus; MPI_Allreduce(&status, &allstatus, 1, MPI_INT, MPI_LOR, BoutComm::get()); @@ -41,7 +43,8 @@ BoutException::~BoutException() { // just clear everything msg_stack.clear(); #if BOUT_USE_BACKTRACE - free(messages); + // Call required for memory allocated by `backtrace_symbols` + free(messages); // NOLINT #endif } From 7290aaeacd5052858878ef1be53cd2cae83f35a8 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 17:12:06 +0000 Subject: [PATCH 263/412] Declare some `PetscLib` static members `inline` Also locally disable buggy clang-tidy warning --- include/bout/petsclib.hxx | 10 ++++++---- src/sys/petsclib.cxx | 6 ------ 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index 043dacb73f..ed59504781 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -124,16 +124,18 @@ public: static BoutException SNESFailure(SNES& snes); private: - static int count; ///< How many instances? + // NOLINTBEGIN(cppcoreguidelines-avoid-non-const-global-variables) + static inline int count = 0; ///< How many instances? // Command-line arguments - static int* pargc; - static char*** pargv; + static inline int* pargc = nullptr; + static inline char*** pargv = nullptr; // Prefix for object-specific options std::string options_prefix; - static PetscLogEvent USER_EVENT; + static inline PetscLogEvent USER_EVENT; + // NOLINTEND(cppcoreguidelines-avoid-non-const-global-variables) void setPetscOptions(Options& options, const std::string& pass_options_prefix); }; diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index 8b92d1abe0..d9568c759e 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -10,12 +10,6 @@ #include "petscsnes.h" -// Define all the static member variables -int PetscLib::count = 0; -int* PetscLib::pargc = nullptr; -char*** PetscLib::pargv = nullptr; -PetscLogEvent PetscLib::USER_EVENT = 0; - namespace { constexpr const char* PetscLibHelp = "BOUT++: Uses finite difference methods to solve plasma fluid " From 61d50c8ad452a8c1aac905b31314f0ce7efa0952 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 13 Feb 2024 17:43:03 +0000 Subject: [PATCH 264/412] Fix a bunch of clang-tidy warnings in `PetscLib` --- include/bout/petsclib.hxx | 32 ++++++++------- src/sys/petsclib.cxx | 83 ++++++++++++++++++++++----------------- 2 files changed, 63 insertions(+), 52 deletions(-) diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index ed59504781..2b6ebef77d 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -43,12 +43,10 @@ * **************************************************************************/ -class PetscLib; +#ifndef BOUT_PETSCLIB_H +#define BOUT_PETSCLIB_H -#ifndef __PETSCLIB_H__ -#define __PETSCLIB_H__ - -#include "bout/build_config.hxx" +#include "bout/build_defines.hxx" class Options; @@ -66,7 +64,8 @@ class Options; #include "bout/boutexception.hxx" -#define BOUT_DO_PETSC(cmd) PetscLib::assertIerr(cmd, #cmd) +// NOLINTNEXTLINE(cppcoreguidelines-macro-usage) +#define BOUT_DO_PETSC(cmd) PetscLib::assertIerr((cmd), #cmd) /*! * Handles initialisation and finalisation of PETSc library. @@ -81,6 +80,11 @@ public: */ explicit PetscLib(Options* opt = nullptr); + PetscLib(const PetscLib&) = default; + PetscLib(PetscLib&&) = default; + PetscLib& operator=(const PetscLib&) = default; + PetscLib& operator=(PetscLib&&) = default; + /*! * Calls PetscFinalize when all PetscLib instances are destroyed */ @@ -92,9 +96,9 @@ public: * PetscLib are created. * The arguments will be passed to PetscInitialize() */ - static void setArgs(int& c, char**& v) { - pargc = &c; - pargv = &v; + static void setArgs(int& argc, char**& argv) { + pargc = &argc; + pargv = &argv; } /// Set options for a KSP linear solver that uses the options specific to this PetscLib, @@ -115,9 +119,9 @@ public: */ static void cleanup(); - static inline void assertIerr(PetscErrorCode ierr, std::string op = "PETSc operation") { - if (ierr) { - throw BoutException("{:s} failed with {:d}", op, ierr); + static inline void assertIerr(PetscErrorCode ierr, const std::string& petsc_op = "PETSc operation") { + if (ierr != 0) { + throw BoutException("{:s} failed with {:d}", petsc_op, ierr); } } @@ -136,8 +140,6 @@ private: static inline PetscLogEvent USER_EVENT; // NOLINTEND(cppcoreguidelines-avoid-non-const-global-variables) - - void setPetscOptions(Options& options, const std::string& pass_options_prefix); }; #ifndef PETSC_VERSION_GE @@ -177,4 +179,4 @@ public: #endif // BOUT_HAS_PETSC -#endif // __PETSCLIB_H__ +#endif // BOUT_PETSCLIB_H diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index d9568c759e..33a0deb3b3 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -3,17 +3,58 @@ #if BOUT_HAS_PETSC #include "bout/boutcomm.hxx" +#include "bout/boutexception.hxx" #include "bout/openmpwrap.hxx" #include "bout/options.hxx" -#include -#include +#include "bout/output.hxx" +#include "bout/petsclib.hxx" -#include "petscsnes.h" +#include +#include +#include +#include +#include +#include +#include + +#include namespace { constexpr const char* PetscLibHelp = "BOUT++: Uses finite difference methods to solve plasma fluid " "problems in curvilinear coordinates"; + +void setPetscOptions(Options& options, const std::string& prefix) { + // Pass all options in the section to PETSc + for (const auto& child : options.getChildren()) { + if (not child.second.isValue()) { + throw BoutException("Found subsection {} in {} when reading PETSc options - only " + "values are allowed in the PETSc options, not subsections", + child.first, options.str()); + } + + // Note, option names in the input file don't start with "-", but need to be passed + // to PETSc with "-" prepended + auto petsc_option_name = "-" + prefix + child.first; + + auto str_value = child.second.as(); + // "true" is the value given to an option with no value, when read from BOUT.inp. Also + // when nullptr is passed to PetscOptionsSetValue for a boolean option, it defaults to + // true so we should always be OK passing nullptr for null or "true". + const char* value = str_value == "true" ? nullptr : str_value.c_str(); + +#if PETSC_VERSION_GE(3, 7, 0) + const auto ierr = PetscOptionsSetValue(nullptr, petsc_option_name.c_str(), value); +#else + // no PetscOptions as first argument + const auto ierr = PetscOptionsSetValue(petsc_option_name.c_str(), value); +#endif + if (ierr != 0) { + throw BoutException("PetscOptionsSetValue returned error code {} when setting {}", + ierr, petsc_option_name); + } + } +} } PetscLib::PetscLib(Options* opt) { @@ -91,43 +132,11 @@ void PetscLib::cleanup() { } } -void PetscLib::setPetscOptions(Options& options, const std::string& prefix) { - // Pass all options in the section to PETSc - for (auto& i : options.getChildren()) { - if (not i.second.isValue()) { - throw BoutException("Found subsection {} in {} when reading PETSc options - only " - "values are allowed in the PETSc options, not subsections", - i.first, options.str()); - } - - // Note, option names in the input file don't start with "-", but need to be passed - // to PETSc with "-" prepended - auto petsc_option_name = "-" + prefix + i.first; - - auto str_value = i.second.as(); - // "true" is the value given to an option with no value, when read from BOUT.inp. Also - // when nullptr is passed to PetscOptionsSetValue for a boolean option, it defaults to - // true so we should always be OK passing nullptr for null or "true". - const char* value = str_value == "true" ? nullptr : str_value.c_str(); - -#if PETSC_VERSION_GE(3, 7, 0) - const auto ierr = PetscOptionsSetValue(nullptr, petsc_option_name.c_str(), value); -#else - // no PetscOptions as first argument - const auto ierr = PetscOptionsSetValue(petsc_option_name.c_str(), value); -#endif - if (ierr) { - throw BoutException("PetscOptionsSetValue returned error code {} when setting {}", - ierr, petsc_option_name); - } - } -} - BoutException PetscLib::SNESFailure(SNES& snes) { - SNESConvergedReason reason; + SNESConvergedReason reason = SNES_CONVERGED_ITERATING; BOUT_DO_PETSC(SNESGetConvergedReason(snes, &reason)); #if PETSC_VERSION_GE(3, 15, 0) - const char* message; + const char* message{nullptr}; BOUT_DO_PETSC(SNESGetConvergedReasonString(snes, &message)); #else const char* message{""}; From 2f25d54dc3e128ce9d6e6f1f9d55491716e60968 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Tue, 13 Feb 2024 17:51:46 +0000 Subject: [PATCH 265/412] Apply clang-format changes --- include/bout/petsclib.hxx | 5 +++-- src/sys/boutexception.cxx | 2 +- src/sys/petsclib.cxx | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index 2b6ebef77d..35334ce773 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -119,7 +119,8 @@ public: */ static void cleanup(); - static inline void assertIerr(PetscErrorCode ierr, const std::string& petsc_op = "PETSc operation") { + static inline void assertIerr(PetscErrorCode ierr, + const std::string& petsc_op = "PETSc operation") { if (ierr != 0) { throw BoutException("{:s} failed with {:d}", petsc_op, ierr); } @@ -129,7 +130,7 @@ public: private: // NOLINTBEGIN(cppcoreguidelines-avoid-non-const-global-variables) - static inline int count = 0; ///< How many instances? + static inline int count = 0; ///< How many instances? // Command-line arguments static inline int* pargc = nullptr; diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx index 8e69e35068..c19ecd7602 100644 --- a/src/sys/boutexception.cxx +++ b/src/sys/boutexception.cxx @@ -17,7 +17,7 @@ #include -namespace{ +namespace { const std::string header{"====== Exception thrown ======\n"}; } diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index 33a0deb3b3..bfcd7d6314 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -55,7 +55,7 @@ void setPetscOptions(Options& options, const std::string& prefix) { } } } -} +} // namespace PetscLib::PetscLib(Options* opt) { BOUT_OMP(critical(PetscLib)) From 407555084e5fa8b760f3958c60b2f7dd673ca3c9 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 13 Feb 2024 11:04:31 -0800 Subject: [PATCH 266/412] Update src/sys/boutexception.cxx Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- src/sys/boutexception.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx index c19ecd7602..825fb37e28 100644 --- a/src/sys/boutexception.cxx +++ b/src/sys/boutexception.cxx @@ -87,7 +87,7 @@ std::string BoutException::getBacktrace() const { while ((retstr = fgets(out.data(), out.size() - 1, file)) != nullptr) { buf += retstr; } - int status = pclose(file); + int const status = pclose(file); if (status == 0) { backtrace_message += buf; } From e8105203f7c0dcc561dc54af7d28da043eae8242 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 14 Feb 2024 09:22:27 -0800 Subject: [PATCH 267/412] CVode solver: Remove accidental Options copy In `create_constraints` the variable options were being copied, so that the `positivity_constraint` documentation was in a copy that was discarded. Should use a reference rather than copy. --- src/solver/impls/cvode/cvode.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 3e53f783e0..c17bed420c 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -485,7 +485,7 @@ CvodeSolver::create_constraints(const std::vector>& fields) { constraints.reserve(fields.size()); std::transform(begin(fields), end(fields), std::back_inserter(constraints), [](const VarStr& f) { - auto f_options = Options::root()[f.name]; + auto& f_options = Options::root()[f.name]; const auto value = f_options["positivity_constraint"] .doc(fmt::format("Constraint to apply to {} if " From cdd72e7b8360e6e57b72cf22a6bf33b04eb8c3c0 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 14 Feb 2024 09:28:06 -0800 Subject: [PATCH 268/412] Options: Add comment to deleted copy constructor & assignment When a compiler error is issued, it will usually print the line where the method is deleted. --- include/bout/options.hxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 7330afdbcb..64bebd0cc0 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -224,7 +224,7 @@ public: using InitializerList = std::initializer_list>; /// Construct with a nested initializer list - /// This allows Options trees to be constructed, using a mix of types. + /// This allows Options trees to be constructed using a mix of types. /// /// Example: { {"key1", 42}, {"key2", field} } /// @@ -238,7 +238,7 @@ public: /// /// Option option2 = option1.copy(); /// - Options(const Options& other) = delete; + Options(const Options& other) = delete; // Use a reference or .copy() method /// Copy assignment must be explicit /// @@ -248,7 +248,7 @@ public: /// /// option2.value = option1.value; /// - Options& operator=(const Options& other) = delete; + Options& operator=(const Options& other) = delete; // Use a reference or .copy() method /// Make a deep copy of this Options, /// recursively copying children. From 46b03c7ad6316d4ae6d22aa6fd44275d9d5581a8 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 15 Feb 2024 21:35:03 +0100 Subject: [PATCH 269/412] Ensure test has zoidberg --- .../test-fci-boundary/CMakeLists.txt | 25 +++++++++++-------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt index 3349d88994..bf25cd7c57 100644 --- a/tests/integrated/test-fci-boundary/CMakeLists.txt +++ b/tests/integrated/test-fci-boundary/CMakeLists.txt @@ -2,18 +2,21 @@ bout_add_mms_test(test-fci-boundary SOURCES get_par_bndry.cxx USE_RUNTEST USE_DATA_BOUT_INP + REQUIRES zoidberg_FOUND PROCESSORS 1 ) -set(gridfile ${CMAKE_CURRENT_BINARY_DIR}/grid.fci.nc) -add_custom_command(OUTPUT ${gridfile} - COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile} - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py - DEPENDS grid.py - IMPLICIT_DEPENDS ${CMAKE_CURRENT_BINARY_DIR} - COMMENT "Creating test-fci-boundary grid file" +if (zoidberg_FOUND) + set(gridfile ${CMAKE_CURRENT_BINARY_DIR}/grid.fci.nc) + add_custom_command(OUTPUT ${gridfile} + COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py + DEPENDS grid.py + IMPLICIT_DEPENDS ${CMAKE_CURRENT_BINARY_DIR} + COMMENT "Creating test-fci-boundary grid file" ) -add_custom_target(test-fci-boundary-grid DEPENDS ${gridfile}) -add_dependencies(test-fci-boundary - test-fci-boundary-grid) + add_custom_target(test-fci-boundary-grid DEPENDS ${gridfile}) + add_dependencies(test-fci-boundary + test-fci-boundary-grid) +endif() From 53cd0cc58c81c85d5053e3467b5d9c91889718e9 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 15 Feb 2024 18:45:48 -0800 Subject: [PATCH 270/412] CopyableOptions: Add constructor from char* C++ compilers can cast char* to bool, rather than std::string. --- include/bout/options.hxx | 3 +++ 1 file changed, 3 insertions(+) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 64bebd0cc0..e8b9cb2085 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -212,6 +212,9 @@ public: template CopyableOptions(T value) : value(std::move(value)) {} + /// Special case for char*, which can otherwise become cast to bool + CopyableOptions(const char* value): value(std::string(value)) {} + CopyableOptions( std::initializer_list> children) : children(children) {} From cc48b1b5a276ff7479e6ab69ed3e20fa78671cb7 Mon Sep 17 00:00:00 2001 From: bendudson Date: Fri, 16 Feb 2024 02:47:07 +0000 Subject: [PATCH 271/412] Apply clang-format changes --- include/bout/options.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index e8b9cb2085..839c847289 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -213,7 +213,7 @@ public: CopyableOptions(T value) : value(std::move(value)) {} /// Special case for char*, which can otherwise become cast to bool - CopyableOptions(const char* value): value(std::string(value)) {} + CopyableOptions(const char* value) : value(std::string(value)) {} CopyableOptions( std::initializer_list> children) From 62f3d2c5b9a0b49273382554e76ae9eec16e86e7 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 20 Feb 2024 09:37:28 +0100 Subject: [PATCH 272/412] Add number of OpenMP threads to dump file --- src/bout++.cxx | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/bout++.cxx b/src/bout++.cxx index 481a928bec..4d5538da14 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -715,6 +715,13 @@ void addBuildFlagsToOptions(Options& options) { options["use_backtrace"].force(bout::build::use_backtrace); options["use_color"].force(bout::build::use_color); options["use_openmp"].force(bout::build::use_openmp); + options["openmp_threads"].force( +#ifdef _OPENMP + omp_get_max_threads() +#else + 1 +#endif + ); options["use_output_debug"].force(bout::build::use_output_debug); options["use_sigfpe"].force(bout::build::use_sigfpe); options["use_signal"].force(bout::build::use_signal); From dc89b520774bd56f9d52322b731d2f16ddfee71a Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Tue, 20 Feb 2024 08:46:03 +0000 Subject: [PATCH 273/412] Apply clang-format changes --- src/bout++.cxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/bout++.cxx b/src/bout++.cxx index 4d5538da14..0a2f2b8696 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -717,11 +717,11 @@ void addBuildFlagsToOptions(Options& options) { options["use_openmp"].force(bout::build::use_openmp); options["openmp_threads"].force( #ifdef _OPENMP - omp_get_max_threads() + omp_get_max_threads() #else - 1 + 1 #endif - ); + ); options["use_output_debug"].force(bout::build::use_output_debug); options["use_sigfpe"].force(bout::build::use_sigfpe); options["use_signal"].force(bout::build::use_signal); From 2d289cc8a0e8e2a3f8f7c5a486d0c9804a3c248b Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 03:00:24 +0100 Subject: [PATCH 274/412] Ignore number of openmp_threads in test --- tests/integrated/test-squash/runtest | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integrated/test-squash/runtest b/tests/integrated/test-squash/runtest index 692d561c59..c79cba0faf 100755 --- a/tests/integrated/test-squash/runtest +++ b/tests/integrated/test-squash/runtest @@ -15,7 +15,7 @@ import os.path # cores: 4 IGNORED_VARS_PATTERN = re.compile( - "(wtime|ncalls|arkode|cvode|run_id|run_restart_from|M.?SUB|N.?PE|iteration|wall_time|has_legacy_netcdf|hist_hi).*" + "(wtime|ncalls|arkode|cvode|run_id|run_restart_from|M.?SUB|N.?PE|iteration|wall_time|has_legacy_netcdf|hist_hi|openmp_threads).*" ) From 2d9858af2e24f1654547c8d349ce7ae6ffc88c58 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 21 Feb 2024 02:12:45 +0000 Subject: [PATCH 275/412] Apply black changes --- tests/MMS/diffusion2/runtest | 2 +- tools/tokamak_grids/all/grid2bout.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest index d915018d8d..6039c6faa6 100755 --- a/tests/MMS/diffusion2/runtest +++ b/tests/MMS/diffusion2/runtest @@ -27,7 +27,7 @@ build_and_log("MMS diffusion test") inputs = [ ("X", ["mesh:nx"]), ("Y", ["mesh:ny"]), - ("Z", ["MZ"]) # , + ("Z", ["MZ"]), # , # ("XYZ", ["mesh:nx", "mesh:ny", "MZ"]) ] diff --git a/tools/tokamak_grids/all/grid2bout.py b/tools/tokamak_grids/all/grid2bout.py index da62a37aeb..6520e8f116 100644 --- a/tools/tokamak_grids/all/grid2bout.py +++ b/tools/tokamak_grids/all/grid2bout.py @@ -3,6 +3,7 @@ """ + from __future__ import print_function from numpy import max From 694d8c010fcf8675e6e3039c7873c308c68e708f Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 10:54:06 +0100 Subject: [PATCH 276/412] Avoid some #if branching for openmp --- include/bout/array.hxx | 8 -------- include/bout/openmpwrap.hxx | 2 ++ src/bout++.cxx | 14 ++------------ .../laplace/impls/multigrid/multigrid_laplace.cxx | 4 ---- 4 files changed, 4 insertions(+), 24 deletions(-) diff --git a/include/bout/array.hxx b/include/bout/array.hxx index 060b4900a1..822ad9af2c 100644 --- a/include/bout/array.hxx +++ b/include/bout/array.hxx @@ -375,17 +375,9 @@ private: * @param[in] cleanup If set to true, deletes all dataBlock and clears the store */ static storeType& store(bool cleanup = false) { -#ifdef _OPENMP static arenaType arena(omp_get_max_threads()); -#else - static arenaType arena(1); -#endif if (!cleanup) { -#ifdef _OPENMP return arena[omp_get_thread_num()]; -#else - return arena[0]; -#endif } // Clean by deleting all data -- possible that just stores.clear() is diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 032705e61a..82f5940afa 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -39,6 +39,8 @@ #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else #define BOUT_OMP(...) +int constexpr omp_get_max_threads(){ return 1; } +int constexpr omp_get_thread_num(){ return 0; } #endif //Perhaps want to cleanup local helpers with below, but DON'T! diff --git a/src/bout++.cxx b/src/bout++.cxx index 0a2f2b8696..ca817d3b51 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -582,11 +582,7 @@ void printCompileTimeOptions() { output_info.write(_("\tSUNDIALS support {}\n"), is_enabled(has_sundials)); output_info.write(_("\tBacktrace in exceptions {}\n"), is_enabled(use_backtrace)); output_info.write(_("\tColour in logs {}\n"), is_enabled(use_color)); - output_info.write(_("\tOpenMP parallelisation {}"), is_enabled(use_openmp)); -#ifdef _OPENMP - output_info.write(_(", using {} threads"), omp_get_max_threads()); -#endif - output_info.write("\n"); + output_info.write(_("\tOpenMP parallelisation {}, using {} threads\n"), is_enabled(use_openmp), omp_get_max_threads()); output_info.write(_("\tExtra debug output {}\n"), is_enabled(use_output_debug)); output_info.write(_("\tFloating-point exceptions {}\n"), is_enabled(use_sigfpe)); output_info.write(_("\tSignal handling support {}\n"), is_enabled(use_signal)); @@ -715,13 +711,7 @@ void addBuildFlagsToOptions(Options& options) { options["use_backtrace"].force(bout::build::use_backtrace); options["use_color"].force(bout::build::use_color); options["use_openmp"].force(bout::build::use_openmp); - options["openmp_threads"].force( -#ifdef _OPENMP - omp_get_max_threads() -#else - 1 -#endif - ); + options["openmp_threads"].force(omp_get_max_threads()); options["use_output_debug"].force(bout::build::use_output_debug); options["use_sigfpe"].force(bout::build::use_sigfpe); options["use_signal"].force(bout::build::use_signal); diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx index beb9262ed8..f124397c78 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx @@ -67,7 +67,6 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ opts->get("atol", atol, pow(10.0, -20), true); opts->get("dtol", dtol, pow(10.0, 5), true); opts->get("smtype", mgsm, 1, true); -#if BOUT_USE_OPENMP if (mgsm != 0 && omp_get_max_threads() > 1) { output_warn << "WARNING: in multigrid Laplace solver, for smtype!=0 the smoothing " "cannot be parallelised with OpenMP threads." @@ -75,7 +74,6 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ << " Consider using smtype=0 instead when using OpenMP threads." << endl; } -#endif opts->get("jacomega", omega, 0.8, true); opts->get("solvertype", mgplag, 1, true); opts->get("cftype", cftype, 0, true); @@ -218,11 +216,9 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ } else { output << "Multigrid solver with merging " << mgmpi << endl; } -#if BOUT_USE_OPENMP BOUT_OMP(parallel) BOUT_OMP(master) { output << "Num threads = " << omp_get_num_threads() << endl; } -#endif } } From 436b6cd56947157228c9bb08318356a4f2af9aa1 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 21 Feb 2024 09:54:49 +0000 Subject: [PATCH 277/412] Apply clang-format changes --- include/bout/openmpwrap.hxx | 4 ++-- src/bout++.cxx | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 82f5940afa..0dd05e53df 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -39,8 +39,8 @@ #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else #define BOUT_OMP(...) -int constexpr omp_get_max_threads(){ return 1; } -int constexpr omp_get_thread_num(){ return 0; } +int constexpr omp_get_max_threads() { return 1; } +int constexpr omp_get_thread_num() { return 0; } #endif //Perhaps want to cleanup local helpers with below, but DON'T! diff --git a/src/bout++.cxx b/src/bout++.cxx index ca817d3b51..a83e278d9c 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -582,7 +582,8 @@ void printCompileTimeOptions() { output_info.write(_("\tSUNDIALS support {}\n"), is_enabled(has_sundials)); output_info.write(_("\tBacktrace in exceptions {}\n"), is_enabled(use_backtrace)); output_info.write(_("\tColour in logs {}\n"), is_enabled(use_color)); - output_info.write(_("\tOpenMP parallelisation {}, using {} threads\n"), is_enabled(use_openmp), omp_get_max_threads()); + output_info.write(_("\tOpenMP parallelisation {}, using {} threads\n"), + is_enabled(use_openmp), omp_get_max_threads()); output_info.write(_("\tExtra debug output {}\n"), is_enabled(use_output_debug)); output_info.write(_("\tFloating-point exceptions {}\n"), is_enabled(use_sigfpe)); output_info.write(_("\tSignal handling support {}\n"), is_enabled(use_signal)); From fe91ff0712f00925798799b19bfc6045fce04bd0 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 11:00:26 +0100 Subject: [PATCH 278/412] Add additional openmp shim --- include/bout/openmpwrap.hxx | 1 + 1 file changed, 1 insertion(+) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 0dd05e53df..3d69e81965 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -40,6 +40,7 @@ #else #define BOUT_OMP(...) int constexpr omp_get_max_threads() { return 1; } +int constexpr omp_get_num_threads() { return 1; } int constexpr omp_get_thread_num() { return 0; } #endif From 3d9a53d2939f37014a78d540473f3fee0a2deb7e Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 11:11:53 +0100 Subject: [PATCH 279/412] function definitions in headers should be inline Co-authored-by: Peter Hill --- include/bout/openmpwrap.hxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 3d69e81965..890d74cdc1 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -39,9 +39,9 @@ #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else #define BOUT_OMP(...) -int constexpr omp_get_max_threads() { return 1; } -int constexpr omp_get_num_threads() { return 1; } -int constexpr omp_get_thread_num() { return 0; } +inline int constexpr omp_get_max_threads() { return 1; } +inline int constexpr omp_get_num_threads() { return 1; } +inline int constexpr omp_get_thread_num() { return 0; } #endif //Perhaps want to cleanup local helpers with below, but DON'T! From 7beb0f17c757ec77182753178c986625dac45b7a Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 14:49:57 +0100 Subject: [PATCH 280/412] remove unneeded forward declaration --- include/bout/invert_laplace.hxx | 1 - 1 file changed, 1 deletion(-) diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index 2cf397cb7f..78417b9fce 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -51,7 +51,6 @@ class Laplacian; #include "bout/dcomplex.hxx" class Solver; -class Datafile; constexpr auto LAPLACE_SPT = "spt"; constexpr auto LAPLACE_TRI = "tri"; From 34af631c83c401961ea6f79d5cc84ba32162feee Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 17:14:18 +0100 Subject: [PATCH 281/412] Use shared_ptr for automatic memory management --- include/bout/mesh.hxx | 4 ++-- src/field/field3d.cxx | 8 ++++---- src/field/field_data.cxx | 3 +-- src/mesh/impls/bout/boutmesh.cxx | 12 ++++-------- src/mesh/impls/bout/boutmesh.hxx | 9 ++++++--- src/mesh/parallel/fci.cxx | 6 +++--- src/mesh/parallel/fci.hxx | 16 ++++++++-------- src/mesh/parallel/shiftedmetricinterp.cxx | 16 ++++++++-------- 8 files changed, 36 insertions(+), 38 deletions(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index ec17fda504..765c2cd9b6 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -491,11 +491,11 @@ public: virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {} /// Get all the parallel (Y) boundaries on this processor - virtual std::vector + virtual std::vector> getBoundariesPar(BoundaryParType type = BoundaryParType::all) = 0; /// Add a parallel(Y) boundary to this processor - virtual void addBoundaryPar(BoundaryRegionPar* UNUSED(bndry), + virtual void addBoundaryPar(std::shared_ptr UNUSED(bndry), BoundaryParType UNUSED(type)) {} /// Branch-cut special handling (experimental) diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index bb8dd2573b..d974029186 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -506,7 +506,7 @@ void Field3D::applyParallelBoundary(const std::string& condition) { /// Loop over the mesh boundary regions for (const auto& reg : fieldmesh->getBoundariesPar()) { auto op = std::unique_ptr{ - dynamic_cast(bfact->create(condition, reg))}; + dynamic_cast(bfact->create(condition, reg.get()))}; op->apply(*this); } } @@ -526,7 +526,7 @@ void Field3D::applyParallelBoundary(const std::string& region, for (const auto& reg : fieldmesh->getBoundariesPar()) { if (reg->label == region) { auto op = std::unique_ptr{ - dynamic_cast(bfact->create(condition, reg))}; + dynamic_cast(bfact->create(condition, reg.get()))}; op->apply(*this); break; } @@ -550,9 +550,9 @@ void Field3D::applyParallelBoundary(const std::string& region, // BoundaryFactory can't create boundaries using Field3Ds, so get temporary // boundary of the right type auto tmp = std::unique_ptr{ - dynamic_cast(bfact->create(condition, reg))}; + dynamic_cast(bfact->create(condition, reg.get()))}; // then clone that with the actual argument - auto op = std::unique_ptr{tmp->clone(reg, f)}; + auto op = std::unique_ptr{tmp->clone(reg.get(), f)}; op->apply(*this); break; } diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx index 88de80cec6..529f595316 100644 --- a/src/field/field_data.cxx +++ b/src/field/field_data.cxx @@ -153,10 +153,9 @@ void FieldData::setBoundary(const std::string& name) { } /// Get the mesh boundary regions - std::vector par_reg = mesh->getBoundariesPar(); /// Loop over the mesh parallel boundary regions for (const auto& reg : mesh->getBoundariesPar()) { - auto* op = dynamic_cast(bfact->createFromOptions(name, reg)); + auto* op = dynamic_cast(bfact->createFromOptions(name, reg.get())); if (op != nullptr) { bndry_op_par.push_back(op); } diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index a0047c0815..16061cd47e 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -72,7 +72,6 @@ If you want the old setting, you have to specify mesh:symmetricGlobalY=false in comm_outer = MPI_COMM_NULL; mpi = bout::globals::mpi; - par_boundary.resize(static_cast(BoundaryParType::SIZE)); } BoutMesh::~BoutMesh() { @@ -83,11 +82,6 @@ BoutMesh::~BoutMesh() { for (const auto& bndry : boundary) { delete bndry; } - if (!par_boundary.empty()) { - for (const auto& bndry : par_boundary[0]) { - delete bndry; - } - } if (comm_x != MPI_COMM_NULL) { MPI_Comm_free(&comm_x); @@ -3016,11 +3010,13 @@ RangeIterator BoutMesh::iterateBndryUpperY() const { std::vector BoutMesh::getBoundaries() { return boundary; } -std::vector BoutMesh::getBoundariesPar(BoundaryParType type) { +std::vector> +BoutMesh::getBoundariesPar(BoundaryParType type) { return par_boundary[static_cast(type)]; } -void BoutMesh::addBoundaryPar(BoundaryRegionPar* bndry, BoundaryParType type) { +void BoutMesh::addBoundaryPar(std::shared_ptr bndry, + BoundaryParType type) { output_info << "Adding new parallel boundary: " << bndry->label << endl; switch (type) { case BoundaryParType::xin_fwd: diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx index 6c9ec5ec40..6afa05652f 100644 --- a/src/mesh/impls/bout/boutmesh.hxx +++ b/src/mesh/impls/bout/boutmesh.hxx @@ -158,8 +158,10 @@ public: // Boundary regions std::vector getBoundaries() override; - std::vector getBoundariesPar(BoundaryParType type) final; - void addBoundaryPar(BoundaryRegionPar* bndry, BoundaryParType type) final; + std::vector> + getBoundariesPar(BoundaryParType type) override; + void addBoundaryPar(std::shared_ptr bndry, + BoundaryParType type) override; std::set getPossibleBoundaries() const override; Field3D smoothSeparatrix(const Field3D& f) override; @@ -394,7 +396,8 @@ protected: private: std::vector boundary; // Vector of boundary regions - std::vector> + std::array>, + static_cast(BoundaryParType::SIZE)> par_boundary; // Vector of parallel boundary regions ////////////////////////////////////////////////// diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index 8e8c574d23..f04ec57a80 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -48,8 +48,8 @@ #include FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, - int offset_, BoundaryRegionPar* inner_boundary, - BoundaryRegionPar* outer_boundary, bool zperiodic) + int offset_, std::shared_ptr inner_boundary, + std::shared_ptr outer_boundary, bool zperiodic) : map_mesh(mesh), offset(offset_), region_no_boundary(map_mesh.getRegion("RGN_NOBNDRY")), corner_boundary_mask(map_mesh) { @@ -227,7 +227,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, // that also means inner. So to differentiate between inner and outer we // need at least 2 points in the domain. ASSERT2(map_mesh.xend - map_mesh.xstart >= 2); - auto* boundary = (xt_prime[i] < map_mesh.xstart) ? inner_boundary : outer_boundary; + auto boundary = (xt_prime[i] < map_mesh.xstart) ? inner_boundary : outer_boundary; boundary->add_point(x, y, z, x + dx, y + 0.5 * offset, z + dz, // Intersection point in local index space 0.5 * dy[i], // Distance to intersection diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index b60e09f2c1..0906bcd2ea 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -44,8 +44,8 @@ class FCIMap { public: FCIMap() = delete; FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, int offset, - BoundaryRegionPar* inner_boundary, BoundaryRegionPar* outer_boundary, - bool zperiodic); + std::shared_ptr inner_boundary, + std::shared_ptr outer_boundary, bool zperiodic); // The mesh this map was created on Mesh& map_mesh; @@ -79,13 +79,13 @@ public: FCITransform::checkInputGrid(); auto forward_boundary_xin = - new BoundaryRegionPar("FCI_forward", BNDRY_PAR_FWD_XIN, +1, &mesh); - auto backward_boundary_xin = - new BoundaryRegionPar("FCI_backward", BNDRY_PAR_BKWD_XIN, -1, &mesh); + std::make_shared("FCI_forward", BNDRY_PAR_FWD_XIN, +1, &mesh); + auto backward_boundary_xin = std::make_shared( + "FCI_backward", BNDRY_PAR_BKWD_XIN, -1, &mesh); auto forward_boundary_xout = - new BoundaryRegionPar("FCI_forward", BNDRY_PAR_FWD_XOUT, +1, &mesh); - auto backward_boundary_xout = - new BoundaryRegionPar("FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh); + std::make_shared("FCI_forward", BNDRY_PAR_FWD_XOUT, +1, &mesh); + auto backward_boundary_xout = std::make_shared( + "FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh); // Add the boundary region to the mesh's vector of parallel boundaries mesh.addBoundaryPar(forward_boundary_xin, BoundaryParType::xin_fwd); diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx index fa3cbb9761..e35fee5486 100644 --- a/src/mesh/parallel/shiftedmetricinterp.cxx +++ b/src/mesh/parallel/shiftedmetricinterp.cxx @@ -119,8 +119,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, // Create regions for parallel boundary conditions Field2D dy; mesh.get(dy, "dy", 1.); - auto forward_boundary_xin = - new BoundaryRegionPar("parallel_forward_xin", BNDRY_PAR_FWD_XIN, +1, &mesh); + auto forward_boundary_xin = std::make_shared( + "parallel_forward_xin", BNDRY_PAR_FWD_XIN, +1, &mesh); for (auto it = mesh.iterateBndryUpperY(); not it.isDone(); it.next()) { for (int z = mesh.zstart; z <= mesh.zend; z++) { forward_boundary_xin->add_point( @@ -136,8 +136,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, ); } } - auto backward_boundary_xin = - new BoundaryRegionPar("parallel_backward_xin", BNDRY_PAR_BKWD_XIN, -1, &mesh); + auto backward_boundary_xin = std::make_shared( + "parallel_backward_xin", BNDRY_PAR_BKWD_XIN, -1, &mesh); for (auto it = mesh.iterateBndryLowerY(); not it.isDone(); it.next()) { for (int z = mesh.zstart; z <= mesh.zend; z++) { backward_boundary_xin->add_point( @@ -154,8 +154,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, } } // Create regions for parallel boundary conditions - auto forward_boundary_xout = - new BoundaryRegionPar("parallel_forward_xout", BNDRY_PAR_FWD_XOUT, +1, &mesh); + auto forward_boundary_xout = std::make_shared( + "parallel_forward_xout", BNDRY_PAR_FWD_XOUT, +1, &mesh); for (auto it = mesh.iterateBndryUpperY(); not it.isDone(); it.next()) { for (int z = mesh.zstart; z <= mesh.zend; z++) { forward_boundary_xout->add_point( @@ -171,8 +171,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in, ); } } - auto backward_boundary_xout = - new BoundaryRegionPar("parallel_backward_xout", BNDRY_PAR_BKWD_XOUT, -1, &mesh); + auto backward_boundary_xout = std::make_shared( + "parallel_backward_xout", BNDRY_PAR_BKWD_XOUT, -1, &mesh); for (auto it = mesh.iterateBndryLowerY(); not it.isDone(); it.next()) { for (int z = mesh.zstart; z <= mesh.zend; z++) { backward_boundary_xout->add_point( From bcb1b503441ab51127c1ead9ad5872c06401e957 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 17:18:48 +0100 Subject: [PATCH 282/412] Update doc string --- include/bout/mesh.hxx | 7 ++++++- tests/integrated/test-fci-boundary/makefile | 6 ------ 2 files changed, 6 insertions(+), 7 deletions(-) delete mode 100644 tests/integrated/test-fci-boundary/makefile diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 765c2cd9b6..d9f33b465e 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -490,7 +490,12 @@ public: /// Add a boundary region to this processor virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {} - /// Get all the parallel (Y) boundaries on this processor + /// Allow to iterate over only spefic parallel boundaries + /// For example: + /// get all regions: + /// mesh->getBoundariesPar(Mesh::BoundaryParType::all) + /// get only xout: + /// mesh->getBoundariesPar(Mesh::BoundaryParType::xout) virtual std::vector> getBoundariesPar(BoundaryParType type = BoundaryParType::all) = 0; diff --git a/tests/integrated/test-fci-boundary/makefile b/tests/integrated/test-fci-boundary/makefile deleted file mode 100644 index c1c6c6f8b8..0000000000 --- a/tests/integrated/test-fci-boundary/makefile +++ /dev/null @@ -1,6 +0,0 @@ - -BOUT_TOP ?= ../../.. - -SOURCEC = get_par_bndry.cxx - -include $(BOUT_TOP)/make.config From 3e737b0b8d851fa31113235f366a27414cf4a7c0 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 20:46:28 +0100 Subject: [PATCH 283/412] Include build_defines Otherwise the header does not expose the correct definitions and macros, leading to potential bugs. --- include/bout/openmpwrap.hxx | 2 ++ 1 file changed, 2 insertions(+) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 890d74cdc1..89c4328df6 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -27,6 +27,8 @@ #ifndef __OPENMPWRAP_H__ #define __OPENMPWRAP_H__ +#include "bout/build_defines.hxx" + //Some helpers for indirection -- required so that the _Pragma gets "omp " //where is any number of valid omp options/environments (e.g. atomic, critical etc.) #define INDIRECT0(a) #a From adbe88aff69abe68a70222cf5f85e28b17e3cc46 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 21:50:19 +0100 Subject: [PATCH 284/412] Include openmp header --- include/bout/openmpwrap.hxx | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 89c4328df6..834d6f7342 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -29,6 +29,10 @@ #include "bout/build_defines.hxx" +#if BOUT_USE_OPENMP + +#include "omp.h" + //Some helpers for indirection -- required so that the _Pragma gets "omp " //where is any number of valid omp options/environments (e.g. atomic, critical etc.) #define INDIRECT0(a) #a @@ -37,7 +41,6 @@ //Define a macro wrapper to the use of `#pragma omp` to avoid unknown pragma //warnings when compiling without openmp support. -#if BOUT_USE_OPENMP #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else #define BOUT_OMP(...) From 09ce12b3e62f48c0db50f8b7a86a1fb80730ecd1 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 22:07:27 +0100 Subject: [PATCH 285/412] Update function signature for mock class --- tests/unit/test_extras.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 480d609844..bc0e8bee31 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -233,8 +233,8 @@ public: RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); } void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); } std::vector getBoundaries() override { return boundaries; } - std::vector getBoundariesPar(BoundaryParType) override { - return std::vector(); + std::vector> getBoundariesPar(BoundaryParType) override { + return std::vector>(); } BoutReal GlobalX(int jx) const override { return jx; } BoutReal GlobalY(int jy) const override { return jy; } From 5889af45d43c659d479d627ed345913f89b0df04 Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Wed, 21 Feb 2024 21:07:57 +0000 Subject: [PATCH 286/412] Apply clang-format changes --- tests/unit/test_extras.hxx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index bc0e8bee31..35cb24a9b6 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -233,7 +233,8 @@ public: RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); } void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); } std::vector getBoundaries() override { return boundaries; } - std::vector> getBoundariesPar(BoundaryParType) override { + std::vector> + getBoundariesPar(BoundaryParType) override { return std::vector>(); } BoutReal GlobalX(int jx) const override { return jx; } From 828552bd7b0a40028b98c7e10d78e2316bf95b80 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 23:04:27 +0100 Subject: [PATCH 287/412] Add -fopenmp to FLAGS if using openmp --- cmake/SetupBOUTThirdParty.cmake | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index ef0fd438d4..a1b1c4620e 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -8,6 +8,8 @@ endif () # determined in SetupCompilers.cmake if (BOUT_USE_OPENMP) target_link_libraries(bout++ PUBLIC OpenMP::OpenMP_CXX) + set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -fopenmp") + set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -fopenmp") endif() # determined in SetupCompilers.cmake From f9b842695a526222de689cd8fb6c9b628370598e Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 23:11:58 +0100 Subject: [PATCH 288/412] Ensure that _OPENMP and BOUT_USE_OPENMP is the same --- include/bout/array.hxx | 2 +- include/bout/openmpwrap.hxx | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/include/bout/array.hxx b/include/bout/array.hxx index 822ad9af2c..b22a19b388 100644 --- a/include/bout/array.hxx +++ b/include/bout/array.hxx @@ -31,7 +31,7 @@ #include #include -#ifdef _OPENMP +#if BOUT_USE_OPENMP #include #endif diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 834d6f7342..eef1cafbf7 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -44,9 +44,13 @@ #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else #define BOUT_OMP(...) +#ifdef _OPENMP inline int constexpr omp_get_max_threads() { return 1; } inline int constexpr omp_get_num_threads() { return 1; } inline int constexpr omp_get_thread_num() { return 0; } +#else +#error OpenMP used but BOUT++ thinks it is disabled +#endif #endif //Perhaps want to cleanup local helpers with below, but DON'T! From 57bb65342bf9b88f214b1c19123753f8dda8bb6f Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 21 Feb 2024 23:17:42 +0100 Subject: [PATCH 289/412] Fix ifdef --- include/bout/openmpwrap.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index eef1cafbf7..5b74f96804 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -45,11 +45,11 @@ #else #define BOUT_OMP(...) #ifdef _OPENMP +#error OpenMP used but BOUT++ thinks it is disabled +#else inline int constexpr omp_get_max_threads() { return 1; } inline int constexpr omp_get_num_threads() { return 1; } inline int constexpr omp_get_thread_num() { return 0; } -#else -#error OpenMP used but BOUT++ thinks it is disabled #endif #endif From 5e100021044329c5881684ab44019f3e29fdf3fc Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 10:07:23 +0100 Subject: [PATCH 290/412] Improve doc string --- include/bout/mesh.hxx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index d9f33b465e..b6faac283a 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -490,7 +490,9 @@ public: /// Add a boundary region to this processor virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {} - /// Allow to iterate over only spefic parallel boundaries + /// Get the list of parallel boundary regions. The option specifies with + /// region to get. Default is to get all regions. All possible options are + /// listed at the top of this file, see BoundaryParType. /// For example: /// get all regions: /// mesh->getBoundariesPar(Mesh::BoundaryParType::all) From 224741dfe486ba6f3d29b716da8bd2337ac58e2f Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 10:18:11 +0100 Subject: [PATCH 291/412] prefer const ref --- src/mesh/parallel/fci.cxx | 4 ++-- src/mesh/parallel/fci.hxx | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx index f04ec57a80..55be0a6a86 100644 --- a/src/mesh/parallel/fci.cxx +++ b/src/mesh/parallel/fci.cxx @@ -48,8 +48,8 @@ #include FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, - int offset_, std::shared_ptr inner_boundary, - std::shared_ptr outer_boundary, bool zperiodic) + int offset_, const std::shared_ptr& inner_boundary, + const std::shared_ptr& outer_boundary, bool zperiodic) : map_mesh(mesh), offset(offset_), region_no_boundary(map_mesh.getRegion("RGN_NOBNDRY")), corner_boundary_mask(map_mesh) { diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 0906bcd2ea..c09a28cc33 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -44,8 +44,8 @@ class FCIMap { public: FCIMap() = delete; FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, int offset, - std::shared_ptr inner_boundary, - std::shared_ptr outer_boundary, bool zperiodic); + const std::shared_ptr& inner_boundary, + const std::shared_ptr& outer_boundary, bool zperiodic); // The mesh this map was created on Mesh& map_mesh; From 3356a5156be9f8a1d76159b31d7198977d854271 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 10:52:52 +0100 Subject: [PATCH 292/412] prefer constexpr Co-authored-by: Peter Hill --- include/bout/parallel_boundary_region.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx index 7dfb650474..0aa69959f1 100644 --- a/include/bout/parallel_boundary_region.hxx +++ b/include/bout/parallel_boundary_region.hxx @@ -188,7 +188,7 @@ public: const int dir; private: - const BoutReal small_value = 1e-2; + constexpr static BoutReal small_value = 1e-2; // BoutReal get(const Field3D& f, int off) const BoutReal& ynext(const Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; } From 82643e25c566e73e2dc68011f8d3e056f558b0c7 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 11:22:06 +0100 Subject: [PATCH 293/412] Track ldflags for shared lib --- CMakeLists.txt | 2 +- cmake/SetupBOUTThirdParty.cmake | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 483672fb67..1f2e3a23cb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -774,7 +774,7 @@ set(BOUT_HAS_PNETCDF OFF) # while for static builds we need the dependencies too if (BUILD_SHARED_LIBS) # Include rpath linker flag so user doesn't need to set LD_LIBRARY_PATH - set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt") + set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt ${CONFIG_LDFLAGS_SHARED}") else() set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS}") endif() diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index a1b1c4620e..53adbec92d 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -9,6 +9,7 @@ endif () if (BOUT_USE_OPENMP) target_link_libraries(bout++ PUBLIC OpenMP::OpenMP_CXX) set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -fopenmp") + set(CONFIG_LDFLAGS_SHARED "${CONFIG_LDFLAGS_SHARED} -fopenmp") set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -fopenmp") endif() From 30cb5468b1586195efe8c3a6c14cabde89f3958d Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 11:22:24 +0100 Subject: [PATCH 294/412] Print --has-openmp in --all for bout-config --- bin/bout-config.in | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/bout-config.in b/bin/bout-config.in index a9045fff39..fa19779cfe 100755 --- a/bin/bout-config.in +++ b/bin/bout-config.in @@ -123,6 +123,7 @@ all() echo " --has-slepc -> $has_slepc" echo " --has-arkode -> $has_arkode" echo " --has-nls -> $has_nls" + echo " --has-openmp -> $has_openmp" echo echo " --petsc-has-sundials -> $petsc_has_sundials" echo From 748998f339439dd2f3879c39472dde4901e4cfff Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 11:24:32 +0100 Subject: [PATCH 295/412] CI: Enable openmp for cuda OpenMP is enabled any way, but if bout is not aware of using openmp, it might misbehave. --- .github/workflows/tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 42965e75e8..5484a224a5 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -264,6 +264,7 @@ jobs: -DCMAKE_CUDA_ARCHITECTURES=80 \ -DCUDA_ARCH=compute_80,code=sm_80 \ -DBOUT_ENABLE_WARNINGS=off \ - -DBOUT_USE_SYSTEM_FMT=on + -DBOUT_USE_SYSTEM_FMT=on \ + -DBOUT_ENABLE_OPENMP=ON cd build make -j 4 From ccf2f78e88b10ad299c3b538d43313684ba7a1ef Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 12:33:13 +0100 Subject: [PATCH 296/412] differentiate openmp usage BOUT_OMP is split in BOUT_OMP_SAFE for cases where we want to ensure that bout++ behaves correctly in an openmp parallel environement. BOUT_OMP_PERF on the other hand enables using openmp for parallel regions. BOUT_OMP_SAFE is enabled whenever openmp is detected, while BOUT_OMP_PERF is a user option. --- .clang-format | 2 + .github/workflows/tests.yml | 3 +- .../iterator-offsets/iterator-offsets.cxx | 6 +- examples/performance/iterator/iterator.cxx | 4 +- include/bout/array.hxx | 2 +- include/bout/cyclic_reduction.hxx | 26 ++-- include/bout/hypre_interface.hxx | 4 +- include/bout/openmpwrap.hxx | 21 +++- include/bout/petsc_interface.hxx | 8 +- include/bout/region.hxx | 2 +- manual/sphinx/developer_docs/data_types.rst | 4 +- src/field/field3d.cxx | 4 +- src/invert/fft_fftw.cxx | 4 +- .../laplace/impls/cyclic/cyclic_laplace.cxx | 40 +++---- .../iterative_parallel_tri.cxx | 2 +- .../laplace/impls/multigrid/multigrid_alg.cxx | 112 +++++++++--------- .../impls/multigrid/multigrid_laplace.cxx | 108 ++++++++--------- .../impls/multigrid/multigrid_solver.cxx | 74 ++++++------ src/invert/laplace/impls/pcr/pcr.cxx | 48 ++++---- .../laplace/impls/pcr_thomas/pcr_thomas.cxx | 40 +++---- .../laplace/impls/serial_band/serial_band.cxx | 2 +- .../laplace/impls/serial_tri/serial_tri.cxx | 2 +- src/invert/laplace/impls/spt/spt.cxx | 10 +- src/mesh/coordinates.cxx | 2 +- src/mesh/difops.cxx | 4 +- src/mesh/index_derivs.cxx | 4 +- src/mesh/mesh.cxx | 6 +- .../impls/adams_bashforth/adams_bashforth.cxx | 8 +- src/solver/impls/euler/euler.cxx | 2 +- src/solver/impls/rk3-ssp/rk3-ssp.cxx | 6 +- src/solver/impls/rk4/rk4.cxx | 10 +- src/solver/impls/rkgeneric/rkgeneric.cxx | 2 +- src/solver/impls/rkgeneric/rkscheme.cxx | 14 +-- src/solver/impls/split-rk/split-rk.cxx | 14 +-- src/sys/hyprelib.cxx | 10 +- src/sys/msg_stack.cxx | 6 +- src/sys/petsclib.cxx | 6 +- .../include/bout/test_hypre_interface.cxx | 2 +- .../unit/include/bout/test_petsc_indexer.cxx | 14 +-- tests/unit/include/bout/test_petsc_matrix.cxx | 2 +- tests/unit/include/bout/test_region.cxx | 8 +- 41 files changed, 331 insertions(+), 317 deletions(-) diff --git a/.clang-format b/.clang-format index f51c5bde87..a80c59bddd 100644 --- a/.clang-format +++ b/.clang-format @@ -109,6 +109,8 @@ SpacesInParentheses: false SpacesInSquareBrackets: false StatementMacros: - BOUT_OMP + - BOUT_OMP_PERF + - BOUT_OMP_SAFE Standard: c++14 TabWidth: 8 UseTab: Never diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5484a224a5..42965e75e8 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -264,7 +264,6 @@ jobs: -DCMAKE_CUDA_ARCHITECTURES=80 \ -DCUDA_ARCH=compute_80,code=sm_80 \ -DBOUT_ENABLE_WARNINGS=off \ - -DBOUT_USE_SYSTEM_FMT=on \ - -DBOUT_ENABLE_OPENMP=ON + -DBOUT_USE_SYSTEM_FMT=on cd build make -j 4 diff --git a/examples/performance/iterator-offsets/iterator-offsets.cxx b/examples/performance/iterator-offsets/iterator-offsets.cxx index 08149f855e..2376b63578 100644 --- a/examples/performance/iterator-offsets/iterator-offsets.cxx +++ b/examples/performance/iterator-offsets/iterator-offsets.cxx @@ -73,7 +73,7 @@ int main(int argc, char** argv) { #if BOUT_USE_OPENMP ITERATOR_TEST_BLOCK( "Nested loop (omp)", - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for(int i=0;iLocalNx;++i) { for (int j = mesh->ystart; j < mesh->yend; ++j) { for (int k = 0; k < mesh->LocalNz; ++k) { @@ -98,7 +98,7 @@ int main(int argc, char** argv) { deriv(a, result, "RGN_NOY");); ITERATOR_TEST_BLOCK( - "Region with stencil", BOUT_OMP(parallel) { + "Region with stencil", BOUT_OMP_PERF(parallel) { stencil s; BOUT_FOR_INNER(i, mesh->getRegion3D("RGN_NOY")) { s.m = a[i.ym()]; @@ -110,7 +110,7 @@ int main(int argc, char** argv) { }); ITERATOR_TEST_BLOCK( - "Region with stencil and function pointer", BOUT_OMP(parallel) { + "Region with stencil and function pointer", BOUT_OMP_PERF(parallel) { stencil s; BOUT_FOR_INNER(i, mesh->getRegion3D("RGN_NOY")) { s.m = a[i.ym()]; diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx index 7f9eb7ce1f..af1163d927 100644 --- a/examples/performance/iterator/iterator.cxx +++ b/examples/performance/iterator/iterator.cxx @@ -66,7 +66,7 @@ int main(int argc, char** argv) { "C loop", for (int j = 0; j < len; ++j) { rd[j] = ad[j] + bd[j]; };); #if BOUT_USE_OPENMP ITERATOR_TEST_BLOCK("C loop (omp)", - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for(int j=0;jLocalNx;++i) { for (int j = 0; j < mesh->LocalNy; ++j) { for (int k = 0; k < mesh->LocalNz; ++k) { diff --git a/include/bout/array.hxx b/include/bout/array.hxx index b22a19b388..d3ff4528cb 100644 --- a/include/bout/array.hxx +++ b/include/bout/array.hxx @@ -382,7 +382,7 @@ private: // Clean by deleting all data -- possible that just stores.clear() is // sufficient rather than looping over each entry. - BOUT_OMP(single) + BOUT_OMP_SAFE(single) { for (auto& stores : arena) { for (auto& p : stores) { diff --git a/include/bout/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx index d4ef958e93..6d26aec3fb 100644 --- a/include/bout/cyclic_reduction.hxx +++ b/include/bout/cyclic_reduction.hxx @@ -101,7 +101,7 @@ public: Matrix bMatrix(1, N); Matrix cMatrix(1, N); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < N; ++i) { aMatrix(0, i) = a[i]; bMatrix(0, i) = b[i]; @@ -126,7 +126,7 @@ public: allocMemory(nprocs, nsys, N); // Fill coefficient array - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int j = 0; j < Nsys; j++) { for (int i = 0; i < N; i++) { coefs(j, 4 * i) = a(j, i); @@ -149,7 +149,7 @@ public: Matrix xMatrix(1, N); // Copy input data into matrix - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < N; ++i) { rhsMatrix(0, i) = rhs[i]; } @@ -158,7 +158,7 @@ public: solve(rhsMatrix, xMatrix); // Copy result back into argument - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < N; ++i) { x[i] = xMatrix(0, i); } @@ -184,7 +184,7 @@ public: // Insert RHS into coefs array. Ordered to allow efficient partitioning // for MPI send/receives - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int j = 0; j < Nsys; j++) { for (int i = 0; i < N; i++) { coefs(j, 4 * i + 3) = rhs(j, i); @@ -230,7 +230,7 @@ public: if (p == myproc) { // Just copy the data - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < myns; i++) { for (int j = 0; j < 8; j++) { ifcs(i, 8 * p + j) = myif(sys0 + i, j); @@ -285,7 +285,7 @@ public: #ifdef DIAGNOSE output << "Copying received data from " << p << endl; #endif - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < myns; i++) { for (int j = 0; j < 8; j++) { #ifdef DIAGNOSE @@ -317,7 +317,7 @@ public: x1.ensureUnique(); xn.ensureUnique(); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < myns; ++i) { // (a b) (x1) = (b1) // (c d) (xn) (bn) @@ -364,7 +364,7 @@ public: if (p == myproc) { // Just copy the data - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < myns; i++) { x1[sys0 + i] = ifx(i, 2 * p); xn[sys0 + i] = ifx(i, 2 * p + 1); @@ -389,7 +389,7 @@ public: // Send data for (int p = 0; p < nprocs; p++) { // Loop over processor if (p != myproc) { - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < myns; i++) { ifp[2 * i] = ifx(i, 2 * p); ifp[2 * i + 1] = ifx(i, 2 * p + 1); @@ -427,7 +427,7 @@ public: nsp++; } - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nsp; i++) { x1[s0 + i] = recvbuffer(fromproc, 2 * i); xn[s0 + i] = recvbuffer(fromproc, 2 * i + 1); @@ -540,7 +540,7 @@ private: } #endif - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int j = 0; j < ns; j++) { // Calculate upper interface equation @@ -619,7 +619,7 @@ private: // Tridiagonal system, solve using serial Thomas algorithm // xa -- Result for each system // co -- Coefficients & rhs for each system - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < ns; i++) { // Loop over systems Array gam(nloc); // Thread-local array T bet = 1.0; diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx index c26548e95e..cd3af7d39c 100644 --- a/include/bout/hypre_interface.hxx +++ b/include/bout/hypre_interface.hxx @@ -480,7 +480,7 @@ public: weights.begin(), weights.end(), std::back_inserter(values), [&value_](BoutReal weight) -> HYPRE_Complex { return weight * value_; }); const HYPRE_BigInt ncolumns = static_cast(positions.size()); - // BOUT_OMP(critical) + // BOUT_OMP_SAFE(critical) for (HYPRE_BigInt i = 0; i < ncolumns; ++i) { matrix->setVal(row, positions[i], values[i]); } @@ -495,7 +495,7 @@ public: weights.begin(), weights.end(), std::back_inserter(values), [&value_](BoutReal weight) -> HYPRE_Complex { return weight * value_; }); const HYPRE_BigInt ncolumns = static_cast(positions.size()); - // BOUT_OMP(critical) + // BOUT_OMP_SAFE(critical) for (HYPRE_BigInt i = 0; i < ncolumns; ++i) { matrix->addVal(row, positions[i], values[i]); } diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 5b74f96804..41f334d2cf 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -30,9 +30,10 @@ #include "bout/build_defines.hxx" #if BOUT_USE_OPENMP - #include "omp.h" +#endif +#ifdef _OPENMP //Some helpers for indirection -- required so that the _Pragma gets "omp " //where is any number of valid omp options/environments (e.g. atomic, critical etc.) #define INDIRECT0(a) #a @@ -41,17 +42,29 @@ //Define a macro wrapper to the use of `#pragma omp` to avoid unknown pragma //warnings when compiling without openmp support. +#define BOUT_OMP_SAFE(...) _Pragma(INDIRECT2(__VA_ARGS__)) #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else +#define BOUT_OMP_SAFE(...) #define BOUT_OMP(...) -#ifdef _OPENMP -#error OpenMP used but BOUT++ thinks it is disabled +#endif + +#if BOUT_USE_OPENMP + +#ifndef INDIRECT2 +#error expected macro INDIRECT2 to be available +#endif + +#define BOUT_OMP_PERF(...) _Pragma(INDIRECT2(__VA_ARGS__)) #else +#define BOUT_OMP_PERF(...) +#endif + +#ifndef _OPENMP inline int constexpr omp_get_max_threads() { return 1; } inline int constexpr omp_get_num_threads() { return 1; } inline int constexpr omp_get_thread_num() { return 0; } #endif -#endif //Perhaps want to cleanup local helpers with below, but DON'T! //This would cause uses of BOUT_OMP to break diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx index 0afcc8a30a..407e5ac18e 100644 --- a/include/bout/petsc_interface.hxx +++ b/include/bout/petsc_interface.hxx @@ -175,7 +175,7 @@ public: #endif BoutReal value = BoutNaN; int status = 0; - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) status = VecGetValues(*get(), 1, &global, &value); if (status != 0) { throw BoutException("Error when getting element of a PETSc vector."); @@ -355,7 +355,7 @@ public: PetscBool assembled = PETSC_FALSE; MatAssembled(*petscMatrix, &assembled); if (assembled == PETSC_TRUE) { - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) MatGetValues(*petscMatrix, 1, &petscRow, 1, &petscCol, &value); } else { value = 0.; @@ -400,7 +400,7 @@ public: [&val](BoutReal weight) -> PetscScalar { return weight * val; }); int status = 0; - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) status = MatSetValues(*petscMatrix, 1, &petscRow, positions.size(), positions.data(), values.data(), mode); if (status != 0) { @@ -467,7 +467,7 @@ public: #endif BoutReal value = BoutNaN; int status = 0; - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) status = MatGetValues(*get(), 1, &global1, 1, &global2, &value); if (status != 0) { throw BoutException("Error when getting elements of a PETSc matrix."); diff --git a/include/bout/region.hxx b/include/bout/region.hxx index cbaf0d0c31..3eabd0a3fd 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -117,7 +117,7 @@ class BoutMask; #if BOUT_USE_OPENMP #define BOUT_FOR_OMP(index, region, omp_pragmas) \ - BOUT_OMP(omp_pragmas) \ + BOUT_OMP_PERF(omp_pragmas) \ for (auto block = region.getBlocks().cbegin(); block < region.getBlocks().cend(); \ ++block) \ for (auto index = block->first; index < block->second; ++index) diff --git a/manual/sphinx/developer_docs/data_types.rst b/manual/sphinx/developer_docs/data_types.rst index 2e303381f9..fa8e9e6ea6 100644 --- a/manual/sphinx/developer_docs/data_types.rst +++ b/manual/sphinx/developer_docs/data_types.rst @@ -300,7 +300,7 @@ verion of the macro:: For loops inside parallel regions, there is ``BOUT_FOR_INNER``:: Field3D f(0.0); - BOUT_OMP(parallel) { + BOUT_OMP_PERF(parallel) { BOUT_FOR_INNER(i, f.getMesh()->getRegion3D("RGN_ALL")) { f[i] = a[i] + b[i]; } @@ -357,7 +357,7 @@ Tuning BOUT_FOR loops The ``BOUT_FOR`` macros use two nested loops: The outer loop is OpenMP parallelised, and iterates over contiguous blocks:: - BOUT_OMP(parallel for schedule(guided)) + BOUT_OMP_PERF(parallel for schedule(guided)) for (auto block = region.getBlocks().cbegin(); block < region.getBlocks().cend(); ++block) diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx index b4bb0d394f..011353f34a 100644 --- a/src/field/field3d.cxx +++ b/src/field/field3d.cxx @@ -618,7 +618,7 @@ Field3D filter(const Field3D& var, int N0, const std::string& rgn) { const Region& region = var.getRegion2D(region_str); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { Array f(ncz / 2 + 1); @@ -668,7 +668,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string const Region& region = var.getRegion2D(region_str); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { Array f(ncz / 2 + 1); diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx index 514396c828..d66f35beee 100644 --- a/src/invert/fft_fftw.cxx +++ b/src/invert/fft_fftw.cxx @@ -258,7 +258,7 @@ void rfft([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length, // use a `single` block here as that requires all threads to reach the // block (implicit barrier) which may not be true in all cases (e.g. // if there are 8 threads but only 4 call the fft routine). - BOUT_OMP(critical(rfft)) + BOUT_OMP_SAFE(critical(rfft)) if ((size != length) || (nthreads < n_th)) { if (size > 0) { // Free all memory @@ -335,7 +335,7 @@ void irfft([[maybe_unused]] const dcomplex* in, [[maybe_unused]] int length, // use a `single` block here as that requires all threads to reach the // block (implicit barrier) which may not be true in all cases (e.g. // if there are 8 threads but only 4 call the fft routine). - BOUT_OMP(critical(irfft)) + BOUT_OMP_SAFE(critical(irfft)) if ((size != length) || (nthreads < n_th)) { if (size > 0) { // Free all memory diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx index 2687bf7187..cf16240c0c 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx @@ -131,7 +131,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } if (dst) { - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( @@ -139,7 +139,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Loop over X indices, including boundaries but not guard cells. (unless periodic // in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d @@ -161,7 +161,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Get elements of the tridiagonal matrix // including boundary conditions BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int kz = 0; kz < nmode; kz++) { // wave number is 1/[rad]; DST has extra 2. BoutReal kwave = kz * 2.0 * PI / (2. * zlen); @@ -181,14 +181,14 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { cr->solve(bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array // ZFFT routine expects input of this length auto k1d = Array(localmesh->LocalNz); - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { for (int kz = 0; kz < nmode; kz++) { k1d[kz] = xcmplx(kz, ix - xs); @@ -206,7 +206,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array // ZFFT routine expects input of this length @@ -214,7 +214,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Loop over X indices, including boundaries but not guard // cells (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d @@ -235,7 +235,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int kz = 0; kz < nmode; kz++) { BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad] tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, @@ -269,7 +269,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { } // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array // ZFFT routine expects input of this length @@ -277,7 +277,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { if (zero_DC) { k1d[0] = 0.; @@ -358,7 +358,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { auto bcmplx3D = Matrix(nsys, nx); if (dst) { - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array // ZFFT routine expects input of this length @@ -366,7 +366,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Loop over X and Y indices, including boundaries but not guard cells. // (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ind = 0; ind < nxny; ++ind) { // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -393,7 +393,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Get elements of the tridiagonal matrix // including boundary conditions const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nsys; ind++) { // ind = (iy - ys) * nmode + kz int iy = ys + ind / nmode; @@ -417,13 +417,13 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { cr->solve(bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array // ZFFT routine expects input of length LocalNz auto k1d = Array(localmesh->LocalNz); - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -445,7 +445,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array // ZFFT routine expects input of this length @@ -454,7 +454,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Loop over X and Y indices, including boundaries but not guard cells // (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ind = 0; ind < nxny; ++ind) { // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -480,7 +480,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nsys; ind++) { // ind = (iy - ys) * nmode + kz int iy = ys + ind / nmode; @@ -524,7 +524,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { } // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -532,7 +532,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx index 2457ff3b8e..b09b67611b 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx @@ -298,7 +298,7 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { const bool invert_outer_boundary = isOuterBoundaryFlagSet(INVERT_SET) and localmesh->lastX(); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int ix = 0; ix < ncx; ix++) { /* This for loop will set the bk (initialized by the constructor) * bk is the z fourier modes of b in z diff --git a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx index 88556e02ad..6eab524b2c 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx @@ -104,14 +104,14 @@ void MultigridAlg::getSolution(BoutReal* x, BoutReal* b, int flag) { Array r(ldim); for (int n = 1; n < flag; n++) { residualVec(level, x, b, std::begin(r)); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { y[i] = 0.0; } cycleMG(level, std::begin(y), std::begin(r)); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { x[i] = x[i] + y[i]; } @@ -135,8 +135,8 @@ void MultigridAlg::cycleMG(int level, BoutReal* sol, BoutReal* rhs) { projection(level, std::begin(r), std::begin(pr)); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < (lnx[level - 1] + 2) * (lnz[level - 1] + 2); i++) { y[i] = 0.0; } @@ -144,8 +144,8 @@ void MultigridAlg::cycleMG(int level, BoutReal* sol, BoutReal* rhs) { cycleMG(level - 1, std::begin(y), std::begin(pr)); prolongation(level - 1, std::begin(y), std::begin(iy)); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < (lnx[level] + 2) * (lnz[level] + 2); i++) { sol[i] += iy[i]; } @@ -156,15 +156,15 @@ void MultigridAlg::cycleMG(int level, BoutReal* sol, BoutReal* rhs) { void MultigridAlg::projection(int level, BoutReal* r, BoutReal* pr) { - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < (lnx[level - 1] + 2) * (lnz[level - 1] + 2); i++) { pr[i] = 0.; } int xend = lnx[level - 1] + 1; int zend = lnz[level - 1] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int i2 = 2 * i - 1; @@ -183,16 +183,16 @@ void MultigridAlg::projection(int level, BoutReal* r, BoutReal* pr) { void MultigridAlg::prolongation(int level, BoutReal* x, BoutReal* ix) { - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < (lnx[level + 1] + 2) * (lnz[level + 1] + 2); i++) { ix[i] = 0.; } int xend = lnx[level] + 1; int zend = lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int i2 = 2 * i - 1; @@ -219,16 +219,16 @@ void MultigridAlg::smoothings(int level, BoutReal* x, BoutReal* b) { dim = mm * (lnx[level] + 2); if (mgsm == 0) { Array x0(dim); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) for (int num = 0; num < 2; num++) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim; i++) { x0[i] = x[i]; } int xend = lnx[level] + 1; int zend = lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int nn = i * mm + k; @@ -313,8 +313,8 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { Array q(ldim); Array r(ldim); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { sol[i] = 0.0; } @@ -335,8 +335,8 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { delete[] v; return; } - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { r[i] = 0.0; } @@ -345,8 +345,8 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { } else { cycleMG(level, std::begin(r), rhs); } - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { v[0][i] = r[i]; } @@ -360,21 +360,21 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { } a0 = 1.0 / a1; g[0] = a1; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { v[0][i] *= a0; } - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 1; i < MAXGM + 1; i++) { g[i] = 0.0; } } for (it = 0; it < MAXGM; it++) { multiAVec(level, v[it], std::begin(q)); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { v[it + 1][i] = 0.0; } @@ -407,8 +407,8 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { } a0 = 1.0 / a1; h[it + 1][it] = a1; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { v[it + 1][i] *= a0; } @@ -444,13 +444,13 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { } y[i] = y[i] / h[i][i]; } - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { p[i] = sol[i]; } - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int k = 0; k < ldim; k++) { for (int i = 0; i <= it; i++) { p[k] += y[i] * v[i][k]; @@ -492,8 +492,8 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { perror = error; } /* Restart with new initial */ - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { v[0][i] = 0.0; } @@ -503,8 +503,8 @@ void MultigridAlg::pGMRES(BoutReal* sol, BoutReal* rhs, int level, int iplag) { cycleMG(level, v[0], std::begin(r)); } - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { sol[i] = p[i]; } @@ -559,11 +559,11 @@ BoutReal MultigridAlg::vectorProd(int level, BoutReal* x, BoutReal* y) { BoutReal val; BoutReal ini_e = 0.0; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { int xend = lnx[level] + 1; int zend = lnz[level] + 1; - BOUT_OMP(for reduction(+:ini_e) collapse(2)) + BOUT_OMP_PERF(for reduction(+:ini_e) collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int ii = i * (lnz[level] + 2) + k; @@ -583,16 +583,16 @@ BoutReal MultigridAlg::vectorProd(int level, BoutReal* x, BoutReal* y) { void MultigridAlg::multiAVec(int level, BoutReal* x, BoutReal* b) { int mm = lnz[level] + 2; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < mm * (lnx[level] + 2); i++) { b[i] = 0.0; } int xend = lnx[level] + 1; int zend = lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int nn = i * mm + k; @@ -614,16 +614,16 @@ void MultigridAlg::residualVec(int level, BoutReal* x, BoutReal* b, BoutReal* r) int mm; mm = lnz[level] + 2; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < mm * (lnx[level] + 2); i++) { r[i] = 0.0; } int xend = lnx[level] + 1; int zend = lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int nn = i * mm + k; @@ -646,16 +646,16 @@ void MultigridAlg::setMatrixC(int level) { BoutReal ratio = 8.0; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < (lnx[level - 1] + 2) * (lnz[level - 1] + 2) * 9; i++) { matmg[level - 1][i] = 0.0; } int xend = lnx[level - 1] + 1; int zend = lnz[level - 1] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < xend; i++) { for (int k = 1; k < zend; k++) { int i2 = 2 * i - 1; @@ -809,8 +809,8 @@ void MultigridAlg::solveMG(BoutReal* sol, BoutReal* rhs, int level) { BoutReal ini_e, perror, error, rederr; int ldim = (lnx[level] + 2) * (lnz[level] + 2); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { sol[i] = 0.0; } @@ -825,22 +825,22 @@ void MultigridAlg::solveMG(BoutReal* sol, BoutReal* rhs, int level) { } Array y(ldim); Array r(ldim); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { r[i] = rhs[i]; } perror = ini_e; for (m = 0; m < MAXIT; m++) { - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { y[i] = 0.0; } cycleMG(level, std::begin(y), std::begin(r)); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { sol[i] = sol[i] + y[i]; } diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx index f124397c78..82273ee7ad 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx @@ -216,8 +216,8 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ } else { output << "Multigrid solver with merging " << mgmpi << endl; } - BOUT_OMP(parallel) - BOUT_OMP(master) + BOUT_OMP_SAFE(parallel) + BOUT_OMP_SAFE(master) { output << "Num threads = " << omp_get_num_threads() << endl; } } } @@ -244,8 +244,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { if (global_flags & INVERT_START_NEW) { // set initial guess to zero - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < lxx + 1; i++) { for (int k = 1; k < lzz + 1; k++) { x[i * lz2 + k] = 0.; @@ -253,8 +253,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // Read initial guess into local array, ignoring guard cells - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < lxx + 1; i++) { for (int k = 1; k < lzz + 1; k++) { int i2 = i - 1 + localmesh->xstart; @@ -265,8 +265,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } // Read RHS into local array - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < lxx + 1; i++) { for (int k = 1; k < lzz + 1; k++) { int i2 = i - 1 + localmesh->xstart; @@ -280,8 +280,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { // Neumann boundary condition if (inner_boundary_flags & INVERT_SET) { // guard cells of x0 specify gradient to set at inner boundary - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; x[k] = -x0(localmesh->xstart - 1, k2) @@ -290,8 +290,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // zero gradient inner boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { // set inner guard cells x[k] = 0.0; @@ -301,8 +301,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { // Dirichlet boundary condition if (inner_boundary_flags & INVERT_SET) { // guard cells of x0 specify value to set at inner boundary - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; x[k] = 2. * x0(localmesh->xstart - 1, k2); @@ -310,8 +310,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // zero value inner boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { // set inner guard cells x[k] = 0.; @@ -324,8 +324,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { // Neumann boundary condition if (inner_boundary_flags & INVERT_SET) { // guard cells of x0 specify gradient to set at outer boundary - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; x[(lxx + 1) * lz2 + k] = x0(localmesh->xend + 1, k2) @@ -335,8 +335,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // zero gradient outer boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { // set outer guard cells x[(lxx + 1) * lz2 + k] = 0.; @@ -346,8 +346,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { // Dirichlet boundary condition if (outer_boundary_flags & INVERT_SET) { // guard cells of x0 specify value to set at outer boundary - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; x[(lxx + 1) * lz2 + k] = 2. * x0(localmesh->xend + 1, k2); @@ -355,8 +355,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // zero value inner boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { // set outer guard cells x[(lxx + 1) * lz2 + k] = 0.; @@ -366,8 +366,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } // Exchange ghost cells of initial guess - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < lxx + 2; i++) { x[i * lz2] = x[(i + 1) * lz2 - 2]; x[(i + 1) * lz2 - 1] = x[i * lz2 + 1]; @@ -467,8 +467,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { #endif // Copy solution into a FieldPerp to return - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < lxx + 1; i++) { for (int k = 1; k < lzz + 1; k++) { int i2 = i - 1 + localmesh->xstart; @@ -482,8 +482,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { if (inner_boundary_flags & INVERT_SET) { // guard cells of x0 specify gradient to set at inner boundary int i2 = -1 + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = x[lz2 + k] @@ -494,8 +494,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } else { // zero gradient inner boundary condition int i2 = -1 + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = x[lz2 + k]; @@ -506,8 +506,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { if (inner_boundary_flags & INVERT_SET) { // guard cells of x0 specify value to set at inner boundary int i2 = -1 + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = 2. * x0(localmesh->xstart - 1, k2) - x[lz2 + k]; @@ -515,8 +515,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } else { // zero value inner boundary condition int i2 = -1 + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = -x[lz2 + k]; @@ -530,8 +530,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { if (inner_boundary_flags & INVERT_SET) { // guard cells of x0 specify gradient to set at outer boundary int i2 = lxx + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = x[lxx * lz2 + k] @@ -542,8 +542,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } else { // zero gradient outer boundary condition int i2 = lxx + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = x[lxx * lz2 + k]; @@ -554,8 +554,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { if (outer_boundary_flags & INVERT_SET) { // guard cells of x0 specify value to set at outer boundary int i2 = lxx + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = 2. * x0(localmesh->xend + 1, k2) - x[lxx * lz2 + k]; @@ -563,8 +563,8 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } else { // zero value inner boundary condition int i2 = lxx + localmesh->xstart; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < lzz + 1; k++) { int k2 = k - 1; result(i2, k2) = -x[lxx * lz2 + k]; @@ -588,8 +588,8 @@ void LaplaceMultigrid::generateMatrixF(int level) { int llx = kMG->lnx[level]; int llz = kMG->lnz[level]; - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for collapse(2)) for (int i = 1; i < llx + 1; i++) { for (int k = 1; k < llz + 1; k++) { int i2 = i - 1 + localmesh->xstart; @@ -653,8 +653,8 @@ void LaplaceMultigrid::generateMatrixF(int level) { if (kMG->rProcI == 0) { if (inner_boundary_flags & INVERT_AC_GRAD) { // Neumann boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < llz + 1; k++) { int ic = llz + 2 + k; mat[ic * 9 + 3] += mat[ic * 9]; @@ -669,8 +669,8 @@ void LaplaceMultigrid::generateMatrixF(int level) { } } else { // Dirichlet boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < llz + 1; k++) { int ic = llz + 2 + k; mat[ic * 9 + 3] -= mat[ic * 9]; @@ -688,8 +688,8 @@ void LaplaceMultigrid::generateMatrixF(int level) { if (kMG->rProcI == kMG->xNP - 1) { if (outer_boundary_flags & INVERT_AC_GRAD) { // Neumann boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < llz + 1; k++) { int ic = llx * (llz + 2) + k; mat[ic * 9 + 3] += mat[ic * 9 + 6]; @@ -704,8 +704,8 @@ void LaplaceMultigrid::generateMatrixF(int level) { } } else { // Dirichlet boundary condition - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int k = 1; k < llz + 1; k++) { int ic = llx * (llz + 2) + k; mat[ic * 9 + 3] -= mat[ic * 9 + 6]; diff --git a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx index 6d448e4db7..0c5ad82d6c 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx @@ -290,15 +290,15 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { int nx = (xProcI % rMG->zNP) * lnx[0]; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; r[i] = 0.0; } - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dimg; i++) { yl[i] = 0.0; yg[i] = 0.0; @@ -306,7 +306,7 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (lnz[0] + 2) + iz; @@ -319,11 +319,11 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { MPI_SUM, comm2D); int nz = (xProcI % rMG->zNP) * (rMG->lnz[level]); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { int xend = rMG->lnx[level] + 1; int zend = rMG->lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = ix * (lnz[0] + 2) + nz + iz; @@ -335,9 +335,9 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { rMG->getSolution(std::begin(y), std::begin(r), 1); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dimg; i++) { yl[i] = 0.0; yg[i] = 0.0; @@ -345,7 +345,7 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { int xend = rMG->lnx[level] + 1; int zend = rMG->lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = ix * (lnz[0] + 2) + nz + iz; @@ -357,11 +357,11 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { bout::globals::mpi->MPI_Allreduce(std::begin(yl), std::begin(yg), dimg, MPI_DOUBLE, MPI_SUM, comm2D); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (lnz[0] + 2) + iz; @@ -377,16 +377,16 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { Array y(dim); Array r(dim); int nx = xProcI * lnx[0]; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; r[i] = 0.0; } int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (lnz[0] + 2) + iz; @@ -397,18 +397,18 @@ void Multigrid1DP::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { } bout::globals::mpi->MPI_Allreduce(std::begin(y), std::begin(r), dim, MPI_DOUBLE, MPI_SUM, commMG); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; } sMG->getSolution(std::begin(y), std::begin(r), 1); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (lnz[0] + 2) + iz; @@ -430,21 +430,21 @@ void Multigrid1DP::convertMatrixF2D(int level) { Array yl(dim * 9); Array yg(dim * 9); int nx = (xProcI % rMG->zNP) * lnx[0]; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim * 9; i++) { yl[i] = 0.0; yg[i] = 0.0; } - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < (rMG->lnx[level] + 2) * (rMG->lnz[level] + 2) * 9; i++) { rMG->matmg[level][i] = 0.0; } int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (lnz[0] + 2) + iz; @@ -494,11 +494,11 @@ void Multigrid1DP::convertMatrixF2D(int level) { } int nz = (xProcI % rMG->zNP) * (rMG->lnz[level]); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { int xend = rMG->lnx[level] + 1; int zend = rMG->lnz[level] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = ix * (lnz[0] + 2) + nz + iz; @@ -517,16 +517,16 @@ void Multigrid1DP::convertMatrixFS(int level) { Array yl(dim * 9); BoutReal* yg = sMG->matmg[level]; int nx = xProcI * lnx[0]; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim * 9; i++) { yl[i] = 0.0; yg[i] = 0.0; } int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (lnz[0] + 2) + iz; @@ -675,9 +675,9 @@ void Multigrid2DPf1D::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { Array r(dim); int nx = xProcI * lnx[0]; int nz = zProcI * lnz[0]; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; r[i] = 0.0; @@ -685,7 +685,7 @@ void Multigrid2DPf1D::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (gnz[0] + 2) + nz + iz; @@ -696,17 +696,17 @@ void Multigrid2DPf1D::lowestSolver(BoutReal* x, BoutReal* b, int UNUSED(plag)) { } bout::globals::mpi->MPI_Allreduce(std::begin(y), std::begin(r), dim, MPI_DOUBLE, MPI_SUM, commMG); - BOUT_OMP(parallel default(shared)) - BOUT_OMP(for) + BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(for) for (int i = 0; i < dim; i++) { y[i] = 0.0; } sMG->getSolution(std::begin(y), std::begin(r), 1); - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (gnz[0] + 2) + nz + iz; @@ -728,16 +728,16 @@ void Multigrid2DPf1D::convertMatrixFS(int level) { BoutReal* yg = sMG->matmg[level]; int nx = xProcI * lnx[0]; int nz = zProcI * lnz[0]; - BOUT_OMP(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) { - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int i = 0; i < dim * 9; i++) { yl[i] = 0.0; yg[i] = 0.0; } int xend = lnx[0] + 1; int zend = lnz[0] + 1; - BOUT_OMP(for collapse(2)) + BOUT_OMP_PERF(for collapse(2)) for (int ix = 1; ix < xend; ix++) { for (int iz = 1; iz < zend; iz++) { int nn = (nx + ix) * (gnz[0] + 2) + nz + iz; diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx index 9402ba9f1b..5c4f8da35b 100644 --- a/src/invert/laplace/impls/pcr/pcr.cxx +++ b/src/invert/laplace/impls/pcr/pcr.cxx @@ -161,7 +161,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { if (dst) { const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( @@ -169,7 +169,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Loop over X indices, including boundaries but not guard cells. (unless periodic // in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d @@ -191,7 +191,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int kz = 0; kz < nmode; kz++) { BoutReal kwave = kz * 2.0 * PI / (2. * zlen); // wave number is 1/[rad]; DST has extra 2. @@ -203,19 +203,19 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } - } // BOUT_OMP(parallel) + } // BOUT_OMP_PERF(parallel) // Solve tridiagonal systems cr_pcr_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { for (int kz = 0; kz < nmode; kz++) { k1d[kz] = xcmplx(kz, ix - xs); @@ -233,7 +233,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -241,7 +241,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Loop over X indices, including boundaries but not guard cells (unless periodic in // x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d @@ -263,7 +263,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int kz = 0; kz < nmode; kz++) { BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad] tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, @@ -273,13 +273,13 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } - } // BOUT_OMP(parallel) + } // BOUT_OMP_PERF(parallel) // Solve tridiagonal systems cr_pcr_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -287,7 +287,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { if (zero_DC) { k1d[0] = 0.; @@ -371,7 +371,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { if (dst) { const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( @@ -379,7 +379,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Loop over X and Y indices, including boundaries but not guard cells. // (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ind = 0; ind < nxny; ++ind) { // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -405,7 +405,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nsys; ind++) { // ind = (iy - ys) * nmode + kz int iy = ys + ind / nmode; @@ -421,19 +421,19 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } - } // BOUT_OMP(parallel) + } // BOUT_OMP_PERF(parallel) // Solve tridiagonal systems cr_pcr_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -455,7 +455,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array(localmesh->LocalNz / 2 @@ -464,7 +464,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Loop over X and Y indices, including boundaries but not guard cells // (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ind = 0; ind < nxny; ++ind) { // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -490,7 +490,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nsys; ind++) { // ind = (iy - ys) * nmode + kz int iy = ys + ind / nmode; @@ -504,13 +504,13 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } - } // BOUT_OMP(parallel) + } // BOUT_OMP_PERF(parallel) // Solve tridiagonal systems cr_pcr_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -518,7 +518,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y int ix = xs + ind / ny; int iy = ys + ind % ny; diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx index 925fb842ce..35a25779a7 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx @@ -157,7 +157,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { if (dst) { const BoutReal zlength = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( @@ -165,7 +165,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Loop over X indices, including boundaries but not guard cells. (unless periodic // in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d @@ -187,7 +187,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int kz = 0; kz < nmode; kz++) { // wave number is 1/[rad]; DST has extra 2. const BoutReal kwave = kz * 2.0 * PI / (2. * zlength); @@ -205,13 +205,13 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { pcr_thomas_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { for (int kz = 0; kz < nmode; kz++) { k1d[kz] = xcmplx(kz, ix - xs); @@ -229,7 +229,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -237,7 +237,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Loop over X indices, including boundaries but not guard cells (unless periodic in // x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d @@ -259,7 +259,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int kz = 0; kz < nmode; kz++) { const BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad] tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, @@ -275,7 +275,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { pcr_thomas_solver(a, b, c, bcmplx, xcmplx); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -283,7 +283,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { if (zero_DC) { k1d[0] = 0.; @@ -367,7 +367,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { if (dst) { const BoutReal zlength = getUniform(coords->dz) * (localmesh->LocalNz - 3); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( @@ -375,7 +375,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Loop over X and Y indices, including boundaries but not guard cells. // (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ind = 0; ind < nxny; ++ind) { // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -401,7 +401,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nsys; ind++) { // ind = (iy - ys) * nmode + kz int iy = ys + ind / nmode; @@ -423,13 +423,13 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { pcr_thomas_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array( localmesh->LocalNz); // ZFFT routine expects input of this length - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -451,7 +451,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { } } else { const BoutReal zlength = getUniform(coords->zlength()); - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array(localmesh->LocalNz / 2 @@ -460,7 +460,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Loop over X and Y indices, including boundaries but not guard cells // (unless periodic in x) - BOUT_OMP(for) + BOUT_OMP_PERF(for) for (int ind = 0; ind < nxny; ++ind) { // ind = (ix - xs)*(ye - ys + 1) + (iy - ys) int ix = xs + ind / ny; @@ -486,7 +486,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Get elements of the tridiagonal matrix // including boundary conditions - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nsys; ind++) { // ind = (iy - ys) * nmode + kz int iy = ys + ind / nmode; @@ -507,7 +507,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { pcr_thomas_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D); // FFT back to real space - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { /// Create a local thread-scope working array auto k1d = Array((localmesh->LocalNz) / 2 @@ -515,7 +515,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; - BOUT_OMP(for nowait) + BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y int ix = xs + ind / ny; int iy = ys + ind % ny; diff --git a/src/invert/laplace/impls/serial_band/serial_band.cxx b/src/invert/laplace/impls/serial_band/serial_band.cxx index 955e9a7ed1..eda76498fc 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.cxx +++ b/src/invert/laplace/impls/serial_band/serial_band.cxx @@ -103,7 +103,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { xbndry = 1; } - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int ix = 0; ix < localmesh->LocalNx; ix++) { // for fixed ix,jy set a complex vector rho(z) diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx index e76650c751..909a47f856 100644 --- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx +++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx @@ -133,7 +133,7 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { auto bvec = Array(ncx); auto cvec = Array(ncx); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int ix = 0; ix < ncx; ix++) { /* This for loop will set the bk (initialized by the constructor) * bk is the z fourier modes of b in z diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index 92959e1194..56ac496271 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -331,7 +331,7 @@ int LaplaceSPT::start(const FieldPerp& b, SPT_data& data) { data.dir = 1; if (localmesh->firstX()) { - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int kz = 0; kz <= maxmode; kz++) { dcomplex bet, u0; // Start tridiagonal solve @@ -382,7 +382,7 @@ int LaplaceSPT::next(SPT_data& data) { if (localmesh->lastX()) { // Last processor, turn-around - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int kz = 0; kz <= maxmode; kz++) { dcomplex bet, u0; dcomplex gp, up; @@ -409,7 +409,7 @@ int LaplaceSPT::next(SPT_data& data) { } else if (data.dir > 0) { // In the middle of X, forward direction - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int kz = 0; kz <= maxmode; kz++) { dcomplex bet, u0; bet = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); @@ -429,7 +429,7 @@ int LaplaceSPT::next(SPT_data& data) { } else if (localmesh->firstX()) { // Back to the start - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int kz = 0; kz <= maxmode; kz++) { dcomplex gp, up; gp = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); @@ -441,7 +441,7 @@ int LaplaceSPT::next(SPT_data& data) { } else { // Middle of X, back-substitution stage - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int kz = 0; kz <= maxmode; kz++) { dcomplex gp = dcomplex(data.buffer[4 * kz], data.buffer[4 * kz + 1]); dcomplex up = dcomplex(data.buffer[4 * kz + 2], data.buffer[4 * kz + 3]); diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx index 5ec0bb79e1..01f0fe46ca 100644 --- a/src/mesh/coordinates.cxx +++ b/src/mesh/coordinates.cxx @@ -925,7 +925,7 @@ void Coordinates::outputVars(Options& output_options) { } const Field2D& Coordinates::zlength() const { - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) if (not zlength_cache) { zlength_cache = std::make_unique(0., localmesh); diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx index f252abe0ea..2e25dfeedb 100644 --- a/src/mesh/difops.cxx +++ b/src/mesh/difops.cxx @@ -774,7 +774,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method, case BRACKET_ARAKAWA_OLD: { #if not(BOUT_USE_METRIC_3D) const int ncz = mesh->LocalNz; - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { for (int jy = mesh->ystart; jy <= mesh->yend; jy++) { const BoutReal partialFactor = 1.0 / (12 * metric->dz(jx, jy)); @@ -1100,7 +1100,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method, Field3D f_temp = f; Field3D g_temp = g; - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { for (int jy = mesh->ystart; jy <= mesh->yend; jy++) { #if not(BOUT_USE_METRIC_3D) diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx index 9cccd6f7d7..ebecb96700 100644 --- a/src/mesh/index_derivs.cxx +++ b/src/mesh/index_derivs.cxx @@ -445,7 +445,7 @@ class FFTDerivativeType { } const int kmax = ncz / 2 - kfilter; // Up to and including this wavenumber index - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { Array cv(ncz / 2 + 1); const BoutReal kwaveFac = TWOPI / ncz; @@ -502,7 +502,7 @@ class FFT2ndDerivativeType { const int ncz = theMesh->getNpoints(direction); const int kmax = ncz / 2; - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { Array cv(ncz / 2 + 1); const BoutReal kwaveFac = TWOPI / ncz; diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx index 0f6315a987..870f3413cd 100644 --- a/src/mesh/mesh.cxx +++ b/src/mesh/mesh.cxx @@ -801,12 +801,12 @@ std::optional Mesh::getCommonRegion(std::optional lhs, */ const size_t pos = (high * (high - 1)) / 2 + low; if (region3Dintersect.size() <= pos) { - BOUT_OMP(critical(mesh_intersection_realloc)) + BOUT_OMP_SAFE(critical(mesh_intersection_realloc)) // By default this function does not need the mutex, however, if we are // going to allocate global memory, we need to use a mutex. // Now that we have the mutex, we need to check again whether a // different thread was faster and already allocated. - // BOUT_OMP(single) would work in most cases, but it would fail if the + // BOUT_OMP_SAFE(single) would work in most cases, but it would fail if the // function is called in parallel with different arguments. While BOUT++ // is not currently doing it, other openmp parallised projects might be // calling BOUT++ in this way. @@ -821,7 +821,7 @@ std::optional Mesh::getCommonRegion(std::optional lhs, return region3Dintersect[pos]; } { - BOUT_OMP(critical(mesh_intersection)) + BOUT_OMP_SAFE(critical(mesh_intersection)) // See comment above why we need to check again in case of OpenMP #if BOUT_USE_OPENMP if (!region3Dintersect[pos].has_value()) diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx index bfdea5e126..79161fcdbf 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx @@ -201,7 +201,7 @@ void AB_integrate_update(Array& update, BoutReal timestep, for (std::size_t j = 0; j < static_cast(order); ++j) { const BoutReal factor = AB_coefficients[j]; - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (std::size_t i = 0; i < static_cast(update.size()); ++i) { update[i] += history[j][i] * factor; } @@ -576,7 +576,7 @@ BoutReal AdamsBashforthSolver::take_step(const BoutReal timeIn, const BoutReal d // std::transform(std::begin(current), std::end(current), std::begin(full_update), // std::begin(result), std::plus{}); if (not(adaptive and followHighOrder)) { - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result[i] = current[i] + full_update[i]; } @@ -614,7 +614,7 @@ BoutReal AdamsBashforthSolver::take_step(const BoutReal timeIn, const BoutReal d // use this to calculate the derivatives at this point. // std::transform(std::begin(current), std::end(current), std::begin(half_update), // std::begin(result2), std::plus{}); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result2[i] = current[i] + half_update[i]; } @@ -639,7 +639,7 @@ BoutReal AdamsBashforthSolver::take_step(const BoutReal timeIn, const BoutReal d // "full" two half step half_update. Rather than using result2 we just replace // result here as we want to use this smaller step result if (followHighOrder) { - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result[i] = current[i] + half_update[i]; } diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx index 7bffcdeb15..3976f4402c 100644 --- a/src/solver/impls/euler/euler.cxx +++ b/src/solver/impls/euler/euler.cxx @@ -144,7 +144,7 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array& star run_rhs(curtime); save_derivs(std::begin(result)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result[i] = start[i] + dt * result[i]; } diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.cxx b/src/solver/impls/rk3-ssp/rk3-ssp.cxx index 27979bc435..e13d996c00 100644 --- a/src/solver/impls/rk3-ssp/rk3-ssp.cxx +++ b/src/solver/impls/rk3-ssp/rk3-ssp.cxx @@ -108,7 +108,7 @@ void RK3SSP::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime); save_derivs(std::begin(L)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { u1[i] = start[i] + dt * L[i]; } @@ -117,7 +117,7 @@ void RK3SSP::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime + dt); save_derivs(std::begin(L)); - BOUT_OMP(parallel for ) + BOUT_OMP_PERF(parallel for ) for (int i = 0; i < nlocal; i++) { u2[i] = 0.75 * start[i] + 0.25 * u1[i] + 0.25 * dt * L[i]; } @@ -126,7 +126,7 @@ void RK3SSP::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime + 0.5 * dt); save_derivs(std::begin(L)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result[i] = (1. / 3) * start[i] + (2. / 3.) * (u2[i] + dt * L[i]); } diff --git a/src/solver/impls/rk4/rk4.cxx b/src/solver/impls/rk4/rk4.cxx index 47bef38f9c..0e7a942a45 100644 --- a/src/solver/impls/rk4/rk4.cxx +++ b/src/solver/impls/rk4/rk4.cxx @@ -105,7 +105,7 @@ int RK4Solver::run() { // Check accuracy BoutReal local_err = 0.; - BOUT_OMP(parallel for reduction(+: local_err) ) + BOUT_OMP_PERF(parallel for reduction(+: local_err) ) for (int i = 0; i < nlocal; i++) { local_err += fabs(f2[i] - f1[i]) / (fabs(f1[i]) + fabs(f2[i]) + atol); } @@ -182,7 +182,7 @@ void RK4Solver::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime); save_derivs(std::begin(k1)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { k5[i] = start[i] + 0.5 * dt * k1[i]; } @@ -191,7 +191,7 @@ void RK4Solver::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime + 0.5 * dt); save_derivs(std::begin(k2)); - BOUT_OMP(parallel for ) + BOUT_OMP_PERF(parallel for ) for (int i = 0; i < nlocal; i++) { k5[i] = start[i] + 0.5 * dt * k2[i]; } @@ -200,7 +200,7 @@ void RK4Solver::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime + 0.5 * dt); save_derivs(std::begin(k3)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { k5[i] = start[i] + dt * k3[i]; } @@ -209,7 +209,7 @@ void RK4Solver::take_step(BoutReal curtime, BoutReal dt, Array& start, run_rhs(curtime + dt); save_derivs(std::begin(k4)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result[i] = start[i] + (1. / 6.) * dt * (k1[i] + 2. * k2[i] + 2. * k3[i] + k4[i]); } diff --git a/src/solver/impls/rkgeneric/rkgeneric.cxx b/src/solver/impls/rkgeneric/rkgeneric.cxx index 8f5e95f0be..1c332d26de 100644 --- a/src/solver/impls/rkgeneric/rkgeneric.cxx +++ b/src/solver/impls/rkgeneric/rkgeneric.cxx @@ -75,7 +75,7 @@ int RKGenericSolver::init() { void RKGenericSolver::resetInternalFields() { //Zero out history - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { tmpState[i] = 0; f2[i] = 0; diff --git a/src/solver/impls/rkgeneric/rkscheme.cxx b/src/solver/impls/rkgeneric/rkscheme.cxx index 25de364533..dd4bd8e7a1 100644 --- a/src/solver/impls/rkgeneric/rkscheme.cxx +++ b/src/solver/impls/rkgeneric/rkscheme.cxx @@ -59,7 +59,7 @@ void RKScheme::setCurState(const Array& start, Array& out, const int curStage, const BoutReal dt) { //Set the initial stage - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { out[i] = start[i]; } @@ -76,7 +76,7 @@ void RKScheme::setCurState(const Array& start, Array& out, } BoutReal fac = stageCoeffs(curStage, j) * dt; - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { out[i] = out[i] + fac * steps(j, i); } @@ -147,7 +147,7 @@ BoutReal RKScheme::getErr(Array& solA, Array& solB) { // we expect slightly different round-off error each time this // is called and hence the nrhs may no longer be exactly // repeatable with this parallelisation. - BOUT_OMP(parallel for reduction(+:local_err)) + BOUT_OMP_PERF(parallel for reduction(+:local_err)) for (int i = 0; i < nlocal; i++) { local_err += std::abs(solA[i] - solB[i]) / (std::abs(solA[i]) + std::abs(solB[i]) + atol); @@ -166,7 +166,7 @@ BoutReal RKScheme::getErr(Array& solA, Array& solB) { void RKScheme::constructOutput(const Array& start, const BoutReal dt, const int index, Array& sol) { //Initialise the return data - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { sol[i] = start[i]; } @@ -177,7 +177,7 @@ void RKScheme::constructOutput(const Array& start, const BoutReal dt, continue; // Real comparison not great } BoutReal fac = dt * resultCoeffs(curStage, index); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { sol[i] = sol[i] + fac * steps(curStage, i); } @@ -188,7 +188,7 @@ void RKScheme::constructOutputs(const Array& start, const BoutReal dt, const int indexFollow, const int indexAlt, Array& solFollow, Array& solAlt) { //Initialise the return data - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { solFollow[i] = start[i]; solAlt[i] = start[i]; @@ -198,7 +198,7 @@ void RKScheme::constructOutputs(const Array& start, const BoutReal dt, for (int curStage = 0; curStage < getStageCount(); curStage++) { BoutReal facFol = dt * resultCoeffs(curStage, indexFollow); BoutReal facAlt = dt * resultCoeffs(curStage, indexAlt); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { solFollow[i] = solFollow[i] + facFol * steps(curStage, i); solAlt[i] = solAlt[i] + facAlt * steps(curStage, i); diff --git a/src/solver/impls/split-rk/split-rk.cxx b/src/solver/impls/split-rk/split-rk.cxx index ef53a12f2e..cd6bd1718c 100644 --- a/src/solver/impls/split-rk/split-rk.cxx +++ b/src/solver/impls/split-rk/split-rk.cxx @@ -113,7 +113,7 @@ int SplitRK::run() { // Check accuracy BoutReal local_err = 0.; - BOUT_OMP(parallel for reduction(+: local_err) ) + BOUT_OMP_PERF(parallel for reduction(+: local_err) ) for (int i = 0; i < nlocal; i++) { local_err += fabs(state2[i] - state1[i]) / (fabs(state1[i]) + fabs(state2[i]) + atol); @@ -220,7 +220,7 @@ void SplitRK::take_diffusion_step(BoutReal curtime, BoutReal dt, Array // Stage j = 1 // y_m2 = y0 + weight/3.0 * f(y0) -> u2 - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < dydt.size(); i++) { u2[i] = start[i] + (weight / 3.0) * dydt[i]; } @@ -231,7 +231,7 @@ void SplitRK::take_diffusion_step(BoutReal curtime, BoutReal dt, Array run_diffusive(curtime + (weight / 3.0) * dt); save_derivs(std::begin(u3)); // f(y_m2) -> u3 - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < u3.size(); i++) { u1[i] = 1.5 * (u2[i] + weight * u3[i]) - 0.5 * start[i] - weight * dydt[i]; } @@ -251,7 +251,7 @@ void SplitRK::take_diffusion_step(BoutReal curtime, BoutReal dt, Array run_diffusive(curtime); save_derivs(std::begin(u3)); // f(y_m1) -> u3 - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < u3.size(); i++) { // Next stage result in u3 u3[i] = mu * (u1[i] + weight * (u3[i] - a_jm1 * dydt[i])) + nu * u2[i] @@ -280,7 +280,7 @@ void SplitRK::take_advection_step(BoutReal curtime, BoutReal dt, Array run_convective(curtime); save_derivs(std::begin(dydt)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { u1[i] = start[i] + dt * dydt[i]; } @@ -289,7 +289,7 @@ void SplitRK::take_advection_step(BoutReal curtime, BoutReal dt, Array run_convective(curtime + dt); save_derivs(std::begin(dydt)); - BOUT_OMP(parallel for ) + BOUT_OMP_PERF(parallel for ) for (int i = 0; i < nlocal; i++) { u2[i] = 0.75 * start[i] + 0.25 * u1[i] + 0.25 * dt * dydt[i]; } @@ -298,7 +298,7 @@ void SplitRK::take_advection_step(BoutReal curtime, BoutReal dt, Array run_convective(curtime + 0.5 * dt); save_derivs(std::begin(dydt)); - BOUT_OMP(parallel for) + BOUT_OMP_PERF(parallel for) for (int i = 0; i < nlocal; i++) { result[i] = (1. / 3) * start[i] + (2. / 3.) * (u2[i] + dt * dydt[i]); } diff --git a/src/sys/hyprelib.cxx b/src/sys/hyprelib.cxx index 691e53230f..7bdeaa47cf 100644 --- a/src/sys/hyprelib.cxx +++ b/src/sys/hyprelib.cxx @@ -27,7 +27,7 @@ static constexpr auto BOUT_HYPRE_MEMORY = HYPRE_MEMORY_HOST; #endif HypreLib::HypreLib() { - BOUT_OMP(critical(HypreLib)) + BOUT_OMP_SAFE(critical(HypreLib)) { if (count == 0) { // Initialise once output_progress.write("Initialising Hypre\n"); @@ -40,7 +40,7 @@ HypreLib::HypreLib() { } HypreLib::HypreLib([[maybe_unused]] const HypreLib& other) noexcept { - BOUT_OMP(critical(HypreLib)) + BOUT_OMP_SAFE(critical(HypreLib)) { // No need to initialise Hypre, because it must already be initialised count++; // Copying, so increase count @@ -48,7 +48,7 @@ HypreLib::HypreLib([[maybe_unused]] const HypreLib& other) noexcept { } HypreLib::HypreLib([[maybe_unused]] HypreLib&& other) noexcept { - BOUT_OMP(critical(HypreLib)) + BOUT_OMP_SAFE(critical(HypreLib)) { // No need to initialise Hypre, because it must already be initialised count++; // Creating a new Hyprelib object; other will be deleted @@ -56,7 +56,7 @@ HypreLib::HypreLib([[maybe_unused]] HypreLib&& other) noexcept { } HypreLib::~HypreLib() { - BOUT_OMP(critical(HypreLib)) + BOUT_OMP_SAFE(critical(HypreLib)) { count--; if (count == 0) { @@ -67,7 +67,7 @@ HypreLib::~HypreLib() { } void HypreLib::cleanup() { - BOUT_OMP(critical(HypreLib)) + BOUT_OMP_SAFE(critical(HypreLib)) { if (count > 0) { output << "Finalising Hypre. Warning: Instances of HypreLib still exist.\n"; diff --git a/src/sys/msg_stack.cxx b/src/sys/msg_stack.cxx index 6ea4c15a8b..502836324c 100644 --- a/src/sys/msg_stack.cxx +++ b/src/sys/msg_stack.cxx @@ -58,7 +58,7 @@ void MsgStack::pop() { if (position <= 0) { return; } - BOUT_OMP(single) + BOUT_OMP_SAFE(single) { --position; } } @@ -78,7 +78,7 @@ void MsgStack::pop(int id) { } void MsgStack::clear() { - BOUT_OMP(single) + BOUT_OMP_SAFE(single) { stack.clear(); position = 0; @@ -86,7 +86,7 @@ void MsgStack::clear() { } void MsgStack::dump() { - BOUT_OMP(single) + BOUT_OMP_SAFE(single) { output << this->getDump(); } } diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx index bfcd7d6314..f1cf1a9d1b 100644 --- a/src/sys/petsclib.cxx +++ b/src/sys/petsclib.cxx @@ -58,7 +58,7 @@ void setPetscOptions(Options& options, const std::string& prefix) { } // namespace PetscLib::PetscLib(Options* opt) { - BOUT_OMP(critical(PetscLib)) + BOUT_OMP_SAFE(critical(PetscLib)) { if (count == 0) { // Initialise PETSc @@ -95,7 +95,7 @@ PetscLib::PetscLib(Options* opt) { } PetscLib::~PetscLib() { - BOUT_OMP(critical(PetscLib)) + BOUT_OMP_SAFE(critical(PetscLib)) { count--; if (count == 0) { @@ -120,7 +120,7 @@ void PetscLib::setOptionsFromInputFile(SNES& snes) { } void PetscLib::cleanup() { - BOUT_OMP(critical(PetscLib)) + BOUT_OMP_SAFE(critical(PetscLib)) { if (count > 0) { output << "Finalising PETSc. Warning: Instances of PetscLib still exist.\n"; diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx index a56f061a6e..e2eefab9a8 100644 --- a/tests/unit/include/bout/test_hypre_interface.cxx +++ b/tests/unit/include/bout/test_hypre_interface.cxx @@ -309,7 +309,7 @@ TYPED_TEST(HypreMatrixTest, SetElements) { auto j_index = static_cast(this->indexer->getGlobal(j)); HYPRE_Int ncolumns{1}; HYPRE_Complex value; - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) { HYPRE_IJMatrixGetValues(raw_matrix, 1, &ncolumns, &i_index, &j_index, &value); } if (i == j) { EXPECT_EQ(static_cast(value), diff --git a/tests/unit/include/bout/test_petsc_indexer.cxx b/tests/unit/include/bout/test_petsc_indexer.cxx index 082acafde6..3c20de9989 100644 --- a/tests/unit/include/bout/test_petsc_indexer.cxx +++ b/tests/unit/include/bout/test_petsc_indexer.cxx @@ -81,15 +81,15 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { BOUT_FOR(i, f.getRegion("RGN_NOBNDRY")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalSquare.insert(global).second); global = this->globalStarIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalStar.insert(global).second); global = this->globalDefaultIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalDefault.insert(global).second); } @@ -97,11 +97,11 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { BOUT_FOR(i, f.getRegion("RGN_XGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalSquare.insert(global).second); global = this->globalStarIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalStar.insert(global).second); EXPECT_LT(this->globalDefaultIndexer.getGlobal(i), 0); } @@ -111,11 +111,11 @@ TYPED_TEST(IndexerTest, TestConvertIndex) { BOUT_FOR(i, f.getRegion("RGN_YGUARDS")) { int global = this->globalSquareIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalSquare.insert(global).second); global = this->globalStarIndexer.getGlobal(i); EXPECT_GE(global, 0); - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) EXPECT_TRUE(indicesGlobalStar.insert(global).second); EXPECT_LT(this->globalDefaultIndexer.getGlobal(i), 0); } diff --git a/tests/unit/include/bout/test_petsc_matrix.cxx b/tests/unit/include/bout/test_petsc_matrix.cxx index cc07145d8e..9ba2475096 100644 --- a/tests/unit/include/bout/test_petsc_matrix.cxx +++ b/tests/unit/include/bout/test_petsc_matrix.cxx @@ -177,7 +177,7 @@ TYPED_TEST(PetscMatrixTest, TestGetElements) { int i_ind = this->indexer->getGlobal(i); int j_ind = this->indexer->getGlobal(j); PetscScalar matContents; - BOUT_OMP(critical) + BOUT_OMP_SAFE(critical) MatGetValues(*rawmat, 1, &i_ind, 1, &j_ind, &matContents); if (i == j) { EXPECT_EQ(matContents, static_cast(i.ind)); diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx index befcc07771..8776dad59a 100644 --- a/tests/unit/include/bout/test_region.cxx +++ b/tests/unit/include/bout/test_region.cxx @@ -262,7 +262,7 @@ TEST_F(RegionTest, regionLoopAllSection) { const auto& region = mesh->getRegion3D("RGN_ALL"); int count = 0; - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { BOUT_FOR_OMP(i, region, for reduction(+:count)) { ++count; @@ -296,7 +296,7 @@ TEST_F(RegionTest, regionLoopNoBndrySection) { const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); int count = 0; - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { BOUT_FOR_OMP(i, region, for reduction(+:count)) { ++count; @@ -313,7 +313,7 @@ TEST_F(RegionTest, regionLoopAllInner) { const auto& region = mesh->getRegion3D("RGN_ALL"); Field3D a{0.}; - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { BOUT_FOR_INNER(i, region) { a[i] = 1.0; } } @@ -331,7 +331,7 @@ TEST_F(RegionTest, regionLoopNoBndryInner) { const auto& region = mesh->getRegion3D("RGN_NOBNDRY"); Field3D a{0.}; - BOUT_OMP(parallel) + BOUT_OMP_PERF(parallel) { BOUT_FOR_INNER(i, region) { a[i] = 1.0; } } From ecef0e6969836cce8b5ab2de845617c9ecdd4cac Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Thu, 22 Feb 2024 11:34:44 +0000 Subject: [PATCH 297/412] Apply clang-format changes --- src/invert/laplace/impls/multigrid/multigrid_alg.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx index 6eab524b2c..fa97a43116 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx @@ -833,7 +833,7 @@ void MultigridAlg::solveMG(BoutReal* sol, BoutReal* rhs, int level) { perror = ini_e; for (m = 0; m < MAXIT; m++) { - BOUT_OMP_PERF(parallel default(shared)) + BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) for (int i = 0; i < ldim; i++) { y[i] = 0.0; From 71e5e4f0a6e3fff1ade583fb7ed82affece6e677 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 12:36:55 +0100 Subject: [PATCH 298/412] Do not specify redundant class in ctor This is an error in C++20 and gcc is warning by default --- include/bout/region.hxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index cbaf0d0c31..fa82deece6 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -516,9 +516,9 @@ public: // Want to make this private to disable but think it may be needed as we put Regions // into maps which seems to need to be able to make "empty" objects. - Region() = default; + Region() = default; - Region(int xstart, int xend, int ystart, int yend, int zstart, int zend, int ny, + Region(int xstart, int xend, int ystart, int yend, int zstart, int zend, int ny, int nz, int maxregionblocksize = MAXREGIONBLOCKSIZE) : ny(ny), nz(nz) { #if CHECK > 1 @@ -560,12 +560,12 @@ public: blocks = getContiguousBlocks(maxregionblocksize); }; - Region(RegionIndices& indices, int maxregionblocksize = MAXREGIONBLOCKSIZE) + Region(RegionIndices& indices, int maxregionblocksize = MAXREGIONBLOCKSIZE) : indices(indices) { blocks = getContiguousBlocks(maxregionblocksize); }; - Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; + Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; bool operator==(const Region& other) const { return std::equal(this->begin(), this->end(), other.begin(), other.end()); From 2a1185d48d2a794ef28fc01420f2c0eb58026f5d Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 12:39:35 +0100 Subject: [PATCH 299/412] Ensure omp functions are always defined --- include/bout/openmpwrap.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 41f334d2cf..da908ca61a 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -29,7 +29,7 @@ #include "bout/build_defines.hxx" -#if BOUT_USE_OPENMP +#if BOUT_USE_OPENMP || defined(_OPENMP) #include "omp.h" #endif From 761ea7e3bf9f5bb1050dfc7164df675721b5562b Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Thu, 22 Feb 2024 11:40:30 +0000 Subject: [PATCH 300/412] Apply clang-format changes --- include/bout/region.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index fa82deece6..53c7320c54 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -518,8 +518,8 @@ public: // into maps which seems to need to be able to make "empty" objects. Region() = default; - Region(int xstart, int xend, int ystart, int yend, int zstart, int zend, int ny, - int nz, int maxregionblocksize = MAXREGIONBLOCKSIZE) + Region(int xstart, int xend, int ystart, int yend, int zstart, int zend, int ny, int nz, + int maxregionblocksize = MAXREGIONBLOCKSIZE) : ny(ny), nz(nz) { #if CHECK > 1 if constexpr (std::is_base_of_v) { From 8abd6dd61bc674078ecfbd183f8d52ffa83de9e3 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 12:45:31 +0100 Subject: [PATCH 301/412] Make check for zoidberg much faster --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 483672fb67..15c7e4ad3b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -366,7 +366,7 @@ else() set(BOUT_GENERATE_FIELDOPS_DEFAULT OFF) endif() -execute_process(COMMAND ${Python3_EXECUTABLE} -c "import zoidberg" +execute_process(COMMAND ${Python3_EXECUTABLE} -c "import importlib.util ; import sys; sys.exit(importlib.util.find_spec(\"zoidberg\") is None)" RESULT_VARIABLE zoidberg_FOUND) if (zoidberg_FOUND EQUAL 0) set(zoidberg_FOUND ON) From e53a8595984dcdcbdaee29f820b115512728a92e Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 22 Feb 2024 16:53:35 +0000 Subject: [PATCH 302/412] Reorder member initialisers for `Region` Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- include/bout/region.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 53c7320c54..e1ce55ac09 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -565,7 +565,7 @@ public: blocks = getContiguousBlocks(maxregionblocksize); }; - Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; + Region(ContiguousBlocks& blocks) : indices(getRegionIndices()), blocks(blocks) { }; bool operator==(const Region& other) const { return std::equal(this->begin(), this->end(), other.begin(), other.end()); From 169a947cebe366eaa507a99ea4e4df9470686c93 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Thu, 22 Feb 2024 16:54:03 +0000 Subject: [PATCH 303/412] Apply clang-format changes --- include/bout/region.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index e1ce55ac09..067878e071 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -565,7 +565,7 @@ public: blocks = getContiguousBlocks(maxregionblocksize); }; - Region(ContiguousBlocks& blocks) : indices(getRegionIndices()), blocks(blocks) { }; + Region(ContiguousBlocks& blocks) : indices(getRegionIndices()), blocks(blocks){}; bool operator==(const Region& other) const { return std::equal(this->begin(), this->end(), other.begin(), other.end()); From af53c5be4c1f369e17a6d47cf0ea24b2b4cfac6b Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 20:33:21 +0100 Subject: [PATCH 304/412] Revert "Reorder member initialisers for `Region`" This reverts commit e53a8595984dcdcbdaee29f820b115512728a92e. --- include/bout/region.hxx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 067878e071..4fd7de3c78 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -565,7 +565,9 @@ public: blocks = getContiguousBlocks(maxregionblocksize); }; - Region(ContiguousBlocks& blocks) : indices(getRegionIndices()), blocks(blocks){}; + // We need to first set the blocks, and only after that call getRegionIndices. + // Do not put in the member initialisation + Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; bool operator==(const Region& other) const { return std::equal(this->begin(), this->end(), other.begin(), other.end()); From 7584a399dc1be4af477d83d27cf49b1171990016 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 22 Feb 2024 20:34:15 +0100 Subject: [PATCH 305/412] Prefer member initialisation --- include/bout/region.hxx | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 4fd7de3c78..8da31978b2 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -561,9 +561,7 @@ public: }; Region(RegionIndices& indices, int maxregionblocksize = MAXREGIONBLOCKSIZE) - : indices(indices) { - blocks = getContiguousBlocks(maxregionblocksize); - }; + : indices(indices), blocks(getContiguousBlocks(maxregionblocksize)){}; // We need to first set the blocks, and only after that call getRegionIndices. // Do not put in the member initialisation From 7abf442ad4b5c2edc0f9e27cd2efe701c5c8e07d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:11:00 +0000 Subject: [PATCH 306/412] Rename header guard --- include/bout/region.hxx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 8da31978b2..29193c9257 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -39,8 +39,8 @@ /// because an Ind2D essentially doesn't keep track of the /// z-dimension. -#ifndef __REGION_H__ -#define __REGION_H__ +#ifndef BOUT_REGION_H +#define BOUT_REGION_H #include #include @@ -979,4 +979,4 @@ unsigned int size(const Region& region) { return region.size(); } -#endif /* __REGION_H__ */ +#endif /* BOUT_REGION_H */ From afde5a48724b9a67b8d4985c88a9341cfd15cda3 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:18:05 +0000 Subject: [PATCH 307/412] CI: Allow `dx, nx` etc as parameter names --- .clang-tidy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index 3be0af4917..6ca5262f41 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -10,7 +10,7 @@ CheckOptions: - key: readability-identifier-length.IgnoredVariableNames value: '^[dn]?[xyz]$' - key: readability-identifier-length.IgnoredParameterNames - value: '^[fijkxyz][01xyz]?$' + value: '^[dfijknxyz][01xyz]?$' - key: readability-identifier-length.IgnoredLoopCounterNames value: '^[ijkxyz_]$' From 0ea866ceccc26060ff8beec0d28a057735b48347 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:19:52 +0000 Subject: [PATCH 308/412] Add some missing headers to `region.hxx` --- include/bout/region.hxx | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 29193c9257..3a2ed43f83 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -44,13 +44,17 @@ #include #include +#include #include #include #include #include "bout/assert.hxx" #include "bout/bout_types.hxx" -#include "bout/openmpwrap.hxx" +#include "bout/boutexception.hxx" +#include "bout/build_defines.hxx" +#include "bout/openmpwrap.hxx" // IWYU pragma: keep + class BoutMask; /// The MAXREGIONBLOCKSIZE value can be tuned to try to optimise From c27eab5ccaff8c6baf5a1098164df24d266a58f5 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:21:06 +0000 Subject: [PATCH 309/412] Explicitly silence some clang-tidy warnings These region macros cannot be implemented as functions, and must take identifiers as their arguments, not expressions The region ctor initialises its members out of order, and the more usual ctor does so in the correct order, so this is the correct implementation --- include/bout/region.hxx | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 3a2ed43f83..e8adc4e4c3 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -57,6 +57,8 @@ class BoutMask; +// NOLINTBEGIN(cppcoreguidelines-macro-usage,bugprone-macro-parentheses) + /// The MAXREGIONBLOCKSIZE value can be tuned to try to optimise /// performance on specific hardware. It determines what the largest /// contiguous block size can be. As we hope the compiler will vectorise @@ -135,6 +137,7 @@ class BoutMask; #define BOUT_FOR_INNER(index, region) \ BOUT_FOR_OMP(index, region, for schedule(BOUT_OPENMP_SCHEDULE) nowait) +// NOLINTEND(cppcoreguidelines-macro-usage,bugprone-macro-parentheses) enum class IND_TYPE { IND_3D = 0, IND_2D = 1, IND_PERP = 2 }; @@ -569,6 +572,7 @@ public: // We need to first set the blocks, and only after that call getRegionIndices. // Do not put in the member initialisation + // NOLINTNEXTLINE(cppcoreguidelines-prefer-member-initializer) Region(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); }; bool operator==(const Region& other) const { From 282306326ce5933de42a3427831f1bf3faa8518f Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:22:01 +0000 Subject: [PATCH 310/412] Apply clang-format --- include/bout/region.hxx | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index e8adc4e4c3..5287466f20 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -489,10 +489,9 @@ template class Region { // Following prevents a Region being created with anything other // than Ind2D, Ind3D or IndPerp as template type - static_assert( - std::is_base_of_v< - Ind2D, T> || std::is_base_of_v || std::is_base_of_v, - "Region must be templated with one of IndPerp, Ind2D or Ind3D"); + static_assert(std::is_base_of_v || std::is_base_of_v + || std::is_base_of_v, + "Region must be templated with one of IndPerp, Ind2D or Ind3D"); public: using data_type = T; From 1af269b1b559bb058296439252b4edebaba6f032 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:23:20 +0000 Subject: [PATCH 311/412] Remove unnecessary `const` on return types --- include/bout/region.hxx | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 5287466f20..a1392c41cc 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -239,7 +239,7 @@ struct SpecificInd { /// and is determined by the `dir` template argument. The offset corresponds /// to the `dd` template argument. template - const inline SpecificInd plus() const { + inline SpecificInd plus() const { static_assert(dir == DIRECTION::X || dir == DIRECTION::Y || dir == DIRECTION::Z || dir == DIRECTION::YAligned || dir == DIRECTION::YOrthogonal, "Unhandled DIRECTION in SpecificInd::plus"); @@ -259,7 +259,7 @@ struct SpecificInd { /// and is determined by the `dir` template argument. The offset corresponds /// to the `dd` template argument. template - const inline SpecificInd minus() const { + inline SpecificInd minus() const { static_assert(dir == DIRECTION::X || dir == DIRECTION::Y || dir == DIRECTION::Z || dir == DIRECTION::YAligned || dir == DIRECTION::YOrthogonal, "Unhandled DIRECTION in SpecificInd::minus"); @@ -275,11 +275,11 @@ struct SpecificInd { } } - const inline SpecificInd xp(int dx = 1) const { return {ind + (dx * ny * nz), ny, nz}; } + inline SpecificInd xp(int dx = 1) const { return {ind + (dx * ny * nz), ny, nz}; } /// The index one point -1 in x - const inline SpecificInd xm(int dx = 1) const { return xp(-dx); } + inline SpecificInd xm(int dx = 1) const { return xp(-dx); } /// The index one point +1 in y - const inline SpecificInd yp(int dy = 1) const { + inline SpecificInd yp(int dy = 1) const { #if CHECK >= 4 if (y() + dy < 0 or y() + dy >= ny) { throw BoutException("Offset in y ({:d}) would go out of bounds at {:d}", dy, ind); @@ -289,12 +289,12 @@ struct SpecificInd { return {ind + (dy * nz), ny, nz}; } /// The index one point -1 in y - const inline SpecificInd ym(int dy = 1) const { return yp(-dy); } + inline SpecificInd ym(int dy = 1) const { return yp(-dy); } /// The index one point +1 in z. Wraps around zend to zstart /// An alternative, non-branching calculation is : /// ind + dz - nz * ((ind + dz) / nz - ind / nz) /// but this appears no faster (and perhaps slower). - const inline SpecificInd zp(int dz = 1) const { + inline SpecificInd zp(int dz = 1) const { ASSERT3(dz >= 0); dz = dz <= nz ? dz : dz % nz; //Fix in case dz > nz, if not force it to be in range return {(ind + dz) % nz < dz ? ind - nz + dz : ind + dz, ny, nz}; @@ -303,22 +303,22 @@ struct SpecificInd { /// An alternative, non-branching calculation is : /// ind - dz + nz * ( (nz + ind) / nz - (nz + ind - dz) / nz) /// but this appears no faster (and perhaps slower). - const inline SpecificInd zm(int dz = 1) const { + inline SpecificInd zm(int dz = 1) const { dz = dz <= nz ? dz : dz % nz; //Fix in case dz > nz, if not force it to be in range ASSERT3(dz >= 0); return {(ind) % nz < dz ? ind + nz - dz : ind - dz, ny, nz}; } // and for 2 cells - const inline SpecificInd xpp() const { return xp(2); } - const inline SpecificInd xmm() const { return xm(2); } - const inline SpecificInd ypp() const { return yp(2); } - const inline SpecificInd ymm() const { return ym(2); } - const inline SpecificInd zpp() const { return zp(2); } - const inline SpecificInd zmm() const { return zm(2); } + inline SpecificInd xpp() const { return xp(2); } + inline SpecificInd xmm() const { return xm(2); } + inline SpecificInd ypp() const { return yp(2); } + inline SpecificInd ymm() const { return ym(2); } + inline SpecificInd zpp() const { return zp(2); } + inline SpecificInd zmm() const { return zm(2); } /// Generic offset of \p index in multiple directions simultaneously - const inline SpecificInd offset(int dx, int dy, int dz) const { + inline SpecificInd offset(int dx, int dy, int dz) const { auto temp = (dz > 0) ? zp(dz) : zm(-dz); return temp.yp(dy).xp(dx); } @@ -387,16 +387,16 @@ using Ind2D = SpecificInd; using IndPerp = SpecificInd; /// Get string representation of Ind3D -inline const std::string toString(const Ind3D& i) { +inline std::string toString(const Ind3D& i) { return "(" + std::to_string(i.x()) + ", " + std::to_string(i.y()) + ", " + std::to_string(i.z()) + ")"; } /// Get string representation of Ind2D -inline const std::string toString(const Ind2D& i) { +inline std::string toString(const Ind2D& i) { return "(" + std::to_string(i.x()) + ", " + std::to_string(i.y()) + ")"; } /// Get string representation of IndPerp -inline const std::string toString(const IndPerp& i) { +inline std::string toString(const IndPerp& i) { return "(" + std::to_string(i.x()) + ", " + std::to_string(i.z()) + ")"; } From 37d22e11e2e807ac08a5ac0c4491982784bb4568 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:28:00 +0000 Subject: [PATCH 312/412] Make some local variables `const` --- include/bout/region.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index a1392c41cc..a7ad2cc3a5 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -767,8 +767,8 @@ public: // globalPos = (index/period) * period; // Find which period block we're in // newIndex = globalPos + localPos; for (unsigned int i = 0; i < newInd.size(); i++) { - int index = newInd[i].ind; - int whichBlock = index / period; + const int index = newInd[i].ind; + const int whichBlock = index / period; newInd[i].ind = ((index + shift) % period) + period * whichBlock; }; From f65ea3bc19a44c2a8c3e6c71de4b5c7d156f96a4 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:28:26 +0000 Subject: [PATCH 313/412] Better names for some local variables --- include/bout/region.hxx | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index a7ad2cc3a5..8a9f0bc712 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -792,8 +792,9 @@ public: std::vector blockSizes(result.numBlocks); // Get the size of each block using lambda to calculate size - std::transform(std::begin(blocks), std::end(blocks), std::begin(blockSizes), - [](const ContiguousBlock& a) { return a.second.ind - a.first.ind; }); + std::transform( + std::begin(blocks), std::end(blocks), std::begin(blockSizes), + [](const ContiguousBlock& block) { return block.second.ind - block.first.ind; }); auto minMaxSize = std::minmax_element(std::begin(blockSizes), std::end(blockSizes)); @@ -860,10 +861,10 @@ private: int z = zstart; bool done = false; - int j = -1; + int ind = -1; while (!done) { - j++; - region[j].ind = (x * ny + y) * nz + z; + ind++; + region[ind].ind = (x * ny + y) * nz + z; if (x == xend && y == yend && z == zend) { done = true; } From c05e8eb2b1ce399a74f976470f79a840554e9c96 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:32:03 +0000 Subject: [PATCH 314/412] Explicitly cast result of `std::count` --- include/bout/region.hxx | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 8a9f0bc712..3de885d92f 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -798,15 +798,15 @@ public: auto minMaxSize = std::minmax_element(std::begin(blockSizes), std::end(blockSizes)); - result.minBlockSize = - *(minMaxSize.first); //Note have to derefence to get actual value - result.numMinBlocks = - std::count(std::begin(blockSizes), std::end(blockSizes), result.minBlockSize); - - result.maxBlockSize = - *(minMaxSize.second); //Note have to derefence to get actual value - result.numMaxBlocks = - std::count(std::begin(blockSizes), std::end(blockSizes), result.maxBlockSize); + // Note have to derefence to get actual value + result.minBlockSize = *(minMaxSize.first); + result.numMinBlocks = static_cast( + std::count(std::begin(blockSizes), std::end(blockSizes), result.minBlockSize)); + + // Note have to derefence to get actual value + result.maxBlockSize = *(minMaxSize.second); + result.numMaxBlocks = static_cast( + std::count(std::begin(blockSizes), std::end(blockSizes), result.maxBlockSize)); result.maxImbalance = static_cast(result.maxBlockSize) / static_cast(result.minBlockSize); From 2d99c6709043bc2c74543422dbede82af3ae204d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 09:40:10 +0000 Subject: [PATCH 315/412] Remove default `Region` dtor --- include/bout/region.hxx | 3 --- 1 file changed, 3 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 3de885d92f..17c3e64259 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -578,9 +578,6 @@ public: return std::equal(this->begin(), this->end(), other.begin(), other.end()); } - /// Destructor - ~Region() = default; - /// Expose the iterator over indices for use in range-based /// for-loops or with STL algorithms, etc. /// From 73f96866bc1ef6b194fe42ef488006b23294aca5 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Fri, 23 Feb 2024 10:16:27 +0000 Subject: [PATCH 316/412] Apply clang-format changes --- include/bout/region.hxx | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 17c3e64259..e9e1885acf 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -489,9 +489,10 @@ template class Region { // Following prevents a Region being created with anything other // than Ind2D, Ind3D or IndPerp as template type - static_assert(std::is_base_of_v || std::is_base_of_v - || std::is_base_of_v, - "Region must be templated with one of IndPerp, Ind2D or Ind3D"); + static_assert( + std::is_base_of_v< + Ind2D, T> || std::is_base_of_v || std::is_base_of_v, + "Region must be templated with one of IndPerp, Ind2D or Ind3D"); public: using data_type = T; From b145b562b6dd08bb70863d755771ec72de5d7f5b Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 23 Feb 2024 10:19:50 +0000 Subject: [PATCH 317/412] Fix all header guards --- include/bout/array.hxx | 6 +++--- include/bout/assert.hxx | 6 +++--- include/bout/boundary_factory.hxx | 6 +++--- include/bout/boundary_region.hxx | 6 +++--- include/bout/boundary_standard.hxx | 6 +++--- include/bout/bout_enum_class.hxx | 6 +++--- include/bout/bout_types.hxx | 6 +++--- include/bout/boutcomm.hxx | 6 +++--- include/bout/constants.hxx | 6 +++--- include/bout/coordinates.hxx | 6 +++--- include/bout/cyclic_reduction.hxx | 6 +++--- include/bout/dcomplex.hxx | 6 +++--- include/bout/derivs.hxx | 6 +++--- include/bout/difops.hxx | 6 +++--- include/bout/expr.hxx | 6 +++--- include/bout/fft.hxx | 6 +++--- include/bout/field2d.hxx | 6 +++--- include/bout/field3d.hxx | 6 +++--- include/bout/field_factory.hxx | 6 +++--- include/bout/fieldgroup.hxx | 6 +++--- include/bout/fieldperp.hxx | 4 ++-- include/bout/fv_ops.hxx | 6 +++--- include/bout/globalfield.hxx | 6 +++--- include/bout/globals.hxx | 6 +++--- include/bout/griddata.hxx | 6 +++--- include/bout/gyro_average.hxx | 6 +++--- include/bout/initialprofiles.hxx | 6 +++--- include/bout/interpolation.hxx | 6 +++--- include/bout/interpolation_xz.hxx | 6 +++--- include/bout/interpolation_z.hxx | 6 +++--- include/bout/invert/laplacexy.hxx | 6 +++--- include/bout/invert/laplacexy2.hxx | 6 +++--- include/bout/invert/laplacexz.hxx | 6 +++--- include/bout/invert_laplace.hxx | 6 +++--- include/bout/invert_parderiv.hxx | 6 +++--- include/bout/invertable_operator.hxx | 4 ++-- include/bout/lapack_routines.hxx | 6 +++--- include/bout/macro_for_each.hxx | 4 ++-- include/bout/mask.hxx | 6 +++--- include/bout/mesh.hxx | 6 +++--- include/bout/monitor.hxx | 6 +++--- include/bout/mpi_wrapper.hxx | 6 +++--- include/bout/msg_stack.hxx | 6 +++--- include/bout/multiostream.hxx | 6 +++--- include/bout/openmpwrap.hxx | 4 ++-- include/bout/operatorstencil.hxx | 6 +++--- include/bout/optionsreader.hxx | 6 +++--- include/bout/output.hxx | 6 +++--- include/bout/parallel_boundary_op.hxx | 6 +++--- include/bout/parallel_boundary_region.hxx | 6 +++--- include/bout/paralleltransform.hxx | 6 +++--- include/bout/physicsmodel.hxx | 6 +++--- include/bout/region.hxx | 6 +++--- include/bout/rkscheme.hxx | 6 +++--- include/bout/rvec.hxx | 6 +++--- include/bout/scorepwrapper.hxx | 4 ++-- include/bout/slepclib.hxx | 6 +++--- include/bout/smoothing.hxx | 6 +++--- include/bout/solverfactory.hxx | 6 +++--- include/bout/sourcex.hxx | 6 +++--- include/bout/stencils.hxx | 6 +++--- include/bout/surfaceiter.hxx | 6 +++--- include/bout/sys/gettext.hxx | 6 +++--- include/bout/sys/range.hxx | 6 +++--- include/bout/sys/timer.hxx | 6 +++--- include/bout/sys/uncopyable.hxx | 6 +++--- include/bout/template_combinations.hxx | 4 ++-- include/bout/unused.hxx | 6 +++--- include/bout/utils.hxx | 6 +++--- include/bout/vecops.hxx | 6 +++--- include/bout/vector2d.hxx | 6 +++--- include/bout/vector3d.hxx | 6 +++--- include/bout/where.hxx | 6 +++--- src/field/fieldgenerators.hxx | 6 +++--- src/invert/laplace/impls/cyclic/cyclic_laplace.hxx | 6 +++--- src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx | 6 +++--- .../impls/iterative_parallel_tri/iterative_parallel_tri.hxx | 6 +++--- src/invert/laplace/impls/multigrid/multigrid_laplace.hxx | 6 +++--- src/invert/laplace/impls/naulin/naulin_laplace.hxx | 6 +++--- src/invert/laplace/impls/petsc/petsc_laplace.hxx | 6 +++--- src/invert/laplace/impls/petsc3damg/petsc3damg.hxx | 6 +++--- src/invert/laplace/impls/serial_band/serial_band.hxx | 6 +++--- src/invert/laplace/impls/serial_tri/serial_tri.hxx | 6 +++--- src/invert/laplace/impls/spt/spt.hxx | 6 +++--- src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx | 6 +++--- src/invert/parderiv/impls/cyclic/cyclic.hxx | 6 +++--- src/mesh/impls/bout/boutmesh.hxx | 6 +++--- src/mesh/parallel/fci.hxx | 6 +++--- src/mesh/parallel/shiftedmetricinterp.hxx | 6 +++--- src/solver/impls/adams_bashforth/adams_bashforth.hxx | 6 +++--- src/solver/impls/arkode/arkode.hxx | 6 +++--- src/solver/impls/cvode/cvode.hxx | 6 +++--- src/solver/impls/euler/euler.hxx | 6 +++--- src/solver/impls/ida/ida.hxx | 6 +++--- src/solver/impls/imex-bdf2/imex-bdf2.hxx | 6 +++--- src/solver/impls/petsc/petsc.hxx | 6 +++--- src/solver/impls/power/power.hxx | 6 +++--- src/solver/impls/pvode/pvode.hxx | 6 +++--- src/solver/impls/rk3-ssp/rk3-ssp.hxx | 6 +++--- src/solver/impls/rk4/rk4.hxx | 6 +++--- src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx | 6 +++--- src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx | 6 +++--- src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx | 6 +++--- src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx | 6 +++--- src/solver/impls/rkgeneric/rkgeneric.hxx | 6 +++--- src/solver/impls/slepc/slepc.hxx | 6 +++--- src/solver/impls/snes/snes.hxx | 6 +++--- src/sys/options/optionparser.hxx | 6 +++--- src/sys/options/options_ini.hxx | 6 +++--- tests/MMS/GBS/gbs.hxx | 6 +++--- tests/integrated/test-laplacexy/loadmetric.hxx | 6 +++--- 111 files changed, 327 insertions(+), 327 deletions(-) diff --git a/include/bout/array.hxx b/include/bout/array.hxx index 060b4900a1..48a966c4b3 100644 --- a/include/bout/array.hxx +++ b/include/bout/array.hxx @@ -23,8 +23,8 @@ * o Added Umpire support, in multiple iterations/variations */ -#ifndef __ARRAY_H__ -#define __ARRAY_H__ +#ifndef BOUT_ARRAY_H +#define BOUT_ARRAY_H #include #include @@ -486,4 +486,4 @@ bool operator==(const Array& lhs, const Array& rhs) { return std::equal(lhs.begin(), lhs.end(), rhs.begin()); } -#endif // __ARRAY_H__ +#endif // BOUT_ARRAY_H diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx index 233641966b..653c44ed42 100644 --- a/include/bout/assert.hxx +++ b/include/bout/assert.hxx @@ -14,8 +14,8 @@ * */ -#ifndef __BOUT_ASSERT_H__ -#define __BOUT_ASSERT_H__ +#ifndef BOUT_ASSERT_H +#define BOUT_ASSERT_H #include "bout/boutexception.hxx" @@ -65,4 +65,4 @@ #define ASSERT3(condition) #endif -#endif // __BOUT_ASSERT_H__ +#endif // BOUT_ASSERT_H diff --git a/include/bout/boundary_factory.hxx b/include/bout/boundary_factory.hxx index 208b7cdb61..9fc2d7f256 100644 --- a/include/bout/boundary_factory.hxx +++ b/include/bout/boundary_factory.hxx @@ -1,8 +1,8 @@ class BoundaryFactory; -#ifndef __BNDRY_FACTORY_H__ -#define __BNDRY_FACTORY_H__ +#ifndef BOUT_BNDRY_FACTORY_H +#define BOUT_BNDRY_FACTORY_H #include "bout/boundary_op.hxx" #include "bout/boundary_region.hxx" @@ -126,4 +126,4 @@ private: // BoundaryModifier* findBoundaryMod(const string &s); }; -#endif // __BNDRY_FACTORY_H__ +#endif // BOUT_BNDRY_FACTORY_H diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx index 542460580c..58de12045e 100644 --- a/include/bout/boundary_region.hxx +++ b/include/bout/boundary_region.hxx @@ -1,8 +1,8 @@ class BoundaryRegion; -#ifndef __BNDRY_REGION_H__ -#define __BNDRY_REGION_H__ +#ifndef BOUT_BNDRY_REGION_H +#define BOUT_BNDRY_REGION_H #include #include @@ -142,4 +142,4 @@ private: int xs, xe; }; -#endif // __BNDRY_REGION_H__ +#endif // BOUT_BNDRY_REGION_H diff --git a/include/bout/boundary_standard.hxx b/include/bout/boundary_standard.hxx index 96d43de24d..b1116e159f 100644 --- a/include/bout/boundary_standard.hxx +++ b/include/bout/boundary_standard.hxx @@ -1,7 +1,7 @@ /// Some standard boundary conditions -#ifndef __BNDRY_STD_H__ -#define __BNDRY_STD_H__ +#ifndef BOUT_BNDRY_STD_H +#define BOUT_BNDRY_STD_H #include "bout/boundary_op.hxx" #include "bout/bout_types.hxx" @@ -516,4 +516,4 @@ public: private: }; -#endif // __BNDRY_STD_H__ +#endif // BOUT_BNDRY_STD_H diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx index ef251b4c2f..f8c9e364c5 100644 --- a/include/bout/bout_enum_class.hxx +++ b/include/bout/bout_enum_class.hxx @@ -19,8 +19,8 @@ * along with BOUT++. If not, see . **************************************************************************/ -#ifndef __BOUT_ENUM_CLASS_H__ -#define __BOUT_ENUM_CLASS_H__ +#ifndef BOUT_ENUM_CLASS_H +#define BOUT_ENUM_CLASS_H #include "bout/boutexception.hxx" #include "bout/macro_for_each.hxx" @@ -100,4 +100,4 @@ return out << toString(e); \ } -#endif // __BOUT_ENUM_CLASS_H__ +#endif // BOUT_ENUM_CLASS_H diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx index 5a00b5144b..c1f06fca7c 100644 --- a/include/bout/bout_types.hxx +++ b/include/bout/bout_types.hxx @@ -19,8 +19,8 @@ * along with BOUT++. If not, see . **************************************************************************/ -#ifndef __BOUT_TYPES_H__ -#define __BOUT_TYPES_H__ +#ifndef BOUT_TYPES_H +#define BOUT_TYPES_H #include #include @@ -140,4 +140,4 @@ struct enumWrapper { /// Boundary condition function using FuncPtr = BoutReal (*)(BoutReal t, BoutReal x, BoutReal y, BoutReal z); -#endif // __BOUT_TYPES_H__ +#endif // BOUT_TYPES_H diff --git a/include/bout/boutcomm.hxx b/include/bout/boutcomm.hxx index fea401af02..9342d29741 100644 --- a/include/bout/boutcomm.hxx +++ b/include/bout/boutcomm.hxx @@ -27,8 +27,8 @@ class BoutComm; -#ifndef __BOUTCOMM_H__ -#define __BOUTCOMM_H__ +#ifndef BOUT_BOUTCOMM_H +#define BOUT_BOUTCOMM_H #include @@ -68,4 +68,4 @@ private: static BoutComm* instance; ///< The only instance of this class (Singleton) }; -#endif // __BOUTCOMM_H__ +#endif // BOUT_BOUTCOMM_H diff --git a/include/bout/constants.hxx b/include/bout/constants.hxx index c811799aef..273ab2270e 100644 --- a/include/bout/constants.hxx +++ b/include/bout/constants.hxx @@ -3,8 +3,8 @@ * **************************************************************************/ -#ifndef __CONSTANTS_H__ -#define __CONSTANTS_H__ +#ifndef BOUT_CONSTANTS_H +#define BOUT_CONSTANTS_H #include @@ -28,4 +28,4 @@ constexpr BoutReal M_Deuterium = 2.01410178 * amu; ///< Mass of a Deuterium atom constexpr BoutReal M_Tritium = 3.0160492 * amu; ///< Mass of a Tritium atom } // namespace SI -#endif // __CONSTANTS_H__ +#endif // BOUT_CONSTANTS_H diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx index 42efcad84c..49feffa0a7 100644 --- a/include/bout/coordinates.hxx +++ b/include/bout/coordinates.hxx @@ -30,8 +30,8 @@ * **************************************************************************/ -#ifndef __COORDINATES_H__ -#define __COORDINATES_H__ +#ifndef BOUT_COORDINATES_H +#define BOUT_COORDINATES_H #include "bout/field2d.hxx" #include "bout/field3d.hxx" @@ -262,4 +262,4 @@ private: }; */ -#endif // __COORDINATES_H__ +#endif // BOUT_COORDINATES_H diff --git a/include/bout/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx index d4ef958e93..6a24ae1409 100644 --- a/include/bout/cyclic_reduction.hxx +++ b/include/bout/cyclic_reduction.hxx @@ -38,8 +38,8 @@ * ************************************************************************/ -#ifndef __CYCLIC_REDUCE_H__ -#define __CYCLIC_REDUCE_H__ +#ifndef BOUT_CYCLIC_REDUCE_H +#define BOUT_CYCLIC_REDUCE_H #ifdef DIAGNOSE #undef DIAGNOSE @@ -640,4 +640,4 @@ private: } }; -#endif // __CYCLIC_REDUCE_H__ +#endif // BOUT_CYCLIC_REDUCE_H diff --git a/include/bout/dcomplex.hxx b/include/bout/dcomplex.hxx index 569b5f2c13..75bc9d26ff 100644 --- a/include/bout/dcomplex.hxx +++ b/include/bout/dcomplex.hxx @@ -29,8 +29,8 @@ * along with BOUT++. If not, see . * */ -#ifndef __DCOMPLEX_H__ -#define __DCOMPLEX_H__ +#ifndef BOUT_DCOMPLEX_H +#define BOUT_DCOMPLEX_H #include "bout/bout_types.hxx" #include @@ -44,4 +44,4 @@ struct fcmplx { BoutReal r, i; }; -#endif // __DCOMPLEX_H__ +#endif // BOUT_DCOMPLEX_H diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx index c01e1562fc..1c360bb9cd 100644 --- a/include/bout/derivs.hxx +++ b/include/bout/derivs.hxx @@ -26,8 +26,8 @@ * **************************************************************************/ -#ifndef __DERIVS_H__ -#define __DERIVS_H__ +#ifndef BOUT_DERIVS_H +#define BOUT_DERIVS_H #include "bout/field2d.hxx" #include "bout/field3d.hxx" @@ -701,4 +701,4 @@ Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY"); -#endif // __DERIVS_H__ +#endif // BOUT_DERIVS_H diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx index 2b5c6746fd..71053d454a 100644 --- a/include/bout/difops.hxx +++ b/include/bout/difops.hxx @@ -33,8 +33,8 @@ * *******************************************************************************/ -#ifndef __DIFOPS_H__ -#define __DIFOPS_H__ +#ifndef BOUT_DIFOPS_H +#define BOUT_DIFOPS_H #include "bout/field2d.hxx" #include "bout/field3d.hxx" @@ -310,4 +310,4 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method = BRAC Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method = BRACKET_STD, CELL_LOC outloc = CELL_DEFAULT, Solver* solver = nullptr); -#endif /* __DIFOPS_H__ */ +#endif /* BOUT_DIFOPS_H */ diff --git a/include/bout/expr.hxx b/include/bout/expr.hxx index e03c07aa49..267af202ed 100644 --- a/include/bout/expr.hxx +++ b/include/bout/expr.hxx @@ -9,8 +9,8 @@ * **************************************************************************/ -#ifndef __EXPR_H__ -#define __EXPR_H__ +#ifndef BOUT_EXPR_H +#define BOUT_EXPR_H #warning expr.hxx is deprecated. Do not use! @@ -205,4 +205,4 @@ const Field3D eval3D(Expr e) { return result; } -#endif // __EXPR_H__ +#endif // BOUT_EXPR_H diff --git a/include/bout/fft.hxx b/include/bout/fft.hxx index 8e74321f2a..fdec8b7bec 100644 --- a/include/bout/fft.hxx +++ b/include/bout/fft.hxx @@ -25,8 +25,8 @@ * *******************************************************************************/ -#ifndef __FFT_H__ -#define __FFT_H__ +#ifndef BOUT_FFT_H +#define BOUT_FFT_H #include "bout/dcomplex.hxx" #include @@ -132,4 +132,4 @@ inline void DST_rev(dcomplex* in, int length, BoutReal* out) { return bout::fft::DST_rev(in, length, out); } -#endif // __FFT_H__ +#endif // BOUT_FFT_H diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx index 5bac67beb2..10b801ef8d 100644 --- a/include/bout/field2d.hxx +++ b/include/bout/field2d.hxx @@ -27,8 +27,8 @@ class Field2D; #pragma once -#ifndef __FIELD2D_H__ -#define __FIELD2D_H__ +#ifndef BOUT_FIELD2D_H +#define BOUT_FIELD2D_H class Mesh; #include "bout/field.hxx" @@ -374,4 +374,4 @@ bool operator==(const Field2D& a, const Field2D& b); std::ostream& operator<<(std::ostream& out, const Field2D& value); -#endif /* __FIELD2D_H__ */ +#endif /* BOUT_FIELD2D_H */ diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx index 9f5326253d..ba8c8e879e 100644 --- a/include/bout/field3d.hxx +++ b/include/bout/field3d.hxx @@ -23,8 +23,8 @@ class Field3D; #pragma once -#ifndef __FIELD3D_H__ -#define __FIELD3D_H__ +#ifndef BOUT_FIELD3D_H +#define BOUT_FIELD3D_H class Mesh; // #include "bout/mesh.hxx" #include "bout/bout_types.hxx" @@ -656,4 +656,4 @@ bool operator==(const Field3D& a, const Field3D& b); /// Output a string describing a Field3D to a stream std::ostream& operator<<(std::ostream& out, const Field3D& value); -#endif /* __FIELD3D_H__ */ +#endif /* BOUT_FIELD3D_H */ diff --git a/include/bout/field_factory.hxx b/include/bout/field_factory.hxx index ee228d836c..2a20226b2e 100644 --- a/include/bout/field_factory.hxx +++ b/include/bout/field_factory.hxx @@ -26,8 +26,8 @@ class FieldFactory; -#ifndef __FIELD_FACTORY_H__ -#define __FIELD_FACTORY_H__ +#ifndef BOUT_FIELD_FACTORY_H +#define BOUT_FIELD_FACTORY_H #include "bout/mesh.hxx" @@ -165,4 +165,4 @@ public: } }; -#endif // __FIELD_FACTORY_H__ +#endif // BOUT_FIELD_FACTORY_H diff --git a/include/bout/fieldgroup.hxx b/include/bout/fieldgroup.hxx index c33bd63e16..184766c6b8 100644 --- a/include/bout/fieldgroup.hxx +++ b/include/bout/fieldgroup.hxx @@ -1,5 +1,5 @@ -#ifndef __FIELDGROUP_H__ -#define __FIELDGROUP_H__ +#ifndef BOUT_FIELDGROUP_H +#define BOUT_FIELDGROUP_H #include "bout/field_data.hxx" #include @@ -190,4 +190,4 @@ private: /// Combine two FieldGroups FieldGroup operator+(const FieldGroup& lhs, const FieldGroup& rhs); -#endif // __FIELDGROUP_H__ +#endif // BOUT_FIELDGROUP_H diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx index 3b8ed45db6..6995308dbe 100644 --- a/include/bout/fieldperp.hxx +++ b/include/bout/fieldperp.hxx @@ -25,8 +25,8 @@ class FieldPerp; -#ifndef __FIELDPERP_H__ -#define __FIELDPERP_H__ +#ifndef BOUT_FIELDPERP_H +#define BOUT_FIELDPERP_H #include "bout/field.hxx" diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx index 5f1e688bd8..94007a57a2 100644 --- a/include/bout/fv_ops.hxx +++ b/include/bout/fv_ops.hxx @@ -2,8 +2,8 @@ Finite-volume discretisation methods. Flux-conservative form */ -#ifndef __FV_OPS_H__ -#define __FV_OPS_H__ +#ifndef BOUT_FV_OPS_H +#define BOUT_FV_OPS_H #include "bout/field3d.hxx" #include "bout/globals.hxx" @@ -525,4 +525,4 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) { */ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT); } // namespace FV -#endif // __FV_OPS_H__ +#endif // BOUT_FV_OPS_H diff --git a/include/bout/globalfield.hxx b/include/bout/globalfield.hxx index 85252f4962..038a0875bf 100644 --- a/include/bout/globalfield.hxx +++ b/include/bout/globalfield.hxx @@ -6,8 +6,8 @@ class GlobalField; class GlobalField2D; -#ifndef __GLOBALFIELD_H__ -#define __GLOBALFIELD_H__ +#ifndef BOUT_GLOBALFIELD_H +#define BOUT_GLOBALFIELD_H #include "mesh.hxx" @@ -257,4 +257,4 @@ private: bool data_valid; }; -#endif // __GLOBALFIELD_H__ +#endif // BOUT_GLOBALFIELD_H diff --git a/include/bout/globals.hxx b/include/bout/globals.hxx index ae7edff298..64b3a09ee3 100644 --- a/include/bout/globals.hxx +++ b/include/bout/globals.hxx @@ -24,8 +24,8 @@ * **************************************************************************/ -#ifndef __GLOBALS_H__ -#define __GLOBALS_H__ +#ifndef BOUT_GLOBALS_H +#define BOUT_GLOBALS_H #include "bout/macro_for_each.hxx" @@ -97,4 +97,4 @@ SETTING(MpiWrapper* mpi, nullptr); ///< The MPI wrapper object } // namespace globals } // namespace bout -#endif // __GLOBALS_H__ +#endif // BOUT_GLOBALS_H diff --git a/include/bout/griddata.hxx b/include/bout/griddata.hxx index 875cb07d7a..29a32e5779 100644 --- a/include/bout/griddata.hxx +++ b/include/bout/griddata.hxx @@ -25,8 +25,8 @@ class GridDataSource; -#ifndef __GRIDDATA_H__ -#define __GRIDDATA_H__ +#ifndef BOUT_GRIDDATA_H +#define BOUT_GRIDDATA_H #include "mesh.hxx" #include "bout/bout_types.hxx" @@ -299,4 +299,4 @@ private: Options* options; }; -#endif // __GRIDDATA_H__ +#endif // BOUT_GRIDDATA_H diff --git a/include/bout/gyro_average.hxx b/include/bout/gyro_average.hxx index 0f9f2a13f7..63ef13279b 100644 --- a/include/bout/gyro_average.hxx +++ b/include/bout/gyro_average.hxx @@ -29,8 +29,8 @@ * **************************************************************/ -#ifndef __GYRO_AVERAGE_H__ -#define __GYRO_AVERAGE_H__ +#ifndef BOUT_GYRO_AVERAGE_H +#define BOUT_GYRO_AVERAGE_H #include "bout/field3d.hxx" #include "bout/invert_laplace.hxx" @@ -115,4 +115,4 @@ Field3D gyroPade2(const Field3D& f, const Field2D& rho, Field3D gyroPade2(const Field3D& f, BoutReal rho, int inner_boundary_flags = GYRO_FLAGS, int outer_boundary_flags = GYRO_FLAGS); -#endif // __GYRO_AVERAGE_H__ +#endif // BOUT_GYRO_AVERAGE_H diff --git a/include/bout/initialprofiles.hxx b/include/bout/initialprofiles.hxx index 71cab22431..a2fc050b15 100644 --- a/include/bout/initialprofiles.hxx +++ b/include/bout/initialprofiles.hxx @@ -23,8 +23,8 @@ * **************************************************************************/ -#ifndef __INITIALPROF_H__ -#define __INITIALPROF_H__ +#ifndef BOUT_INITIALPROF_H +#define BOUT_INITIALPROF_H #include @@ -113,4 +113,4 @@ void initial_profile(const std::string& name, Vector2D& var); */ void initial_profile(const std::string& name, Vector3D& var); -#endif // __INITIALPROF_H__ +#endif // BOUT_INITIALPROF_H diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx index aab3f61281..1f4b0a51b5 100644 --- a/include/bout/interpolation.hxx +++ b/include/bout/interpolation.hxx @@ -23,8 +23,8 @@ * **************************************************************************/ -#ifndef __INTERP_H__ -#define __INTERP_H__ +#ifndef BOUT_INTERP_H +#define BOUT_INTERP_H #include "bout/mesh.hxx" @@ -202,4 +202,4 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL return result; } -#endif // __INTERP_H__ +#endif // BOUT_INTERP_H diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx index 3f8e37d3fd..52dc38f174 100644 --- a/include/bout/interpolation_xz.hxx +++ b/include/bout/interpolation_xz.hxx @@ -21,8 +21,8 @@ * **************************************************************************/ -#ifndef __INTERP_XZ_H__ -#define __INTERP_XZ_H__ +#ifndef BOUT_INTERP_XZ_H +#define BOUT_INTERP_XZ_H #include "bout/mask.hxx" @@ -286,4 +286,4 @@ public: template using RegisterXZInterpolation = XZInterpolationFactory::RegisterInFactory; -#endif // __INTERP_XZ_H__ +#endif // BOUT_INTERP_XZ_H diff --git a/include/bout/interpolation_z.hxx b/include/bout/interpolation_z.hxx index b11d7ff5b6..68cf5b0b06 100644 --- a/include/bout/interpolation_z.hxx +++ b/include/bout/interpolation_z.hxx @@ -20,8 +20,8 @@ * **************************************************************************/ -#ifndef __INTERP_Z_H__ -#define __INTERP_Z_H__ +#ifndef BOUT_INTERP_Z_H +#define BOUT_INTERP_Z_H #include "bout/generic_factory.hxx" #include "bout/paralleltransform.hxx" @@ -125,4 +125,4 @@ private: Field3D h11; }; -#endif // __INTERP_Z_H__ +#endif // BOUT_INTERP_Z_H diff --git a/include/bout/invert/laplacexy.hxx b/include/bout/invert/laplacexy.hxx index c07db58478..19da48dd4d 100644 --- a/include/bout/invert/laplacexy.hxx +++ b/include/bout/invert/laplacexy.hxx @@ -30,8 +30,8 @@ * **************************************************************************/ -#ifndef __LAPLACE_XY_H__ -#define __LAPLACE_XY_H__ +#ifndef BOUT_LAPLACE_XY_H +#define BOUT_LAPLACE_XY_H #include "bout/build_config.hxx" @@ -222,4 +222,4 @@ private: }; #endif // BOUT_HAS_PETSC -#endif // __LAPLACE_XY_H__ +#endif // BOUT_LAPLACE_XY_H diff --git a/include/bout/invert/laplacexy2.hxx b/include/bout/invert/laplacexy2.hxx index 6945de7b99..51f75f467d 100644 --- a/include/bout/invert/laplacexy2.hxx +++ b/include/bout/invert/laplacexy2.hxx @@ -30,8 +30,8 @@ * **************************************************************************/ -#ifndef __LAPLACE_XY2_H__ -#define __LAPLACE_XY2_H__ +#ifndef BOUT_LAPLACE_XY2_H +#define BOUT_LAPLACE_XY2_H #include "bout/build_defines.hxx" @@ -141,4 +141,4 @@ private: }; #endif // BOUT_HAS_PETSC -#endif // __LAPLACE_XY_H__ +#endif // BOUT_LAPLACE_XY2_H diff --git a/include/bout/invert/laplacexz.hxx b/include/bout/invert/laplacexz.hxx index 1b1ebef832..11f1c69330 100644 --- a/include/bout/invert/laplacexz.hxx +++ b/include/bout/invert/laplacexz.hxx @@ -28,8 +28,8 @@ * **************************************************************************/ -#ifndef __LAPLACEXZ_H__ -#define __LAPLACEXZ_H__ +#ifndef BOUT_LAPLACEXZ_H +#define BOUT_LAPLACEXZ_H #include #include @@ -91,4 +91,4 @@ protected: private: }; -#endif // __LAPLACEXZ_H__ +#endif // BOUT_LAPLACEXZ_H diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index 78417b9fce..f7b9501a81 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -31,8 +31,8 @@ class Laplacian; -#ifndef __LAPLACE_H__ -#define __LAPLACE_H__ +#ifndef BOUT_LAPLACE_H +#define BOUT_LAPLACE_H #include "bout/build_config.hxx" @@ -374,4 +374,4 @@ void laplace_tridag_coefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcom const Field2D* ccoef = nullptr, const Field2D* d = nullptr, CELL_LOC loc = CELL_DEFAULT); -#endif // __LAPLACE_H__ +#endif // BOUT_LAPLACE_H diff --git a/include/bout/invert_parderiv.hxx b/include/bout/invert_parderiv.hxx index 5a83a7f4e8..e9623e0f9f 100644 --- a/include/bout/invert_parderiv.hxx +++ b/include/bout/invert_parderiv.hxx @@ -28,8 +28,8 @@ * ************************************************************************/ -#ifndef __INV_PAR_H__ -#define __INV_PAR_H__ +#ifndef BOUT_INV_PAR_H +#define BOUT_INV_PAR_H #include "bout/field2d.hxx" #include "bout/field3d.hxx" @@ -189,4 +189,4 @@ protected: private: }; -#endif // __INV_PAR_H__ +#endif // BOUT_INV_PAR_H diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx index 1940177bca..a45fc3565f 100644 --- a/include/bout/invertable_operator.hxx +++ b/include/bout/invertable_operator.hxx @@ -30,8 +30,8 @@ class InvertableOperator; }; }; // namespace bout -#ifndef __INVERTABLE_OPERATOR_H__ -#define __INVERTABLE_OPERATOR_H__ +#ifndef BOUT_INVERTABLE_OPERATOR_H +#define BOUT_INVERTABLE_OPERATOR_H #include "bout/build_config.hxx" diff --git a/include/bout/lapack_routines.hxx b/include/bout/lapack_routines.hxx index 70a3128f81..d81c0b422d 100644 --- a/include/bout/lapack_routines.hxx +++ b/include/bout/lapack_routines.hxx @@ -20,8 +20,8 @@ * **************************************************************************/ -#ifndef __LAPACK_ROUTINES_H__ -#define __LAPACK_ROUTINES_H__ +#ifndef BOUT_LAPACK_ROUTINES_H +#define BOUT_LAPACK_ROUTINES_H #include @@ -56,4 +56,4 @@ void cyclic_tridag(dcomplex* a, dcomplex* b, dcomplex* c, dcomplex* r, dcomplex* /// Complex band matrix solver void cband_solve(Matrix& a, int n, int m1, int m2, Array& b); -#endif // __LAPACK_ROUTINES_H__ +#endif // BOUT_LAPACK_ROUTINES_H diff --git a/include/bout/macro_for_each.hxx b/include/bout/macro_for_each.hxx index 10cbd21818..1cfe373c3f 100644 --- a/include/bout/macro_for_each.hxx +++ b/include/bout/macro_for_each.hxx @@ -1,6 +1,6 @@ -#ifndef __MACRO_FOR_EACH_H__ -#define __MACRO_FOR_EACH_H__ +#ifndef BOUT_MACRO_FOR_EACH_H +#define BOUT_MACRO_FOR_EACH_H // Provides a macro MACRO_FOR_EACH which applies a // macro to each argument in a VA_ARGS list diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx index 89197ddcf2..4250d21105 100644 --- a/include/bout/mask.hxx +++ b/include/bout/mask.hxx @@ -19,8 +19,8 @@ * along with BOUT++. If not, see . **************************************************************************/ -#ifndef __MASK_H__ -#define __MASK_H__ +#ifndef BOUT_MASK_H +#define BOUT_MASK_H #include @@ -79,4 +79,4 @@ inline std::unique_ptr> regionFromMask(const BoutMask& mask, } return std::make_unique>(indices); } -#endif //__MASK_H__ +#endif //BOUT_MASK_H diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx index 8f73552ea5..3bc01d3787 100644 --- a/include/bout/mesh.hxx +++ b/include/bout/mesh.hxx @@ -40,8 +40,8 @@ class Mesh; -#ifndef __MESH_H__ -#define __MESH_H__ +#ifndef BOUT_MESH_H +#define BOUT_MESH_H #include "mpi.h" @@ -853,4 +853,4 @@ Mesh::getRegion(const std::string& region_name) const { return getRegionPerp(region_name); } -#endif // __MESH_H__ +#endif // BOUT_MESH_H diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx index 5bc4fc7e12..359096e74f 100644 --- a/include/bout/monitor.hxx +++ b/include/bout/monitor.hxx @@ -1,5 +1,5 @@ -#ifndef __MONITOR_H__ -#define __MONITOR_H__ +#ifndef BOUT_MONITOR_H +#define BOUT_MONITOR_H #include "bout/assert.hxx" #include "bout/bout_types.hxx" @@ -125,4 +125,4 @@ public: void writeProgress(BoutReal simtime, bool output_split); }; -#endif // __MONITOR_H__ +#endif // BOUT_MONITOR_H diff --git a/include/bout/mpi_wrapper.hxx b/include/bout/mpi_wrapper.hxx index 65b14cf84f..826405d8da 100644 --- a/include/bout/mpi_wrapper.hxx +++ b/include/bout/mpi_wrapper.hxx @@ -27,8 +27,8 @@ class MpiWrapper; -#ifndef __MPIWRAPPER_H__ -#define __MPIWRAPPER_H__ +#ifndef BOUT_MPIWRAPPER_H +#define BOUT_MPIWRAPPER_H #include @@ -153,4 +153,4 @@ public: virtual double MPI_Wtime() { return ::MPI_Wtime(); } }; -#endif // __MPIWRAPPER_H__ +#endif // BOUT_MPIWRAPPER_H diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx index e8158c3200..adbf1bbbcb 100644 --- a/include/bout/msg_stack.hxx +++ b/include/bout/msg_stack.hxx @@ -26,8 +26,8 @@ class MsgStack; -#ifndef __MSG_STACK_H__ -#define __MSG_STACK_H__ +#ifndef BOUT_MSG_STACK_H +#define BOUT_MSG_STACK_H #include "bout/build_config.hxx" @@ -212,4 +212,4 @@ private: */ #define AUTO_TRACE() TRACE(__thefunc__) // NOLINT -#endif // __MSG_STACK_H__ +#endif // BOUT_MSG_STACK_H diff --git a/include/bout/multiostream.hxx b/include/bout/multiostream.hxx index b90ccf9419..ca3cc2d0c7 100644 --- a/include/bout/multiostream.hxx +++ b/include/bout/multiostream.hxx @@ -1,5 +1,5 @@ -#ifndef __MULTIOSTREAM_H__ -#define __MULTIOSTREAM_H__ +#ifndef BOUT_MULTIOSTREAM_H +#define BOUT_MULTIOSTREAM_H #include #include @@ -89,4 +89,4 @@ public: using cmultiostream = multiostream; using wmultiostream = multiostream; -#endif // __MULTIOSTREAM_H__ +#endif // BOUT_MULTIOSTREAM_H diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx index 032705e61a..59e6f1f2b4 100644 --- a/include/bout/openmpwrap.hxx +++ b/include/bout/openmpwrap.hxx @@ -24,8 +24,8 @@ * **************************************************************************/ -#ifndef __OPENMPWRAP_H__ -#define __OPENMPWRAP_H__ +#ifndef BOUT_OPENMPWRAP_H +#define BOUT_OPENMPWRAP_H //Some helpers for indirection -- required so that the _Pragma gets "omp " //where is any number of valid omp options/environments (e.g. atomic, critical etc.) diff --git a/include/bout/operatorstencil.hxx b/include/bout/operatorstencil.hxx index 9a60f94ca7..118dc7a068 100644 --- a/include/bout/operatorstencil.hxx +++ b/include/bout/operatorstencil.hxx @@ -27,8 +27,8 @@ * **************************************************************************/ -#ifndef __OPERATORSTENCIL_H__ -#define __OPERATORSTENCIL_H__ +#ifndef BOUT_OPERATORSTENCIL_H +#define BOUT_OPERATORSTENCIL_H #include #include @@ -322,4 +322,4 @@ OperatorStencil starStencil(Mesh* localmesh) { return stencil; } -#endif // __OPERATORSTENCIL_H__ +#endif // BOUT_OPERATORSTENCIL_H diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx index 32c302a3f7..de3d40514d 100644 --- a/include/bout/optionsreader.hxx +++ b/include/bout/optionsreader.hxx @@ -31,8 +31,8 @@ class OptionsReader; -#ifndef __OPTIONSREADER_H__ -#define __OPTIONSREADER_H__ +#ifndef BOUT_OPTIONSREADER_H +#define BOUT_OPTIONSREADER_H #include "bout/options.hxx" @@ -108,4 +108,4 @@ private: static OptionsReader* instance; }; -#endif // __OPTIONSREADER_H__ +#endif // BOUT_OPTIONSREADER_H diff --git a/include/bout/output.hxx b/include/bout/output.hxx index a44e987197..2862899067 100644 --- a/include/bout/output.hxx +++ b/include/bout/output.hxx @@ -26,8 +26,8 @@ class Output; #pragma once -#ifndef __OUTPUT_H__ -#define __OUTPUT_H__ +#ifndef BOUT_OUTPUT_H +#define BOUT_OUTPUT_H #include "bout/multiostream.hxx" #include @@ -304,4 +304,4 @@ extern ConditionalOutput output_verbose; ///< less interesting messages /// Generic output, given the same level as output_progress extern ConditionalOutput output; -#endif // __OUTPUT_H__ +#endif // BOUT_OUTPUT_H diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx index d17aa8e48a..2bcb660802 100644 --- a/include/bout/parallel_boundary_op.hxx +++ b/include/bout/parallel_boundary_op.hxx @@ -1,5 +1,5 @@ -#ifndef __PAR_BNDRY_OP_H__ -#define __PAR_BNDRY_OP_H__ +#ifndef BOUT_PAR_BNDRY_OP_H +#define BOUT_PAR_BNDRY_OP_H #include "bout/boundary_op.hxx" #include "bout/bout_types.hxx" @@ -136,4 +136,4 @@ public: void apply(Field3D& f, BoutReal t) override; }; -#endif // __PAR_BNDRY_OP_H__ +#endif // BOUT_PAR_BNDRY_OP_H diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx index 3d5525a303..ea609c7b55 100644 --- a/include/bout/parallel_boundary_region.hxx +++ b/include/bout/parallel_boundary_region.hxx @@ -1,5 +1,5 @@ -#ifndef __PAR_BNDRY_H__ -#define __PAR_BNDRY_H__ +#ifndef BOUT_PAR_BNDRY_H +#define BOUT_PAR_BNDRY_H #include "bout/boundary_region.hxx" #include "bout/bout_types.hxx" @@ -70,4 +70,4 @@ public: const int dir; }; -#endif // __PAR_BNDRY_H__ +#endif // BOUT_PAR_BNDRY_H diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx index 4a7e4989c8..0aafa04303 100644 --- a/include/bout/paralleltransform.hxx +++ b/include/bout/paralleltransform.hxx @@ -3,8 +3,8 @@ * values along Y */ -#ifndef __PARALLELTRANSFORM_H__ -#define __PARALLELTRANSFORM_H__ +#ifndef BOUT_PARALLELTRANSFORM_H +#define BOUT_PARALLELTRANSFORM_H #include "bout/bout_types.hxx" #include "bout/field3d.hxx" @@ -317,4 +317,4 @@ private: const std::vector& phases) const; }; -#endif // __PARALLELTRANSFORM_H__ +#endif // BOUT_PARALLELTRANSFORM_H diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx index ada97fc6fc..9fa25d8b0f 100644 --- a/include/bout/physicsmodel.hxx +++ b/include/bout/physicsmodel.hxx @@ -34,8 +34,8 @@ class PhysicsModel; -#ifndef __PHYSICS_MODEL_H__ -#define __PHYSICS_MODEL_H__ +#ifndef BOUT_PHYSICS_MODEL_H +#define BOUT_PHYSICS_MODEL_H #include "solver.hxx" #include "bout/bout.hxx" @@ -566,4 +566,4 @@ private: #define SAVE_REPEAT(...) \ { MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__) } -#endif // __PHYSICS_MODEL_H__ +#endif // BOUT_PHYSICS_MODEL_H diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 8da31978b2..29193c9257 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -39,8 +39,8 @@ /// because an Ind2D essentially doesn't keep track of the /// z-dimension. -#ifndef __REGION_H__ -#define __REGION_H__ +#ifndef BOUT_REGION_H +#define BOUT_REGION_H #include #include @@ -979,4 +979,4 @@ unsigned int size(const Region& region) { return region.size(); } -#endif /* __REGION_H__ */ +#endif /* BOUT_REGION_H */ diff --git a/include/bout/rkscheme.hxx b/include/bout/rkscheme.hxx index f4e5959aff..ba818c04fe 100644 --- a/include/bout/rkscheme.hxx +++ b/include/bout/rkscheme.hxx @@ -32,8 +32,8 @@ class RKScheme; -#ifndef __RKSCHEME_H__ -#define __RKSCHEME_H__ +#ifndef BOUT_RKSCHEME_H +#define BOUT_RKSCHEME_H #include "bout/generic_factory.hxx" #include @@ -140,4 +140,4 @@ private: void zeroSteps(); }; -#endif // __RKSCHEME_H__ +#endif // BOUT_RKSCHEME_H diff --git a/include/bout/rvec.hxx b/include/bout/rvec.hxx index 0b611d64bf..492228b9ea 100644 --- a/include/bout/rvec.hxx +++ b/include/bout/rvec.hxx @@ -1,11 +1,11 @@ #pragma once -#ifndef __RVEC_H__ -#define __RVEC_H__ +#ifndef BOUT_RVEC_H +#define BOUT_RVEC_H #include #include using rvec = std::vector; -#endif // __RVEC_H__ +#endif // BOUT_RVEC_H diff --git a/include/bout/scorepwrapper.hxx b/include/bout/scorepwrapper.hxx index 210d48e49f..2eb67cda30 100644 --- a/include/bout/scorepwrapper.hxx +++ b/include/bout/scorepwrapper.hxx @@ -1,5 +1,5 @@ -#ifndef __BOUT_SCOREP_H__ -#define __BOUT_SCOREP_H__ +#ifndef BOUT_SCOREP_H +#define BOUT_SCOREP_H #include "bout/build_config.hxx" diff --git a/include/bout/slepclib.hxx b/include/bout/slepclib.hxx index f6df9ce98c..e59a9c2913 100644 --- a/include/bout/slepclib.hxx +++ b/include/bout/slepclib.hxx @@ -42,8 +42,8 @@ class SlepcLib; -#ifndef __SLEPCLIB_H__ -#define __SLEPCLIB_H__ +#ifndef BOUT_SLEPCLIB_H +#define BOUT_SLEPCLIB_H #include "bout/build_config.hxx" @@ -89,4 +89,4 @@ public: #endif // BOUT_HAS_SLEPC -#endif // __SLEPCLIB_H__ +#endif // BOUT_SLEPCLIB_H diff --git a/include/bout/smoothing.hxx b/include/bout/smoothing.hxx index 8a0d6e81b8..9485602053 100644 --- a/include/bout/smoothing.hxx +++ b/include/bout/smoothing.hxx @@ -25,8 +25,8 @@ * **************************************************************/ -#ifndef __SMOOTHING_H__ -#define __SMOOTHING_H__ +#ifndef BOUT_SMOOTHING_H +#define BOUT_SMOOTHING_H #include "bout/field3d.hxx" @@ -135,4 +135,4 @@ const Field3D nl_filter_z(const Field3D& f, BoutReal w = 1.0); */ const Field3D nl_filter(const Field3D& f, BoutReal w = 1.0); -#endif // __SMOOTHING_H__ +#endif // BOUT_SMOOTHING_H diff --git a/include/bout/solverfactory.hxx b/include/bout/solverfactory.hxx index a628aed0c1..a0ecd646b8 100644 --- a/include/bout/solverfactory.hxx +++ b/include/bout/solverfactory.hxx @@ -1,5 +1,5 @@ -#ifndef __SOLVER_FACTORY_H__ -#define __SOLVER_FACTORY_H__ +#ifndef BOUT_SOLVER_FACTORY_H +#define BOUT_SOLVER_FACTORY_H #ifndef _MSC_VER #warning("Deprecated header: use #include instead") @@ -9,4 +9,4 @@ #include -#endif // __SOLVER_FACTORY_H__ +#endif // BOUT_SOLVER_FACTORY_H diff --git a/include/bout/sourcex.hxx b/include/bout/sourcex.hxx index 6727c8bcc9..e01c469af6 100644 --- a/include/bout/sourcex.hxx +++ b/include/bout/sourcex.hxx @@ -2,8 +2,8 @@ * Radial mask operators **************************************************************/ -#ifndef __MASKX_H__ -#define __MASKX_H__ +#ifndef BOUT_MASKX_H +#define BOUT_MASKX_H #include "bout/field3d.hxx" @@ -21,4 +21,4 @@ const Field3D sink_tanhxr(const Field2D& f0, const Field3D& f, BoutReal swidth, const Field3D buff_x(const Field3D& f, bool BoutRealspace = true); -#endif // __MASKX_H__ +#endif // BOUT_MASKX_H diff --git a/include/bout/stencils.hxx b/include/bout/stencils.hxx index fa55e7dd2d..2466047297 100644 --- a/include/bout/stencils.hxx +++ b/include/bout/stencils.hxx @@ -25,8 +25,8 @@ * **************************************************************************/ -#ifndef __STENCILS_H__ -#define __STENCILS_H__ +#ifndef BOUT_STENCILS_H +#define BOUT_STENCILS_H #include "bout/bout_types.hxx" @@ -125,4 +125,4 @@ stencil inline populateStencil(const FieldType& f, const typename FieldType::ind populateStencil(s, f, i); return s; } -#endif /* __STENCILS_H__ */ +#endif /* BOUT_STENCILS_H */ diff --git a/include/bout/surfaceiter.hxx b/include/bout/surfaceiter.hxx index ebe33b9864..a031b30ba6 100644 --- a/include/bout/surfaceiter.hxx +++ b/include/bout/surfaceiter.hxx @@ -4,8 +4,8 @@ class SurfaceIter; -#ifndef __SURFACEITER_H__ -#define __SURFACEITER_H__ +#ifndef BOUT_SURFACEITER_H +#define BOUT_SURFACEITER_H #include "mesh.hxx" @@ -63,4 +63,4 @@ private: const int lastpos; }; -#endif // __SURFACEITER_H__ +#endif // BOUT_SURFACEITER_H diff --git a/include/bout/sys/gettext.hxx b/include/bout/sys/gettext.hxx index 2ada87ab63..a17412118c 100644 --- a/include/bout/sys/gettext.hxx +++ b/include/bout/sys/gettext.hxx @@ -1,7 +1,7 @@ /// Support for i18n using GNU gettext -#ifndef __BOUT_GETTEXT_H__ -#define __BOUT_GETTEXT_H__ +#ifndef BOUT_GETTEXT_H +#define BOUT_GETTEXT_H #include "bout/build_config.hxx" @@ -19,4 +19,4 @@ #define _(string) string #endif // BOUT_HAS_GETTEXT -#endif // __BOUT_GETTEXT_H__ +#endif // BOUT_GETTEXT_H diff --git a/include/bout/sys/range.hxx b/include/bout/sys/range.hxx index a210983f25..9d8aa96cd7 100644 --- a/include/bout/sys/range.hxx +++ b/include/bout/sys/range.hxx @@ -21,8 +21,8 @@ */ -#ifndef __RANGE_H__ -#define __RANGE_H__ +#ifndef BOUT_RANGE_H +#define BOUT_RANGE_H class RangeIterator { public: @@ -74,4 +74,4 @@ private: bool delete_next = false; // Flag to delete this->n if we created it }; -#endif // __RANGE_H__ +#endif // BOUT_RANGE_H diff --git a/include/bout/sys/timer.hxx b/include/bout/sys/timer.hxx index 6f04630c9d..f3beba27b1 100644 --- a/include/bout/sys/timer.hxx +++ b/include/bout/sys/timer.hxx @@ -1,5 +1,5 @@ -#ifndef __TIMER_H__ -#define __TIMER_H__ +#ifndef BOUT_TIMER_H +#define BOUT_TIMER_H #include #include @@ -134,4 +134,4 @@ public: }; #define AUTO_TIME() Timer CONCATENATE(time_, __LINE__)(__thefunc__) -#endif // __TIMER_H__ +#endif // BOUT_TIMER_H diff --git a/include/bout/sys/uncopyable.hxx b/include/bout/sys/uncopyable.hxx index 76606620ed..35418cb7f6 100644 --- a/include/bout/sys/uncopyable.hxx +++ b/include/bout/sys/uncopyable.hxx @@ -1,7 +1,7 @@ // From Scott Meyers' "Effective C++, third edition" -#ifndef __UNCOPYABLE_H__ -#define __UNCOPYABLE_H__ +#ifndef BOUT_UNCOPYABLE_H +#define BOUT_UNCOPYABLE_H /// Inherit from this class (private) to prevent copying class Uncopyable { @@ -14,4 +14,4 @@ public: Uncopyable& operator=(const Uncopyable&) = delete; }; -#endif // __UNCOPYABLE_H__ +#endif // BOUT_UNCOPYABLE_H diff --git a/include/bout/template_combinations.hxx b/include/bout/template_combinations.hxx index 81848cf252..49a42e6bca 100644 --- a/include/bout/template_combinations.hxx +++ b/include/bout/template_combinations.hxx @@ -27,8 +27,8 @@ * **************************************************************************/ -#ifndef __TEMPLATE_COMBINATIONS_H__ -#define __TEMPLATE_COMBINATIONS_H__ +#ifndef BOUT_TEMPLATE_COMBINATIONS_H +#define BOUT_TEMPLATE_COMBINATIONS_H #include diff --git a/include/bout/unused.hxx b/include/bout/unused.hxx index 74fd3c2f98..7ef67cfe84 100644 --- a/include/bout/unused.hxx +++ b/include/bout/unused.hxx @@ -1,5 +1,5 @@ -#ifndef __UNUSED_H__ -#define __UNUSED_H__ +#ifndef BOUT_UNUSED_H +#define BOUT_UNUSED_H /// Mark a function parameter as unused in the function body /// @@ -37,4 +37,4 @@ #define UNUSED(x) x #endif -#endif //__UNUSED_H__ +#endif //BOUT_UNUSED_H diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 034657423a..3172f1cf7a 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -26,8 +26,8 @@ * **************************************************************************/ -#ifndef __UTILS_H__ -#define __UTILS_H__ +#ifndef BOUT_UTILS_H +#define BOUT_UTILS_H #include "bout/bout_types.hxx" #include "bout/boutexception.hxx" @@ -712,4 +712,4 @@ inline bool flagSet(int bitset, int flag) { return (bitset & flag) != 0; } } // namespace utils } // namespace bout -#endif // __UTILS_H__ +#endif // BOUT_UTILS_H diff --git a/include/bout/vecops.hxx b/include/bout/vecops.hxx index 4a03d06b5e..9166503855 100644 --- a/include/bout/vecops.hxx +++ b/include/bout/vecops.hxx @@ -26,8 +26,8 @@ * **************************************************************************/ -#ifndef __VECOPS_H__ -#define __VECOPS_H__ +#ifndef BOUT_VECOPS_H +#define BOUT_VECOPS_H #include "bout/bout_types.hxx" #include "bout/coordinates.hxx" @@ -129,4 +129,4 @@ Vector3D V_dot_Grad(const Vector2D& v, const Vector3D& a); Vector3D V_dot_Grad(const Vector3D& v, const Vector2D& a); Vector3D V_dot_Grad(const Vector3D& v, const Vector3D& a); -#endif // __VECOPS_H__ +#endif // BOUT_VECOPS_H diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx index 974c5f81db..bdc375e698 100644 --- a/include/bout/vector2d.hxx +++ b/include/bout/vector2d.hxx @@ -34,8 +34,8 @@ class Vector2D; #pragma once -#ifndef __VECTOR2D_H__ -#define __VECTOR2D_H__ +#ifndef BOUT_VECTOR2D_H +#define BOUT_VECTOR2D_H class Field2D; class Field3D; @@ -217,4 +217,4 @@ inline Vector2D zeroFrom(const Vector2D& v) { */ inline Vector2D& ddt(Vector2D& f) { return *(f.timeDeriv()); } -#endif // __VECTOR2D_H__ +#endif // BOUT_VECTOR2D_H diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx index 93ee798663..0c71dcffa5 100644 --- a/include/bout/vector3d.hxx +++ b/include/bout/vector3d.hxx @@ -30,8 +30,8 @@ class Vector3D; #pragma once -#ifndef __VECTOR3D_H__ -#define __VECTOR3D_H__ +#ifndef BOUT_VECTOR3D_H +#define BOUT_VECTOR3D_H class Field2D; class Vector2D; @@ -237,4 +237,4 @@ inline Vector3D zeroFrom(const Vector3D& v) { */ inline Vector3D& ddt(Vector3D& f) { return *(f.timeDeriv()); } -#endif // __VECTOR3D_H__ +#endif // BOUT_VECTOR3D_H diff --git a/include/bout/where.hxx b/include/bout/where.hxx index 504dc028b1..c798d75de8 100644 --- a/include/bout/where.hxx +++ b/include/bout/where.hxx @@ -25,8 +25,8 @@ * **************************************************************************/ -#ifndef __WHERE_H__ -#define __WHERE_H__ +#ifndef BOUT_WHERE_H +#define BOUT_WHERE_H #include "bout/field.hxx" #include "bout/field2d.hxx" @@ -85,4 +85,4 @@ auto where(const T& test, BoutReal gt0, BoutReal le0) -> ResultType { return result; } -#endif // __WHERE_H__ +#endif // BOUT_WHERE_H diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx index 66ef11a855..2485b4b82d 100644 --- a/src/field/fieldgenerators.hxx +++ b/src/field/fieldgenerators.hxx @@ -4,8 +4,8 @@ * These classes are used by FieldFactory */ -#ifndef __FIELDGENERATORS_H__ -#define __FIELDGENERATORS_H__ +#ifndef BOUT_FIELDGENERATORS_H +#define BOUT_FIELDGENERATORS_H #include #include @@ -352,4 +352,4 @@ private: FieldGeneratorPtr test, gt0, lt0; }; -#endif // __FIELDGENERATORS_H__ +#endif // BOUT_FIELDGENERATORS_H diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx index 841f0a4e05..febffa7d18 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx @@ -28,8 +28,8 @@ class LaplaceCyclic; -#ifndef __LAP_CYCLIC_H__ -#define __LAP_CYCLIC_H__ +#ifndef BOUT_LAP_CYCLIC_H +#define BOUT_LAP_CYCLIC_H #include "bout/build_config.hxx" #include "bout/invert_laplace.hxx" @@ -125,4 +125,4 @@ private: #endif // BOUT_USE_METRIC_3D -#endif // __SPT_H__ +#endif // BOUT_LAP_CYCLIC_H diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx index c9c44ac19e..05a0604c4f 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx @@ -30,8 +30,8 @@ class LaplaceHypre3d; #include "bout/build_config.hxx" -#ifndef __LAPLACE_HYPRE3D_H__ -#define __LAPLACE_HYPRE3D_H__ +#ifndef BOUT_LAPLACE_HYPRE3D_H +#define BOUT_LAPLACE_HYPRE3D_H #if BOUT_HAS_HYPRE @@ -227,4 +227,4 @@ public: #endif // BOUT_HAS_HYPRE -#endif //__LAPLACE_HYPRE3D_H__ +#endif //BOUT_LAPLACE_HYPRE3D_H diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx index 563ae7e61f..1c6bb7a02e 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx @@ -26,8 +26,8 @@ class LaplaceIPT; -#ifndef __IPT_H__ -#define __IPT_H__ +#ifndef BOUT_IPT_H +#define BOUT_IPT_H #include "bout/build_config.hxx" #include "bout/invert_laplace.hxx" @@ -246,4 +246,4 @@ private: #endif // BOUT_USE_METRIC_3D -#endif // __IPT_H__ +#endif // BOUT_IPT_H diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx index 4186147874..f0b3cfc5c1 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.hxx @@ -28,8 +28,8 @@ * **************************************************************************/ -#ifndef __MULTIGRID_LAPLACE_H__ -#define __MULTIGRID_LAPLACE_H__ +#ifndef BOUT_MULTIGRID_LAPLACE_H +#define BOUT_MULTIGRID_LAPLACE_H #include "bout/build_config.hxx" #include "bout/invert_laplace.hxx" @@ -246,4 +246,4 @@ RegisterLaplace registerlaplacemultigrid(LAPLACE_MULTIGRID); #endif // BOUT_USE_METRIC_3D -#endif // __MULTIGRID_LAPLACE_H__ +#endif // BOUT_MULTIGRID_LAPLACE_H diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx index f544e74336..e464ef18e7 100644 --- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx +++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx @@ -25,8 +25,8 @@ class LaplaceNaulin; -#ifndef __LAP_NAULIN_H__ -#define __LAP_NAULIN_H__ +#ifndef BOUT_LAP_NAULIN_H +#define BOUT_LAP_NAULIN_H #include #include @@ -179,4 +179,4 @@ private: void copy_x_boundaries(Field3D& x, const Field3D& x0, Mesh* mesh); }; -#endif // __LAP_NAULIN_H__ +#endif // BOUT_LAP_NAULIN_H diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx index 3b1d3bcb49..011f8971df 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx @@ -26,8 +26,8 @@ * **************************************************************************/ -#ifndef __PETSC_LAPLACE_H__ -#define __PETSC_LAPLACE_H__ +#ifndef BOUT_PETSC_LAPLACE_H +#define BOUT_PETSC_LAPLACE_H #include "bout/build_config.hxx" #include "bout/invert_laplace.hxx" @@ -262,4 +262,4 @@ private: #endif //BOUT_HAS_PETSC -#endif //__PETSC_LAPLACE_H__ +#endif //BOUT_PETSC_LAPLACE_H diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx index 99a04bd2dd..456b85b5e6 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.hxx @@ -27,8 +27,8 @@ **************************************************************************/ class LaplacePetsc3dAmg; -#ifndef __PETSC_LAPLACE_3DAMG_H__ -#define __PETSC_LAPLACE_3DAMG_H__ +#ifndef BOUT_PETSC_LAPLACE_3DAMG_H +#define BOUT_PETSC_LAPLACE_3DAMG_H #include "bout/build_config.hxx" #include "bout/invert_laplace.hxx" @@ -228,4 +228,4 @@ private: #endif //BOUT_HAS_PETSC -#endif //__PETSC_LAPLACE_3DAMG_H__ +#endif //BOUT_PETSC_LAPLACE_3DAMG_H diff --git a/src/invert/laplace/impls/serial_band/serial_band.hxx b/src/invert/laplace/impls/serial_band/serial_band.hxx index 186e716a95..d1f0fc7c65 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.hxx +++ b/src/invert/laplace/impls/serial_band/serial_band.hxx @@ -26,8 +26,8 @@ class LaplaceSerialBand; -#ifndef __SERIAL_BAND_H__ -#define __SERIAL_BAND_H__ +#ifndef BOUT_SERIAL_BAND_H +#define BOUT_SERIAL_BAND_H #include "bout/build_config.hxx" #include "bout/invert_laplace.hxx" @@ -95,4 +95,4 @@ private: #endif // BOUT_USE_METRIC_3D -#endif // __SERIAL_BAND_H__ +#endif // BOUT_SERIAL_BAND_H diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.hxx b/src/invert/laplace/impls/serial_tri/serial_tri.hxx index 05fa375de7..5b0419fa27 100644 --- a/src/invert/laplace/impls/serial_tri/serial_tri.hxx +++ b/src/invert/laplace/impls/serial_tri/serial_tri.hxx @@ -26,8 +26,8 @@ class LaplaceSerialTri; -#ifndef __SERIAL_TRI_H__ -#define __SERIAL_TRI_H__ +#ifndef BOUT_SERIAL_TRI_H +#define BOUT_SERIAL_TRI_H #include #include @@ -80,4 +80,4 @@ private: Field2D A, C, D; }; -#endif // __SERIAL_TRI_H__ +#endif // BOUT_SERIAL_TRI_H diff --git a/src/invert/laplace/impls/spt/spt.hxx b/src/invert/laplace/impls/spt/spt.hxx index 27e9c8100c..c6aa8fd404 100644 --- a/src/invert/laplace/impls/spt/spt.hxx +++ b/src/invert/laplace/impls/spt/spt.hxx @@ -38,8 +38,8 @@ class LaplaceSPT; -#ifndef __SPT_H__ -#define __SPT_H__ +#ifndef BOUT_SPT_H +#define BOUT_SPT_H #include #include @@ -159,4 +159,4 @@ namespace { RegisterLaplace registerlaplacespt(LAPLACE_SPT); } // namespace -#endif // __SPT_H__ +#endif // BOUT_SPT_H diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx index 47967390f9..7e15be5a34 100644 --- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx +++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx @@ -6,8 +6,8 @@ class LaplaceXZpetsc; -#ifndef __LAPLACEXZ_PETSC_H__ -#define __LAPLACEXZ_PETSC_H__ +#ifndef BOUT_LAPLACEXZ_PETSC_H +#define BOUT_LAPLACEXZ_PETSC_H #include "bout/build_config.hxx" #include "bout/invert/laplacexz.hxx" @@ -73,4 +73,4 @@ private: }; #endif // BOUT_HAS_PETSC -#endif // __LAPLACEXZ_PETSC_H__ +#endif // BOUT_LAPLACEXZ_PETSC_H diff --git a/src/invert/parderiv/impls/cyclic/cyclic.hxx b/src/invert/parderiv/impls/cyclic/cyclic.hxx index 0c581adc52..6493a3b945 100644 --- a/src/invert/parderiv/impls/cyclic/cyclic.hxx +++ b/src/invert/parderiv/impls/cyclic/cyclic.hxx @@ -39,8 +39,8 @@ * ************************************************************************/ -#ifndef __INV_PAR_CR_H__ -#define __INV_PAR_CR_H__ +#ifndef BOUT_INV_PAR_CR_H +#define BOUT_INV_PAR_CR_H #include "bout/build_config.hxx" #include "bout/invert_parderiv.hxx" @@ -110,4 +110,4 @@ RegisterInvertPar registerinvertparcyclic{PARDERIVCYCLIC}; #endif // BOUT_USE_METRIC_3D -#endif // __INV_PAR_CR_H__ +#endif // BOUT_INV_PAR_CR_H diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx index 20bf1d7d46..59c6ecbfbd 100644 --- a/src/mesh/impls/bout/boutmesh.hxx +++ b/src/mesh/impls/bout/boutmesh.hxx @@ -1,6 +1,6 @@ -#ifndef __BOUTMESH_H__ -#define __BOUTMESH_H__ +#ifndef BOUT_BOUTMESH_H +#define BOUT_BOUTMESH_H #include "mpi.h" @@ -485,4 +485,4 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny, int ny_inner); } // namespace bout -#endif // __BOUTMESH_H__ +#endif // BOUT_BOUTMESH_H diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index a749c084cc..dd647d939d 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -23,8 +23,8 @@ * **************************************************************************/ -#ifndef __FCITRANSFORM_H__ -#define __FCITRANSFORM_H__ +#ifndef BOUT_FCITRANSFORM_H +#define BOUT_FCITRANSFORM_H #include #include @@ -142,4 +142,4 @@ private: std::vector field_line_maps; }; -#endif // __FCITRANSFORM_H__ +#endif // BOUT_FCITRANSFORM_H diff --git a/src/mesh/parallel/shiftedmetricinterp.hxx b/src/mesh/parallel/shiftedmetricinterp.hxx index 93ea2f07be..6852ea15a9 100644 --- a/src/mesh/parallel/shiftedmetricinterp.hxx +++ b/src/mesh/parallel/shiftedmetricinterp.hxx @@ -24,8 +24,8 @@ * **************************************************************************/ -#ifndef __SHIFTEDINTERP_H__ -#define __SHIFTEDINTERP_H__ +#ifndef BOUT_SHIFTEDINTERP_H +#define BOUT_SHIFTEDINTERP_H #include #include @@ -129,4 +129,4 @@ private: const std::size_t ydown_index; }; -#endif // __SHIFTEDINTERP_H__ +#endif // BOUT_SHIFTEDINTERP_H diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.hxx b/src/solver/impls/adams_bashforth/adams_bashforth.hxx index ad8e77ed1c..60b3b2b05e 100644 --- a/src/solver/impls/adams_bashforth/adams_bashforth.hxx +++ b/src/solver/impls/adams_bashforth/adams_bashforth.hxx @@ -25,8 +25,8 @@ class AdamsBashforthSolver; -#ifndef __ADAMSBASHFORTH_SOLVER_H__ -#define __ADAMSBASHFORTH_SOLVER_H__ +#ifndef BOUT_ADAMSBASHFORTH_SOLVER_H +#define BOUT_ADAMSBASHFORTH_SOLVER_H #include #include @@ -96,4 +96,4 @@ private: int nlocal, neq; // Number of variables on local processor and in total }; -#endif // __ADAMSBASHFORTH_SOLVER_H__ +#endif // BOUT_ADAMSBASHFORTH_SOLVER_H diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index afdce0b701..302413d8aa 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -26,8 +26,8 @@ * **************************************************************************/ -#ifndef __ARKODE_SOLVER_H__ -#define __ARKODE_SOLVER_H__ +#ifndef BOUT_ARKODE_SOLVER_H +#define BOUT_ARKODE_SOLVER_H #include "bout/build_config.hxx" #include "bout/solver.hxx" @@ -160,4 +160,4 @@ private: }; #endif // BOUT_HAS_ARKODE -#endif // __ARKODE_SOLVER_H__ +#endif // BOUT_ARKODE_SOLVER_H diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx index fa8b972bca..89c3a613a8 100644 --- a/src/solver/impls/cvode/cvode.hxx +++ b/src/solver/impls/cvode/cvode.hxx @@ -25,8 +25,8 @@ * **************************************************************************/ -#ifndef __SUNDIAL_SOLVER_H__ -#define __SUNDIAL_SOLVER_H__ +#ifndef BOUT_SUNDIAL_SOLVER_H +#define BOUT_SUNDIAL_SOLVER_H #include "bout/build_config.hxx" #include "bout/solver.hxx" @@ -157,4 +157,4 @@ private: }; #endif // BOUT_HAS_CVODE -#endif // __SUNDIAL_SOLVER_H__ +#endif // BOUT_SUNDIAL_SOLVER_H diff --git a/src/solver/impls/euler/euler.hxx b/src/solver/impls/euler/euler.hxx index bfa0be9bb3..0ee81a3d33 100644 --- a/src/solver/impls/euler/euler.hxx +++ b/src/solver/impls/euler/euler.hxx @@ -27,8 +27,8 @@ class EulerSolver; -#ifndef __EULER_SOLVER_H__ -#define __EULER_SOLVER_H__ +#ifndef BOUT_EULER_SOLVER_H +#define BOUT_EULER_SOLVER_H #include "mpi.h" @@ -66,4 +66,4 @@ private: Array& result); }; -#endif // __KARNIADAKIS_SOLVER_H__ +#endif // BOUT_KARNIADAKIS_SOLVER_H diff --git a/src/solver/impls/ida/ida.hxx b/src/solver/impls/ida/ida.hxx index 83ee4d83e6..b00054d157 100644 --- a/src/solver/impls/ida/ida.hxx +++ b/src/solver/impls/ida/ida.hxx @@ -27,8 +27,8 @@ * **************************************************************************/ -#ifndef __IDA_SOLVER_H__ -#define __IDA_SOLVER_H__ +#ifndef BOUT_IDA_SOLVER_H +#define BOUT_IDA_SOLVER_H #include "bout/build_config.hxx" #include "bout/solver.hxx" @@ -97,4 +97,4 @@ private: }; #endif // BOUT_HAS_IDA -#endif // __IDA_SOLVER_H__ +#endif // BOUT_IDA_SOLVER_H diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.hxx b/src/solver/impls/imex-bdf2/imex-bdf2.hxx index 4126c48265..f0e1b2faee 100644 --- a/src/solver/impls/imex-bdf2/imex-bdf2.hxx +++ b/src/solver/impls/imex-bdf2/imex-bdf2.hxx @@ -32,8 +32,8 @@ * **************************************************************************/ -#ifndef __IMEXBDF2_SOLVER_H__ -#define __IMEXBDF2_SOLVER_H__ +#ifndef BOUT_IMEXBDF2_SOLVER_H +#define BOUT_IMEXBDF2_SOLVER_H #include "bout/build_config.hxx" #include "bout/solver.hxx" @@ -221,6 +221,6 @@ private: void saveDerivs(BoutReal* u); }; -#endif // __IMEXBDF2_SOLVER_H__ +#endif // BOUT_IMEXBDF2_SOLVER_H #endif // BOUT_HAS_PETSC diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx index 349f40bad8..7239126abb 100644 --- a/src/solver/impls/petsc/petsc.hxx +++ b/src/solver/impls/petsc/petsc.hxx @@ -24,8 +24,8 @@ * **************************************************************************/ -#ifndef __PETSC_SOLVER_H__ -#define __PETSC_SOLVER_H__ +#ifndef BOUT_PETSC_SOLVER_H +#define BOUT_PETSC_SOLVER_H #include "bout/build_config.hxx" #include "bout/solver.hxx" @@ -149,4 +149,4 @@ private: #endif // BOUT_HAS_PETSC -#endif // __PETSC_SOLVER_H__ +#endif // BOUT_PETSC_SOLVER_H diff --git a/src/solver/impls/power/power.hxx b/src/solver/impls/power/power.hxx index 757befeec5..6f56c20f43 100644 --- a/src/solver/impls/power/power.hxx +++ b/src/solver/impls/power/power.hxx @@ -26,8 +26,8 @@ class PowerSolver; -#ifndef __POWER_SOLVER_H__ -#define __POWER_SOLVER_H__ +#ifndef BOUT_POWER_SOLVER_H +#define BOUT_POWER_SOLVER_H #include #include @@ -60,4 +60,4 @@ private: void divide(Array& in, BoutReal value); }; -#endif // __KARNIADAKIS_SOLVER_H__ +#endif // BOUT_KARNIADAKIS_SOLVER_H diff --git a/src/solver/impls/pvode/pvode.hxx b/src/solver/impls/pvode/pvode.hxx index 2ff02c22bf..d29135d02e 100644 --- a/src/solver/impls/pvode/pvode.hxx +++ b/src/solver/impls/pvode/pvode.hxx @@ -30,8 +30,8 @@ class PvodeSolver; -#ifndef __PVODE_SOLVER_H__ -#define __PVODE_SOLVER_H__ +#ifndef BOUT_PVODE_SOLVER_H +#define BOUT_PVODE_SOLVER_H #include #include @@ -81,6 +81,6 @@ private: bool pvode_initialised = false; }; -#endif // __PVODE_SOLVER_H__ +#endif // BOUT_PVODE_SOLVER_H #endif diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.hxx b/src/solver/impls/rk3-ssp/rk3-ssp.hxx index 4080b17bb5..3682d5cbde 100644 --- a/src/solver/impls/rk3-ssp/rk3-ssp.hxx +++ b/src/solver/impls/rk3-ssp/rk3-ssp.hxx @@ -33,8 +33,8 @@ class RK3SSP; -#ifndef __RK3SSP_SOLVER_H__ -#define __RK3SSP_SOLVER_H__ +#ifndef BOUT_RK3SSP_SOLVER_H +#define BOUT_RK3SSP_SOLVER_H #include "mpi.h" @@ -72,4 +72,4 @@ private: Array u1, u2, u3, L; //< Time-stepping arrays }; -#endif // __RK4_SOLVER_H__ +#endif // BOUT_RK3SSP_SOLVER_H diff --git a/src/solver/impls/rk4/rk4.hxx b/src/solver/impls/rk4/rk4.hxx index 5838b24e8e..7ec7e6dd45 100644 --- a/src/solver/impls/rk4/rk4.hxx +++ b/src/solver/impls/rk4/rk4.hxx @@ -27,8 +27,8 @@ class RK4Solver; -#ifndef __RK4_SOLVER_H__ -#define __RK4_SOLVER_H__ +#ifndef BOUT_RK4_SOLVER_H +#define BOUT_RK4_SOLVER_H #include "mpi.h" @@ -68,4 +68,4 @@ private: Array k1, k2, k3, k4, k5; //< Time-stepping arrays }; -#endif // __RK4_SOLVER_H__ +#endif // BOUT_RK4_SOLVER_H diff --git a/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx b/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx index 32072f1fc7..76042174f9 100644 --- a/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx +++ b/src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx @@ -1,8 +1,8 @@ class CASHKARPScheme; -#ifndef __CASHKARP_SCHEME_H__ -#define __CASHKARP_SCHEME_H__ +#ifndef BOUT_CASHKARP_SCHEME_H +#define BOUT_CASHKARP_SCHEME_H #include #include @@ -16,4 +16,4 @@ namespace { RegisterRKScheme registerrkschemecashkarp(RKSCHEME_CASHKARP); } -#endif // __CASHKARP_SCHEME_H__ +#endif // BOUT_CASHKARP_SCHEME_H diff --git a/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx b/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx index 126fa0912c..9fc0fc0604 100644 --- a/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx +++ b/src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx @@ -1,8 +1,8 @@ class RK4SIMPLEScheme; -#ifndef __RK4SIMPLE_SCHEME_H__ -#define __RK4SIMPLE_SCHEME_H__ +#ifndef BOUT_RK4SIMPLE_SCHEME_H +#define BOUT_RK4SIMPLE_SCHEME_H #include #include @@ -19,4 +19,4 @@ namespace { RegisterRKScheme registerrkscheme4simple(RKSCHEME_RK4); } -#endif // __RK4SIMPLE_SCHEME_H__ +#endif // BOUT_RK4SIMPLE_SCHEME_H diff --git a/src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx b/src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx index 9de022b865..6840c4f5b4 100644 --- a/src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx +++ b/src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx @@ -1,8 +1,8 @@ class RKF34Scheme; -#ifndef __RKF34_SCHEME_H__ -#define __RKF34_SCHEME_H__ +#ifndef BOUT_RKF34_SCHEME_H +#define BOUT_RKF34_SCHEME_H #include #include @@ -16,4 +16,4 @@ namespace { RegisterRKScheme registerrkschemef34(RKSCHEME_RKF34); } -#endif // __RKF34_SCHEME_H__ +#endif // BOUT_RKF34_SCHEME_H diff --git a/src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx b/src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx index ea752877e0..70150a2a40 100644 --- a/src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx +++ b/src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx @@ -1,8 +1,8 @@ class RKF45Scheme; -#ifndef __RKF45_SCHEME_H__ -#define __RKF45_SCHEME_H__ +#ifndef BOUT_RKF45_SCHEME_H +#define BOUT_RKF45_SCHEME_H #include #include @@ -16,4 +16,4 @@ namespace { RegisterRKScheme registerrkschemef45(RKSCHEME_RKF45); } -#endif // __RKF45_SCHEME_H__ +#endif // BOUT_RKF45_SCHEME_H diff --git a/src/solver/impls/rkgeneric/rkgeneric.hxx b/src/solver/impls/rkgeneric/rkgeneric.hxx index a18678e724..9df9a4a396 100644 --- a/src/solver/impls/rkgeneric/rkgeneric.hxx +++ b/src/solver/impls/rkgeneric/rkgeneric.hxx @@ -25,8 +25,8 @@ class RKGenericSolver; -#ifndef __RKGENERIC_SOLVER_H__ -#define __RKGENERIC_SOLVER_H__ +#ifndef BOUT_RKGENERIC_SOLVER_H +#define BOUT_RKGENERIC_SOLVER_H #include "mpi.h" @@ -77,4 +77,4 @@ private: std::unique_ptr scheme{nullptr}; }; -#endif // __RKGENERIC_SOLVER_H__ +#endif // BOUT_RKGENERIC_SOLVER_H diff --git a/src/solver/impls/slepc/slepc.hxx b/src/solver/impls/slepc/slepc.hxx index 88f35a04f9..619c873132 100644 --- a/src/solver/impls/slepc/slepc.hxx +++ b/src/solver/impls/slepc/slepc.hxx @@ -24,8 +24,8 @@ * **************************************************************************/ -#ifndef __SLEPC_SOLVER_H__ -#define __SLEPC_SOLVER_H__ +#ifndef BOUT_SLEPC_SOLVER_H +#define BOUT_SLEPC_SOLVER_H #include "bout/build_config.hxx" #include "bout/solver.hxx" @@ -234,4 +234,4 @@ private: #endif // BOUT_HAS_SLEPC -#endif // __SLEPC_SOLVER_H__ +#endif // BOUT_SLEPC_SOLVER_H diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx index 2021402cd7..601eaaaa25 100644 --- a/src/solver/impls/snes/snes.hxx +++ b/src/solver/impls/snes/snes.hxx @@ -25,8 +25,8 @@ * **************************************************************************/ -#ifndef __SNES_SOLVER_H__ -#define __SNES_SOLVER_H__ +#ifndef BOUT_SNES_SOLVER_H +#define BOUT_SNES_SOLVER_H #include #include @@ -143,4 +143,4 @@ RegisterUnavailableSolver #endif // BOUT_HAS_PETSC -#endif // __SNES_SOLVER_H__ +#endif // BOUT_SNES_SOLVER_H diff --git a/src/sys/options/optionparser.hxx b/src/sys/options/optionparser.hxx index ff5bb61a6f..bc61ef7297 100644 --- a/src/sys/options/optionparser.hxx +++ b/src/sys/options/optionparser.hxx @@ -39,8 +39,8 @@ class OptionParser; -#ifndef __OPTIONPARSER_H__ -#define __OPTIONPARSER_H__ +#ifndef BOUT_OPTIONPARSER_H +#define BOUT_OPTIONPARSER_H #include "bout/bout_types.hxx" #include "bout/options.hxx" @@ -61,4 +61,4 @@ public: private: }; -#endif // __OPTIONPARSER_H__ +#endif // BOUT_OPTIONPARSER_H diff --git a/src/sys/options/options_ini.hxx b/src/sys/options/options_ini.hxx index d06a700f09..092ed9320a 100644 --- a/src/sys/options/options_ini.hxx +++ b/src/sys/options/options_ini.hxx @@ -33,8 +33,8 @@ class OptionINI; -#ifndef __OPTIONS_INI_H__ -#define __OPTIONS_INI_H__ +#ifndef BOUT_OPTIONS_INI_H +#define BOUT_OPTIONS_INI_H #include "optionparser.hxx" @@ -59,4 +59,4 @@ private: std::string getNextLine(std::ifstream& fin); }; -#endif // __OPTIONS_INI_H__ +#endif // BOUT_OPTIONS_INI_H diff --git a/tests/MMS/GBS/gbs.hxx b/tests/MMS/GBS/gbs.hxx index e711e3ea83..468a5e579c 100644 --- a/tests/MMS/GBS/gbs.hxx +++ b/tests/MMS/GBS/gbs.hxx @@ -1,8 +1,8 @@ class GBS; -#ifndef __GBS_H__ -#define __GBS_H__ +#ifndef BOUT_GBS_H +#define BOUT_GBS_H #include @@ -96,4 +96,4 @@ private: std::unique_ptr aparSolver{nullptr}; }; -#endif // __GBS_H__ +#endif // BOUT_GBS_H diff --git a/tests/integrated/test-laplacexy/loadmetric.hxx b/tests/integrated/test-laplacexy/loadmetric.hxx index 141269d8b8..25e55fc8e8 100644 --- a/tests/integrated/test-laplacexy/loadmetric.hxx +++ b/tests/integrated/test-laplacexy/loadmetric.hxx @@ -1,8 +1,8 @@ -#ifndef __LOADMETRIC_H__ -#define __LOADMETRIC_H__ +#ifndef BOUT_LOADMETRIC_H +#define BOUT_LOADMETRIC_H #include void LoadMetric(BoutReal Lnorm, BoutReal Bnorm); -#endif // __LOADMETRIC_H__ +#endif // BOUT_LOADMETRIC_H From 572287ded330129a5670f5a4d3176cdbae11338b Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 1 Mar 2024 20:35:10 -0800 Subject: [PATCH 318/412] elm-pb: Fix sheath boundary conditions Need to shift to/from field-aligned coordinates when applying parallel boundary conditions. --- examples/elm-pb/elm_pb.cxx | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index e81742747a..ea8737ebc8 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -1427,23 +1427,30 @@ class ELMpb : public PhysicsModel { if (sheath_boundaries) { + // Need to shift into field-aligned coordinates before applying + // parallel boundary conditions + + auto phi_fa = toFieldAligned(phi); + auto P_fa = toFieldAligned(P); + auto Jpar_fa = toFieldAligned(Jpar); + // At y = ystart (lower boundary) for (RangeIterator r = mesh->iterateBndryLowerY(); !r.isDone(); r++) { for (int jz = 0; jz < mesh->LocalNz; jz++) { // Zero-gradient potential - BoutReal phisheath = phi(r.ind, mesh->ystart, jz); + BoutReal phisheath = phi_fa(r.ind, mesh->ystart, jz); BoutReal jsheath = -(sqrt(mi_me) / (2. * sqrt(PI))) * phisheath; // Apply boundary condition half-way between cells for (int jy = mesh->ystart - 1; jy >= 0; jy--) { // Neumann conditions - P(r.ind, jy, jz) = P(r.ind, mesh->ystart, jz); - phi(r.ind, jy, jz) = phisheath; + P_fa(r.ind, jy, jz) = P_fa(r.ind, mesh->ystart, jz); + phi_fa(r.ind, jy, jz) = phisheath; // Dirichlet condition on Jpar - Jpar(r.ind, jy, jz) = 2. * jsheath - Jpar(r.ind, mesh->ystart, jz); + Jpar_fa(r.ind, jy, jz) = 2. * jsheath - Jpar_fa(r.ind, mesh->ystart, jz); } } } @@ -1454,22 +1461,27 @@ class ELMpb : public PhysicsModel { for (int jz = 0; jz < mesh->LocalNz; jz++) { // Zero-gradient potential - BoutReal phisheath = phi(r.ind, mesh->yend, jz); + BoutReal phisheath = phi_fa(r.ind, mesh->yend, jz); BoutReal jsheath = (sqrt(mi_me) / (2. * sqrt(PI))) * phisheath; // Apply boundary condition half-way between cells for (int jy = mesh->yend + 1; jy < mesh->LocalNy; jy++) { // Neumann conditions - P(r.ind, jy, jz) = P(r.ind, mesh->yend, jz); - phi(r.ind, jy, jz) = phisheath; + P_fa(r.ind, jy, jz) = P_fa(r.ind, mesh->yend, jz); + phi_fa(r.ind, jy, jz) = phisheath; // Dirichlet condition on Jpar // WARNING: this is not correct if staggered grids are used ASSERT3(not mesh->StaggerGrids); - Jpar(r.ind, jy, jz) = 2. * jsheath - Jpar(r.ind, mesh->yend, jz); + Jpar_fa(r.ind, jy, jz) = 2. * jsheath - Jpar_fa(r.ind, mesh->yend, jz); } } } + + // Shift back from field aligned coordinates + phi = fromFieldAligned(phi_fa); + P = fromFieldAligned(P_fa); + Jpar = fromFieldAligned(Jpar_fa); } //////////////////////////////////////////////////// From f77fef5c8f945c14e6958f03165851faa8fb201c Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Fri, 1 Mar 2024 21:06:51 -0800 Subject: [PATCH 319/412] Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- examples/elm-pb/elm_pb.cxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx index ea8737ebc8..f108e58e2f 100644 --- a/examples/elm-pb/elm_pb.cxx +++ b/examples/elm-pb/elm_pb.cxx @@ -1440,7 +1440,7 @@ class ELMpb : public PhysicsModel { for (int jz = 0; jz < mesh->LocalNz; jz++) { // Zero-gradient potential - BoutReal phisheath = phi_fa(r.ind, mesh->ystart, jz); + BoutReal const phisheath = phi_fa(r.ind, mesh->ystart, jz); BoutReal jsheath = -(sqrt(mi_me) / (2. * sqrt(PI))) * phisheath; @@ -1461,7 +1461,7 @@ class ELMpb : public PhysicsModel { for (int jz = 0; jz < mesh->LocalNz; jz++) { // Zero-gradient potential - BoutReal phisheath = phi_fa(r.ind, mesh->yend, jz); + BoutReal const phisheath = phi_fa(r.ind, mesh->yend, jz); BoutReal jsheath = (sqrt(mi_me) / (2. * sqrt(PI))) * phisheath; From 06eb590b6c977d5d2a7d8844545adcb9814f284a Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 18 Mar 2024 14:31:48 +0100 Subject: [PATCH 320/412] CI: Adopt for no sudo in container --- .ci_fedora.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_fedora.sh b/.ci_fedora.sh index 452afb4b7e..b8805abb15 100755 --- a/.ci_fedora.sh +++ b/.ci_fedora.sh @@ -50,7 +50,7 @@ then cp -a /tmp/BOUT-dev /home/test/ chown -R test /home/test chmod u+rwX /home/test -R - sudo -u test ${0/\/tmp/\/home\/test} $mpi + su - test -c "${0/\/tmp/\/home\/test} $mpi" ## If we are called as normal user, run test else . /etc/profile.d/modules.sh From 21fbe05f37de9e3811336f5f0c8c7f6bd413f0eb Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 3 Nov 2023 11:51:22 +0100 Subject: [PATCH 321/412] ignore cmake cache stuff --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 7ddf9526ab..934da1c0de 100644 --- a/.gitignore +++ b/.gitignore @@ -85,3 +85,5 @@ coverage/ /_version.txt /BOUT++-v*.tar.gz /BOUT++-v*.tar.xz +/CMakeCache.txt +/CMakeFiles/cmake.check_cache From 4153b2d5d853df57598318ab6fce84da4cb44073 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 3 Nov 2023 11:49:59 +0100 Subject: [PATCH 322/412] Fix comment --- src/mesh/fv_ops.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx index 0a5d5f9624..cd5b924e9e 100644 --- a/src/mesh/fv_ops.cxx +++ b/src/mesh/fv_ops.cxx @@ -22,7 +22,7 @@ Slices makeslices(bool use_slices, const T& field) { namespace FV { -// Div ( a Grad_perp(f) ) -- ∇⊥ ( a ⋅ ∇⊥ f) -- Vorticity +// Div ( a Grad_perp(f) ) -- ∇ ⋅ ( a ∇⊥ f) -- Vorticity Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) { ASSERT2(a.getLocation() == f.getLocation()); From 999124255a7eaee0f10b03ba8939f51b94544b2c Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 3 Nov 2023 11:49:01 +0100 Subject: [PATCH 323/412] Fix license tag --- include/bout/sundials_backports.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index c4f4aa59ef..6442dd1900 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -3,7 +3,7 @@ // These are common backports shared between the CVode, ARKode, and IDA solvers // // Copyright 2022 Peter Hill, BOUT++ Team -// SPDX-License-Identifier: LGPLv3 +// SPDX-License-Identifier: LGPL-3.0-or-later #ifndef BOUT_SUNDIALS_BACKPORTS_H #define BOUT_SUNDIALS_BACKPORTS_H From d74a18889418bca1318354346d5cc388b4f05b16 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 19 Jun 2023 09:20:02 +0200 Subject: [PATCH 324/412] More const awareness --- include/bout/options.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 839c847289..62aeed4294 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -364,7 +364,7 @@ public: /// {"long_name", "some velocity"} /// }); Options& setAttributes( - std::initializer_list> attrs) { + const std::initializer_list>& attrs) { for (const auto& attr : attrs) { attributes[attr.first] = attr.second; } From d32be809271507c75974ae1a57307d5822cbed8e Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 16 Dec 2021 12:00:05 +0100 Subject: [PATCH 325/412] Provide non-const [] operator --- include/bout/utils.hxx | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx index 3172f1cf7a..b45152fbcc 100644 --- a/include/bout/utils.hxx +++ b/include/bout/utils.hxx @@ -362,6 +362,14 @@ public: return data[i.ind]; } + T& operator[](Ind3D i) { + // ny and nz are private :-( + // ASSERT2(i.nz == n3); + // ASSERT2(i.ny == n2); + ASSERT2(0 <= i.ind && i.ind < n1 * n2 * n3); + return data[i.ind]; + } + Tensor& operator=(const T& val) { for (auto& i : data) { i = val; From df29b37921b7425554fe3287fca6b72f289d7fe7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20Schw=C3=B6rer?= Date: Fri, 19 Nov 2021 10:31:31 +0100 Subject: [PATCH 326/412] Update comments --- include/bout/single_index_ops.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/bout/single_index_ops.hxx b/include/bout/single_index_ops.hxx index 6a9089510b..60bd78bc36 100644 --- a/include/bout/single_index_ops.hxx +++ b/include/bout/single_index_ops.hxx @@ -16,7 +16,7 @@ using EXEC_POL = RAJA::cuda_exec; using EXEC_POL = RAJA::loop_exec; #endif // end BOUT_USE_CUDA ////-----------CUDA settings------------------------------------------------------end -#endif +#endif // end BOUT_HAS_RAJA // Ind3D: i.zp(): BOUT_HOST_DEVICE inline int i_zp(const int id, const int nz) { From bdb24ce02740bc083c41024905b7b4e60441e3ae Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Tue, 19 Mar 2024 15:17:56 +0000 Subject: [PATCH 327/412] Apply clang-format changes --- include/bout/options.hxx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 62aeed4294..2078c5cb63 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -364,7 +364,8 @@ public: /// {"long_name", "some velocity"} /// }); Options& setAttributes( - const std::initializer_list>& attrs) { + const std::initializer_list>& + attrs) { for (const auto& attr : attrs) { attributes[attr.first] = attr.second; } From 2c01f109a0322b43b77e8e43b738121c24c84607 Mon Sep 17 00:00:00 2001 From: David Bold Date: Thu, 21 Mar 2024 10:50:44 +0100 Subject: [PATCH 328/412] Reintroduce removed copy function marked deprecated This gives dependend codes more time to adopt. --- include/bout/options.hxx | 6 ++++-- src/sys/options.cxx | 30 ++++++++++++++++++++++++++++++ 2 files changed, 34 insertions(+), 2 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index 839c847289..7f736a506d 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -241,7 +241,8 @@ public: /// /// Option option2 = option1.copy(); /// - Options(const Options& other) = delete; // Use a reference or .copy() method + [[deprecated("Please use a reference or .copy() instead")]] Options( + const Options& other); /// Copy assignment must be explicit /// @@ -251,7 +252,8 @@ public: /// /// option2.value = option1.value; /// - Options& operator=(const Options& other) = delete; // Use a reference or .copy() method + [[deprecated("Please use a reference or .copy() instead")]] Options& + operator=(const Options& other); // Use a reference or .copy() method /// Make a deep copy of this Options, /// recursively copying children. diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 49a81cfa88..1d18a0e462 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -221,6 +221,36 @@ Options::fuzzyFind(const std::string& name, std::string::size_type distance) con return matches; } +Options::Options(const Options& other) { (*this) = other.copy(); } + +Options& Options::operator=(const Options& other) { + if (this == &other) { + return *this; + } + + // Note: Here can't do copy-and-swap because pointers to parents are stored + + value = other.value; + + // Assigning the attributes. + // The simple assignment operator fails to compile with Apple Clang 12 + // attributes = other.attributes; + attributes.clear(); + attributes.insert(other.attributes.begin(), other.attributes.end()); + + full_name = other.full_name; + is_section = other.is_section; + children = other.children; + value_used = other.value_used; + + // Ensure that this is the parent of all children, + // otherwise will point to the original Options instance + for (auto& child : children) { + child.second.parent_instance = this; + } + return *this; +} + Options& Options::operator=(Options&& other) noexcept { if (this == &other) { return *this; From ab4928e9989682160062b2e66e9acab512fdc2bf Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 22 Mar 2024 12:04:28 +0100 Subject: [PATCH 329/412] Remove unused option for blob2d --- examples/blob2d/blob2d.cxx | 2 -- examples/blob2d/delta_0.25/BOUT.inp | 2 -- examples/blob2d/delta_1/BOUT.inp | 2 -- examples/blob2d/delta_10/BOUT.inp | 2 -- examples/boutpp/blob2d.py | 2 -- 5 files changed, 10 deletions(-) diff --git a/examples/blob2d/blob2d.cxx b/examples/blob2d/blob2d.cxx index f41f857d46..7007bbeb77 100644 --- a/examples/blob2d/blob2d.cxx +++ b/examples/blob2d/blob2d.cxx @@ -25,7 +25,6 @@ class Blob2D : public PhysicsModel { BoutReal rho_s; ///< Bohm gyro radius BoutReal Omega_i; ///< Ion cyclotron frequency BoutReal c_s; ///< Bohm sound speed - BoutReal n0; ///< Reference density // Constants to calculate the parameters BoutReal Te0; ///< Isothermal temperature [eV] @@ -61,7 +60,6 @@ class Blob2D : public PhysicsModel { m_i = options["m_i"].withDefault(2 * 1.667e-27); m_e = options["m_e"].withDefault(9.11e-31); - n0 = options["n0"].doc("Background density in cubic m").withDefault(1e19); D_vort = options["D_vort"].doc("Viscous diffusion coefficient").withDefault(0.0); D_n = options["D_n"].doc("Density diffusion coefficient").withDefault(0.0); diff --git a/examples/blob2d/delta_0.25/BOUT.inp b/examples/blob2d/delta_0.25/BOUT.inp index 58d1e36741..841fcaf235 100644 --- a/examples/blob2d/delta_0.25/BOUT.inp +++ b/examples/blob2d/delta_0.25/BOUT.inp @@ -87,8 +87,6 @@ flags = 49152 # set_rhs i.e. identity matrix in boundaries Te0 = 5 # Electron Temperature (eV) -n0 = 2e+18 # Background plasma density (m^-3) - compressible = false # Compressibility? boussinesq = true # Boussinesq approximation (no perturbed n in vorticity) diff --git a/examples/blob2d/delta_1/BOUT.inp b/examples/blob2d/delta_1/BOUT.inp index 417911271d..39213ddd36 100644 --- a/examples/blob2d/delta_1/BOUT.inp +++ b/examples/blob2d/delta_1/BOUT.inp @@ -87,8 +87,6 @@ flags = 49152 # set_rhs i.e. identity matrix in boundaries Te0 = 5 # Electron Temperature (eV) -n0 = 2e+18 # Background plasma density (m^-3) - compressible = false # Compressibility? boussinesq = true # Boussinesq approximation (no perturbed n in vorticity) diff --git a/examples/blob2d/delta_10/BOUT.inp b/examples/blob2d/delta_10/BOUT.inp index 353c28c3b2..f4507b871b 100644 --- a/examples/blob2d/delta_10/BOUT.inp +++ b/examples/blob2d/delta_10/BOUT.inp @@ -87,8 +87,6 @@ flags = 49152 # set_rhs i.e. identity matrix in boundaries Te0 = 5 # Electron Temperature (eV) -n0 = 2e+18 # Background plasma density (m^-3) - compressible = false # Compressibility? boussinesq = true # Boussinesq approximation (no perturbed n in vorticity) diff --git a/examples/boutpp/blob2d.py b/examples/boutpp/blob2d.py index d5f370a454..7d8f2441bf 100755 --- a/examples/boutpp/blob2d.py +++ b/examples/boutpp/blob2d.py @@ -245,8 +245,6 @@ def ensure_blob(): Te0 = 5 # Electron Temperature (eV) -n0 = 2e18 # Background plasma density (m^-3) - compressible = false # Compressibility? boussinesq = true # Boussinesq approximation (no perturbed n in vorticity) From 3969836786c3fb938fe386d4fe829d3bb6f91ee1 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 22 Mar 2024 12:04:57 +0100 Subject: [PATCH 330/412] Update boutpp/blob2d for recent updates --- examples/boutpp/blob2d.py | 46 ++++++++++++++++++++++----------------- 1 file changed, 26 insertions(+), 20 deletions(-) diff --git a/examples/boutpp/blob2d.py b/examples/boutpp/blob2d.py index 7d8f2441bf..9d3a063afb 100755 --- a/examples/boutpp/blob2d.py +++ b/examples/boutpp/blob2d.py @@ -24,7 +24,7 @@ def init(self, restart): self.phiSolver = bc.Laplacian() - options = bc.Options("model") + options = bc.Options.root("model") # Temperature in eV Te0 = options.get("Te0", 30) e = options.get("e", 1.602e-19) @@ -70,12 +70,20 @@ def init(self, restart): # /************ Create a solver for potential ********/ + opts_boussinesq = bc.Options.root("phiBoussinesq") + opts_non_boussinesq = bc.Options.root("phiSolver") + if self.boussinesq: # BOUT.inp section "phiBoussinesq" - self.phiSolver = bc.Laplacian(bc.Options("phiBoussinesq")) + opts_used = opts_boussinesq + opts_unused = opts_non_boussinesq else: # BOUT.inp section "phiSolver" - self.phiSolver = bc.Laplacian(bc.Options("phiSolver")) + opts_used = opts_non_boussinesq + opts_unused = opts_boussinesq + + self.phiSolver = bc.Laplacian(opts_used) + opts_unused.setConditionallyUsed() # Starting guess for first solve (if iterative) self.phi = bc.create3D("0") @@ -165,8 +173,8 @@ def ensure_blob(): # settings used by the core code -NOUT = 50 # number of time-steps -TIMESTEP = 50 # time between outputs [1/wci] +nout = 50 # number of time-steps +timestep = 50 # time between outputs [1/wci] MXG = 2 # Number of X guard cells @@ -198,8 +206,8 @@ def ensure_blob(): [mesh:ddz] -first = FFT -second = FFT +first = C2 +second = C2 upwind = W3 ################################################### @@ -207,8 +215,8 @@ def ensure_blob(): [solver] -ATOL = 1.0e-10 # absolute tolerance -RTOL = 1.0e-5 # relative tolerance +atol = 1e-10 # absolute tolerance +rtol = 1e-05 # relative tolerance mxstep = 10000 # Maximum internal steps per output ################################################### @@ -221,22 +229,20 @@ def ensure_blob(): fourth_order = true # 4th order or 2nd order -flags = 0 # inversion flags for phi - # 0 = Zero value - # 10 = Zero gradient AC inner & outer - # 15 = Zero gradient AC and DC - # 768 = Zero laplace inner & outer +# 0 = Zero value +# 10 = Zero gradient AC inner & outer +# 15 = Zero gradient AC and DC +# 768 = Zero laplace inner & outer [phiSolver:precon] # Preconditioner (if pctype=user) -filter = 0. # Must not filter solution -flags = 49152 # set_rhs i.e. identity matrix in boundaries +filter = 0.0 # Must not filter solution +flags = 49152 # set_rhs i.e. identity matrix in boundaries ################################################### # Electrostatic potential solver (Boussinesq) [phiBoussinesq] # By default type is tri (serial) or spt (parallel) -flags = 0 ################################################## # general settings for the model @@ -249,8 +255,8 @@ def ensure_blob(): boussinesq = true # Boussinesq approximation (no perturbed n in vorticity) -D_vort = 1e-6 # Viscosity -D_n = 1e-6 # Diffusion +D_vort = 1e-06 # Viscosity +D_n = 1e-06 # Diffusion R_c = 1.5 # Radius of curvature (m) @@ -259,7 +265,7 @@ def ensure_blob(): # These can be overridden for individual variables in # a section of that name. -[All] +[all] scale = 0.0 # default size of initial perturbations bndry_all = neumann # Zero-gradient on all boundaries From ba720948e5e02bff3fae3ca4aa4c88bbbf9f68c8 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 22 Mar 2024 12:05:12 +0100 Subject: [PATCH 331/412] Always ensure folder gets created --- examples/boutpp/blob2d.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/examples/boutpp/blob2d.py b/examples/boutpp/blob2d.py index 9d3a063afb..4dc8ea60ac 100755 --- a/examples/boutpp/blob2d.py +++ b/examples/boutpp/blob2d.py @@ -282,9 +282,8 @@ def ensure_blob(): if __name__ == "__main__": - if "--create" in sys.argv: - sys.argv.remove("--create") - ensure_blob() + ensure_blob() + bc.init("-d blob".split(" ") + sys.argv[1:]) # Create an instance From 2e07aa2a561bb08b96c26e1b9cbd3be2631026f3 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 22 Mar 2024 12:43:31 +0100 Subject: [PATCH 332/412] Copy boutpp example files --- examples/CMakeLists.txt | 1 + examples/boutpp/CMakeLists.txt | 10 ++++++++++ examples/boutpp/data/BOUT.inp | 9 +++++++++ 3 files changed, 20 insertions(+) create mode 100644 examples/boutpp/CMakeLists.txt create mode 100644 examples/boutpp/data/BOUT.inp diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt index 3849d34852..022b16e248 100644 --- a/examples/CMakeLists.txt +++ b/examples/CMakeLists.txt @@ -11,6 +11,7 @@ add_subdirectory(backtrace) add_subdirectory(blob2d) add_subdirectory(blob2d-outerloop) add_subdirectory(blob2d-laplacexz) +add_subdirectory(boutpp) add_subdirectory(boundary-conditions/advection) add_subdirectory(conducting-wall-mode) add_subdirectory(conduction) diff --git a/examples/boutpp/CMakeLists.txt b/examples/boutpp/CMakeLists.txt new file mode 100644 index 0000000000..e46a7ae990 --- /dev/null +++ b/examples/boutpp/CMakeLists.txt @@ -0,0 +1,10 @@ +cmake_minimum_required(VERSION 3.13) + +if (NOT TARGET bout++::bout++) + find_package(bout++ REQUIRED) +endif() + +bout_copy_file(runexample) +bout_copy_file(blob2d.py) +bout_copy_file(simulation.py) +bout_copy_file(data/BOUT.inp) diff --git a/examples/boutpp/data/BOUT.inp b/examples/boutpp/data/BOUT.inp new file mode 100644 index 0000000000..d91707ec1b --- /dev/null +++ b/examples/boutpp/data/BOUT.inp @@ -0,0 +1,9 @@ +nout=10 +timestep=10 + +[mesh] +nx=160 +ny=1 +nz=n/n + +MYG=0 From f79c5913f061c26eebecfde519ed68a62e989d56 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 22 Mar 2024 12:43:51 +0100 Subject: [PATCH 333/412] expose setConditionallyUsed --- tools/pylib/_boutpp_build/bout_options.pxd | 1 + tools/pylib/_boutpp_build/boutpp.pyx.jinja | 14 ++++++++++++-- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/tools/pylib/_boutpp_build/bout_options.pxd b/tools/pylib/_boutpp_build/bout_options.pxd index be17608cea..365e08bcc7 100644 --- a/tools/pylib/_boutpp_build/bout_options.pxd +++ b/tools/pylib/_boutpp_build/bout_options.pxd @@ -43,6 +43,7 @@ cdef extern from "bout/options.hxx": void get(string, double&, double) void get(string, bool&, bool) void cleanCache() + void setConditionallyUsed() cdef extern from "bout/optionsreader.hxx": diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja index 3aeb1428eb..8e2957eb39 100644 --- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja +++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja @@ -1209,8 +1209,9 @@ def finalise(): else: for ourClass in ourClasses: if isinstance(obj, ourClass): - ourClass.__boutpp_dealloc(obj) - break + if hasattr(ourClass, "__boutpp_dealloc"): + ourClass.__boutpp_dealloc(obj) + break del objects # Actually finalise if wasInit: @@ -1715,6 +1716,15 @@ cdef class Options: opt.get(key, ret_str, default_) return ret_str.decode() + def setConditionallyUsed(self): + """Set the attribute "conditionally used" to be true for \p options + and all its children/sections, causing `Options::getUnused` to + assume those options have been used. This is useful to ignore + options when checking for typos etc. + """ + cdef c.Options* opt = self.cobj + opt.setConditionallyUsed() + def __dealloc__(self): self.__boutpp_dealloc() From 651bac3e94c6d1e30ae7925c0e8a9c712a8eb8a3 Mon Sep 17 00:00:00 2001 From: David Bold Date: Fri, 22 Mar 2024 12:46:01 +0100 Subject: [PATCH 334/412] Ensure errors in solve and rhs are catchable Fixes GH#2890 --- tools/pylib/_boutpp_build/boutcpp.pxd.jinja | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja index 12e210a5b5..8f838b864c 100644 --- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja +++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja @@ -148,10 +148,10 @@ cdef extern from "bout/physicsmodel.hxx": ctypedef void (*Method)(void *param, void *user_data) cdef extern from "helper.h": cppclass PythonModel(PhysicsModel): - int rhs(double t) + int rhs(double t) except +raise_bout_py_error void pyinit() void free() - void solve() + void solve() except +raise_bout_py_error Solver * getSolver() void set_rhs_func(PythonModelCallback*) void set_init_func(PythonModelCallback*) From 5fd38b592c2c07d69bf76bed7fabd9b5d13be550 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 25 Mar 2024 09:29:16 +0100 Subject: [PATCH 335/412] Do not use python preserved __ prefix --- tools/pylib/_boutpp_build/boutpp.pyx.jinja | 48 +++++++++++----------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja index 8e2957eb39..9aedbb291a 100644 --- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja +++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja @@ -583,9 +583,9 @@ cdef class {{ field.field_type }}: {% endfor %} def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.isSelfOwned and self.cobj != NULL: del self.cobj self.cobj = NULL @@ -645,9 +645,9 @@ cdef class {{ vec }}: def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.isSelfOwned and self.cobj != NULL: del self.cobj self.cobj=NULL @@ -742,9 +742,9 @@ cdef class Mesh: return msh def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.cobj and self.isSelfOwned: del self.cobj self.cobj = NULL @@ -850,9 +850,9 @@ cdef class Coordinates: {% endfor %} def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.cobj and self.isSelfOwned: del self.cobj self.cobj = NULL @@ -931,9 +931,9 @@ cdef class FieldFactory: checkInit() cobj=< c.FieldFactory*>0 def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.cobj != NULL: del self.cobj self.cobj = NULL @@ -965,9 +965,9 @@ cdef class PythonModelCallback: self.cobj = new c.PythonModelCallback(callback, method) def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.cobj: del self.cobj self.cobj = NULL @@ -1037,12 +1037,12 @@ cdef class PhysicsModelBase(object): self.cmodel.set_init_func(self.callbackinit) def __dealloc__(self): - if hasattr(self, "__boutpp_dealloc"): - self.__boutpp_dealloc() + if hasattr(self, "_boutpp_dealloc"): + self._boutpp_dealloc() else: - PhysicsModelBase.__boutpp_dealloc(self) + PhysicsModelBase._boutpp_dealloc(self) - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.cmodel != 0: self.cmodel.free() del self.cmodel @@ -1123,8 +1123,8 @@ class PhysicsModel(PhysicsModelBase): def __dealloc__(self): super(PhysicsModel,self).__dealloc__() - def __boutpp_dealloc(self): - super(PhysicsModel,self).__boutpp_dealloc() + def _boutpp_dealloc(self): + super(PhysicsModel,self)._boutpp_dealloc() cdef extern from "bout/bout.hxx": int BoutInitialise(int&, char **&) except +raise_bout_py_error @@ -1204,13 +1204,13 @@ def finalise(): PythonModelCallback) for obj in objects: if isinstance(obj, ourClasses): - if hasattr(obj, "__boutpp_dealloc"): - obj.__boutpp_dealloc() + if hasattr(obj, "_boutpp_dealloc"): + obj._boutpp_dealloc() else: for ourClass in ourClasses: if isinstance(obj, ourClass): - if hasattr(ourClass, "__boutpp_dealloc"): - ourClass.__boutpp_dealloc(obj) + if hasattr(ourClass, "_boutpp_dealloc"): + ourClass._boutpp_dealloc(obj) break del objects # Actually finalise @@ -1726,9 +1726,9 @@ cdef class Options: opt.setConditionallyUsed() def __dealloc__(self): - self.__boutpp_dealloc() + self._boutpp_dealloc() - def __boutpp_dealloc(self): + def _boutpp_dealloc(self): if self.isSelfOwned and self.cobj != NULL: del self.cobj self.cobj = NULL From b4c255553bd2274dcef7682725f831d362829424 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Thu, 18 Jan 2024 17:13:57 -0800 Subject: [PATCH 336/412] Add warnings about SUNDIALS versions <4 --- cmake/FindSUNDIALS.cmake | 4 ++++ manual/sphinx/user_docs/advanced_install.rst | 7 ++++--- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake index 1ecb5db429..29da3e5ca7 100644 --- a/cmake/FindSUNDIALS.cmake +++ b/cmake/FindSUNDIALS.cmake @@ -121,6 +121,10 @@ if (SUNDIALS_INCLUDE_DIR) set(SUNDIALS_VERSION "${SUNDIALS_VERSION_MAJOR}.${SUNDIALS_VERSION_MINOR}.${SUNDIALS_VERSION_PATCH}" CACHE STRING "SUNDIALS version") endif() +if("${SUNDIALS_VERSION_MAJOR}" LESS 4) + message(WARNING "SUNDIALS versions <4 are depricated and will not be supported in the next release") +endif() + if (SUNDIALS_DEBUG) message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " " SUNDIALS_VERSION = ${SUNDIALS_VERSION}") diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst index e25be12b4b..57ac5f8e3f 100644 --- a/manual/sphinx/user_docs/advanced_install.rst +++ b/manual/sphinx/user_docs/advanced_install.rst @@ -306,9 +306,10 @@ solver. Currently, BOUT++ also supports the SUNDIALS solvers CVODE, IDA and ARKODE which are available from https://computation.llnl.gov/casc/sundials/main.html. -.. note:: BOUT++ currently supports SUNDIALS > 2.6, up to 5.4.0 as of - September 2020. It is advisable to use the highest possible - version +.. note:: BOUT++ currently supports SUNDIALS > 2.6, up to 6.7.0 as of + January 2024. It is advisable to use the highest possible + version. Support for SUNDIALS versions < 4 will be removed + in the next release. The full installation guide is found in the downloaded ``.tar.gz``, but we will provide a step-by-step guide to install it and make it From 2730aec12e8f7d530e45379be392803ff459cfa1 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 12 Feb 2024 10:36:00 -0800 Subject: [PATCH 337/412] Remove sundials + #include #include #include #include - -#if SUNDIALS_VERSION_MAJOR >= 3 #include -#endif - -#if SUNDIALS_VERSION_MAJOR >= 4 #include #include #include + +#if SUNDIALS_VERSION_MAJOR >= 6 +#include #endif #include "bout/unused.hxx" -#if SUNDIALS_VERSION_MAJOR < 3 -using SUNLinearSolver = int*; -inline void SUNLinSolFree([[maybe_unused]] SUNLinearSolver solver) {} -using sunindextype = long int; -#endif - -#if SUNDIALS_VERSION_MAJOR < 4 -using SUNNonlinearSolver = int*; -inline void SUNNonlinSolFree([[maybe_unused]] SUNNonlinearSolver solver) {} +static_assert(std::is_same::value, + "BOUT++ and SUNDIALS real types do not match"); #if SUNDIALS_VERSION_MAJOR < 6 -namespace sundials { -struct Context { - Context(void* comm [[maybe_unused]]) {} -}; -} // namespace sundials - -using SUNContext = sundials::Context; - constexpr auto SUN_PREC_RIGHT = PREC_RIGHT; constexpr auto SUN_PREC_LEFT = PREC_LEFT; constexpr auto SUN_PREC_NONE = PREC_NONE; -inline N_Vector N_VNew_Parallel(MPI_Comm comm, sunindextype local_length, - sunindextype global_length, - [[maybe_unused]] SUNContext sunctx) { - return N_VNew_Parallel(comm, local_length, global_length); -} +namespace sundials { +using Context = std::nullptr_t; +} // namespace sundials +#endif -#if SUNDIALS_VERSION_MAJOR >= 3 -inline SUNLinearSolver SUNLinSol_SPGMR(N_Vector y, int pretype, int maxl, - [[maybe_unused]] SUNContext sunctx) { -#if SUNDIALS_VERSION_MAJOR == 3 - return SUNSPGMR(y, pretype, maxl); +inline sundials::Context createSUNContext(MAYBE_UNUSED(MPI_Comm& comm)) { +#if SUNDIALS_VERSION_MAJOR < 6 + return nullptr; +#elif SUNDIALS_VERSION_MAJOR < 7 + return sundials::Context(static_cast(&comm)); #else - return SUNLinSol_SPGMR(y, pretype, maxl); + return sundials::Context(comm); #endif } -#if SUNDIALS_VERSION_MAJOR >= 4 -inline SUNNonlinearSolver SUNNonlinSol_FixedPoint(N_Vector y, int m, - [[maybe_unused]] SUNContext sunctx) { - return SUNNonlinSol_FixedPoint(y, m); -} -inline SUNNonlinearSolver SUNNonlinSol_Newton(N_Vector y, - [[maybe_unused]] SUNContext sunctx) { - return SUNNonlinSol_Newton(y); +template +inline decltype(auto) callWithSUNContext(Func f, + MAYBE_UNUSED(sundials::Context& ctx), + Args&&... args) { +#if SUNDIALS_VERSION_MAJOR < 6 + return f(std::forward(args)...); +#else + return f(std::forward(args)..., ctx); +#endif } -#endif // SUNDIALS_VERSION_MAJOR >= 4 -#endif // SUNDIALS_VERSION_MAJOR >= 3 -#endif // SUNDIALS_VERSION_MAJOR < 6 #endif // BOUT_SUNDIALS_BACKPORTS_H diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index aabe2ae050..076b8655af 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -41,17 +41,7 @@ #include "bout/unused.hxx" #include "bout/utils.hxx" -#if SUNDIALS_VERSION_MAJOR >= 4 #include -#else -#include -#if SUNDIALS_VERSION_MAJOR >= 3 -#include -#else -#include -#endif -#endif - #include #include #include @@ -61,110 +51,18 @@ class Field2D; -#define ZERO RCONST(0.) -#define ONE RCONST(1.0) - -#ifndef ARKODEINT -#if SUNDIALS_VERSION_MAJOR < 3 -using ARKODEINT = bout::utils::function_traits::arg_t<0>; -#else -using ARKODEINT = sunindextype; -#endif -#endif - static int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); static int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int arkode_bbd_rhs(ARKODEINT Nlocal, BoutReal t, N_Vector u, N_Vector du, +static int arkode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, void* user_data); static int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int lr, void* user_data); -#if SUNDIALS_VERSION_MAJOR < 3 -// Shim for earlier versions -inline static int arkode_pre_shim(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, - N_Vector zvec, BoutReal gamma, BoutReal delta, int lr, - void* user_data, N_Vector UNUSED(tmp)) { - return arkode_pre(t, yy, yp, rvec, zvec, gamma, delta, lr, user_data); -} -#else -// Alias for newer versions -constexpr auto& arkode_pre_shim = arkode_pre; -#endif -static int arkode_jac(N_Vector v, N_Vector Jv, realtype t, N_Vector y, N_Vector fy, +static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); -#if SUNDIALS_VERSION_MAJOR < 4 -// Shim for earlier versions -inline int ARKStepSetJacTimes(void* arkode_mem, std::nullptr_t, - ARKSpilsJacTimesVecFn jtimes) { -#if SUNDIALS_VERSION_MAJOR < 3 - return ARKSpilsSetJacTimesVecFn(arkode_mem, jtimes); -#else - return ARKSpilsSetJacTimes(arkode_mem, nullptr, jtimes); -#endif -} -#endif - -#if SUNDIALS_VERSION_MAJOR < 4 -void* ARKStepCreate(ARKRhsFn fe, ARKRhsFn fi, BoutReal t0, N_Vector y0) { - auto arkode_mem = ARKodeCreate(); - - if (arkode_mem == nullptr) { - throw BoutException("ARKodeCreate failed\n"); - } - if (ARKodeInit(arkode_mem, fe, fi, t0, y0) != ARK_SUCCESS) { - throw BoutException("ARKodeInit failed\n"); - } - return arkode_mem; -} - -#if SUNDIALS_VERSION_MAJOR == 3 -int ARKStepSetLinearSolver(void* arkode_mem, SUNLinearSolver LS, std::nullptr_t) { - return ARKSpilsSetLinearSolver(arkode_mem, LS); -} -#endif -// Aliases for older versions -// In SUNDIALS 4, ARKode has become ARKStep, hence all the renames -constexpr auto& ARKStepEvolve = ARKode; -constexpr auto& ARKStepFree = ARKodeFree; -constexpr auto& ARKStepGetCurrentTime = ARKodeGetCurrentTime; -constexpr auto& ARKStepGetDky = ARKodeGetDky; -constexpr auto& ARKStepGetLastStep = ARKodeGetLastStep; -constexpr auto& ARKStepGetNumLinIters = ARKSpilsGetNumLinIters; -constexpr auto& ARKStepGetNumNonlinSolvIters = ARKodeGetNumNonlinSolvIters; -constexpr auto& ARKStepGetNumPrecEvals = ARKSpilsGetNumPrecEvals; -constexpr auto& ARKStepGetNumRhsEvals = ARKodeGetNumRhsEvals; -constexpr auto& ARKStepGetNumSteps = ARKodeGetNumSteps; -constexpr auto& ARKStepReInit = ARKodeReInit; -constexpr auto& ARKStepSStolerances = ARKodeSStolerances; -constexpr auto& ARKStepSVtolerances = ARKodeSVtolerances; -constexpr auto& ARKStepSetAdaptivityMethod = ARKodeSetAdaptivityMethod; -constexpr auto& ARKStepSetCFLFraction = ARKodeSetCFLFraction; -constexpr auto& ARKStepSetEpsLin = ARKSpilsSetEpsLin; -constexpr auto& ARKStepSetExplicit = ARKodeSetExplicit; -constexpr auto& ARKStepSetFixedPoint = ARKodeSetFixedPoint; -constexpr auto& ARKStepSetFixedStep = ARKodeSetFixedStep; -constexpr auto& ARKStepSetImEx = ARKodeSetImEx; -constexpr auto& ARKStepSetImplicit = ARKodeSetImplicit; -constexpr auto& ARKStepSetInitStep = ARKodeSetInitStep; -constexpr auto& ARKStepSetLinear = ARKodeSetLinear; -constexpr auto& ARKStepSetMaxNumSteps = ARKodeSetMaxNumSteps; -constexpr auto& ARKStepSetMaxStep = ARKodeSetMaxStep; -constexpr auto& ARKStepSetMinStep = ARKodeSetMinStep; -constexpr auto& ARKStepSetOptimalParams = ARKodeSetOptimalParams; -constexpr auto& ARKStepSetOrder = ARKodeSetOrder; -constexpr auto& ARKStepSetPreconditioner = ARKSpilsSetPreconditioner; -constexpr auto& ARKStepSetUserData = ARKodeSetUserData; -#endif - -#if SUNDIALS_VERSION_MAJOR < 6 -void* ARKStepCreate(ARKRhsFn fe, ARKRhsFn fi, BoutReal t0, N_Vector y0, - [[maybe_unused]] SUNContext context) { - return ARKStepCreate(fe, fi, t0, y0); -} -#endif ArkodeSolver::ArkodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] @@ -226,7 +124,7 @@ ArkodeSolver::ArkodeSolver(Options* opts) .withDefault(false)), optimize( (*options)["optimize"].doc("Use ARKode optimal parameters").withDefault(false)), - suncontext(static_cast(&BoutComm::get())) { + suncontext(createSUNContext(BoutComm::get())) { has_constraints = false; // This solver doesn't have constraints // Add diagnostics to output @@ -274,7 +172,8 @@ int ArkodeSolver::init() { n2Dvars(), neq, local_N); // Allocate memory - if ((uvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext)) == nullptr) { + uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq); + if (uvec == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } @@ -298,8 +197,8 @@ int ArkodeSolver::init() { } }(); - if ((arkode_mem = ARKStepCreate(explicit_rhs, implicit_rhs, simtime, uvec, suncontext)) - == nullptr) { + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, explicit_rhs, implicit_rhs, simtime, uvec); + if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); } @@ -374,7 +273,7 @@ int ArkodeSolver::init() { return Options::root()[f3.name]["atol"].withDefault(abstol); }); - N_Vector abstolvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext); + N_Vector abstolvec = N_VClone(uvec); if (abstolvec == nullptr) { throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n"); } @@ -416,51 +315,35 @@ int ArkodeSolver::init() { // ARKStepSetPredictorMethod(arkode_mem,4); -#if SUNDIALS_VERSION_MAJOR < 4 if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); - if (ARKodeSetFixedPoint(arkode_mem, 3.0)) { - throw BoutException("ARKodeSetFixedPoint failed\n"); - } - } else { - output.write("\tUsing Newton iteration\n"); - if (ARKodeSetNewton(arkode_mem)) { - throw BoutException("ARKodeSetNewton failed\n"); - } - } -#else - if (fixed_point) { - output.write("\tUsing accelerated fixed point solver\n"); - if ((nonlinear_solver = SUNNonlinSol_FixedPoint(uvec, 3, suncontext)) == nullptr) { + nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); + if (nonlinear_solver == nullptr) { throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); } } else { output.write("\tUsing Newton iteration\n"); - if ((nonlinear_solver = SUNNonlinSol_Newton(uvec, suncontext)) == nullptr) { + nonlinear_solver = callWithSUNContext(SUNNonlinSol_Newton, suncontext, uvec); + if (nonlinear_solver == nullptr) { throw BoutException("Creating SUNDIALS Newton nonlinear solver failed\n"); } } if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { throw BoutException("ARKStepSetNonlinearSolver failed\n"); } -#endif /// Set Preconditioner + // TODO: only set of linear solver with Newton's method if (use_precon) { const int prectype = rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT; -#if SUNDIALS_VERSION_MAJOR >= 3 - if ((sun_solver = SUNLinSol_SPGMR(uvec, prectype, maxl, suncontext)) == nullptr) { + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); + if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) { throw BoutException("ARKStepSetLinearSolver failed\n"); } -#else - if (ARKSpgmr(arkode_mem, prectype, maxl) != ARKSPILS_SUCCESS) { - throw BoutException("ARKSpgmr failed\n"); - } -#endif if (!hasPreconditioner()) { output.write("\tUsing BBD preconditioner\n"); @@ -495,7 +378,7 @@ int ArkodeSolver::init() { "approximate Jacobian block") .withDefault(n3Dvars() + n2Dvars()); - if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, ZERO, + if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, arkode_bbd_rhs, nullptr) != ARK_SUCCESS) { throw BoutException("ARKBBDPrecInit failed\n"); @@ -504,7 +387,7 @@ int ArkodeSolver::init() { } else { output.write("\tUsing user-supplied preconditioner\n"); - if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre_shim) != ARK_SUCCESS) { + if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARK_SUCCESS) { throw BoutException("ARKStepSetPreconditioner failed\n"); } } @@ -513,19 +396,13 @@ int ArkodeSolver::init() { output.write("\tNo preconditioning\n"); -#if SUNDIALS_VERSION_MAJOR >= 3 - if ((sun_solver = SUNLinSol_SPGMR(uvec, SUN_PREC_NONE, maxl, suncontext)) - == nullptr) { + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, SUN_PREC_NONE, maxl); + if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) { throw BoutException("ARKStepSetLinearSolver failed\n"); } -#else - if (ARKSpgmr(arkode_mem, SUN_PREC_NONE, maxl) != ARKSPILS_SUCCESS) { - throw BoutException("ARKSpgmr failed\n"); - } -#endif } /// Set Jacobian-vector multiplication function @@ -815,7 +692,7 @@ static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { } /// RHS function for BBD preconditioner -static int arkode_bbd_rhs(ARKODEINT UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, +static int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, void* user_data) { return arkode_rhs_implicit(t, u, du, user_data); } @@ -837,7 +714,7 @@ static int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rve } /// Jacobian-vector multiplication function -static int arkode_jac(N_Vector v, N_Vector Jv, realtype t, N_Vector y, +static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { BoutReal* ydata = NV_DATA_P(y); ///< System state BoutReal* vdata = NV_DATA_P(v); ///< Input vector diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index c17bed420c..aeed7ab3af 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -44,14 +44,8 @@ #include "fmt/core.h" #include - -#if SUNDIALS_VERSION_MAJOR >= 3 #include #include -#else -#include -#endif - #include #include @@ -61,69 +55,19 @@ class Field2D; -#define ZERO RCONST(0.) -#define ONE RCONST(1.0) - -#ifndef CVODEINT -#if SUNDIALS_VERSION_MAJOR < 3 -using CVODEINT = bout::utils::function_traits::arg_t<0>; -#else -using CVODEINT = sunindextype; -#endif -#endif - BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative, non_positive); static int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int cvode_bbd_rhs(CVODEINT Nlocal, BoutReal t, N_Vector u, N_Vector du, +static int cvode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, void* user_data); static int cvode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int lr, void* user_data); -#if SUNDIALS_VERSION_MAJOR < 3 -// Shim for earlier versions -inline static int cvode_pre_shim(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, - N_Vector zvec, BoutReal gamma, BoutReal delta, int lr, - void* user_data, N_Vector UNUSED(tmp)) { - return cvode_pre(t, yy, yp, rvec, zvec, gamma, delta, lr, user_data); -} -#else -// Alias for newer versions -constexpr auto& cvode_pre_shim = cvode_pre; -#endif - -static int cvode_jac(N_Vector v, N_Vector Jv, realtype t, N_Vector y, N_Vector fy, +static int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); -#if SUNDIALS_VERSION_MAJOR < 3 -// Shim for earlier versions -inline int CVSpilsSetJacTimes(void* arkode_mem, std::nullptr_t, - CVSpilsJacTimesVecFn jtimes) { - return CVSpilsSetJacTimesVecFn(arkode_mem, jtimes); -} -#endif - -#if SUNDIALS_VERSION_MAJOR >= 4 -// Shim for newer versions -constexpr auto CV_FUNCTIONAL = 0; -constexpr auto CV_NEWTON = 0; -#endif - -#if SUNDIALS_VERSION_MAJOR >= 3 -void* CVodeCreate(int lmm, [[maybe_unused]] int iter, - [[maybe_unused]] SUNContext context) { -#if SUNDIALS_VERSION_MAJOR == 3 - return CVodeCreate(lmm, iter); -#elif SUNDIALS_VERSION_MAJOR == 4 || SUNDIALS_VERSION_MAJOR == 5 - return CVodeCreate(lmm); -#else - return CVodeCreate(lmm, context); -#endif -} -#endif - CvodeSolver::CvodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] .doc("Print solver diagnostic information?") @@ -184,7 +128,7 @@ CvodeSolver::CvodeSolver(Options* opts) .doc("Factor by which the Krylov linear solver’s convergence test constant " "is reduced from the nonlinear solver test constant.") .withDefault(0.05)), - suncontext(static_cast(&BoutComm::get())) { + suncontext(createSUNContext(BoutComm::get())) { has_constraints = false; // This solver doesn't have constraints canReset = true; @@ -242,7 +186,8 @@ int CvodeSolver::init() { n3Dvars(), n2Dvars(), neq, local_N); // Allocate memory - if ((uvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext)) == nullptr) { + uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq); + if (uvec == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } @@ -258,9 +203,9 @@ int CvodeSolver::init() { } const auto lmm = adams_moulton ? CV_ADAMS : CV_BDF; - const auto iter = func_iter ? CV_FUNCTIONAL : CV_NEWTON; - - if ((cvode_mem = CVodeCreate(lmm, iter, suncontext)) == nullptr) { + + cvode_mem = callWithSUNContext(CVodeCreate, suncontext, lmm); + if (cvode_mem == nullptr) { throw BoutException("CVodeCreate failed\n"); } @@ -307,7 +252,7 @@ int CvodeSolver::init() { return Options::root()[f3.name]["atol"].withDefault(abstol); }); - N_Vector abstolvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext); + N_Vector abstolvec = N_VClone(uvec); if (abstolvec == nullptr) { throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n"); } @@ -347,17 +292,11 @@ int CvodeSolver::init() { CVodeSetMaxNonlinIters(cvode_mem, max_nonlinear_iterations); } -#if not(SUNDIALS_VERSION_MAJOR >= 3 and SUNDIALS_VERSION_MINOR >= 2) - if (apply_positivity_constraints) { - throw BoutException("The apply_positivity_constraints option is only available with " - "SUNDIALS>=3.2.0"); - } -#else if (apply_positivity_constraints) { auto f2d_constraints = create_constraints(f2d); auto f3d_constraints = create_constraints(f3d); - N_Vector constraints_vec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext); + N_Vector constraints_vec = N_VClone(uvec); if (constraints_vec == nullptr) { throw BoutException("SUNDIALS memory allocation (positivity constraints vector) " "failed\n"); @@ -372,7 +311,6 @@ int CvodeSolver::init() { N_VDestroy_Parallel(constraints_vec); } -#endif /// Newton method can include Preconditioners and Jacobian function if (!func_iter) { @@ -381,18 +319,13 @@ int CvodeSolver::init() { if (use_precon) { const int prectype = rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT; -#if SUNDIALS_VERSION_MAJOR >= 3 - if ((sun_solver = SUNLinSol_SPGMR(uvec, prectype, maxl, suncontext)) == nullptr) { + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); + if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) { throw BoutException("CVSpilsSetLinearSolver failed\n"); } -#else - if (CVSpgmr(cvode_mem, prectype, maxl) != CVSPILS_SUCCESS) { - throw BoutException("CVSpgmr failed\n"); - } -#endif if (!hasPreconditioner()) { output_info.write("\tUsing BBD preconditioner\n"); @@ -415,7 +348,7 @@ int CvodeSolver::init() { const auto mukeep = (*options)["mukeep"].withDefault(n3Dvars() + n2Dvars()); const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars()); - if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, ZERO, + if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, cvode_bbd_rhs, nullptr)) { throw BoutException("CVBBDPrecInit failed\n"); } @@ -423,26 +356,20 @@ int CvodeSolver::init() { } else { output_info.write("\tUsing user-supplied preconditioner\n"); - if (CVSpilsSetPreconditioner(cvode_mem, nullptr, cvode_pre_shim)) { + if (CVSpilsSetPreconditioner(cvode_mem, nullptr, cvode_pre)) { throw BoutException("CVSpilsSetPreconditioner failed\n"); } } } else { output_info.write("\tNo preconditioning\n"); -#if SUNDIALS_VERSION_MAJOR >= 3 - if ((sun_solver = SUNLinSol_SPGMR(uvec, SUN_PREC_NONE, maxl, suncontext)) - == nullptr) { + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, SUN_PREC_NONE, maxl); + if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) { throw BoutException("CVSpilsSetLinearSolver failed\n"); } -#else - if (CVSpgmr(cvode_mem, SUN_PREC_NONE, maxl) != CVSPILS_SUCCESS) { - throw BoutException("CVSpgmr failed\n"); - } -#endif } /// Set Jacobian-vector multiplication function @@ -457,15 +384,14 @@ int CvodeSolver::init() { } } else { output_info.write("\tUsing Functional iteration\n"); -#if SUNDIALS_VERSION_MAJOR >= 4 - if ((nonlinear_solver = SUNNonlinSol_FixedPoint(uvec, 0, suncontext)) == nullptr) { + nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 0); + if (nonlinear_solver == nullptr) { throw BoutException("SUNNonlinSol_FixedPoint failed\n"); } if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver)) { throw BoutException("CVodeSetNonlinearSolver failed\n"); } -#endif } // Set internal tolerance factors @@ -748,7 +674,7 @@ static int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { } /// RHS function for BBD preconditioner -static int cvode_bbd_rhs(CVODEINT UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, +static int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, void* user_data) { return cvode_rhs(t, u, du, user_data); } @@ -770,7 +696,7 @@ static int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec } /// Jacobian-vector multiplication function -static int cvode_jac(N_Vector v, N_Vector Jv, realtype t, N_Vector y, N_Vector UNUSED(fy), +static int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { BoutReal* ydata = NV_DATA_P(y); ///< System state BoutReal* vdata = NV_DATA_P(v); ///< Input vector diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 189a103bbe..6168c984f9 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -40,53 +40,21 @@ #include "bout/unused.hxx" #include - -#if SUNDIALS_VERSION_MAJOR >= 3 #include #include -#else -#include -#endif - #include #include #include #include -#define ZERO RCONST(0.) -#define ONE RCONST(1.0) - -#ifndef IDAINT -#if SUNDIALS_VERSION_MAJOR < 3 -using IDAINT = bout::utils::function_traits::arg_t<0>; -#else -using IDAINT = sunindextype; -#endif -#endif - static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); -static int ida_bbd_res(IDAINT Nlocal, BoutReal t, N_Vector u, N_Vector du, N_Vector rr, +static int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); static int ida_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data); -#if SUNDIALS_VERSION_MAJOR < 3 -// Shim for earlier versions -inline static int ida_pre_shim(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, - N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, - void* user_data, N_Vector UNUSED(tmp)) { - return ida_pre(t, yy, yp, rr, rvec, zvec, cj, delta, user_data); -} -#else -// Alias for newer versions -constexpr auto& ida_pre_shim = ida_pre; -#endif - -#if SUNDIALS_VERSION_MAJOR < 6 -void* IDACreate([[maybe_unused]] SUNContext) { return IDACreate(); } -#endif IdaSolver::IdaSolver(Options* opts) : Solver(opts), @@ -101,7 +69,7 @@ IdaSolver::IdaSolver(Options* opts) correct_start((*options)["correct_start"] .doc("Correct the initial values") .withDefault(true)), - suncontext(static_cast(&BoutComm::get())) { + suncontext(createSUNContext(BoutComm::get())) { has_constraints = true; // This solver has constraints } @@ -144,13 +112,14 @@ int IdaSolver::init() { neq, local_N); // Allocate memory - if ((uvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext)) == nullptr) { + uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq); + if (uvec == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } - if ((duvec = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext)) == nullptr) { + if ((duvec = N_VClone(uvec)) == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } - if ((id = N_VNew_Parallel(BoutComm::get(), local_N, neq, suncontext)) == nullptr) { + if ((id = N_VClone(uvec)) == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } @@ -167,7 +136,8 @@ int IdaSolver::init() { set_id(NV_DATA_P(id)); // Call IDACreate to initialise - if ((idamem = IDACreate(suncontext)) == nullptr) { + idamem = callWithSUNContext(IDACreate, suncontext); + if (idamem == nullptr) { throw BoutException("IDACreate failed\n"); } @@ -192,18 +162,13 @@ int IdaSolver::init() { // Call IDASpgmr to specify the IDA linear solver IDASPGMR const auto maxl = (*options)["maxl"].withDefault(6 * n3d); -#if SUNDIALS_VERSION_MAJOR >= 3 - if ((sun_solver = SUNLinSol_SPGMR(uvec, SUN_PREC_NONE, maxl, suncontext)) == nullptr) { + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, SUN_PREC_NONE, maxl); + if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } if (IDASpilsSetLinearSolver(idamem, sun_solver) != IDA_SUCCESS) { throw BoutException("IDASpilsSetLinearSolver failed\n"); } -#else - if (IDASpgmr(idamem, maxl)) { - throw BoutException("IDASpgmr failed\n"); - } -#endif if (use_precon) { if (!hasPreconditioner()) { @@ -225,13 +190,13 @@ int IdaSolver::init() { const auto mldq = (*options)["mldq"].withDefault(band_width_default); const auto mukeep = (*options)["mukeep"].withDefault(n3d); const auto mlkeep = (*options)["mlkeep"].withDefault(n3d); - if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, ZERO, ida_bbd_res, + if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, 0, ida_bbd_res, nullptr)) { throw BoutException("IDABBDPrecInit failed\n"); } } else { output.write("\tUsing user-supplied preconditioner\n"); - if (IDASpilsSetPreconditioner(idamem, nullptr, ida_pre_shim)) { + if (IDASpilsSetPreconditioner(idamem, nullptr, ida_pre)) { throw BoutException("IDASpilsSetPreconditioner failed\n"); } } @@ -381,7 +346,7 @@ static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_d } /// Residual function for BBD preconditioner -static int ida_bbd_res(IDAINT UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, +static int ida_bbd_res(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { return idares(t, u, du, rr, user_data); } From db5f0d877a3cb5bde4bce387737f30581896d614 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 18 Mar 2024 15:34:18 -0700 Subject: [PATCH 338/412] Remove old spils API for linear solvers --- src/solver/impls/arkode/arkode.cxx | 4 +- src/solver/impls/cvode/cvode.cxx | 137 ++++++++++++++--------------- src/solver/impls/ida/ida.cxx | 15 ++-- 3 files changed, 73 insertions(+), 83 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 076b8655af..e63faef6f4 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -141,7 +141,7 @@ ArkodeSolver::ArkodeSolver(Options* opts) } ArkodeSolver::~ArkodeSolver() { - N_VDestroy_Parallel(uvec); + N_VDestroy(uvec); ARKStepFree(&arkode_mem); SUNLinSolFree(sun_solver); SUNNonlinSolFree(nonlinear_solver); @@ -284,7 +284,7 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSVtolerances failed\n"); } - N_VDestroy_Parallel(abstolvec); + N_VDestroy(abstolvec); } else { if (ARKStepSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) { throw BoutException("ARKStepSStolerances failed\n"); diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index aeed7ab3af..4108b4ecbd 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -44,7 +44,6 @@ #include "fmt/core.h" #include -#include #include #include #include @@ -154,7 +153,7 @@ CvodeSolver::CvodeSolver(Options* opts) CvodeSolver::~CvodeSolver() { if (cvode_initialised) { - N_VDestroy_Parallel(uvec); + N_VDestroy(uvec); CVodeFree(&cvode_mem); SUNLinSolFree(sun_solver); SUNNonlinSolFree(nonlinear_solver); @@ -210,24 +209,20 @@ int CvodeSolver::init() { } // For callbacks, need pointer to solver object - if (CVodeSetUserData(cvode_mem, this) < 0) { + if (CVodeSetUserData(cvode_mem, this) != CV_SUCCESS) { throw BoutException("CVodeSetUserData failed\n"); } - if (CVodeInit(cvode_mem, cvode_rhs, simtime, uvec) < 0) { + if (CVodeInit(cvode_mem, cvode_rhs, simtime, uvec) != CV_SUCCESS) { throw BoutException("CVodeInit failed\n"); } - if (max_order > 0) { - if (CVodeSetMaxOrd(cvode_mem, max_order) < 0) { - throw BoutException("CVodeSetMaxOrder failed\n"); - } + if (CVodeSetMaxOrd(cvode_mem, max_order) != CV_SUCCESS) { + throw BoutException("CVodeSetMaxOrder failed\n"); } - if (stablimdet) { - if (CVodeSetStabLimDet(cvode_mem, stablimdet) < 0) { - throw BoutException("CVodeSetStabLimDet failed\n"); - } + if (CVodeSetStabLimDet(cvode_mem, stablimdet) != CV_SUCCESS) { + throw BoutException("CVodeSetStabLimDet failed\n"); } if (use_vector_abstol) { @@ -259,37 +254,35 @@ int CvodeSolver::init() { set_vector_option_values(NV_DATA_P(abstolvec), f2dtols, f3dtols); - if (CVodeSVtolerances(cvode_mem, reltol, abstolvec) < 0) { + if (CVodeSVtolerances(cvode_mem, reltol, abstolvec) != CV_SUCCESS) { throw BoutException("CVodeSVtolerances failed\n"); } - N_VDestroy_Parallel(abstolvec); + N_VDestroy(abstolvec); } else { - if (CVodeSStolerances(cvode_mem, reltol, abstol) < 0) { + if (CVodeSStolerances(cvode_mem, reltol, abstol) != CV_SUCCESS) { throw BoutException("CVodeSStolerances failed\n"); } } - CVodeSetMaxNumSteps(cvode_mem, mxsteps); - - if (max_timestep > 0.0) { - CVodeSetMaxStep(cvode_mem, max_timestep); + if (CVodeSetMaxNumSteps(cvode_mem, mxsteps) != CV_SUCCESS) { + throw BoutException("CVodeSetMaxNumSteps failed\n"); } - if (min_timestep > 0.0) { - CVodeSetMinStep(cvode_mem, min_timestep); + if (CVodeSetMaxStep(cvode_mem, max_timestep) != CV_SUCCESS) { + throw BoutException("CVodeSetMaxStep failed\n"); } - if (start_timestep > 0.0) { - CVodeSetInitStep(cvode_mem, start_timestep); + if (CVodeSetMinStep(cvode_mem, min_timestep) != CV_SUCCESS) { + throw BoutException("CVodeSetMinStep failed\n"); } - if (mxorder > 0) { - CVodeSetMaxOrd(cvode_mem, mxorder); + if (CVodeSetInitStep(cvode_mem, start_timestep) != CV_SUCCESS) { + throw BoutException("CVodeSetInitStep failed\n"); } - if (max_nonlinear_iterations > 0) { - CVodeSetMaxNonlinIters(cvode_mem, max_nonlinear_iterations); + if (CVodeSetMaxNonlinIters(cvode_mem, max_nonlinear_iterations) != CV_SUCCESS) { + throw BoutException("CVodeSetMaxNonlinIters failed\n"); } if (apply_positivity_constraints) { @@ -305,29 +298,47 @@ int CvodeSolver::init() { set_vector_option_values(NV_DATA_P(constraints_vec), f2d_constraints, f3d_constraints); - if (CVodeSetConstraints(cvode_mem, constraints_vec) < 0) { + if (CVodeSetConstraints(cvode_mem, constraints_vec) != CV_SUCCESS) { throw BoutException("CVodeSetConstraints failed\n"); } - N_VDestroy_Parallel(constraints_vec); + N_VDestroy(constraints_vec); } /// Newton method can include Preconditioners and Jacobian function - if (!func_iter) { + if (func_iter) { + output_info.write("\tUsing Functional iteration\n"); + nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 0); + if (nonlinear_solver == nullptr) { + throw BoutException("SUNNonlinSol_FixedPoint failed\n"); + } + + if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver)) { + throw BoutException("CVodeSetNonlinearSolver failed\n"); + } + } else { output_info.write("\tUsing Newton iteration\n"); TRACE("Setting preconditioner"); - if (use_precon) { - const int prectype = rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT; - sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); - if (sun_solver == nullptr) { - throw BoutException("Creating SUNDIALS linear solver failed\n"); - } - if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) { - throw BoutException("CVSpilsSetLinearSolver failed\n"); - } + const auto prectype = use_prec ? + (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : + SUN_PREC_NONE; + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); + if (sun_solver == nullptr) { + throw BoutException("Creating SUNDIALS linear solver failed\n"); + } + if (CVodeSetLinearSolver(cvode_mem, sun_solver, nullptr) != CVLS_SUCCESS) { + throw BoutException("CVodeSetLinearSolver failed\n"); + } - if (!hasPreconditioner()) { + if (use_precon) { + if (hasPreconditioner()) { + output_info.write("\tUsing user-supplied preconditioner\n"); + + if (CVodeSetPreconditioner(cvode_mem, nullptr, cvode_pre) != CVLS_SUCCESS) { + throw BoutException("CVodeSetPreconditioner failed\n"); + } + } else { output_info.write("\tUsing BBD preconditioner\n"); /// Get options @@ -349,54 +360,34 @@ int CvodeSolver::init() { const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars()); if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, - cvode_bbd_rhs, nullptr)) { + cvode_bbd_rhs, nullptr) != CVLS_SUCCESS) { throw BoutException("CVBBDPrecInit failed\n"); } - - } else { - output_info.write("\tUsing user-supplied preconditioner\n"); - - if (CVSpilsSetPreconditioner(cvode_mem, nullptr, cvode_pre)) { - throw BoutException("CVSpilsSetPreconditioner failed\n"); - } } } else { output_info.write("\tNo preconditioning\n"); - - sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, SUN_PREC_NONE, maxl); - if (sun_solver == nullptr) { - throw BoutException("Creating SUNDIALS linear solver failed\n"); - } - if (CVSpilsSetLinearSolver(cvode_mem, sun_solver) != CV_SUCCESS) { - throw BoutException("CVSpilsSetLinearSolver failed\n"); - } } /// Set Jacobian-vector multiplication function if (use_jacobian and hasJacobian()) { output_info.write("\tUsing user-supplied Jacobian function\n"); - if (CVSpilsSetJacTimes(cvode_mem, nullptr, cvode_jac) != CV_SUCCESS) { - throw BoutException("CVSpilsSetJacTimesVecFn failed\n"); + if (CVodeSetJacTimes(cvode_mem, nullptr, cvode_jac) != CVLS_SUCCESS) { + throw BoutException("CVodeSetJacTimes failed\n"); } } else { output_info.write("\tUsing difference quotient approximation for Jacobian\n"); } - } else { - output_info.write("\tUsing Functional iteration\n"); - nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 0); - if (nonlinear_solver == nullptr) { - throw BoutException("SUNNonlinSol_FixedPoint failed\n"); - } - - if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver)) { - throw BoutException("CVodeSetNonlinearSolver failed\n"); - } } // Set internal tolerance factors - CVodeSetNonlinConvCoef(cvode_mem, cvode_nonlinear_convergence_coef); - CVodeSetEpsLin(cvode_mem, cvode_linear_convergence_coef); + if (CVodeSetNonlinConvCoef(cvode_mem, cvode_nonlinear_convergence_coef) != CV_SUCCESS) { + throw BoutException("CVodeSetNonlinConvCoef failed\n"); + } + + if (CVodeSetEpsLin(cvode_mem, cvode_linear_convergence_coef) != CV_SUCCESS) { + throw BoutException("CVodeSetEpsLin failed\n"); + } cvode_initialised = true; @@ -470,9 +461,9 @@ int CvodeSolver::run() { nfevals = int(temp_long_int); CVodeGetNumNonlinSolvIters(cvode_mem, &temp_long_int); nniters = int(temp_long_int); - CVSpilsGetNumPrecSolves(cvode_mem, &temp_long_int); + CVodeGetNumPrecSolves(cvode_mem, &temp_long_int); npevals = int(temp_long_int); - CVSpilsGetNumLinIters(cvode_mem, &temp_long_int); + CVodeGetNumLinIters(cvode_mem, &temp_long_int); nliters = int(temp_long_int); // Last step size @@ -757,7 +748,7 @@ void CvodeSolver::resetInternalFields() { TRACE("CvodeSolver::resetInternalFields"); save_vars(NV_DATA_P(uvec)); - if (CVodeReInit(cvode_mem, simtime, uvec) < 0) { + if (CVodeReInit(cvode_mem, simtime, uvec) != CV_SUCCESS) { throw BoutException("CVodeReInit failed\n"); } } diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 6168c984f9..02c86e9624 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -40,7 +40,6 @@ #include "bout/unused.hxx" #include -#include #include #include #include @@ -75,9 +74,9 @@ IdaSolver::IdaSolver(Options* opts) IdaSolver::~IdaSolver() { if (initialised) { - N_VDestroy_Parallel(uvec); - N_VDestroy_Parallel(duvec); - N_VDestroy_Parallel(id); + N_VDestroy(uvec); + N_VDestroy(duvec); + N_VDestroy(id); IDAFree(&idamem); SUNLinSolFree(sun_solver); } @@ -166,8 +165,8 @@ int IdaSolver::init() { if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } - if (IDASpilsSetLinearSolver(idamem, sun_solver) != IDA_SUCCESS) { - throw BoutException("IDASpilsSetLinearSolver failed\n"); + if (IDASetLinearSolver(idamem, sun_solver, nullptr) != IDALS_SUCCESS) { + throw BoutException("IDASetLinearSolver failed\n"); } if (use_precon) { @@ -196,8 +195,8 @@ int IdaSolver::init() { } } else { output.write("\tUsing user-supplied preconditioner\n"); - if (IDASpilsSetPreconditioner(idamem, nullptr, ida_pre)) { - throw BoutException("IDASpilsSetPreconditioner failed\n"); + if (IDASetPreconditioner(idamem, nullptr, ida_pre) != IDALS_SUCCESS) { + throw BoutException("IDASetPreconditioner failed\n"); } } } From 92ccf9989923071d06503b04abd68f66ab21716f Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 18 Mar 2024 16:17:50 -0700 Subject: [PATCH 339/412] Update IDA calls --- src/solver/impls/cvode/cvode.cxx | 51 +++++++++++++++--------------- src/solver/impls/ida/ida.cxx | 54 +++++++++++++++++--------------- 2 files changed, 54 insertions(+), 51 deletions(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 4108b4ecbd..17ff9c55f0 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -79,7 +79,7 @@ CvodeSolver::CvodeSolver(Options* opts) .doc("Use functional iteration instead of Newton") .withDefault(adams_moulton)), max_order((*options)["cvode_max_order"] - .doc("Maximum order of method to use. < 0 means no limit.") + .doc("Maximum order of method to use. <= 0 means default limit.") .withDefault(-1)), stablimdet((*options)["cvode_stability_limit_detection"].withDefault(false)), abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)), @@ -91,19 +91,18 @@ CvodeSolver::CvodeSolver(Options* opts) .doc("Maximum number of internal steps between outputs.") .withDefault(500)), max_timestep( - (*options)["max_timestep"].doc("Maximum time step size").withDefault(-1.0)), + (*options)["max_timestep"].doc("Maximum time step size").withDefault(0.0)), min_timestep( - (*options)["min_timestep"].doc("Minimum time step size").withDefault(-1.0)), + (*options)["min_timestep"].doc("Minimum time step size").withDefault(0.0)), start_timestep((*options)["start_timestep"] - .doc("Starting time step. < 0 then chosen by CVODE.") - .withDefault(-1.0)), + .doc("Starting time step. = 0 then chosen by CVODE.") + .withDefault(0.0)), mxorder((*options)["mxorder"].doc("Maximum order").withDefault(-1)), max_nonlinear_iterations( (*options)["max_nonlinear_iterations"] .doc("Maximum number of nonlinear iterations allowed by CVODE before " - "reducing " - "timestep. CVODE default (used if this option is negative) is 3.") - .withDefault(-1)), + "reducing timestep.") + .withDefault(3)), apply_positivity_constraints( (*options)["apply_positivity_constraints"] .doc("Use CVODE function CVodeSetConstraints to constrain variables - the " @@ -191,7 +190,7 @@ int CvodeSolver::init() { } // Put the variables into uvec - save_vars(NV_DATA_P(uvec)); + save_vars(N_VGetArrayPointer(uvec)); if (adams_moulton) { // By default use functional iteration for Adams-Moulton @@ -217,8 +216,10 @@ int CvodeSolver::init() { throw BoutException("CVodeInit failed\n"); } - if (CVodeSetMaxOrd(cvode_mem, max_order) != CV_SUCCESS) { - throw BoutException("CVodeSetMaxOrder failed\n"); + if (max_order > 0) { + if (CVodeSetMaxOrd(cvode_mem, max_order) != CV_SUCCESS) { + throw BoutException("CVodeSetMaxOrder failed\n"); + } } if (CVodeSetStabLimDet(cvode_mem, stablimdet) != CV_SUCCESS) { @@ -252,7 +253,7 @@ int CvodeSolver::init() { throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n"); } - set_vector_option_values(NV_DATA_P(abstolvec), f2dtols, f3dtols); + set_vector_option_values(N_VGetArrayPointer(abstolvec), f2dtols, f3dtols); if (CVodeSVtolerances(cvode_mem, reltol, abstolvec) != CV_SUCCESS) { throw BoutException("CVodeSVtolerances failed\n"); @@ -295,7 +296,7 @@ int CvodeSolver::init() { "failed\n"); } - set_vector_option_values(NV_DATA_P(constraints_vec), f2d_constraints, + set_vector_option_values(N_VGetArrayPointer(constraints_vec), f2d_constraints, f3d_constraints); if (CVodeSetConstraints(cvode_mem, constraints_vec) != CV_SUCCESS) { @@ -320,7 +321,7 @@ int CvodeSolver::init() { output_info.write("\tUsing Newton iteration\n"); TRACE("Setting preconditioner"); - const auto prectype = use_prec ? + const auto prectype = use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); @@ -551,7 +552,7 @@ BoutReal CvodeSolver::run(BoutReal tout) { } // Copy variables - load_vars(NV_DATA_P(uvec)); + load_vars(N_VGetArrayPointer(uvec)); // Call rhs function to get extra variables at this time run_rhs(simtime); @@ -595,7 +596,7 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udat BoutReal tstart = bout::globals::mpi->MPI_Wtime(); - int N = NV_LOCLENGTH_P(uvec); + int N = N_VGetLocalLength(uvec); if (!hasPreconditioner()) { // Identity (but should never happen) @@ -650,8 +651,8 @@ void CvodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jv static int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { - BoutReal* udata = NV_DATA_P(u); - BoutReal* dudata = NV_DATA_P(du); + BoutReal* udata = N_VGetArrayPointer(u); + BoutReal* dudata = N_VGetArrayPointer(du); auto* s = static_cast(user_data); @@ -674,9 +675,9 @@ static int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_ static int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) { - BoutReal* udata = NV_DATA_P(yy); - BoutReal* rdata = NV_DATA_P(rvec); - BoutReal* zdata = NV_DATA_P(zvec); + BoutReal* udata = N_VGetArrayPointer(yy); + BoutReal* rdata = N_VGetArrayPointer(rvec); + BoutReal* zdata = N_VGetArrayPointer(zvec); auto* s = static_cast(user_data); @@ -689,9 +690,9 @@ static int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec /// Jacobian-vector multiplication function static int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { - BoutReal* ydata = NV_DATA_P(y); ///< System state - BoutReal* vdata = NV_DATA_P(v); ///< Input vector - BoutReal* Jvdata = NV_DATA_P(Jv); ///< Jacobian*vector output + BoutReal* ydata = N_VGetArrayPointer(y); ///< System state + BoutReal* vdata = N_VGetArrayPointer(v); ///< Input vector + BoutReal* Jvdata = N_VGetArrayPointer(Jv); ///< Jacobian*vector output auto* s = static_cast(user_data); @@ -746,7 +747,7 @@ void CvodeSolver::loop_vector_option_values_op(Ind2D UNUSED(i2d), BoutReal* opti void CvodeSolver::resetInternalFields() { TRACE("CvodeSolver::resetInternalFields"); - save_vars(NV_DATA_P(uvec)); + save_vars(N_VGetArrayPointer(uvec)); if (CVodeReInit(cvode_mem, simtime, uvec) != CV_SUCCESS) { throw BoutException("CVodeReInit failed\n"); diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 02c86e9624..3a24bbb28b 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -123,16 +123,16 @@ int IdaSolver::init() { } // Put the variables into uvec - save_vars(NV_DATA_P(uvec)); + save_vars(N_VGetArrayPointer(uvec)); // Get the starting time derivative run_rhs(simtime); // Put the time-derivatives into duvec - save_derivs(NV_DATA_P(duvec)); + save_derivs(N_VGetArrayPointer(duvec)); // Set the equation type in id(Differential or Algebraic. This is optional) - set_id(NV_DATA_P(id)); + set_id(N_VGetArrayPointer(id)); // Call IDACreate to initialise idamem = callWithSUNContext(IDACreate, suncontext); @@ -141,23 +141,25 @@ int IdaSolver::init() { } // For callbacks, need pointer to solver object - if (IDASetUserData(idamem, this) < 0) { + if (IDASetUserData(idamem, this) != IDA_SUCCESS) { throw BoutException("IDASetUserData failed\n"); } - if (IDASetId(idamem, id) < 0) { + if (IDASetId(idamem, id) != IDA_SUCCESS) { throw BoutException("IDASetID failed\n"); } - if (IDAInit(idamem, idares, simtime, uvec, duvec) < 0) { + if (IDAInit(idamem, idares, simtime, uvec, duvec) != IDA_SUCCESS) { throw BoutException("IDAInit failed\n"); } - if (IDASStolerances(idamem, reltol, abstol) < 0) { + if (IDASStolerances(idamem, reltol, abstol) != IDA_SUCCESS) { throw BoutException("IDASStolerances failed\n"); } - IDASetMaxNumSteps(idamem, mxsteps); + if (IDASetMaxNumSteps(idamem, mxsteps) != IDA_SUCCESS) { + throw BoutException("IDASetMaxNumSteps failed\n"); + } // Call IDASpgmr to specify the IDA linear solver IDASPGMR const auto maxl = (*options)["maxl"].withDefault(6 * n3d); @@ -170,7 +172,12 @@ int IdaSolver::init() { } if (use_precon) { - if (!hasPreconditioner()) { + if (hasPreconditioner()) { + output.write("\tUsing user-supplied preconditioner\n"); + if (IDASetPreconditioner(idamem, nullptr, ida_pre) != IDALS_SUCCESS) { + throw BoutException("IDASetPreconditioner failed\n"); + } + } else { output.write("\tUsing BBD preconditioner\n"); /// Get options // Compute band_width_default from actually added fields, to allow for multiple Mesh @@ -190,20 +197,15 @@ int IdaSolver::init() { const auto mukeep = (*options)["mukeep"].withDefault(n3d); const auto mlkeep = (*options)["mlkeep"].withDefault(n3d); if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, 0, ida_bbd_res, - nullptr)) { + nullptr) != IDALS_SUCCESS) { throw BoutException("IDABBDPrecInit failed\n"); } - } else { - output.write("\tUsing user-supplied preconditioner\n"); - if (IDASetPreconditioner(idamem, nullptr, ida_pre) != IDALS_SUCCESS) { - throw BoutException("IDASetPreconditioner failed\n"); - } } } // Call IDACalcIC (with default options) to correct the initial values if (correct_start) { - if (IDACalcIC(idamem, IDA_YA_YDP_INIT, 1e-6)) { + if (IDACalcIC(idamem, IDA_YA_YDP_INIT, 1e-6) != IDA_SUCCESS) { throw BoutException("IDACalcIC failed\n"); } } @@ -255,7 +257,7 @@ BoutReal IdaSolver::run(BoutReal tout) { const int flag = IDASolve(idamem, tout, &simtime, uvec, duvec, IDA_NORMAL); // Copy variables - load_vars(NV_DATA_P(uvec)); + load_vars(N_VGetArrayPointer(uvec)); // Call rhs function to get extra variables at this time run_rhs(simtime); @@ -286,8 +288,8 @@ void IdaSolver::res(BoutReal t, BoutReal* udata, BoutReal* dudata, BoutReal* rda save_derivs(rdata); // If a differential equation, subtract dudata - const int N = NV_LOCLENGTH_P(id); - const BoutReal* idd = NV_DATA_P(id); + const auto N = N_VGetLocalLength(id); + const BoutReal* idd = N_VGetArrayPointer(id); for (int i = 0; i < N; i++) { if (idd[i] > 0.5) { // 1 -> differential, 0 -> algebraic rdata[i] -= dudata[i]; @@ -307,7 +309,7 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, if (!hasPreconditioner()) { // Identity (but should never happen) - const int N = NV_LOCLENGTH_P(id); + const int N = N_VGetLocalLength(id); std::copy(rvec, rvec + N, zvec); return; } @@ -332,9 +334,9 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, **************************************************************************/ static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { - BoutReal* udata = NV_DATA_P(u); - BoutReal* dudata = NV_DATA_P(du); - BoutReal* rdata = NV_DATA_P(rr); + BoutReal* udata = N_VGetArrayPointer(u); + BoutReal* dudata = N_VGetArrayPointer(du); + BoutReal* rdata = N_VGetArrayPointer(rr); auto* s = static_cast(user_data); @@ -354,9 +356,9 @@ static int ida_bbd_res(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Ve static int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr), N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data) { - BoutReal* udata = NV_DATA_P(yy); - BoutReal* rdata = NV_DATA_P(rvec); - BoutReal* zdata = NV_DATA_P(zvec); + BoutReal* udata = N_VGetArrayPointer(yy); + BoutReal* rdata = N_VGetArrayPointer(rvec); + BoutReal* zdata = N_VGetArrayPointer(zvec); auto* s = static_cast(user_data); From bd794f7792ee97cf143339f650201bc093672126 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 18 Mar 2024 17:28:10 -0700 Subject: [PATCH 340/412] Use new adaptivity controller with ARKODE --- include/bout/sundials_backports.hxx | 2 + src/solver/impls/arkode/arkode.cxx | 210 +++++++++++++++------------- src/solver/impls/arkode/arkode.hxx | 6 +- 3 files changed, 123 insertions(+), 95 deletions(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index 81ec98b1ac..df3234944a 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -34,6 +34,8 @@ static_assert(std::is_same::value, "BOUT++ and SUNDIALS real types do not match"); +#define SUNDIALS_CONTROLLER_SUPPORT (SUNDIALS_VERSION_MAJOR > 5 || SUNDIALS_VERSION_MAJOR == 5 && SUNDIALS_VERSION_MINOR >= 7) + #if SUNDIALS_VERSION_MAJOR < 6 constexpr auto SUN_PREC_RIGHT = PREC_RIGHT; constexpr auto SUN_PREC_LEFT = PREC_LEFT; diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index e63faef6f4..ae136d207f 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -145,6 +145,10 @@ ArkodeSolver::~ArkodeSolver() { ARKStepFree(&arkode_mem); SUNLinSolFree(sun_solver); SUNNonlinSolFree(nonlinear_solver); + +#if SUNDIALS_CONTROLLER_SUPPORT + SUNAdaptController_Destroy(controller); +#endif } /************************************************************************** @@ -178,7 +182,7 @@ int ArkodeSolver::init() { } // Put the variables into uvec - save_vars(NV_DATA_P(uvec)); + save_vars(N_VGetArrayPointer(uvec)); ASSERT1(solve_explicit or solve_implicit); @@ -224,11 +228,8 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetUserData failed\n"); } - if (set_linear) { - output.write("\tSetting ARKStep implicit solver to Linear\n"); - if (ARKStepSetLinear(arkode_mem, 1) != ARK_SUCCESS) { - throw BoutException("ARKStepSetLinear failed\n"); - } + if (ARKStepSetLinear(arkode_mem, 1) != ARK_SUCCESS) { + throw BoutException("ARKStepSetLinear failed\n"); } if (fixed_step) { @@ -247,9 +248,44 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetCFLFraction failed\n"); } + +#if SUNDIALS_CONTROLLER_SUPPORT + switch (adap_method) { + case 0: + controller = SUNAdaptController_PID(suncontext); + break; + case 1: + controller = SUNAdaptController_PI(suncontext); + break; + case 2: + controller = SUNAdaptController_I(suncontext); + break; + case 3: + controller = SUNAdaptController_ExpGus(suncontext); + break; + case 4: + controller = SUNAdaptController_ImpGus(suncontext); + break; + case 5: + controller = SUNAdaptController_ImExGus(suncontext); + break; + + default: + throw BoutException("Invalid adap_method\n"); + } + + if (ARKStepSetAdaptController(arkode_mem, controller) != ARK_SUCCESS) { + throw BoutException("ARKStepSetAdaptController failed\n"); + } + + if (ARKStepSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) { + throw BoutException("ARKStepSetAdaptivityAdjustment failed\n"); + } +#else if (ARKStepSetAdaptivityMethod(arkode_mem, adap_method, 1, 1, nullptr) != ARK_SUCCESS) { throw BoutException("ARKStepSetAdaptivityMethod failed\n"); } +#endif if (use_vector_abstol) { std::vector f2dtols; @@ -278,7 +314,7 @@ int ArkodeSolver::init() { throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n"); } - set_abstol_values(NV_DATA_P(abstolvec), f2dtols, f3dtols); + set_abstol_values(N_VGetArrayPointer(abstolvec), f2dtols, f3dtols); if (ARKStepSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) { throw BoutException("ARKStepSVtolerances failed\n"); @@ -313,95 +349,81 @@ int ArkodeSolver::init() { } } - // ARKStepSetPredictorMethod(arkode_mem,4); - if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); if (nonlinear_solver == nullptr) { throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); + + } + if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { + throw BoutException("ARKStepSetNonlinearSolver failed\n"); } } else { output.write("\tUsing Newton iteration\n"); - nonlinear_solver = callWithSUNContext(SUNNonlinSol_Newton, suncontext, uvec); - if (nonlinear_solver == nullptr) { - throw BoutException("Creating SUNDIALS Newton nonlinear solver failed\n"); - } - } - if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { - throw BoutException("ARKStepSetNonlinearSolver failed\n"); - } - - /// Set Preconditioner - // TODO: only set of linear solver with Newton's method - if (use_precon) { - const int prectype = rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT; + const auto prectype = use_precon ? + (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : + SUN_PREC_NONE; sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); } - if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) { + if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { throw BoutException("ARKStepSetLinearSolver failed\n"); } - if (!hasPreconditioner()) { - output.write("\tUsing BBD preconditioner\n"); - - /// Get options - // Compute band_width_default from actually added fields, to allow for multiple - // Mesh objects - // - // Previous implementation was equivalent to: - // int MXSUB = mesh->xend - mesh->xstart + 1; - // int band_width_default = n3Dvars()*(MXSUB+2); - const int band_width_default = std::accumulate( - begin(f3d), end(f3d), 0, [](int a, const VarStr& fvar) { - Mesh* localmesh = fvar.var->getMesh(); - return a + localmesh->xend - localmesh->xstart + 3; - }); - - const auto mudq = (*options)["mudq"] - .doc("Upper half-bandwidth to be used in the difference " - "quotient Jacobian approximation") - .withDefault(band_width_default); - const auto mldq = (*options)["mldq"] - .doc("Lower half-bandwidth to be used in the difference " - "quotient Jacobian approximation") - .withDefault(band_width_default); - const auto mukeep = (*options)["mukeep"] - .doc("Upper half-bandwidth of the retained banded " - "approximate Jacobian block") - .withDefault(n3Dvars() + n2Dvars()); - const auto mlkeep = (*options)["mlkeep"] - .doc("Lower half-bandwidth of the retained banded " - "approximate Jacobian block") - .withDefault(n3Dvars() + n2Dvars()); - - if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, - arkode_bbd_rhs, nullptr) - != ARK_SUCCESS) { - throw BoutException("ARKBBDPrecInit failed\n"); - } - - } else { - output.write("\tUsing user-supplied preconditioner\n"); + /// Set Preconditioner + if (use_precon) { + if (hasPreconditioner()) { + output.write("\tUsing user-supplied preconditioner\n"); + + if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetPreconditioner failed\n"); + } + } else { + output.write("\tUsing BBD preconditioner\n"); + + /// Get options + // Compute band_width_default from actually added fields, to allow for multiple + // Mesh objects + // + // Previous implementation was equivalent to: + // int MXSUB = mesh->xend - mesh->xstart + 1; + // int band_width_default = n3Dvars()*(MXSUB+2); + const int band_width_default = std::accumulate( + begin(f3d), end(f3d), 0, [](int a, const VarStr& fvar) { + Mesh* localmesh = fvar.var->getMesh(); + return a + localmesh->xend - localmesh->xstart + 3; + }); + + const auto mudq = (*options)["mudq"] + .doc("Upper half-bandwidth to be used in the difference " + "quotient Jacobian approximation") + .withDefault(band_width_default); + const auto mldq = (*options)["mldq"] + .doc("Lower half-bandwidth to be used in the difference " + "quotient Jacobian approximation") + .withDefault(band_width_default); + const auto mukeep = (*options)["mukeep"] + .doc("Upper half-bandwidth of the retained banded " + "approximate Jacobian block") + .withDefault(n3Dvars() + n2Dvars()); + const auto mlkeep = (*options)["mlkeep"] + .doc("Lower half-bandwidth of the retained banded " + "approximate Jacobian block") + .withDefault(n3Dvars() + n2Dvars()); + + if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, + arkode_bbd_rhs, nullptr) + != ARKLS_SUCCESS) { + throw BoutException("ARKBBDPrecInit failed\n"); + } - if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARK_SUCCESS) { - throw BoutException("ARKStepSetPreconditioner failed\n"); } - } - } else { - // Not using preconditioning - - output.write("\tNo preconditioning\n"); - - sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, SUN_PREC_NONE, maxl); - if (sun_solver == nullptr) { - throw BoutException("Creating SUNDIALS linear solver failed\n"); - } - if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARK_SUCCESS) { - throw BoutException("ARKStepSetLinearSolver failed\n"); + } else { + // Not using preconditioning + output.write("\tNo preconditioning\n"); } } @@ -410,8 +432,8 @@ int ArkodeSolver::init() { if (use_jacobian and hasJacobian()) { output.write("\tUsing user-supplied Jacobian function\n"); - if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARK_SUCCESS) { - throw BoutException("ARKStepSetJacTimesVecFn failed\n"); + if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetJacTimes failed\n"); } } else { output.write("\tUsing difference quotient approximation for Jacobian\n"); @@ -522,7 +544,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) { } // Copy variables - load_vars(NV_DATA_P(uvec)); + load_vars(N_VGetArrayPointer(uvec)); // Call rhs function to get extra variables at this time run_rhs(simtime); // run_diffusive(simtime); @@ -595,7 +617,7 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* uda if (!hasPreconditioner()) { // Identity (but should never happen) - const int N = NV_LOCLENGTH_P(uvec); + const int N = N_VGetLocalLength(uvec); std::copy(rvec, rvec + N, zvec); return; } @@ -645,8 +667,8 @@ void ArkodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* J static int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { - BoutReal* udata = NV_DATA_P(u); - BoutReal* dudata = NV_DATA_P(du); + BoutReal* udata = N_VGetArrayPointer(u); + BoutReal* dudata = N_VGetArrayPointer(du); auto* s = static_cast(user_data); @@ -661,8 +683,8 @@ static int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_d static int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { - BoutReal* udata = NV_DATA_P(u); - BoutReal* dudata = NV_DATA_P(du); + BoutReal* udata = N_VGetArrayPointer(u); + BoutReal* dudata = N_VGetArrayPointer(du); auto* s = static_cast(user_data); @@ -677,8 +699,8 @@ static int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_d static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { - BoutReal* udata = NV_DATA_P(u); - BoutReal* dudata = NV_DATA_P(du); + BoutReal* udata = N_VGetArrayPointer(u); + BoutReal* dudata = N_VGetArrayPointer(du); auto* s = static_cast(user_data); @@ -701,9 +723,9 @@ static int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N static int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) { - BoutReal* udata = NV_DATA_P(yy); - BoutReal* rdata = NV_DATA_P(rvec); - BoutReal* zdata = NV_DATA_P(zvec); + BoutReal* udata = N_VGetArrayPointer(yy); + BoutReal* rdata = N_VGetArrayPointer(rvec); + BoutReal* zdata = N_VGetArrayPointer(zvec); auto* s = static_cast(user_data); @@ -716,9 +738,9 @@ static int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rve /// Jacobian-vector multiplication function static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { - BoutReal* ydata = NV_DATA_P(y); ///< System state - BoutReal* vdata = NV_DATA_P(v); ///< Input vector - BoutReal* Jvdata = NV_DATA_P(Jv); ///< Jacobian*vector output + BoutReal* ydata = N_VGetArrayPointer(y); ///< System state + BoutReal* vdata = N_VGetArrayPointer(v); ///< Input vector + BoutReal* Jvdata = N_VGetArrayPointer(Jv); ///< Jacobian*vector output auto* s = static_cast(user_data); diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index 302413d8aa..b1b1819d11 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -153,8 +153,12 @@ private: /// SPGMR solver structure SUNLinearSolver sun_solver{nullptr}; - /// Solver for functional iterations for Adams-Moulton + /// Solver for implicit stages SUNNonlinearSolver nonlinear_solver{nullptr}; +#if SUNDIALS_CONTROLLER_SUPPORT + /// Timestep controller + SUNAdaptController controller{nullptr}; +#endif /// Context for SUNDIALS memory allocations sundials::Context suncontext; }; From 87c4caefb928eaf4ca6438271b8bb7f94babca84 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 18 Mar 2024 17:36:31 -0700 Subject: [PATCH 341/412] Fix local length for old SUNDIALS versions --- src/solver/impls/arkode/arkode.cxx | 2 +- src/solver/impls/cvode/cvode.cxx | 2 +- src/solver/impls/ida/ida.cxx | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index ae136d207f..f9ea90a483 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -617,7 +617,7 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* uda if (!hasPreconditioner()) { // Identity (but should never happen) - const int N = N_VGetLocalLength(uvec); + const int N = N_VGetLocalLength_Parallel(uvec); std::copy(rvec, rvec + N, zvec); return; } diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 17ff9c55f0..930842fbc7 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -596,7 +596,7 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udat BoutReal tstart = bout::globals::mpi->MPI_Wtime(); - int N = N_VGetLocalLength(uvec); + int N = N_VGetLocalLength_Parallel(uvec); if (!hasPreconditioner()) { // Identity (but should never happen) diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 3a24bbb28b..76431f2d6d 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -288,7 +288,7 @@ void IdaSolver::res(BoutReal t, BoutReal* udata, BoutReal* dudata, BoutReal* rda save_derivs(rdata); // If a differential equation, subtract dudata - const auto N = N_VGetLocalLength(id); + const auto N = N_VGetLocalLength_Parallel(id); const BoutReal* idd = N_VGetArrayPointer(id); for (int i = 0; i < N; i++) { if (idd[i] > 0.5) { // 1 -> differential, 0 -> algebraic @@ -309,7 +309,7 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, if (!hasPreconditioner()) { // Identity (but should never happen) - const int N = N_VGetLocalLength(id); + const int N = N_VGetLocalLength_Parallel(id); std::copy(rvec, rvec + N, zvec); return; } From 2c3df119b2bd6cfa4c74b593d0816f71e926dffe Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 18 Mar 2024 17:42:11 -0700 Subject: [PATCH 342/412] Update SUNDIALS download source --- cmake/SetupBOUTThirdParty.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 53adbec92d..6de83e854b 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -281,8 +281,8 @@ if (BOUT_USE_SUNDIALS) include(FetchContent) FetchContent_Declare( sundials - GIT_REPOSITORY https://github.com/ZedThree/sundials - GIT_TAG cmake-export-fixes + GIT_REPOSITORY https://github.com/LLNL/sundials + GIT_TAG v7.0.0 ) # Note: These are settings for building SUNDIALS set(EXAMPLES_ENABLE_C OFF CACHE BOOL "" FORCE) From 3ee3526cb102e497a005e14d3197fc8b21d47871 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 18 Mar 2024 18:03:16 -0700 Subject: [PATCH 343/412] Add missing header --- include/bout/sundials_backports.hxx | 2 +- src/solver/impls/arkode/arkode.hxx | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index df3234944a..44b4809e6c 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -34,7 +34,7 @@ static_assert(std::is_same::value, "BOUT++ and SUNDIALS real types do not match"); -#define SUNDIALS_CONTROLLER_SUPPORT (SUNDIALS_VERSION_MAJOR > 5 || SUNDIALS_VERSION_MAJOR == 5 && SUNDIALS_VERSION_MINOR >= 7) +#define SUNDIALS_CONTROLLER_SUPPORT (SUNDIALS_VERSION_MAJOR > 6 || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 7) #if SUNDIALS_VERSION_MAJOR < 6 constexpr auto SUN_PREC_RIGHT = PREC_RIGHT; diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index b1b1819d11..e8e0369368 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -47,6 +47,10 @@ RegisterUnavailableSolver #include #include +#if SUNDIALS_CONTROLLER_SUPPORT +#include +#endif + #include class ArkodeSolver; From eac0acb3eb062d25c27ebf5ef6677a5b6d2b1d4f Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Tue, 19 Mar 2024 12:33:04 -0700 Subject: [PATCH 344/412] Fix bug with ARKODE always treating problem as linear --- src/solver/impls/arkode/arkode.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index f9ea90a483..34064bac0c 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -228,7 +228,7 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetUserData failed\n"); } - if (ARKStepSetLinear(arkode_mem, 1) != ARK_SUCCESS) { + if (ARKStepSetLinear(arkode_mem, set_linear) != ARK_SUCCESS) { throw BoutException("ARKStepSetLinear failed\n"); } From 4cbc34ead5141d5a8a3a02eb2dc8142d5b45b14d Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Tue, 19 Mar 2024 12:37:45 -0700 Subject: [PATCH 345/412] Apply suggestions from code review Co-authored-by: Daniel R. Reynolds --- src/solver/impls/cvode/cvode.cxx | 2 +- src/solver/impls/ida/ida.cxx | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 930842fbc7..68984ebf64 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -360,7 +360,7 @@ int CvodeSolver::init() { const auto mukeep = (*options)["mukeep"].withDefault(n3Dvars() + n2Dvars()); const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars()); - if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, + if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0.0, cvode_bbd_rhs, nullptr) != CVLS_SUCCESS) { throw BoutException("CVBBDPrecInit failed\n"); } diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 76431f2d6d..a47afaa85a 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -196,7 +196,7 @@ int IdaSolver::init() { const auto mldq = (*options)["mldq"].withDefault(band_width_default); const auto mukeep = (*options)["mukeep"].withDefault(n3d); const auto mlkeep = (*options)["mlkeep"].withDefault(n3d); - if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, 0, ida_bbd_res, + if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, 0.0, ida_bbd_res, nullptr) != IDALS_SUCCESS) { throw BoutException("IDABBDPrecInit failed\n"); } From 0b8e47b280bf3f1d36f5cc2bcf1be20721510516 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Tue, 19 Mar 2024 12:43:39 -0700 Subject: [PATCH 346/412] CMake requires SUNDIALS v4+ --- cmake/FindSUNDIALS.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake index 29da3e5ca7..a4e163bc9c 100644 --- a/cmake/FindSUNDIALS.cmake +++ b/cmake/FindSUNDIALS.cmake @@ -122,7 +122,7 @@ if (SUNDIALS_INCLUDE_DIR) endif() if("${SUNDIALS_VERSION_MAJOR}" LESS 4) - message(WARNING "SUNDIALS versions <4 are depricated and will not be supported in the next release") + message(FATAL_ERROR "SUNDIALS versions <4 are not supported") endif() if (SUNDIALS_DEBUG) From 9c05cc93992bedfbf3244bb7f8b552fbe09a610b Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Tue, 19 Mar 2024 12:50:15 -0700 Subject: [PATCH 347/412] Add missing period --- cmake/FindSUNDIALS.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake index a4e163bc9c..9277ba17c9 100644 --- a/cmake/FindSUNDIALS.cmake +++ b/cmake/FindSUNDIALS.cmake @@ -122,7 +122,7 @@ if (SUNDIALS_INCLUDE_DIR) endif() if("${SUNDIALS_VERSION_MAJOR}" LESS 4) - message(FATAL_ERROR "SUNDIALS versions <4 are not supported") + message(FATAL_ERROR "SUNDIALS versions <4 are not supported.") endif() if (SUNDIALS_DEBUG) From e905f6a83b3c404c64bf460190f9a1b6d3babdcd Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Wed, 20 Mar 2024 15:14:25 -0700 Subject: [PATCH 348/412] Apply suggestions from code review Co-authored-by: Peter Hill --- include/bout/sundials_backports.hxx | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index 44b4809e6c..77ced8bb58 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -25,14 +25,13 @@ #include "bout/unused.hxx" -static_assert(std::is_same::value, - "BOUT++ and SUNDIALS real types do not match"); + +static_assert(std::is_same_v, "BOUT++ and SUNDIALS real types do not match"); #define SUNDIALS_CONTROLLER_SUPPORT (SUNDIALS_VERSION_MAJOR > 6 || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 7) From 173456cdad3fac597f05f2f396f5015643be258a Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Wed, 20 Mar 2024 15:23:31 -0700 Subject: [PATCH 349/412] Switch to [[maybe_unused]] --- include/bout/sundials_backports.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index 77ced8bb58..7245514f04 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -45,7 +45,7 @@ using Context = std::nullptr_t; } // namespace sundials #endif -inline sundials::Context createSUNContext(MAYBE_UNUSED(MPI_Comm& comm)) { +inline sundials::Context createSUNContext([[maybe_unused]] MPI_Comm& comm) { #if SUNDIALS_VERSION_MAJOR < 6 return nullptr; #elif SUNDIALS_VERSION_MAJOR < 7 @@ -57,7 +57,7 @@ inline sundials::Context createSUNContext(MAYBE_UNUSED(MPI_Comm& comm)) { template inline decltype(auto) callWithSUNContext(Func f, - MAYBE_UNUSED(sundials::Context& ctx), + [[maybe_unused]] sundials::Context& ctx, Args&&... args) { #if SUNDIALS_VERSION_MAJOR < 6 return f(std::forward(args)...); From 90ceeecbb2b31480c310281351fa7d50d0fc663a Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Wed, 20 Mar 2024 16:50:18 -0700 Subject: [PATCH 350/412] Simplify SUNDIALS cmake --- cmake/FindSUNDIALS.cmake | 16 ++-------------- cmake/SetupBOUTThirdParty.cmake | 2 +- 2 files changed, 3 insertions(+), 15 deletions(-) diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake index 9277ba17c9..15b266d06a 100644 --- a/cmake/FindSUNDIALS.cmake +++ b/cmake/FindSUNDIALS.cmake @@ -104,16 +104,8 @@ endforeach() if (SUNDIALS_INCLUDE_DIR) file(READ "${SUNDIALS_INCLUDE_DIR}/sundials_config.h" SUNDIALS_CONFIG_FILE) - string(FIND "${SUNDIALS_CONFIG_FILE}" "SUNDIALS_PACKAGE_VERSION" index) - if("${index}" LESS 0) - # Version >3 - set(SUNDIALS_VERSION_REGEX_PATTERN - ".*#define SUNDIALS_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*") - else() - # Version <3 - set(SUNDIALS_VERSION_REGEX_PATTERN - ".*#define SUNDIALS_PACKAGE_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*") - endif() + set(SUNDIALS_VERSION_REGEX_PATTERN + ".*#define SUNDIALS_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*") string(REGEX MATCH ${SUNDIALS_VERSION_REGEX_PATTERN} _ "${SUNDIALS_CONFIG_FILE}") set(SUNDIALS_VERSION_MAJOR ${CMAKE_MATCH_1} CACHE STRING "") set(SUNDIALS_VERSION_MINOR ${CMAKE_MATCH_2} CACHE STRING "") @@ -121,10 +113,6 @@ if (SUNDIALS_INCLUDE_DIR) set(SUNDIALS_VERSION "${SUNDIALS_VERSION_MAJOR}.${SUNDIALS_VERSION_MINOR}.${SUNDIALS_VERSION_PATCH}" CACHE STRING "SUNDIALS version") endif() -if("${SUNDIALS_VERSION_MAJOR}" LESS 4) - message(FATAL_ERROR "SUNDIALS versions <4 are not supported.") -endif() - if (SUNDIALS_DEBUG) message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] " " SUNDIALS_VERSION = ${SUNDIALS_VERSION}") diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 6de83e854b..83f8a52e85 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -297,7 +297,7 @@ if (BOUT_USE_SUNDIALS) FetchContent_MakeAvailable(sundials) message(STATUS "SUNDIALS done configuring") else() - find_package(SUNDIALS REQUIRED) + find_package(SUNDIALS 4 REQUIRED) endif() target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel) target_link_libraries(bout++ PUBLIC SUNDIALS::cvode) From c749ec4e4dc52ce40e23546c95011c280c9309a0 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Wed, 20 Mar 2024 18:04:23 -0700 Subject: [PATCH 351/412] Add options to set Butcher tables by name --- include/bout/sundials_backports.hxx | 1 + src/solver/impls/arkode/arkode.cxx | 18 ++++++++++++++++++ src/solver/impls/arkode/arkode.hxx | 4 ++++ 3 files changed, 23 insertions(+) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index 7245514f04..fed11ccef6 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -34,6 +34,7 @@ using sundials_real_type = sunrealtype; static_assert(std::is_same_v, "BOUT++ and SUNDIALS real types do not match"); #define SUNDIALS_CONTROLLER_SUPPORT (SUNDIALS_VERSION_MAJOR > 6 || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 7) +#define SUNDIALS_TABLE_BY_NAME_SUPPORT (SUNDIALS_VERSION_MAJOR > 6 || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 4) #if SUNDIALS_VERSION_MAJOR < 6 constexpr auto SUN_PREC_RIGHT = PREC_RIGHT; diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 34064bac0c..18dc4516e0 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -85,6 +85,14 @@ ArkodeSolver::ArkodeSolver(Options* opts) "not recommended except for code comparison") .withDefault(false)), order((*options)["order"].doc("Order of internal step").withDefault(4)), +#if SUNDIALS_TABLE_BY_NAME_SUPPORT + implicit_table((*options)["implicit_table"] + .doc("Name of the implicit Butcher table") + .withDefault("")), + explicit_table((*options)["explicit_table"] + .doc("Name of the explicit Butcher table") + .withDefault("")), +#endif cfl_frac((*options)["cfl_frac"] .doc("Fraction of the estimated explicitly stable step to use") .withDefault(-1.0)), @@ -244,6 +252,16 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetOrder failed\n"); } +#if SUNDIALS_TABLE_BY_NAME_SUPPORT + if (!implicit_table.empty() || !explicit_table.empty()) { + if (ARKStepSetTableName(arkode_mem, + implicit_table.empty() ? "ARKODE_DIRK_NONE" : implicit_table.c_str(), + explicit_table.empty() ? "ARKODE_ERK_NONE" : explicit_table.c_str()) != ARK_SUCCESS) { + throw BoutException("ARKStepSetTableName failed\n"); + } + } +#endif + if (ARKStepSetCFLFraction(arkode_mem, cfl_frac) != ARK_SUCCESS) { throw BoutException("ARKStepSetCFLFraction failed\n"); } diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index e8e0369368..08bb3ea729 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -106,6 +106,10 @@ private: bool fixed_step; /// Order of internal step int order; + /// Name of the implicit Butcher table + std::string implicit_table; + /// Name of the explicit Butcher table + std::string explicit_table; /// Fraction of the estimated explicitly stable step to use BoutReal cfl_frac; /// Set timestep adaptivity function: From d1ff45214f41b6c626cb34a073f90beed17cc1a6 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 28 Mar 2024 15:52:40 +0000 Subject: [PATCH 352/412] Apply clang-format --- include/bout/sundials_backports.hxx | 20 +++++--- src/solver/impls/arkode/arkode.cxx | 78 ++++++++++++++--------------- src/solver/impls/cvode/cvode.cxx | 12 ++--- src/solver/impls/ida/ida.cxx | 10 ++-- 4 files changed, 61 insertions(+), 59 deletions(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index fed11ccef6..19140e2453 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -13,9 +13,9 @@ #include #include #include +#include #include #include -#include #include #include @@ -31,10 +31,15 @@ using sundials_real_type = realtype; using sundials_real_type = sunrealtype; #endif -static_assert(std::is_same_v, "BOUT++ and SUNDIALS real types do not match"); +static_assert(std::is_same_v, + "BOUT++ and SUNDIALS real types do not match"); -#define SUNDIALS_CONTROLLER_SUPPORT (SUNDIALS_VERSION_MAJOR > 6 || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 7) -#define SUNDIALS_TABLE_BY_NAME_SUPPORT (SUNDIALS_VERSION_MAJOR > 6 || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 4) +#define SUNDIALS_CONTROLLER_SUPPORT \ + (SUNDIALS_VERSION_MAJOR > 6 \ + || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 7) +#define SUNDIALS_TABLE_BY_NAME_SUPPORT \ + (SUNDIALS_VERSION_MAJOR > 6 \ + || SUNDIALS_VERSION_MAJOR == 6 && SUNDIALS_VERSION_MINOR >= 4) #if SUNDIALS_VERSION_MAJOR < 6 constexpr auto SUN_PREC_RIGHT = PREC_RIGHT; @@ -56,10 +61,9 @@ inline sundials::Context createSUNContext([[maybe_unused]] MPI_Comm& comm) { #endif } -template -inline decltype(auto) callWithSUNContext(Func f, - [[maybe_unused]] sundials::Context& ctx, - Args&&... args) { +template +inline decltype(auto) callWithSUNContext(Func f, [[maybe_unused]] sundials::Context& ctx, + Args&&... args) { #if SUNDIALS_VERSION_MAJOR < 6 return f(std::forward(args)...); #else diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 18dc4516e0..e639dfca1d 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -63,7 +63,6 @@ static int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vec static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); - ArkodeSolver::ArkodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] .doc("Print some additional diagnostics") @@ -209,7 +208,8 @@ int ArkodeSolver::init() { } }(); - arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, explicit_rhs, implicit_rhs, simtime, uvec); + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, explicit_rhs, implicit_rhs, + simtime, uvec); if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); } @@ -254,9 +254,11 @@ int ArkodeSolver::init() { #if SUNDIALS_TABLE_BY_NAME_SUPPORT if (!implicit_table.empty() || !explicit_table.empty()) { - if (ARKStepSetTableName(arkode_mem, - implicit_table.empty() ? "ARKODE_DIRK_NONE" : implicit_table.c_str(), - explicit_table.empty() ? "ARKODE_ERK_NONE" : explicit_table.c_str()) != ARK_SUCCESS) { + if (ARKStepSetTableName( + arkode_mem, + implicit_table.empty() ? "ARKODE_DIRK_NONE" : implicit_table.c_str(), + explicit_table.empty() ? "ARKODE_ERK_NONE" : explicit_table.c_str()) + != ARK_SUCCESS) { throw BoutException("ARKStepSetTableName failed\n"); } } @@ -266,36 +268,35 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetCFLFraction failed\n"); } - #if SUNDIALS_CONTROLLER_SUPPORT switch (adap_method) { - case 0: - controller = SUNAdaptController_PID(suncontext); - break; - case 1: - controller = SUNAdaptController_PI(suncontext); - break; - case 2: - controller = SUNAdaptController_I(suncontext); - break; - case 3: - controller = SUNAdaptController_ExpGus(suncontext); - break; - case 4: - controller = SUNAdaptController_ImpGus(suncontext); - break; - case 5: - controller = SUNAdaptController_ImExGus(suncontext); - break; - - default: - throw BoutException("Invalid adap_method\n"); + case 0: + controller = SUNAdaptController_PID(suncontext); + break; + case 1: + controller = SUNAdaptController_PI(suncontext); + break; + case 2: + controller = SUNAdaptController_I(suncontext); + break; + case 3: + controller = SUNAdaptController_ExpGus(suncontext); + break; + case 4: + controller = SUNAdaptController_ImpGus(suncontext); + break; + case 5: + controller = SUNAdaptController_ImExGus(suncontext); + break; + + default: + throw BoutException("Invalid adap_method\n"); } if (ARKStepSetAdaptController(arkode_mem, controller) != ARK_SUCCESS) { throw BoutException("ARKStepSetAdaptController failed\n"); } - + if (ARKStepSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) { throw BoutException("ARKStepSetAdaptivityAdjustment failed\n"); } @@ -372,7 +373,6 @@ int ArkodeSolver::init() { nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); if (nonlinear_solver == nullptr) { throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); - } if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { throw BoutException("ARKStepSetNonlinearSolver failed\n"); @@ -380,9 +380,8 @@ int ArkodeSolver::init() { } else { output.write("\tUsing Newton iteration\n"); - const auto prectype = use_precon ? - (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : - SUN_PREC_NONE; + const auto prectype = + use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); @@ -417,27 +416,26 @@ int ArkodeSolver::init() { const auto mudq = (*options)["mudq"] .doc("Upper half-bandwidth to be used in the difference " - "quotient Jacobian approximation") + "quotient Jacobian approximation") .withDefault(band_width_default); const auto mldq = (*options)["mldq"] .doc("Lower half-bandwidth to be used in the difference " - "quotient Jacobian approximation") + "quotient Jacobian approximation") .withDefault(band_width_default); const auto mukeep = (*options)["mukeep"] .doc("Upper half-bandwidth of the retained banded " - "approximate Jacobian block") + "approximate Jacobian block") .withDefault(n3Dvars() + n2Dvars()); const auto mlkeep = (*options)["mlkeep"] .doc("Lower half-bandwidth of the retained banded " - "approximate Jacobian block") + "approximate Jacobian block") .withDefault(n3Dvars() + n2Dvars()); if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, - arkode_bbd_rhs, nullptr) + arkode_bbd_rhs, nullptr) != ARKLS_SUCCESS) { throw BoutException("ARKBBDPrecInit failed\n"); } - } } else { // Not using preconditioning @@ -732,8 +730,8 @@ static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { } /// RHS function for BBD preconditioner -static int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, - void* user_data) { +static int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, + N_Vector du, void* user_data) { return arkode_rhs_implicit(t, u, du, user_data); } diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 68984ebf64..d8f292fade 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -44,9 +44,9 @@ #include "fmt/core.h" #include -#include #include #include +#include #include #include @@ -201,7 +201,7 @@ int CvodeSolver::init() { } const auto lmm = adams_moulton ? CV_ADAMS : CV_BDF; - + cvode_mem = callWithSUNContext(CVodeCreate, suncontext, lmm); if (cvode_mem == nullptr) { throw BoutException("CVodeCreate failed\n"); @@ -321,9 +321,8 @@ int CvodeSolver::init() { output_info.write("\tUsing Newton iteration\n"); TRACE("Setting preconditioner"); - const auto prectype = use_precon ? - (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : - SUN_PREC_NONE; + const auto prectype = + use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); if (sun_solver == nullptr) { throw BoutException("Creating SUNDIALS linear solver failed\n"); @@ -361,7 +360,8 @@ int CvodeSolver::init() { const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars()); if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0.0, - cvode_bbd_rhs, nullptr) != CVLS_SUCCESS) { + cvode_bbd_rhs, nullptr) + != CVLS_SUCCESS) { throw BoutException("CVBBDPrecInit failed\n"); } } diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index a47afaa85a..ebf8633c03 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -40,21 +40,20 @@ #include "bout/unused.hxx" #include -#include #include #include #include +#include #include static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); -static int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, N_Vector rr, - void* user_data); +static int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, + N_Vector rr, void* user_data); static int ida_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data); - IdaSolver::IdaSolver(Options* opts) : Solver(opts), abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)), @@ -197,7 +196,8 @@ int IdaSolver::init() { const auto mukeep = (*options)["mukeep"].withDefault(n3d); const auto mlkeep = (*options)["mlkeep"].withDefault(n3d); if (IDABBDPrecInit(idamem, local_N, mudq, mldq, mukeep, mlkeep, 0.0, ida_bbd_res, - nullptr) != IDALS_SUCCESS) { + nullptr) + != IDALS_SUCCESS) { throw BoutException("IDABBDPrecInit failed\n"); } } From 4ef1ddd95a8c0621d7a0be7e6af06aa78d428286 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 09:46:49 +0100 Subject: [PATCH 353/412] Include header for `BoutReal`; remove unused header --- include/bout/sundials_backports.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx index 19140e2453..4ec334f4d4 100644 --- a/include/bout/sundials_backports.hxx +++ b/include/bout/sundials_backports.hxx @@ -8,6 +8,8 @@ #ifndef BOUT_SUNDIALS_BACKPORTS_H #define BOUT_SUNDIALS_BACKPORTS_H +#include "bout/bout_types.hxx" + #include #include @@ -23,8 +25,6 @@ #include #endif -#include "bout/unused.hxx" - #if SUNDIALS_VERSION_MAJOR < 6 using sundials_real_type = realtype; #else From 35cae4a12cefd633b9a99a8f72f6bf492e4d144c Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 09:56:56 +0100 Subject: [PATCH 354/412] CI: Remove deprecated clang-tidy option --- .clang-tidy | 1 - 1 file changed, 1 deletion(-) diff --git a/.clang-tidy b/.clang-tidy index 6ca5262f41..0117c20e42 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -2,7 +2,6 @@ Checks: 'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters' WarningsAsErrors: '' HeaderFilterRegex: '' -AnalyzeTemporaryDtors: false FormatStyle: file CheckOptions: From c027a638a56b0d5f8d683c0abf3cb26a5a462f87 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 10:00:36 +0100 Subject: [PATCH 355/412] Move some static functions to anonymous namespace --- src/solver/impls/arkode/arkode.cxx | 28 ++++++++++++++++------------ src/solver/impls/cvode/cvode.cxx | 20 ++++++++++++-------- src/solver/impls/ida/ida.cxx | 17 +++++++++++------ 3 files changed, 39 insertions(+), 26 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index e639dfca1d..e6a076dac7 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -51,17 +51,19 @@ class Field2D; -static int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); +namespace { +int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); +int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); +int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int arkode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, +int arkode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, +int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int lr, void* user_data); -static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, +int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); +} ArkodeSolver::ArkodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] @@ -681,7 +683,8 @@ void ArkodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* J * ARKODE explicit RHS functions **************************************************************************/ -static int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { +namespace { +int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); BoutReal* dudata = N_VGetArrayPointer(du); @@ -697,7 +700,7 @@ static int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_d return 0; } -static int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { +int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); BoutReal* dudata = N_VGetArrayPointer(du); @@ -713,7 +716,7 @@ static int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_d return 0; } -static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { +int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); BoutReal* dudata = N_VGetArrayPointer(du); @@ -730,13 +733,13 @@ static int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { } /// RHS function for BBD preconditioner -static int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, +int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, void* user_data) { return arkode_rhs_implicit(t, u, du, user_data); } /// Preconditioner function -static int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, +int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) { BoutReal* udata = N_VGetArrayPointer(yy); @@ -752,7 +755,7 @@ static int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rve } /// Jacobian-vector multiplication function -static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, +int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { BoutReal* ydata = N_VGetArrayPointer(y); ///< System state BoutReal* vdata = N_VGetArrayPointer(v); ///< Input vector @@ -764,6 +767,7 @@ static int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, return 0; } +} /************************************************************************** * vector abstol functions diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index d8f292fade..375575df5c 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -57,15 +57,17 @@ class Field2D; BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative, non_positive); -static int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int cvode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, +namespace { +int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); +int cvode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, void* user_data); -static int cvode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, +int cvode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int lr, void* user_data); -static int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, +int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); +} CvodeSolver::CvodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] @@ -649,7 +651,8 @@ void CvodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jv * CVODE RHS functions **************************************************************************/ -static int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { +namespace { +int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); BoutReal* dudata = N_VGetArrayPointer(du); @@ -666,13 +669,13 @@ static int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { } /// RHS function for BBD preconditioner -static int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, +int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, void* user_data) { return cvode_rhs(t, u, du, user_data); } /// Preconditioner function -static int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, +int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) { BoutReal* udata = N_VGetArrayPointer(yy); @@ -688,7 +691,7 @@ static int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec } /// Jacobian-vector multiplication function -static int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), +int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { BoutReal* ydata = N_VGetArrayPointer(y); ///< System state BoutReal* vdata = N_VGetArrayPointer(v); ///< Input vector @@ -700,6 +703,7 @@ static int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector U return 0; } +} /************************************************************************** * CVODE vector option functions diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index ebf8633c03..a115006ae2 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -47,12 +47,15 @@ #include -static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); -static int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, +namespace { +int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); +int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); -static int ida_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector rvec, +int ida_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data); +} + IdaSolver::IdaSolver(Options* opts) : Solver(opts), @@ -333,7 +336,8 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, * IDA res function **************************************************************************/ -static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { +namespace { +int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); BoutReal* dudata = N_VGetArrayPointer(du); BoutReal* rdata = N_VGetArrayPointer(rr); @@ -347,13 +351,13 @@ static int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_d } /// Residual function for BBD preconditioner -static int ida_bbd_res(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, +int ida_bbd_res(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { return idares(t, u, du, rr, user_data); } // Preconditioner function -static int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr), +int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr), N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data) { BoutReal* udata = N_VGetArrayPointer(yy); @@ -367,5 +371,6 @@ static int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED return 0; } +} #endif From 5a0a311f7d556ee0867e68d9062659cb36c57665 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 10:00:59 +0100 Subject: [PATCH 356/412] CI: Suppress some warnings about short identifiers --- src/solver/impls/arkode/arkode.cxx | 4 ++++ src/solver/impls/cvode/cvode.cxx | 4 ++++ src/solver/impls/ida/ida.cxx | 5 ++++- 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index e6a076dac7..e71138fce4 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -51,6 +51,7 @@ class Field2D; +// NOLINTBEGIN(readability-identifier-length) namespace { int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); @@ -64,6 +65,7 @@ int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zve int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); } +// NOLINTEND(readability-identifier-length) ArkodeSolver::ArkodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] @@ -683,6 +685,7 @@ void ArkodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* J * ARKODE explicit RHS functions **************************************************************************/ +// NOLINTBEGIN(readability-identifier-length) namespace { int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) { @@ -768,6 +771,7 @@ int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, return 0; } } +// NOLINTEND(readability-identifier-length) /************************************************************************** * vector abstol functions diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 375575df5c..862b71f4e5 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -57,6 +57,7 @@ class Field2D; BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative, non_positive); +// NOLINTBEGIN(readability-identifier-length) namespace { int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); int cvode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, @@ -68,6 +69,7 @@ int cvode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, void* user_data, N_Vector tmp); } +// NOLINTEND(readability-identifier-length) CvodeSolver::CvodeSolver(Options* opts) : Solver(opts), diagnose((*options)["diagnose"] @@ -651,6 +653,7 @@ void CvodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jv * CVODE RHS functions **************************************************************************/ +// NOLINTBEGIN(readability-identifier-length) namespace { int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { @@ -704,6 +707,7 @@ int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(f return 0; } } +// NOLINTEND(readability-identifier-length) /************************************************************************** * CVODE vector option functions diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index a115006ae2..0d8b8391ce 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -47,6 +47,7 @@ #include +// NOLINTBEGIN(readability-identifier-length) namespace { int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, @@ -55,7 +56,7 @@ int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, int ida_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data); } - +// NOLINTEND(readability-identifier-length) IdaSolver::IdaSolver(Options* opts) : Solver(opts), @@ -336,6 +337,7 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, * IDA res function **************************************************************************/ +// NOLINTBEGIN(readability-identifier-length) namespace { int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); @@ -372,5 +374,6 @@ int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr), return 0; } } +// NOLINTEND(readability-identifier-length) #endif From 4ed2164a501c8a3f1cc1d18a5e48321b27988b92 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 10:15:30 +0100 Subject: [PATCH 357/412] Make a couple of implicit casts explicit --- src/solver/impls/cvode/cvode.cxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 862b71f4e5..b66b4c8fb4 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -226,7 +226,7 @@ int CvodeSolver::init() { } } - if (CVodeSetStabLimDet(cvode_mem, stablimdet) != CV_SUCCESS) { + if (CVodeSetStabLimDet(cvode_mem, static_cast(stablimdet)) != CV_SUCCESS) { throw BoutException("CVodeSetStabLimDet failed\n"); } @@ -318,7 +318,7 @@ int CvodeSolver::init() { throw BoutException("SUNNonlinSol_FixedPoint failed\n"); } - if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver)) { + if (CVodeSetNonlinearSolver(cvode_mem, nonlinear_solver) != 0) { throw BoutException("CVodeSetNonlinearSolver failed\n"); } } else { From 84db34d861e9b547b7cd4e7cb20e966b07203bb1 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 10:15:59 +0100 Subject: [PATCH 358/412] Fix some short identifiers --- src/solver/impls/arkode/arkode.cxx | 8 ++++---- src/solver/impls/cvode/cvode.cxx | 4 ++-- src/solver/impls/ida/ida.cxx | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index e71138fce4..42af78ead1 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -413,9 +413,9 @@ int ArkodeSolver::init() { // int MXSUB = mesh->xend - mesh->xstart + 1; // int band_width_default = n3Dvars()*(MXSUB+2); const int band_width_default = std::accumulate( - begin(f3d), end(f3d), 0, [](int a, const VarStr& fvar) { + begin(f3d), end(f3d), 0, [](int acc, const VarStr& fvar) { Mesh* localmesh = fvar.var->getMesh(); - return a + localmesh->xend - localmesh->xstart + 3; + return acc + localmesh->xend - localmesh->xstart + 3; }); const auto mudq = (*options)["mudq"] @@ -637,8 +637,8 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* uda if (!hasPreconditioner()) { // Identity (but should never happen) - const int N = N_VGetLocalLength_Parallel(uvec); - std::copy(rvec, rvec + N, zvec); + const auto length = N_VGetLocalLength_Parallel(uvec); + std::copy(rvec, rvec + length, zvec); return; } diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index b66b4c8fb4..197837cd4f 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -600,11 +600,11 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udat BoutReal tstart = bout::globals::mpi->MPI_Wtime(); - int N = N_VGetLocalLength_Parallel(uvec); + const auto length = N_VGetLocalLength_Parallel(uvec); if (!hasPreconditioner()) { // Identity (but should never happen) - for (int i = 0; i < N; i++) { + for (int i = 0; i < length; i++) { zvec[i] = rvec[i]; } return; diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 0d8b8391ce..9fcbfa3d69 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -292,9 +292,9 @@ void IdaSolver::res(BoutReal t, BoutReal* udata, BoutReal* dudata, BoutReal* rda save_derivs(rdata); // If a differential equation, subtract dudata - const auto N = N_VGetLocalLength_Parallel(id); + const auto length = N_VGetLocalLength_Parallel(id); const BoutReal* idd = N_VGetArrayPointer(id); - for (int i = 0; i < N; i++) { + for (int i = 0; i < length; i++) { if (idd[i] > 0.5) { // 1 -> differential, 0 -> algebraic rdata[i] -= dudata[i]; } @@ -313,8 +313,8 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, if (!hasPreconditioner()) { // Identity (but should never happen) - const int N = N_VGetLocalLength_Parallel(id); - std::copy(rvec, rvec + N, zvec); + const auto length = N_VGetLocalLength_Parallel(id); + std::copy(rvec, rvec + length, zvec); return; } From 9436af84e57ce44bb8d0b1ba6b7828594f79d279 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 8 Apr 2024 10:16:43 +0100 Subject: [PATCH 359/412] Silence warning about assignment in `if` statement Yes, I know it's fine --- src/solver/impls/ida/ida.cxx | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 9fcbfa3d69..9dff394093 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -118,10 +118,12 @@ int IdaSolver::init() { if (uvec == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } - if ((duvec = N_VClone(uvec)) == nullptr) { + duvec = N_VClone(uvec); + if (duvec == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } - if ((id = N_VClone(uvec)) == nullptr) { + id = N_VClone(uvec); + if (id == nullptr) { throw BoutException("SUNDIALS memory allocation failed\n"); } From 2c0c60daac276ea36c5597874da2c82c7d1e7785 Mon Sep 17 00:00:00 2001 From: ZedThree Date: Mon, 8 Apr 2024 09:18:05 +0000 Subject: [PATCH 360/412] Apply clang-format changes --- src/solver/impls/arkode/arkode.cxx | 23 +++++++++++------------ src/solver/impls/cvode/cvode.cxx | 19 +++++++++---------- src/solver/impls/ida/ida.cxx | 15 +++++++-------- 3 files changed, 27 insertions(+), 30 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 42af78ead1..bc3be6f80a 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -58,13 +58,13 @@ int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data); int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); int arkode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, - void* user_data); + void* user_data); int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, - BoutReal gamma, BoutReal delta, int lr, void* user_data); + BoutReal gamma, BoutReal delta, int lr, void* user_data); int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, - void* user_data, N_Vector tmp); -} + void* user_data, N_Vector tmp); +} // namespace // NOLINTEND(readability-identifier-length) ArkodeSolver::ArkodeSolver(Options* opts) @@ -736,15 +736,14 @@ int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { } /// RHS function for BBD preconditioner -int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, - N_Vector du, void* user_data) { +int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, + void* user_data) { return arkode_rhs_implicit(t, u, du, user_data); } /// Preconditioner function -int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, - N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr), - void* user_data) { +int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec, + BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) { BoutReal* udata = N_VGetArrayPointer(yy); BoutReal* rdata = N_VGetArrayPointer(rvec); BoutReal* zdata = N_VGetArrayPointer(zvec); @@ -758,8 +757,8 @@ int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, } /// Jacobian-vector multiplication function -int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, - N_Vector UNUSED(fy), void* user_data, N_Vector UNUSED(tmp)) { +int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), + void* user_data, N_Vector UNUSED(tmp)) { BoutReal* ydata = N_VGetArrayPointer(y); ///< System state BoutReal* vdata = N_VGetArrayPointer(v); ///< Input vector BoutReal* Jvdata = N_VGetArrayPointer(Jv); ///< Jacobian*vector output @@ -770,7 +769,7 @@ int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, return 0; } -} +} // namespace // NOLINTEND(readability-identifier-length) /************************************************************************** diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 197837cd4f..22f7f154f7 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -61,14 +61,14 @@ BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative, namespace { int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); int cvode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, - void* user_data); + void* user_data); int cvode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec, - BoutReal gamma, BoutReal delta, int lr, void* user_data); + BoutReal gamma, BoutReal delta, int lr, void* user_data); int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy, - void* user_data, N_Vector tmp); -} + void* user_data, N_Vector tmp); +} // namespace // NOLINTEND(readability-identifier-length) CvodeSolver::CvodeSolver(Options* opts) @@ -673,14 +673,13 @@ int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { /// RHS function for BBD preconditioner int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, - void* user_data) { + void* user_data) { return cvode_rhs(t, u, du, user_data); } /// Preconditioner function -int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, - N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr), - void* user_data) { +int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec, + BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) { BoutReal* udata = N_VGetArrayPointer(yy); BoutReal* rdata = N_VGetArrayPointer(rvec); BoutReal* zdata = N_VGetArrayPointer(zvec); @@ -695,7 +694,7 @@ int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, /// Jacobian-vector multiplication function int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy), - void* user_data, N_Vector UNUSED(tmp)) { + void* user_data, N_Vector UNUSED(tmp)) { BoutReal* ydata = N_VGetArrayPointer(y); ///< System state BoutReal* vdata = N_VGetArrayPointer(v); ///< Input vector BoutReal* Jvdata = N_VGetArrayPointer(Jv); ///< Jacobian*vector output @@ -706,7 +705,7 @@ int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(f return 0; } -} +} // namespace // NOLINTEND(readability-identifier-length) /************************************************************************** diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx index 9dff394093..cfc978f755 100644 --- a/src/solver/impls/ida/ida.cxx +++ b/src/solver/impls/ida/ida.cxx @@ -50,12 +50,12 @@ // NOLINTBEGIN(readability-identifier-length) namespace { int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data); -int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, - N_Vector rr, void* user_data); +int ida_bbd_res(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, N_Vector rr, + void* user_data); int ida_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector rvec, - N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data); -} + N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data); +} // namespace // NOLINTEND(readability-identifier-length) IdaSolver::IdaSolver(Options* opts) @@ -356,14 +356,13 @@ int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) { /// Residual function for BBD preconditioner int ida_bbd_res(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, - N_Vector rr, void* user_data) { + N_Vector rr, void* user_data) { return idares(t, u, du, rr, user_data); } // Preconditioner function int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr), - N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, - void* user_data) { + N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data) { BoutReal* udata = N_VGetArrayPointer(yy); BoutReal* rdata = N_VGetArrayPointer(rvec); BoutReal* zdata = N_VGetArrayPointer(zvec); @@ -375,7 +374,7 @@ int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr), return 0; } -} +} // namespace // NOLINTEND(readability-identifier-length) #endif From 394491383b8854f2f32a3fc8c961d58d2d3226e5 Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 9 Apr 2024 14:32:14 +0200 Subject: [PATCH 361/412] Update tests/unit/test_extras.hxx --- tests/unit/test_extras.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx index 3415b239be..700b977ac8 100644 --- a/tests/unit/test_extras.hxx +++ b/tests/unit/test_extras.hxx @@ -234,7 +234,7 @@ public: void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); } std::vector getBoundaries() override { return boundaries; } std::vector> - getBoundariesPar(BoundaryParType) override { + getBoundariesPar(BoundaryParType UNUSED(type)) override { return std::vector>(); } BoutReal GlobalX(int jx) const override { return jx; } From 33c22849f0605ea2fd7b71f9fc898a259595817b Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 22 Apr 2024 12:03:15 +0200 Subject: [PATCH 362/412] Prefer ADIOS2 over ADIOS in more cases Using ADIOS was confusing, as can be seen that the test got it wrong. --- .github/workflows/tests.yml | 2 +- CMakeLists.txt | 2 +- bin/bout-config.in | 24 +++++++++---------- bout++Config.cmake.in | 2 +- cmake/SetupBOUTThirdParty.cmake | 14 +++++------ cmake_build_defines.hxx.in | 2 +- include/bout/adios_object.hxx | 4 ++-- include/bout/build_config.hxx | 2 +- include/bout/options_io.hxx | 2 +- manual/sphinx/user_docs/adios2.rst | 6 ++--- manual/sphinx/user_docs/installing.rst | 2 +- src/bout++.cxx | 8 +++---- src/sys/adios_object.cxx | 4 ++-- src/sys/options/options_adios.cxx | 4 ++-- src/sys/options/options_adios.hxx | 4 ++-- .../test-options-adios/CMakeLists.txt | 2 +- tests/integrated/test-options-adios/runtest | 2 +- 17 files changed, 43 insertions(+), 43 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 42965e75e8..bdaeb3dc4f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -39,7 +39,7 @@ jobs: is_cron: - ${{ github.event_name == 'cron' }} config: - - name: "CMake, PETSc unreleased, ADIOS" + - name: "CMake, PETSc unreleased, ADIOS2" os: ubuntu-20.04 cmake_options: "-DBUILD_SHARED_LIBS=ON -DBOUT_ENABLE_METRIC_3D=ON diff --git a/CMakeLists.txt b/CMakeLists.txt index c1c82ea4e3..f57a78a14a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -935,7 +935,7 @@ message(" SUNDIALS support : ${BOUT_HAS_SUNDIALS} HYPRE support : ${BOUT_HAS_HYPRE} NetCDF support : ${BOUT_HAS_NETCDF} - ADIOS support : ${BOUT_HAS_ADIOS} + ADIOS2 support : ${BOUT_HAS_ADIOS2} FFTW support : ${BOUT_HAS_FFTW} LAPACK support : ${BOUT_HAS_LAPACK} OpenMP support : ${BOUT_USE_OPENMP} diff --git a/bin/bout-config.in b/bin/bout-config.in index fa19779cfe..b5a62a42eb 100755 --- a/bin/bout-config.in +++ b/bin/bout-config.in @@ -29,7 +29,7 @@ idlpath="@IDLCONFIGPATH@" pythonpath="@PYTHONCONFIGPATH@" has_netcdf="@BOUT_HAS_NETCDF@" -has_adios="@BOUT_HAS_ADIOS@" +has_adios2="@BOUT_HAS_ADIOS2@" has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@" has_pnetcdf="@BOUT_HAS_PNETCDF@" has_pvode="@BOUT_HAS_PVODE@" @@ -71,18 +71,18 @@ Available values for OPTION include: --idl IDL path --python Python path - --has-netcdf NetCDF file support - --has-adios ADIOS file support + --has-netcdf NetCDF file support + --has-adios2 ADIOS2 file support --has-legacy-netcdf Legacy NetCDF file support - --has-pnetcdf Parallel NetCDF file support - --has-pvode PVODE solver support - --has-cvode SUNDIALS CVODE solver support - --has-ida SUNDIALS IDA solver support - --has-lapack LAPACK support - --has-petsc PETSc support - --has-hypre Hypre support - --has-slepc SLEPc support - --has-nls Natural Language Support + --has-pnetcdf Parallel NetCDF file support + --has-pvode PVODE solver support + --has-cvode SUNDIALS CVODE solver support + --has-ida SUNDIALS IDA solver support + --has-lapack LAPACK support + --has-petsc PETSc support + --has-hypre Hypre support + --has-slepc SLEPc support + --has-nls Natural Language Support --petsc-has-sundials diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in index 3d824e455f..5af0dc43ea 100644 --- a/bout++Config.cmake.in +++ b/bout++Config.cmake.in @@ -15,7 +15,7 @@ set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@) set(BOUT_HAS_PVODE @BOUT_HAS_PVODE@) set(BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@) -set(BOUT_HAS_ADIOS @BOUT_HAS_ADIOS@) +set(BOUT_HAS_ADIOS2 @BOUT_HAS_ADIOS2@) set(BOUT_HAS_FFTW @BOUT_HAS_FFTW@) set(BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@) set(BOUT_HAS_PETSC @BOUT_HAS_PETSC@) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 83f8a52e85..127fbda765 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -190,10 +190,10 @@ endif() message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}") set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF}) -option(BOUT_USE_ADIOS "Enable support for ADIOS output" ON) -option(BOUT_DOWNLOAD_ADIOS "Download and build ADIOS2" OFF) -if (BOUT_USE_ADIOS) - if (BOUT_DOWNLOAD_ADIOS) +option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" ON) +option(BOUT_DOWNLOAD_ADIOS2 "Download and build ADIOS2" OFF) +if (BOUT_USE_ADIOS2) + if (BOUT_DOWNLOAD_ADIOS2) message(STATUS "Downloading and configuring ADIOS2") include(FetchContent) FetchContent_Declare( @@ -220,12 +220,12 @@ if (BOUT_USE_ADIOS) find_package(MPI REQUIRED COMPONENTS C) target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C) else() - set(BOUT_USE_ADIOS OFF) + set(BOUT_USE_ADIOS2 OFF) endif() endif() endif() -message(STATUS "ADIOS support: ${BOUT_USE_ADIOS}") -set(BOUT_HAS_ADIOS ${BOUT_USE_ADIOS}) +message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}") +set(BOUT_HAS_ADIOS2 ${BOUT_USE_ADIOS2}) option(BOUT_USE_FFTW "Enable support for FFTW" ON) diff --git a/cmake_build_defines.hxx.in b/cmake_build_defines.hxx.in index ed6e8685f6..4d63a01b7d 100644 --- a/cmake_build_defines.hxx.in +++ b/cmake_build_defines.hxx.in @@ -13,7 +13,7 @@ #cmakedefine01 BOUT_HAS_IDA #cmakedefine01 BOUT_HAS_LAPACK #cmakedefine01 BOUT_HAS_NETCDF -#cmakedefine01 BOUT_HAS_ADIOS +#cmakedefine01 BOUT_HAS_ADIOS2 #cmakedefine01 BOUT_HAS_PETSC #cmakedefine01 BOUT_HAS_PRETTY_FUNCTION #cmakedefine01 BOUT_HAS_PVODE diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx index 9d2f545b46..4750930373 100755 --- a/include/bout/adios_object.hxx +++ b/include/bout/adios_object.hxx @@ -14,7 +14,7 @@ #include "bout/build_config.hxx" -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS2 #include #include @@ -79,5 +79,5 @@ void ADIOSSetParameters(const std::string& input, const char delimKeyValue, } // namespace bout -#endif //BOUT_HAS_ADIOS +#endif //BOUT_HAS_ADIOS2 #endif //ADIOS_OBJECT_HXX diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx index c97962f7cf..08158d00e9 100644 --- a/include/bout/build_config.hxx +++ b/include/bout/build_config.hxx @@ -17,7 +17,7 @@ constexpr auto has_gettext = static_cast(BOUT_HAS_GETTEXT); constexpr auto has_lapack = static_cast(BOUT_HAS_LAPACK); constexpr auto has_legacy_netcdf = static_cast(BOUT_HAS_LEGACY_NETCDF); constexpr auto has_netcdf = static_cast(BOUT_HAS_NETCDF); -constexpr auto has_adios = static_cast(BOUT_HAS_ADIOS); +constexpr auto has_adios2 = static_cast(BOUT_HAS_ADIOS2); constexpr auto has_petsc = static_cast(BOUT_HAS_PETSC); constexpr auto has_hypre = static_cast(BOUT_HAS_HYPRE); constexpr auto has_umpire = static_cast(BOUT_HAS_UMPIRE); diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx index 4c70159514..57be8bbaae 100644 --- a/include/bout/options_io.hxx +++ b/include/bout/options_io.hxx @@ -111,7 +111,7 @@ public: static constexpr auto default_type = #if BOUT_HAS_NETCDF "netcdf"; -#elif BOUT_HAS_ADIOS +#elif BOUT_HAS_ADIOS2 "adios"; #else "invalid"; diff --git a/manual/sphinx/user_docs/adios2.rst b/manual/sphinx/user_docs/adios2.rst index 8a6228cd3a..d8e0135c0d 100644 --- a/manual/sphinx/user_docs/adios2.rst +++ b/manual/sphinx/user_docs/adios2.rst @@ -11,14 +11,14 @@ Installation The easiest way to configure BOUT++ with ADIOS2 is to tell CMake to download and build it with this flag:: - -DBOUT_DOWNLOAD_ADIOS=ON + -DBOUT_DOWNLOAD_ADIOS2=ON The ``master`` branch will be downloaded from `Github `_, configured and built with BOUT++. -Alternatively, if ADIOS is already installed then the following flags can be used:: +Alternatively, if ADIOS2 is already installed then the following flags can be used:: - -DBOUT_USE_ADIOS=ON -DADIOS2_ROOT=/path/to/adios2 + -DBOUT_USE_ADIOS2=ON -DADIOS2_ROOT=/path/to/adios2 Output files ------------ diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst index eb155909bf..10f5d9b9f1 100644 --- a/manual/sphinx/user_docs/installing.rst +++ b/manual/sphinx/user_docs/installing.rst @@ -373,7 +373,7 @@ For SUNDIALS, use ``-DBOUT_DOWNLOAD_SUNDIALS=ON``. If using ``ccmake`` this opti may not appear initially. This automatically sets ``BOUT_USE_SUNDIALS=ON``, and configures SUNDIALS to use MPI. -For ADIOS2, use ``-DBOUT_DOWNLOAD_ADIOS=ON``. This will download and +For ADIOS2, use ``-DBOUT_DOWNLOAD_ADIOS2=ON``. This will download and configure `ADIOS2 `_, enabling BOUT++ to read and write this high-performance parallel file format. diff --git a/src/bout++.cxx b/src/bout++.cxx index a83e278d9c..7fc53bac8a 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -59,7 +59,7 @@ const char DEFAULT_DIR[] = "data"; #include "bout/bout.hxx" #undef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS2 #include "bout/adios_object.hxx" #endif @@ -165,7 +165,7 @@ int BoutInitialise(int& argc, char**& argv) { savePIDtoFile(args.data_dir, MYPE); -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS2 bout::ADIOSInit(BoutComm::get()); #endif @@ -572,7 +572,7 @@ void printCompileTimeOptions() { constexpr auto netcdf_flavour = has_netcdf ? (has_legacy_netcdf ? " (Legacy)" : " (NetCDF4)") : ""; output_info.write(_("\tNetCDF support {}{}\n"), is_enabled(has_netcdf), netcdf_flavour); - output_info.write(_("\tADIOS support {}\n"), is_enabled(has_adios)); + output_info.write(_("\tADIOS2 support {}\n"), is_enabled(has_adios2)); output_info.write(_("\tPETSc support {}\n"), is_enabled(has_petsc)); output_info.write(_("\tPretty function name support {}\n"), is_enabled(has_pretty_function)); @@ -795,7 +795,7 @@ int BoutFinalise(bool write_settings) { // Call HYPER_Finalize if not already called bout::HypreLib::cleanup(); -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS2 bout::ADIOSFinalize(); #endif diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx index c7d6dab9aa..477dae14ef 100644 --- a/src/sys/adios_object.cxx +++ b/src/sys/adios_object.cxx @@ -1,6 +1,6 @@ #include "bout/build_config.hxx" -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS2 #include "bout/adios_object.hxx" #include "bout/boutexception.hxx" @@ -95,4 +95,4 @@ void ADIOSSetParameters(const std::string& input, const char delimKeyValue, } } // namespace bout -#endif //BOUT_HAS_ADIOS +#endif //BOUT_HAS_ADIOS2 diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx index b313d7bc79..88df92df04 100644 --- a/src/sys/options/options_adios.cxx +++ b/src/sys/options/options_adios.cxx @@ -1,6 +1,6 @@ #include "bout/build_config.hxx" -#if BOUT_HAS_ADIOS +#if BOUT_HAS_ADIOS2 #include "options_adios.hxx" #include "bout/adios_object.hxx" @@ -628,4 +628,4 @@ void OptionsADIOS::write(const Options& options, const std::string& time_dim) { } // namespace bout -#endif // BOUT_HAS_ADIOS +#endif // BOUT_HAS_ADIOS2 diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx index eddb3976ff..a942e6fed9 100644 --- a/src/sys/options/options_adios.hxx +++ b/src/sys/options/options_adios.hxx @@ -8,7 +8,7 @@ #include "bout/options.hxx" #include "bout/options_io.hxx" -#if !BOUT_HAS_ADIOS +#if !BOUT_HAS_ADIOS2 namespace { bout::RegisterUnavailableOptionsIO @@ -79,5 +79,5 @@ RegisterOptionsIO registeroptionsadios("adios"); } // namespace bout -#endif // BOUT_HAS_ADIOS +#endif // BOUT_HAS_ADIOS2 #endif // OPTIONS_ADIOS_H diff --git a/tests/integrated/test-options-adios/CMakeLists.txt b/tests/integrated/test-options-adios/CMakeLists.txt index 110773d6fd..cc61fabe57 100644 --- a/tests/integrated/test-options-adios/CMakeLists.txt +++ b/tests/integrated/test-options-adios/CMakeLists.txt @@ -2,5 +2,5 @@ bout_add_integrated_test(test-options-adios SOURCES test-options-adios.cxx USE_RUNTEST USE_DATA_BOUT_INP - REQUIRES BOUT_HAS_ADIOS + REQUIRES BOUT_HAS_ADIOS2 ) diff --git a/tests/integrated/test-options-adios/runtest b/tests/integrated/test-options-adios/runtest index 1621c686a3..03a83fc0ba 100755 --- a/tests/integrated/test-options-adios/runtest +++ b/tests/integrated/test-options-adios/runtest @@ -34,7 +34,7 @@ assert result["int"] == 42 assert math.isclose(result["real"], 3.1415) assert result["string"] == "hello" -print("Checking saved ADIOS test-out file -- Not implemented") +print("Checking saved ADIOS2 test-out file -- Not implemented") # Check the output NetCDF file # with DataFile("test-out.nc") as f: From 0589919d026c8cfc205f057a526259e58a57fad3 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 22 Apr 2024 12:06:41 +0200 Subject: [PATCH 363/412] Fix missed adios --- src/bout++.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/bout++.cxx b/src/bout++.cxx index 7fc53bac8a..ff25b1163e 100644 --- a/src/bout++.cxx +++ b/src/bout++.cxx @@ -698,7 +698,7 @@ void addBuildFlagsToOptions(Options& options) { options["has_gettext"].force(bout::build::has_gettext); options["has_lapack"].force(bout::build::has_lapack); options["has_netcdf"].force(bout::build::has_netcdf); - options["has_adios"].force(bout::build::has_adios); + options["has_adios2"].force(bout::build::has_adios2); options["has_petsc"].force(bout::build::has_petsc); options["has_hypre"].force(bout::build::has_hypre); options["has_umpire"].force(bout::build::has_umpire); From 7db76aabbe5e614bf45e6c810bd57190e9df30c6 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 24 Apr 2024 14:19:36 -0700 Subject: [PATCH 364/412] Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- src/mesh/parallel/fci.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 6e9638d849..f226b9c40b 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -103,8 +103,8 @@ public: ASSERT0(mesh.ystart == 1); BoundaryRegionPar* bndries[]{forward_boundary_xin, forward_boundary_xout, backward_boundary_xin, backward_boundary_xout}; - for (auto bndry : bndries) { - for (auto bndry2 : bndries) { + for (auto *bndry : bndries) { + for (auto *bndry2 : bndries) { if (bndry->dir == bndry2->dir) { continue; } From f8a94bf7c62e6b0f564899276f7b550dfa71374e Mon Sep 17 00:00:00 2001 From: bendudson Date: Wed, 24 Apr 2024 21:20:07 +0000 Subject: [PATCH 365/412] Apply clang-format changes --- src/mesh/parallel/fci.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index f226b9c40b..bd18f92fd6 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -103,8 +103,8 @@ public: ASSERT0(mesh.ystart == 1); BoundaryRegionPar* bndries[]{forward_boundary_xin, forward_boundary_xout, backward_boundary_xin, backward_boundary_xout}; - for (auto *bndry : bndries) { - for (auto *bndry2 : bndries) { + for (auto* bndry : bndries) { + for (auto* bndry2 : bndries) { if (bndry->dir == bndry2->dir) { continue; } From d99183eacb279c83d8191866d4efc160142f18ae Mon Sep 17 00:00:00 2001 From: dschwoerer Date: Mon, 29 Apr 2024 08:24:14 +0000 Subject: [PATCH 366/412] Apply clang-format changes --- src/mesh/parallel/fci.hxx | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx index 6837702496..3ec3321a6a 100644 --- a/src/mesh/parallel/fci.hxx +++ b/src/mesh/parallel/fci.hxx @@ -101,8 +101,9 @@ public: backward_boundary_xout, zperiodic); } ASSERT0(mesh.ystart == 1); - std::shared_ptr bndries[]{forward_boundary_xin, forward_boundary_xout, - backward_boundary_xin, backward_boundary_xout}; + std::shared_ptr bndries[]{ + forward_boundary_xin, forward_boundary_xout, backward_boundary_xin, + backward_boundary_xout}; for (auto& bndry : bndries) { for (const auto& bndry2 : bndries) { if (bndry->dir == bndry2->dir) { From f68950c937c5df77de06fe6d9031d13c0de57b02 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Mon, 20 May 2024 09:57:31 -0700 Subject: [PATCH 367/412] invert_laplace: Fix outer boundary metrics Was using metric tensors at wrong cell index when NXPE > 1. Only matters when setting boundaries to specific gradients. --- src/invert/laplace/invert_laplace.cxx | 32 +++++++++++++-------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index 505b04cc4f..017c35e1b5 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -668,10 +668,10 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco && (outer_boundary_flags & INVERT_SET || outer_boundary_flags & INVERT_RHS)) { // Zero gradient at outer boundary for (int ix = 0; ix < outbndry; ix++) { - avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) - / coords->dx(ncx - ix, jy); - bvec[ncx - ix] = dcomplex(1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) - / coords->dx(ncx - ix, jy); + avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(xe - ix, jy)) + / coords->dx(xe - ix, jy); + bvec[ncx - ix] = dcomplex(1., 0.) / sqrt(coords->g_11(xe - ix, jy)) + / coords->dx(xe - ix, jy); cvec[ncx - ix] = dcomplex(0., 0.); } } else if (outer_boundary_flags & INVERT_DC_GRAD) { @@ -681,19 +681,19 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco bvec[ncx - ix] = dcomplex(-1., 0.); cvec[ncx - ix] = dcomplex(0., 0.); } - } else if (inner_boundary_flags & INVERT_DC_GRADPAR) { + } else if (outer_boundary_flags & INVERT_DC_GRADPAR) { for (int ix = 0; ix < inbndry; ix++) { - avec[ncx - ix] = 1.0 / sqrt(coords->g_22(ncx - ix + 1, jy)); - bvec[ncx - ix] = -1.0 / sqrt(coords->g_22(ncx - ix, jy)); + avec[ncx - ix] = 1.0 / sqrt(coords->g_22(xe - ix - 1, jy)); + bvec[ncx - ix] = -1.0 / sqrt(coords->g_22(xe - ix, jy)); cvec[ncx - ix] = 0.0; } - } else if (inner_boundary_flags & INVERT_DC_GRADPARINV) { + } else if (outer_boundary_flags & INVERT_DC_GRADPARINV) { for (int ix = 0; ix < inbndry; ix++) { - avec[ncx - ix] = sqrt(coords->g_22(ncx - ix - 1, jy)); - bvec[ncx - ix] = -sqrt(coords->g_22(ncx - ix, jy)); + avec[ncx - ix] = sqrt(coords->g_22(xe - ix - 1, jy)); + bvec[ncx - ix] = -sqrt(coords->g_22(xe - ix, jy)); cvec[ncx - ix] = 0.0; } - } else if (inner_boundary_flags & INVERT_DC_LAP) { + } else if (outer_boundary_flags & INVERT_DC_LAP) { // Decaying boundary conditions BoutReal k = 0.0; if (a != nullptr) { @@ -707,7 +707,7 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco cvec[ncx - ix] = 0.; bvec[ncx - ix] = 1.; avec[ncx - ix] = - -exp(-k * coords->dx(ncx - ix, jy) / sqrt(coords->g11(ncx - ix, jy))); + -exp(-k * coords->dx(xe - ix, jy) / sqrt(coords->g11(xe - ix, jy))); } } else { // Order 2 dirichlet BC (boundary half between points) @@ -726,10 +726,10 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco && (outer_boundary_flags & INVERT_SET || outer_boundary_flags & INVERT_RHS)) { // Zero gradient at outer boundary for (int ix = 0; ix < outbndry; ix++) { - avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) - / coords->dx(ncx - ix, jy); - bvec[ncx - ix] = dcomplex(1., 0.) / sqrt(coords->g_11(ncx - ix, jy)) - / coords->dx(ncx - ix, jy); + avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(xe - ix, jy)) + / coords->dx(xe - ix, jy); + bvec[ncx - ix] = dcomplex(1., 0.) / sqrt(coords->g_11(xe - ix, jy)) + / coords->dx(xe - ix, jy); cvec[ncx - ix] = dcomplex(0., 0.); } } else if (outer_boundary_flags & INVERT_AC_GRAD) { From 863abe8e0fbe2cbb39d453f5330506e38cff0c50 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 23 May 2024 17:55:27 +0100 Subject: [PATCH 368/412] Add methods to `Laplacian` for checking if flags are set --- include/bout/invert_laplace.hxx | 11 ++++ .../laplace/impls/cyclic/cyclic_laplace.cxx | 34 +++++------ .../laplace/impls/hypre3d/hypre3d_laplace.cxx | 12 ++-- .../iterative_parallel_tri.hxx | 8 --- .../impls/multigrid/multigrid_laplace.cxx | 43 +++++++------ .../laplace/impls/naulin/naulin_laplace.cxx | 2 +- src/invert/laplace/impls/pcr/pcr.cxx | 36 +++++------ src/invert/laplace/impls/pcr/pcr.hxx | 8 --- .../laplace/impls/pcr_thomas/pcr_thomas.cxx | 36 +++++------ .../laplace/impls/pcr_thomas/pcr_thomas.hxx | 8 --- .../laplace/impls/petsc/petsc_laplace.cxx | 30 +++++----- .../laplace/impls/petsc3damg/petsc3damg.cxx | 10 ++-- .../laplace/impls/serial_band/serial_band.cxx | 36 +++++------ .../laplace/impls/serial_tri/serial_tri.cxx | 14 ++--- src/invert/laplace/impls/spt/spt.cxx | 20 +++---- src/invert/laplace/invert_laplace.cxx | 60 ++++++++++--------- 16 files changed, 174 insertions(+), 194 deletions(-) diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index f7b9501a81..e47b195d0d 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -308,6 +308,17 @@ protected: int extra_yguards_lower; ///< exclude some number of points at the lower boundary, useful for staggered grids or when boundary conditions make inversion redundant int extra_yguards_upper; ///< exclude some number of points at the upper boundary, useful for staggered grids or when boundary conditions make inversion redundant + /// Return true if global/default \p flag is set + bool isGlobalFlagSet(int flag) const { return (global_flags & flag) != 0; } + /// Return true if \p flag is set for the inner boundary condition + bool isInnerBoundaryFlagSet(int flag) const { + return (inner_boundary_flags & flag) != 0; + } + /// Return true if \p flag is set for the outer boundary condition + bool isOuterBoundaryFlagSet(int flag) const { + return (outer_boundary_flags & flag) != 0; + } + int global_flags; ///< Default flags int inner_boundary_flags; ///< Flags to set inner boundary condition int outer_boundary_flags; ///< Flags to set outer boundary condition diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx index cf16240c0c..98c5e7c400 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx @@ -120,13 +120,13 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { // If the flags to assign that only one guard cell should be used is set int inbndry = localmesh->xstart, outbndry = localmesh->xstart; - if (((global_flags & INVERT_BOTH_BNDRY_ONE) != 0) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if ((inner_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if ((outer_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -143,9 +143,9 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && (inner_boundary_flags & INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && (outer_boundary_flags & INVERT_SET) && localmesh->lastX())) { + && (isOuterBoundaryFlagSet(INVERT_SET)) && localmesh->lastX())) { // Use the values in x0 in the boundary DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -218,9 +218,9 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && (inner_boundary_flags & INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && (outer_boundary_flags & INVERT_SET) && localmesh->lastX())) { + && (isOuterBoundaryFlagSet(INVERT_SET)) && localmesh->lastX())) { // Use the values in x0 in the boundary rfft(x0[ix], localmesh->LocalNz, std::begin(k1d)); } else { @@ -275,7 +275,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { // ZFFT routine expects input of this length auto k1d = Array((localmesh->LocalNz) / 2 + 1); - const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; + const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC); BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { @@ -316,13 +316,13 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // If the flags to assign that only one guard cell should be used is set int inbndry = localmesh->xstart, outbndry = localmesh->xstart; - if (((global_flags & INVERT_BOTH_BNDRY_ONE) != 0) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if ((inner_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if ((outer_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -374,10 +374,9 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -462,10 +461,9 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d)); } else { @@ -530,7 +528,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length - const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; + const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC); BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx index c74e184be3..d789e5e408 100644 --- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx +++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx @@ -99,7 +99,7 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, // Set up boundary conditions in operator BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) { - if (inner_boundary_flags & INVERT_AC_GRAD) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann on inner X boundary operator3D(i, i) = -1. / coords->dx[i] / sqrt(coords->g_11[i]); operator3D(i, i.xp()) = 1. / coords->dx[i] / sqrt(coords->g_11[i]); @@ -111,7 +111,7 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, } BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) { - if (outer_boundary_flags & INVERT_AC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann on outer X boundary operator3D(i, i) = 1. / coords->dx[i] / sqrt(coords->g_11[i]); operator3D(i, i.xm()) = -1. / coords->dx[i] / sqrt(coords->g_11[i]); @@ -180,9 +180,9 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) { // Adjust vectors to represent boundary conditions and check that // boundary cells are finite BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) { - const BoutReal val = (inner_boundary_flags & INVERT_SET) ? x0[i] : 0.; + const BoutReal val = isInnerBoundaryFlagSet(INVERT_SET) ? x0[i] : 0.; ASSERT1(std::isfinite(val)); - if (!(inner_boundary_flags & INVERT_RHS)) { + if (!(isInnerBoundaryFlagSet(INVERT_RHS))) { b[i] = val; } else { ASSERT1(std::isfinite(b[i])); @@ -190,9 +190,9 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) { } BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) { - const BoutReal val = (outer_boundary_flags & INVERT_SET) ? x0[i] : 0.; + const BoutReal val = (isOuterBoundaryFlagSet(INVERT_SET)) ? x0[i] : 0.; ASSERT1(std::isfinite(val)); - if (!(outer_boundary_flags & INVERT_RHS)) { + if (!(isOuterBoundaryFlagSet(INVERT_RHS))) { b[i] = val; } else { ASSERT1(std::isfinite(b[i])); diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx index 1c6bb7a02e..02e3eca06c 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx @@ -234,14 +234,6 @@ private: /// First and last interior points xstart, xend int xs, xe; - - bool isGlobalFlagSet(int flag) const { return (global_flags & flag) != 0; } - bool isInnerBoundaryFlagSet(int flag) const { - return (inner_boundary_flags & flag) != 0; - } - bool isOuterBoundaryFlagSet(int flag) const { - return (outer_boundary_flags & flag) != 0; - } }; #endif // BOUT_USE_METRIC_3D diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx index 82273ee7ad..c5076cd499 100644 --- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx +++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx @@ -84,19 +84,18 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_ // Initialize, allocate memory, etc. comms_tagbase = 385; // Some random number - int implemented_global_flags = INVERT_START_NEW; - if (global_flags & ~implemented_global_flags) { + constexpr int implemented_global_flags = INVERT_START_NEW; + if (isGlobalFlagSet(~implemented_global_flags)) { throw BoutException("Attempted to set Laplacian inversion flag that is not " "implemented in LaplaceMultigrid."); } - int implemented_boundary_flags = - INVERT_AC_GRAD + INVERT_SET - + INVERT_DC_GRAD; // INVERT_DC_GRAD does not actually do anything, but harmless to set while comparing to Fourier solver with Neumann boundary conditions - if (inner_boundary_flags & ~implemented_boundary_flags) { + // INVERT_DC_GRAD does not actually do anything, but harmless to set while comparing to Fourier solver with Neumann boundary conditions + constexpr int implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_DC_GRAD; + if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) { throw BoutException("Attempted to set Laplacian inner boundary inversion flag that " "is not implemented in LaplaceMultigrid."); } - if (outer_boundary_flags & ~implemented_boundary_flags) { + if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) { throw BoutException("Attempted to set Laplacian outer boundary inversion flag that " "is not implemented in LaplaceMultigrid."); } @@ -242,7 +241,7 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { int lz2 = lzz + 2; int lxx = kMG->lnx[level]; - if (global_flags & INVERT_START_NEW) { + if (isGlobalFlagSet(INVERT_START_NEW)) { // set initial guess to zero BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for collapse(2)) @@ -276,9 +275,9 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } if (localmesh->firstX()) { - if (inner_boundary_flags & INVERT_AC_GRAD) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann boundary condition - if (inner_boundary_flags & INVERT_SET) { + if (isInnerBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify gradient to set at inner boundary BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) @@ -299,7 +298,7 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // Dirichlet boundary condition - if (inner_boundary_flags & INVERT_SET) { + if (isInnerBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify value to set at inner boundary BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) @@ -320,9 +319,9 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } if (localmesh->lastX()) { - if (outer_boundary_flags & INVERT_AC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann boundary condition - if (inner_boundary_flags & INVERT_SET) { + if (isInnerBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify gradient to set at outer boundary BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) @@ -344,7 +343,7 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // Dirichlet boundary condition - if (outer_boundary_flags & INVERT_SET) { + if (isOuterBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify value to set at outer boundary BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) @@ -477,9 +476,9 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } if (localmesh->firstX()) { - if (inner_boundary_flags & INVERT_AC_GRAD) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann boundary condition - if (inner_boundary_flags & INVERT_SET) { + if (isInnerBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify gradient to set at inner boundary int i2 = -1 + localmesh->xstart; BOUT_OMP_PERF(parallel default(shared)) @@ -503,7 +502,7 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // Dirichlet boundary condition - if (inner_boundary_flags & INVERT_SET) { + if (isInnerBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify value to set at inner boundary int i2 = -1 + localmesh->xstart; BOUT_OMP_PERF(parallel default(shared)) @@ -525,9 +524,9 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } if (localmesh->lastX()) { - if (outer_boundary_flags & INVERT_AC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann boundary condition - if (inner_boundary_flags & INVERT_SET) { + if (isInnerBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify gradient to set at outer boundary int i2 = lxx + localmesh->xstart; BOUT_OMP_PERF(parallel default(shared)) @@ -551,7 +550,7 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) { } } else { // Dirichlet boundary condition - if (outer_boundary_flags & INVERT_SET) { + if (isOuterBoundaryFlagSet(INVERT_SET)) { // guard cells of x0 specify value to set at outer boundary int i2 = lxx + localmesh->xstart; BOUT_OMP_PERF(parallel default(shared)) @@ -651,7 +650,7 @@ void LaplaceMultigrid::generateMatrixF(int level) { // Here put boundary conditions if (kMG->rProcI == 0) { - if (inner_boundary_flags & INVERT_AC_GRAD) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann boundary condition BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) @@ -686,7 +685,7 @@ void LaplaceMultigrid::generateMatrixF(int level) { } } if (kMG->rProcI == kMG->xNP - 1) { - if (outer_boundary_flags & INVERT_AC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Neumann boundary condition BOUT_OMP_PERF(parallel default(shared)) BOUT_OMP_PERF(for) diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx index d82f874cbb..585d78a0fc 100644 --- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx +++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx @@ -258,7 +258,7 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) { // Note take a copy of the 'b' argument, because we want to return a copy of it in the // result - if ((inner_boundary_flags & INVERT_SET) || (outer_boundary_flags & INVERT_SET)) { + if (isInnerBoundaryFlagSet(INVERT_SET) || isOuterBoundaryFlagSet(INVERT_SET)) { // This passes in the boundary conditions from x0's guard cells copy_x_boundaries(x_guess, x0, localmesh); } diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx index 5c4f8da35b..da92351a45 100644 --- a/src/invert/laplace/impls/pcr/pcr.cxx +++ b/src/invert/laplace/impls/pcr/pcr.cxx @@ -149,13 +149,13 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { // If the flags to assign that only one guard cell should be used is set inbndry = localmesh->xstart; outbndry = localmesh->xstart; - if (((global_flags & INVERT_BOTH_BNDRY_ONE) != 0) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if ((inner_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if ((outer_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -173,10 +173,9 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -245,10 +244,9 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary rfft(x0[ix], localmesh->LocalNz, std::begin(k1d)); } else { @@ -285,7 +283,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length - const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; + const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC); BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { @@ -327,13 +325,13 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // If the flags to assign that only one guard cell should be used is set inbndry = localmesh->xstart; outbndry = localmesh->xstart; - if (((global_flags & INVERT_BOTH_BNDRY_ONE) != 0) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if ((inner_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if ((outer_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -387,10 +385,9 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -472,10 +469,9 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d)); } else { @@ -516,7 +512,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length - const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; + const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC); BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y diff --git a/src/invert/laplace/impls/pcr/pcr.hxx b/src/invert/laplace/impls/pcr/pcr.hxx index 38b7c356d3..ec4637f56c 100644 --- a/src/invert/laplace/impls/pcr/pcr.hxx +++ b/src/invert/laplace/impls/pcr/pcr.hxx @@ -172,14 +172,6 @@ private: /// First and last interior points xstart, xend int xs, xe; - bool isGlobalFlagSet(int flag) const { return (global_flags & flag) != 0; } - bool isInnerBoundaryFlagSet(int flag) const { - return (inner_boundary_flags & flag) != 0; - } - bool isOuterBoundaryFlagSet(int flag) const { - return (outer_boundary_flags & flag) != 0; - } - bool dst{false}; }; diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx index 35a25779a7..579decce43 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx @@ -145,13 +145,13 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { // If the flags to assign that only one guard cell should be used is set int inbndry = localmesh->xstart; int outbndry = localmesh->xstart; - if (((global_flags & INVERT_BOTH_BNDRY_ONE) != 0) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if ((inner_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if ((outer_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -169,10 +169,9 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -241,10 +240,9 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary rfft(x0[ix], localmesh->LocalNz, std::begin(k1d)); } else { @@ -281,7 +279,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length - const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; + const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC); BOUT_OMP_PERF(for nowait) for (int ix = xs; ix <= xe; ix++) { @@ -323,13 +321,13 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // If the flags to assign that only one guard cell should be used is set int inbndry = localmesh->xstart; int outbndry = localmesh->xstart; - if (((global_flags & INVERT_BOTH_BNDRY_ONE) != 0) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if ((inner_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if ((outer_boundary_flags & INVERT_BNDRY_ONE) != 0) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -383,10 +381,9 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -468,10 +465,9 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && ((inner_boundary_flags & INVERT_SET) != 0) - && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) || ((localmesh->LocalNx - ix - 1 < outbndry) - && ((outer_boundary_flags & INVERT_SET) != 0) && localmesh->lastX())) { + && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { // Use the values in x0 in the boundary rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d)); } else { @@ -513,7 +509,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { auto k1d = Array((localmesh->LocalNz) / 2 + 1); // ZFFT routine expects input of this length - const bool zero_DC = (global_flags & INVERT_ZERO_DC) != 0; + const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC); BOUT_OMP_PERF(for nowait) for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx index 009a1def2b..e12a647789 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx @@ -175,14 +175,6 @@ private: /// First and last interior points xstart, xend int xs, xe; - bool isGlobalFlagSet(int flag) const { return (global_flags & flag) != 0; } - bool isInnerBoundaryFlagSet(int flag) const { - return (inner_boundary_flags & flag) != 0; - } - bool isOuterBoundaryFlagSet(int flag) const { - return (outer_boundary_flags & flag) != 0; - } - bool dst{false}; }; diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx index d125b90694..c5a81b03d6 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx @@ -84,8 +84,8 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_RHS; // Checking flags are set to something which is not implemented // This is done binary (which is possible as each flag is a power of 2) - if (global_flags & ~implemented_flags) { - if (global_flags & INVERT_4TH_ORDER) { + if (isGlobalFlagSet(~implemented_flags)) { + if (isGlobalFlagSet(INVERT_4TH_ORDER)) { output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " "setting INVERT_4TH_ORDER flag" << endl; @@ -93,11 +93,11 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, throw BoutException("Attempted to set Laplacian inversion flag that is not " "implemented in petsc_laplace.cxx"); } - if (inner_boundary_flags & ~implemented_boundary_flags) { + if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) { throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " "implemented in petsc_laplace.cxx"); } - if (outer_boundary_flags & ~implemented_boundary_flags) { + if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) { throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " "implemented in petsc_laplace.cxx"); } @@ -362,8 +362,8 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { #if CHECK > 0 // Checking flags are set to something which is not implemented (see // constructor for details) - if (global_flags & !implemented_flags) { - if (global_flags & INVERT_4TH_ORDER) { + if (isGlobalFlagSet(~implemented_flags)) { + if (isGlobalFlagSet(INVERT_4TH_ORDER)) { output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " "setting INVERT_4TH_ORDER flag" << endl; @@ -371,11 +371,11 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { throw BoutException("Attempted to set Laplacian inversion flag that is not " "implemented in petsc_laplace.cxx"); } - if (inner_boundary_flags & ~implemented_boundary_flags) { + if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) { throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " "implemented in petsc_laplace.cxx"); } - if (outer_boundary_flags & ~implemented_boundary_flags) { + if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) { throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " "implemented in petsc_laplace.cxx"); } @@ -415,7 +415,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { for (int z = 0; z < localmesh->LocalNz; z++) { PetscScalar val; // Value of element to be set in the matrix // If Neumann Boundary Conditions are set. - if (inner_boundary_flags & INVERT_AC_GRAD) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Set values corresponding to nodes adjacent in x if (fourth_order) { // Fourth Order Accuracy on Boundary @@ -472,9 +472,9 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { // Set Components of RHS // If the inner boundary value should be set by b or x0 - if (inner_boundary_flags & INVERT_RHS) { + if (isInnerBoundaryFlagSet(INVERT_RHS)) { val = b[x][z]; - } else if (inner_boundary_flags & INVERT_SET) { + } else if (isInnerBoundaryFlagSet(INVERT_SET)) { val = x0[x][z]; } @@ -680,7 +680,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { Element(i, x, z, 0, 0, val, MatA); // If Neumann Boundary Conditions are set. - if (outer_boundary_flags & INVERT_AC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Set values corresponding to nodes adjacent in x if (fourth_order) { // Fourth Order Accuracy on Boundary @@ -733,9 +733,9 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { // Set Components of RHS // If the inner boundary value should be set by b or x0 val = 0; - if (outer_boundary_flags & INVERT_RHS) { + if (isOuterBoundaryFlagSet(INVERT_RHS)) { val = b[x][z]; - } else if (outer_boundary_flags & INVERT_SET) { + } else if (isOuterBoundaryFlagSet(INVERT_SET)) { val = x0[x][z]; } @@ -812,7 +812,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { KSPSetTolerances(ksp, rtol, atol, dtol, maxits); // If the initial guess is not set to zero - if (!(global_flags & INVERT_START_NEW)) { + if (!isGlobalFlagSet(INVERT_START_NEW)) { KSPSetInitialGuessNonzero(ksp, static_cast(true)); } diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index d1e2207725..40e3b5fbe8 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -84,12 +84,12 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes #if CHECK > 0 // Checking flags are set to something which is not implemented // This is done binary (which is possible as each flag is a power of 2) - if (flagSet(global_flags, INVERT_4TH_ORDER)) { + if (isGlobalFlagSet(INVERT_4TH_ORDER)) { output.write("For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " "setting INVERT_4TH_ORDER flag\n"); } - if (flagSet(global_flags, ~implemented_flags)) { + if (isGlobalFlagSet(~implemented_flags)) { throw BoutException("Attempted to set global Laplacian inversion flag that is not " "implemented in petsc_laplace.cxx"); } @@ -119,7 +119,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes } // Set up boundary conditions in operator - const bool inner_X_neumann = flagSet(inner_boundary_flags, INVERT_AC_GRAD); + const bool inner_X_neumann = isInnerBoundaryFlagSet(INVERT_AC_GRAD); const auto inner_X_BC = inner_X_neumann ? -1. / coords->dx / sqrt(coords->g_11) : 0.5; const auto inner_X_BC_plus = inner_X_neumann ? -inner_X_BC : 0.5; @@ -128,7 +128,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes operator3D(i, i.xp()) = inner_X_BC_plus[i]; } - const bool outer_X_neumann = flagSet(outer_boundary_flags, INVERT_AC_GRAD); + const bool outer_X_neumann = isOuterBoundaryFlagSet(INVERT_AC_GRAD); const auto outer_X_BC = outer_X_neumann ? 1. / coords->dx / sqrt(coords->g_11) : 0.5; const auto outer_X_BC_minus = outer_X_neumann ? -outer_X_BC : 0.5; @@ -460,7 +460,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() { KSPSetTolerances(ksp, rtol, atol, dtol, maxits); // If the initial guess is not set to zero - if ((global_flags & INVERT_START_NEW) == 0) { + if (!isGlobalFlagSet(INVERT_START_NEW)) { KSPSetInitialGuessNonzero(ksp, (PetscBool) true); } diff --git a/src/invert/laplace/impls/serial_band/serial_band.cxx b/src/invert/laplace/impls/serial_band/serial_band.cxx index eda76498fc..4e7bb4c63f 100644 --- a/src/invert/laplace/impls/serial_band/serial_band.cxx +++ b/src/invert/laplace/impls/serial_band/serial_band.cxx @@ -99,7 +99,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { int xbndry = localmesh->xstart; // Width of the x boundary // If the flags to assign that only one guard cell should be used is set - if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; } @@ -107,8 +107,8 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { for (int ix = 0; ix < localmesh->LocalNx; ix++) { // for fixed ix,jy set a complex vector rho(z) - if (((ix < xbndry) && (inner_boundary_flags & INVERT_SET)) - || ((ncx - ix < xbndry) && (outer_boundary_flags & INVERT_SET))) { + if (((ix < xbndry) && isInnerBoundaryFlagSet(INVERT_SET)) + || ((ncx - ix < xbndry) && (isOuterBoundaryFlagSet(INVERT_SET)))) { // Use the values in x0 in the boundary rfft(x0[ix], ncz, &bk(ix, 0)); } else { @@ -247,10 +247,10 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { for (int ix = 0; ix < xbndry; ix++) { // Set zero-value. Change to zero-gradient if needed - if (!(inner_boundary_flags & (INVERT_RHS | INVERT_SET))) { + if (!isInnerBoundaryFlagSet(INVERT_RHS | INVERT_SET)) { bk1d[ix] = 0.0; } - if (!(outer_boundary_flags & (INVERT_RHS | INVERT_SET))) { + if (!isOuterBoundaryFlagSet(INVERT_RHS | INVERT_SET)) { bk1d[ncx - ix] = 0.0; } @@ -265,8 +265,8 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { // DC // Inner boundary - if (inner_boundary_flags & (INVERT_DC_GRAD + INVERT_SET) - || inner_boundary_flags & (INVERT_DC_GRAD + INVERT_RHS)) { + if (isInnerBoundaryFlagSet(INVERT_DC_GRAD + INVERT_SET) + || isInnerBoundaryFlagSet(INVERT_DC_GRAD + INVERT_RHS)) { // Zero gradient at inner boundary. 2nd-order accurate // Boundary at midpoint for (int ix = 0; ix < xbndry; ix++) { @@ -277,7 +277,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ix, 4) = 0.; } - } else if (inner_boundary_flags & INVERT_DC_GRAD) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_GRAD)) { // Zero gradient at inner boundary. 2nd-order accurate // Boundary at midpoint for (int ix = 0; ix < xbndry; ix++) { @@ -288,7 +288,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ix, 4) = 0.; } - } else if (inner_boundary_flags & INVERT_DC_GRADPAR) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_GRADPAR)) { for (int ix = 0; ix < xbndry; ix++) { A(ix, 0) = 0.; A(ix, 1) = 0.; @@ -296,7 +296,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ix, 3) = 4. / sqrt(coords->g_22(ix + 1, jy)); A(ix, 4) = -1. / sqrt(coords->g_22(ix + 2, jy)); } - } else if (inner_boundary_flags & INVERT_DC_GRADPARINV) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_GRADPARINV)) { for (int ix = 0; ix < xbndry; ix++) { A(ix, 0) = 0.; A(ix, 1) = 0.; @@ -304,7 +304,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { A(ix, 3) = 4. * sqrt(coords->g_22(ix + 1, jy)); A(ix, 4) = -sqrt(coords->g_22(ix + 2, jy)); } - } else if (inner_boundary_flags & INVERT_DC_LAP) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_LAP)) { for (int ix = 0; ix < xbndry; ix++) { A(ix, 0) = 0.; A(ix, 1) = 0.; @@ -315,7 +315,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { } // Outer boundary - if (outer_boundary_flags & INVERT_DC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_DC_GRAD)) { // Zero gradient at outer boundary for (int ix = 0; ix < xbndry; ix++) { A(ncx - ix, 1) = -1.0; @@ -326,12 +326,12 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { // AC // Inner boundarySQ(kwave)*coef2 - if (inner_boundary_flags & INVERT_AC_GRAD) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Zero gradient at inner boundary for (int ix = 0; ix < xbndry; ix++) { A(ix, 3) = -1.0; } - } else if (inner_boundary_flags & INVERT_AC_LAP) { + } else if (isInnerBoundaryFlagSet(INVERT_AC_LAP)) { // Enforce zero laplacian for 2nd and 4th-order int ix = 1; @@ -369,12 +369,12 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { } // Outer boundary - if (outer_boundary_flags & INVERT_AC_GRAD) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Zero gradient at outer boundary for (int ix = 0; ix < xbndry; ix++) { A(ncx - ix, 1) = -1.0; } - } else if (outer_boundary_flags & INVERT_AC_LAP) { + } else if (isOuterBoundaryFlagSet(INVERT_AC_LAP)) { // Enforce zero laplacian for 2nd and 4th-order // NOTE: Currently ignoring XZ term and coef4 assumed zero on boundary // FIX THIS IF IT WORKS @@ -417,7 +417,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { // Perform inversion cband_solve(A, localmesh->LocalNx, 2, 2, bk1d); - if ((global_flags & INVERT_KX_ZERO) && (iz == 0)) { + if (isGlobalFlagSet(INVERT_KX_ZERO) && (iz == 0)) { // Set the Kx = 0, n = 0 component to zero. For now just subtract // Should do in the inversion e.g. Sherman-Morrison formula @@ -440,7 +440,7 @@ FieldPerp LaplaceSerialBand::solve(const FieldPerp& b, const FieldPerp& x0) { // Done inversion, transform back for (int ix = 0; ix <= ncx; ix++) { - if (global_flags & INVERT_ZERO_DC) { + if (isGlobalFlagSet(INVERT_ZERO_DC)) { xk(ix, 0) = 0.0; } diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx index 909a47f856..816723e08a 100644 --- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx +++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx @@ -91,13 +91,13 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { int inbndry = localmesh->xstart, outbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if (inner_boundary_flags & INVERT_BNDRY_ONE) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if (outer_boundary_flags & INVERT_BNDRY_ONE) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -140,8 +140,8 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { * If the INVERT_SET flag is set (meaning that x0 will be used to set the * bounadry values), */ - if (((ix < inbndry) && (inner_boundary_flags & INVERT_SET)) - || ((ncx - 1 - ix < outbndry) && (outer_boundary_flags & INVERT_SET))) { + if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET)) + || ((ncx - 1 - ix < outbndry) && (isOuterBoundaryFlagSet(INVERT_SET)))) { // Use the values in x0 in the boundary // x0 is the input @@ -208,7 +208,7 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { } // If the global flag is set to INVERT_KX_ZERO - if ((global_flags & INVERT_KX_ZERO) && (kz == 0)) { + if (isGlobalFlagSet(INVERT_KX_ZERO) && (kz == 0)) { dcomplex offset(0.0); for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) { offset += xk1d[ix]; @@ -228,7 +228,7 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { // Done inversion, transform back for (int ix = 0; ix < ncx; ix++) { - if (global_flags & INVERT_ZERO_DC) { + if (isGlobalFlagSet(INVERT_ZERO_DC)) { xk(ix, 0) = 0.0; } diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index 56ac496271..e352dcab00 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -90,15 +90,15 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) { FieldPerp x{emptyFrom(b)}; - if ((inner_boundary_flags & INVERT_SET) || (outer_boundary_flags & INVERT_SET)) { + if (isInnerBoundaryFlagSet(INVERT_SET) || isOuterBoundaryFlagSet(INVERT_SET)) { FieldPerp bs = copy(b); int xbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; } - if ((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) { + if (isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) { // Copy x0 inner boundary into bs for (int ix = 0; ix < xbndry; ix++) { for (int iz = 0; iz < localmesh->LocalNz; iz++) { @@ -106,7 +106,7 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) { } } } - if ((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) { + if (isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX()) { // Copy x0 outer boundary into bs for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) { for (int iz = 0; iz < localmesh->LocalNz; iz++) { @@ -173,17 +173,17 @@ Field3D LaplaceSPT::solve(const Field3D& b) { Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { ASSERT1(localmesh == b.getMesh() && localmesh == x0.getMesh()); - if (((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) - || ((outer_boundary_flags & INVERT_SET) && localmesh->lastX())) { + if ((isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + || (isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { Field3D bs = copy(b); int xbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; } - if ((inner_boundary_flags & INVERT_SET) && localmesh->firstX()) { + if (isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) { // Copy x0 inner boundary into bs for (int ix = 0; ix < xbndry; ix++) { for (int iy = 0; iy < localmesh->LocalNy; iy++) { @@ -193,7 +193,7 @@ Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { } } } - if ((outer_boundary_flags & INVERT_SET) && localmesh->lastX()) { + if (isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX()) { // Copy x0 outer boundary into bs for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) { for (int iy = 0; iy < localmesh->LocalNy; iy++) { @@ -516,7 +516,7 @@ void LaplaceSPT::finish(SPT_data& data, FieldPerp& x) { dc1d[kz] = 0.0; } - if (global_flags & INVERT_ZERO_DC) { + if (isGlobalFlagSet(INVERT_ZERO_DC)) { dc1d[0] = 0.0; } diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index 017c35e1b5..72e1671cd2 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -469,13 +469,13 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco int inbndry = localmesh->xstart, outbndry = localmesh->xstart; // If the flags to assign that only one guard cell should be used is set - if ((global_flags & INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { + if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { inbndry = outbndry = 1; } - if (inner_boundary_flags & INVERT_BNDRY_ONE) { + if (isInnerBoundaryFlagSet(INVERT_BNDRY_ONE)) { inbndry = 1; } - if (outer_boundary_flags & INVERT_BNDRY_ONE) { + if (isOuterBoundaryFlagSet(INVERT_BNDRY_ONE)) { outbndry = 1; } @@ -497,7 +497,7 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco // If no user specified value is set on inner boundary, set the first // element in b (in the equation AX=b) to 0 - if (!(inner_boundary_flags & (INVERT_RHS | INVERT_SET))) { + if (!isInnerBoundaryFlagSet(INVERT_RHS | INVERT_SET)) { for (int ix = 0; ix < inbndry; ix++) { bk[ix] = 0.; } @@ -506,34 +506,35 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco // DC i.e. kz = 0 (the offset mode) if (kz == 0) { - if (inner_boundary_flags & INVERT_DC_GRAD - && (inner_boundary_flags & INVERT_SET || inner_boundary_flags & INVERT_RHS)) { + if (isInnerBoundaryFlagSet(INVERT_DC_GRAD) + && (isInnerBoundaryFlagSet(INVERT_SET) + || isInnerBoundaryFlagSet(INVERT_RHS))) { // Zero gradient at inner boundary for (int ix = 0; ix < inbndry; ix++) { avec[ix] = 0.; bvec[ix] = -1. / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); cvec[ix] = 1. / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); } - } else if (inner_boundary_flags & INVERT_DC_GRAD) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_GRAD)) { // Zero gradient at inner boundary for (int ix = 0; ix < inbndry; ix++) { avec[ix] = 0.; bvec[ix] = -1.; cvec[ix] = 1.; } - } else if (inner_boundary_flags & INVERT_DC_GRADPAR) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_GRADPAR)) { for (int ix = 0; ix < inbndry; ix++) { avec[ix] = 0.0; bvec[ix] = 1.0 / sqrt(coords->g_22(ix, jy)); cvec[ix] = -1.0 / sqrt(coords->g_22(ix + 1, jy)); } - } else if (inner_boundary_flags & INVERT_DC_GRADPARINV) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_GRADPARINV)) { for (int ix = 0; ix < inbndry; ix++) { avec[ix] = 0.0; bvec[ix] = sqrt(coords->g_22(ix, jy)); cvec[ix] = -sqrt(coords->g_22(ix + 1, jy)); } - } else if (inner_boundary_flags & INVERT_DC_LAP) { + } else if (isInnerBoundaryFlagSet(INVERT_DC_LAP)) { // Decaying boundary conditions BoutReal k = 0.0; if (a != nullptr) { @@ -548,7 +549,7 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco bvec[ix] = 1.; cvec[ix] = -exp(-k * coords->dx(ix, jy) / sqrt(coords->g11(ix, jy))); } - } else if (inner_boundary_flags & INVERT_IN_CYLINDER) { + } else if (isInnerBoundaryFlagSet(INVERT_IN_CYLINDER)) { // Condition for inner radial boundary for cylindrical coordinates /* Explanation: * The discrete fourier transform is defined as @@ -602,8 +603,9 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco // AC i.e. kz =/= 0 (all other modes than the offset mode) else { - if (inner_boundary_flags & INVERT_AC_GRAD - && (inner_boundary_flags & INVERT_SET || inner_boundary_flags & INVERT_RHS)) { + if (isInnerBoundaryFlagSet(INVERT_AC_GRAD) + && (isInnerBoundaryFlagSet(INVERT_SET) + || isInnerBoundaryFlagSet(INVERT_RHS))) { // Zero gradient at inner boundary for (int ix = 0; ix < inbndry; ix++) { avec[ix] = dcomplex(0., 0.); @@ -611,14 +613,14 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco dcomplex(-1., 0.) / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); cvec[ix] = dcomplex(1., 0.) / sqrt(coords->g_11(ix, jy)) / coords->dx(ix, jy); } - } else if (inner_boundary_flags & INVERT_AC_GRAD) { + } else if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) { // Zero gradient at inner boundary for (int ix = 0; ix < inbndry; ix++) { avec[ix] = dcomplex(0., 0.); bvec[ix] = dcomplex(-1., 0.); cvec[ix] = dcomplex(1., 0.); } - } else if (inner_boundary_flags & INVERT_AC_LAP) { + } else if (isInnerBoundaryFlagSet(INVERT_AC_LAP)) { // Use decaying zero-Laplacian solution in the boundary for (int ix = 0; ix < inbndry; ix++) { avec[ix] = 0.0; @@ -626,9 +628,9 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco cvec[ix] = -exp(-1.0 * sqrt(coords->g33(ix, jy) / coords->g11(ix, jy)) * kwave * coords->dx(ix, jy)); } - } else if (inner_boundary_flags & INVERT_IN_CYLINDER) { + } else if (isInnerBoundaryFlagSet(INVERT_IN_CYLINDER)) { // Condition for inner radial boundary for cylindrical coordinates - // Explanation under "if (inner_boundary_flags & INVERT_IN_CYLINDER)" + // Explanation under "if (isInnerBoundaryFlagSet(INVERT_IN_CYLINDER))" for (int ix = 0; ix < inbndry; ix++) { avec[ix] = 0.; bvec[ix] = 1.; @@ -655,7 +657,7 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco // If no user specified value is set on outer boundary, set the last // element in b (in the equation AX=b) to 0 - if (!(outer_boundary_flags & (INVERT_RHS | INVERT_SET))) { + if (!isOuterBoundaryFlagSet(INVERT_RHS | INVERT_SET)) { for (int ix = 0; ix < outbndry; ix++) { bk[ncx - ix] = 0.; } @@ -664,8 +666,9 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco // DC i.e. kz = 0 (the offset mode) if (kz == 0) { - if (outer_boundary_flags & INVERT_DC_GRAD - && (outer_boundary_flags & INVERT_SET || outer_boundary_flags & INVERT_RHS)) { + if (isOuterBoundaryFlagSet(INVERT_DC_GRAD) + && (isOuterBoundaryFlagSet(INVERT_SET) + || isOuterBoundaryFlagSet(INVERT_RHS))) { // Zero gradient at outer boundary for (int ix = 0; ix < outbndry; ix++) { avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(xe - ix, jy)) @@ -674,26 +677,26 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco / coords->dx(xe - ix, jy); cvec[ncx - ix] = dcomplex(0., 0.); } - } else if (outer_boundary_flags & INVERT_DC_GRAD) { + } else if (isOuterBoundaryFlagSet(INVERT_DC_GRAD)) { // Zero gradient at outer boundary for (int ix = 0; ix < outbndry; ix++) { avec[ncx - ix] = dcomplex(1., 0.); bvec[ncx - ix] = dcomplex(-1., 0.); cvec[ncx - ix] = dcomplex(0., 0.); } - } else if (outer_boundary_flags & INVERT_DC_GRADPAR) { + } else if (isOuterBoundaryFlagSet(INVERT_DC_GRADPAR)) { for (int ix = 0; ix < inbndry; ix++) { avec[ncx - ix] = 1.0 / sqrt(coords->g_22(xe - ix - 1, jy)); bvec[ncx - ix] = -1.0 / sqrt(coords->g_22(xe - ix, jy)); cvec[ncx - ix] = 0.0; } - } else if (outer_boundary_flags & INVERT_DC_GRADPARINV) { + } else if (isOuterBoundaryFlagSet(INVERT_DC_GRADPARINV)) { for (int ix = 0; ix < inbndry; ix++) { avec[ncx - ix] = sqrt(coords->g_22(xe - ix - 1, jy)); bvec[ncx - ix] = -sqrt(coords->g_22(xe - ix, jy)); cvec[ncx - ix] = 0.0; } - } else if (outer_boundary_flags & INVERT_DC_LAP) { + } else if (isOuterBoundaryFlagSet(INVERT_DC_LAP)) { // Decaying boundary conditions BoutReal k = 0.0; if (a != nullptr) { @@ -722,8 +725,9 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco // AC i.e. kz =/= 0 (all other modes than the offset mode) else { - if (outer_boundary_flags & INVERT_AC_GRAD - && (outer_boundary_flags & INVERT_SET || outer_boundary_flags & INVERT_RHS)) { + if (isOuterBoundaryFlagSet(INVERT_AC_GRAD) + && (isOuterBoundaryFlagSet(INVERT_SET) + || isOuterBoundaryFlagSet(INVERT_RHS))) { // Zero gradient at outer boundary for (int ix = 0; ix < outbndry; ix++) { avec[ncx - ix] = dcomplex(-1., 0.) / sqrt(coords->g_11(xe - ix, jy)) @@ -732,14 +736,14 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco / coords->dx(xe - ix, jy); cvec[ncx - ix] = dcomplex(0., 0.); } - } else if (outer_boundary_flags & INVERT_AC_GRAD) { + } else if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) { // Zero gradient at outer boundary for (int ix = 0; ix < outbndry; ix++) { avec[ncx - ix] = dcomplex(1., 0.); bvec[ncx - ix] = dcomplex(-1., 0.); cvec[ncx - ix] = dcomplex(0., 0.); } - } else if (outer_boundary_flags & INVERT_AC_LAP) { + } else if (isOuterBoundaryFlagSet(INVERT_AC_LAP)) { // Use decaying zero-Laplacian solution in the boundary for (int ix = 0; ix < outbndry; ix++) { avec[ncx - ix] = From d8032863b4621e700360129d68b2467701b9e38e Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 23 May 2024 18:02:03 +0100 Subject: [PATCH 369/412] Add helper method for checking inner/outer flags on `first/lastX` --- include/bout/invert_laplace.hxx | 7 +++++++ .../laplace/impls/cyclic/cyclic_laplace.cxx | 16 ++++++++-------- .../iterative_parallel_tri.cxx | 6 ++---- src/invert/laplace/impls/pcr/pcr.cxx | 16 ++++++++-------- .../laplace/impls/pcr_thomas/pcr_thomas.cxx | 16 ++++++++-------- src/invert/laplace/impls/spt/spt.cxx | 12 ++++++------ src/invert/laplace/invert_laplace.cxx | 7 +++++++ 7 files changed, 46 insertions(+), 34 deletions(-) diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index e47b195d0d..3d3ead038b 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -319,6 +319,13 @@ protected: return (outer_boundary_flags & flag) != 0; } + /// Return true if \p flag is set for the inner boundary condition + /// on the inner processor(s) + bool isInnerBoundaryFlagSetOnFirstX(int flag) const; + /// Return true if \p flag is set for the outer boundary condition + /// on the outer processor(s) + bool isOuterBoundaryFlagSetOnLastX(int flag) const; + int global_flags; ///< Default flags int inner_boundary_flags; ///< Flags to set inner boundary condition int outer_boundary_flags; ///< Flags to set outer boundary condition diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx index 98c5e7c400..d3e2497905 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx @@ -143,9 +143,9 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && (isOuterBoundaryFlagSet(INVERT_SET)) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -218,9 +218,9 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && (isOuterBoundaryFlagSet(INVERT_SET)) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0[ix], localmesh->LocalNz, std::begin(k1d)); } else { @@ -374,9 +374,9 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -461,9 +461,9 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d)); } else { diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx index b09b67611b..be94709cf7 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx @@ -293,10 +293,8 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { */ auto bcmplx = Matrix(nmode, ncx); - const bool invert_inner_boundary = - isInnerBoundaryFlagSet(INVERT_SET) and localmesh->firstX(); - const bool invert_outer_boundary = - isOuterBoundaryFlagSet(INVERT_SET) and localmesh->lastX(); + const bool invert_inner_boundary = isInnerBoundaryFlagSetOnFirstX(INVERT_SET); + const bool invert_outer_boundary = isOuterBoundaryFlagSetOnLastX(INVERT_SET); BOUT_OMP_PERF(parallel for) for (int ix = 0; ix < ncx; ix++) { diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx index da92351a45..a12054c53e 100644 --- a/src/invert/laplace/impls/pcr/pcr.cxx +++ b/src/invert/laplace/impls/pcr/pcr.cxx @@ -173,9 +173,9 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -244,9 +244,9 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0[ix], localmesh->LocalNz, std::begin(k1d)); } else { @@ -385,9 +385,9 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -469,9 +469,9 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d)); } else { diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx index 579decce43..77501f35ea 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx @@ -169,9 +169,9 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -240,9 +240,9 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { for (int ix = xs; ix <= xe; ix++) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0[ix], localmesh->LocalNz, std::begin(k1d)); } else { @@ -381,9 +381,9 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Take DST in Z direction and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d)); } else { @@ -465,9 +465,9 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { // Take FFT in Z direction, apply shift, and put result in k1d - if (((ix < inbndry) && isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) + if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) || ((localmesh->LocalNx - ix - 1 < outbndry) - && isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) { // Use the values in x0 in the boundary rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d)); } else { diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index e352dcab00..093fe993fb 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -98,7 +98,7 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) { if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) { xbndry = 1; } - if (isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) { + if (isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) { // Copy x0 inner boundary into bs for (int ix = 0; ix < xbndry; ix++) { for (int iz = 0; iz < localmesh->LocalNz; iz++) { @@ -106,7 +106,7 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) { } } } - if (isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX()) { + if (isOuterBoundaryFlagSetOnLastX(INVERT_SET)) { // Copy x0 outer boundary into bs for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) { for (int iz = 0; iz < localmesh->LocalNz; iz++) { @@ -173,8 +173,8 @@ Field3D LaplaceSPT::solve(const Field3D& b) { Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { ASSERT1(localmesh == b.getMesh() && localmesh == x0.getMesh()); - if ((isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) - || (isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX())) { + if ((isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) + || isOuterBoundaryFlagSetOnLastX(INVERT_SET)) { Field3D bs = copy(b); int xbndry = localmesh->xstart; @@ -183,7 +183,7 @@ Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { xbndry = 1; } - if (isInnerBoundaryFlagSet(INVERT_SET) && localmesh->firstX()) { + if (isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) { // Copy x0 inner boundary into bs for (int ix = 0; ix < xbndry; ix++) { for (int iy = 0; iy < localmesh->LocalNy; iy++) { @@ -193,7 +193,7 @@ Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) { } } } - if (isOuterBoundaryFlagSet(INVERT_SET) && localmesh->lastX()) { + if (isOuterBoundaryFlagSetOnLastX(INVERT_SET)) { // Copy x0 outer boundary into bs for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) { for (int iy = 0; iy < localmesh->LocalNy; iy++) { diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index 72e1671cd2..f58023df2f 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -799,6 +799,13 @@ void Laplacian::LaplacianMonitor::outputVars(Options& output_options, laplacian->outputVars(output_options, time_dimension); } +bool Laplacian::isInnerBoundaryFlagSetOnFirstX(int flag) const { + return isInnerBoundaryFlagSet(flag) and localmesh->firstX(); +} +bool Laplacian::isOuterBoundaryFlagSetOnLastX(int flag) const { + return isOuterBoundaryFlagSet(flag) and localmesh->lastX(); +} + /********************************************************************************** * LEGACY INTERFACE * From bdbd5289b44f787f3addbd9941adc06e8231a706 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 24 May 2024 09:00:33 +0100 Subject: [PATCH 370/412] Remove flags arguments from `Laplacian::tridagMatrix` Use members directly --- include/bout/invert_laplace.hxx | 10 ++++------ .../laplace/impls/cyclic/cyclic_laplace.cxx | 12 ++++-------- .../iterative_parallel_tri.cxx | 3 +-- src/invert/laplace/impls/pcr/pcr.cxx | 12 ++++-------- .../laplace/impls/pcr_thomas/pcr_thomas.cxx | 12 ++++-------- .../laplace/impls/serial_tri/serial_tri.cxx | 3 +-- src/invert/laplace/impls/spt/spt.cxx | 3 +-- src/invert/laplace/invert_laplace.cxx | 16 ++++++---------- 8 files changed, 25 insertions(+), 46 deletions(-) diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index 3d3ead038b..d041403ffb 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -340,15 +340,13 @@ protected: CELL_LOC loc = CELL_DEFAULT); void tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk, int jy, - int kz, BoutReal kwave, int flags, int inner_boundary_flags, - int outer_boundary_flags, const Field2D* a, const Field2D* ccoef, + int kz, BoutReal kwave, const Field2D* a, const Field2D* ccoef, const Field2D* d, bool includeguards = true, bool zperiodic = true) { - tridagMatrix(avec, bvec, cvec, bk, jy, kz, kwave, flags, inner_boundary_flags, - outer_boundary_flags, a, ccoef, ccoef, d, includeguards, zperiodic); + tridagMatrix(avec, bvec, cvec, bk, jy, kz, kwave, a, ccoef, ccoef, d, includeguards, + zperiodic); } void tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk, int jy, - int kz, BoutReal kwave, int flags, int inner_boundary_flags, - int outer_boundary_flags, const Field2D* a, const Field2D* c1coef, + int kz, BoutReal kwave, const Field2D* a, const Field2D* c1coef, const Field2D* c2coef, const Field2D* d, bool includeguards = true, bool zperiodic = true); CELL_LOC location; ///< staggered grid location of this solver diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx index d3e2497905..a9bf0536ca 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx @@ -169,8 +169,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, kz, // wave number index kwave, // kwave (inverse wave length) - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false, // Don't include guard cells in arrays false); // Z domain not periodic } @@ -241,8 +240,7 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) { tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, kz, // True for the component constant (DC) in Z kwave, // Z wave number - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } @@ -404,8 +402,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy, kz, // wave number index kwave, // kwave (inverse wave length) - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false, // Don't include guard cells in arrays false); // Z domain not periodic } @@ -488,8 +485,7 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy, kz, // True for the component constant (DC) in Z kwave, // Z wave number - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx index be94709cf7..f79463769a 100644 --- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx +++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx @@ -343,8 +343,7 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) { kz, // wave number (different from kz only if we are taking a part // of the z-domain [and not from 0 to 2*pi]) - kz * kwaveFactor, global_flags, inner_boundary_flags, - outer_boundary_flags, &A, &C, &D); + kz * kwaveFactor, &A, &C, &D); // Patch up internal boundaries if (not localmesh->lastX()) { diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx index a12054c53e..48bbdbac4b 100644 --- a/src/invert/laplace/impls/pcr/pcr.cxx +++ b/src/invert/laplace/impls/pcr/pcr.cxx @@ -198,8 +198,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, kz, // wave number index kwave, // kwave (inverse wave length) - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } // BOUT_OMP_PERF(parallel) @@ -267,8 +266,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) { tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, kz, // True for the component constant (DC) in Z kwave, // Z wave number - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } // BOUT_OMP_PERF(parallel) @@ -414,8 +412,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy, kz, // wave number index kwave, // kwave (inverse wave length) - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } // BOUT_OMP_PERF(parallel) @@ -496,8 +493,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) { tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy, kz, // True for the component constant (DC) in Z kwave, // Z wave number - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } // BOUT_OMP_PERF(parallel) diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx index 77501f35ea..61c8f58694 100644 --- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx +++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx @@ -194,8 +194,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, kz, // wave number index kwave, // kwave (inverse wave length) - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } @@ -263,8 +262,7 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) { tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy, kz, // True for the component constant (DC) in Z kwave, // Z wave number - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } @@ -410,8 +408,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy, kz, // wave number index kwave, // kwave (inverse wave length) - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } @@ -493,8 +490,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) { tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy, kz, // True for the component constant (DC) in Z kwave, // Z wave number - global_flags, inner_boundary_flags, outer_boundary_flags, &Acoef, - &C1coef, &C2coef, &Dcoef, + &Acoef, &C1coef, &C2coef, &Dcoef, false); // Don't include guard cells in arrays } } diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx index 816723e08a..f46a0a46e5 100644 --- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx +++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx @@ -185,8 +185,7 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) { kz, // wave number (different from kz only if we are taking a part // of the z-domain [and not from 0 to 2*pi]) - kz * kwaveFactor, global_flags, inner_boundary_flags, - outer_boundary_flags, &A, &C, &D); + kz * kwaveFactor, &A, &C, &D); ///////// PERFORM INVERSION ///////// if (!localmesh->periodicX) { diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index 093fe993fb..2426b362f6 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -323,8 +323,7 @@ int LaplaceSPT::start(const FieldPerp& b, SPT_data& data) { /// Set matrix elements for (int kz = 0; kz <= maxmode; kz++) { tridagMatrix(&data.avec(kz, 0), &data.bvec(kz, 0), &data.cvec(kz, 0), &data.bk(kz, 0), - data.jy, kz, kz * kwaveFactor, global_flags, inner_boundary_flags, - outer_boundary_flags, &Acoef, &Ccoef, &Dcoef); + data.jy, kz, kz * kwaveFactor, &Acoef, &Ccoef, &Dcoef); } data.proc = 0; //< Starts at processor 0 diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx index f58023df2f..4032499781 100644 --- a/src/invert/laplace/invert_laplace.cxx +++ b/src/invert/laplace/invert_laplace.cxx @@ -424,20 +424,16 @@ void Laplacian::tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomple #if BOUT_USE_METRIC_3D void Laplacian::tridagMatrix(dcomplex* /*avec*/, dcomplex* /*bvec*/, dcomplex* /*cvec*/, dcomplex* /*bk*/, int /*jy*/, int /*kz*/, BoutReal /*kwave*/, - int /*global_flags*/, int /*inner_boundary_flags*/, - int /*outer_boundary_flags*/, const Field2D* /*a*/, - const Field2D* /*c1coef*/, const Field2D* /*c2coef*/, - const Field2D* /*d*/, bool /*includeguards*/, - bool /*zperiodic*/) { + const Field2D* /*a*/, const Field2D* /*c1coef*/, + const Field2D* /*c2coef*/, const Field2D* /*d*/, + bool /*includeguards*/, bool /*zperiodic*/) { throw BoutException("Error: tridagMatrix does not yet work with 3D metric."); } #else void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk, - int jy, int kz, BoutReal kwave, int global_flags, - int inner_boundary_flags, int outer_boundary_flags, - const Field2D* a, const Field2D* c1coef, - const Field2D* c2coef, const Field2D* d, bool includeguards, - bool zperiodic) { + int jy, int kz, BoutReal kwave, const Field2D* a, + const Field2D* c1coef, const Field2D* c2coef, + const Field2D* d, bool includeguards, bool zperiodic) { ASSERT1(a->getLocation() == location); ASSERT1(c1coef->getLocation() == location); ASSERT1(c2coef->getLocation() == location); From fe30f47f7bc3a7ef2b9e754c4119d6665e91e59a Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 24 May 2024 09:03:54 +0100 Subject: [PATCH 371/412] Add getters for Laplacian flags, make data members private --- include/bout/invert_laplace.hxx | 12 ++++++++---- src/invert/laplace/impls/naulin/naulin_laplace.cxx | 6 +++--- src/invert/laplace/impls/petsc3damg/petsc3damg.cxx | 8 ++++---- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index d041403ffb..b1ff84782f 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -238,6 +238,10 @@ public: virtual void setInnerBoundaryFlags(int f) { inner_boundary_flags = f; } virtual void setOuterBoundaryFlags(int f) { outer_boundary_flags = f; } + virtual int getGlobalFlags() const { return global_flags; } + virtual int getInnerBoundaryFlags() const { return inner_boundary_flags; } + virtual int getOuterBoundaryFlags() const { return outer_boundary_flags; } + /// Does this solver use Field3D coefficients (true) or only their DC component (false) virtual bool uses3DCoefs() const { return false; } @@ -326,10 +330,6 @@ protected: /// on the outer processor(s) bool isOuterBoundaryFlagSetOnLastX(int flag) const; - int global_flags; ///< Default flags - int inner_boundary_flags; ///< Flags to set inner boundary condition - int outer_boundary_flags; ///< Flags to set outer boundary condition - void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, dcomplex& c, const Field2D* ccoef = nullptr, const Field2D* d = nullptr, CELL_LOC loc = CELL_DEFAULT) { @@ -355,6 +355,10 @@ protected: /// localmesh->getCoordinates(location) once private: + int global_flags; ///< Default flags + int inner_boundary_flags; ///< Flags to set inner boundary condition + int outer_boundary_flags; ///< Flags to set outer boundary condition + /// Singleton instance static std::unique_ptr instance; /// Name for writing performance infomation; default taken from diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx index 585d78a0fc..e315d3c771 100644 --- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx +++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx @@ -174,9 +174,9 @@ LaplaceNaulin::LaplaceNaulin(Options* opt, const CELL_LOC loc, Mesh* mesh_in, // invert Delp2 and we will not converge ASSERT0(delp2type == "cyclic" || delp2type == "spt" || delp2type == "tri"); // Use same flags for FFT solver as for NaulinSolver - delp2solver->setGlobalFlags(global_flags); - delp2solver->setInnerBoundaryFlags(inner_boundary_flags); - delp2solver->setOuterBoundaryFlags(outer_boundary_flags); + delp2solver->setGlobalFlags(getGlobalFlags()); + delp2solver->setInnerBoundaryFlags(getInnerBoundaryFlags()); + delp2solver->setOuterBoundaryFlags(getOuterBoundaryFlags()); static int naulinsolver_count = 1; setPerformanceName(fmt::format("{}{}", "naulinsolver", ++naulinsolver_count)); diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx index 40e3b5fbe8..a7bfd209ee 100644 --- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx +++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx @@ -102,8 +102,8 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes name); } }; - unimplementedBoundaryFlag(inner_boundary_flags, "inner"); - unimplementedBoundaryFlag(outer_boundary_flags, "outer"); + unimplementedBoundaryFlag(getInnerBoundaryFlags(), "inner"); + unimplementedBoundaryFlag(getOuterBoundaryFlags(), "outer"); unimplementedBoundaryFlag(lower_boundary_flags, "lower"); unimplementedBoundaryFlag(upper_boundary_flags, "upper"); @@ -191,8 +191,8 @@ Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) { // Adjust vectors to represent boundary conditions and check that // boundary cells are finite - setBC(rhs, b_in, indexer->getRegionInnerX(), inner_boundary_flags, x0); - setBC(rhs, b_in, indexer->getRegionOuterX(), outer_boundary_flags, x0); + setBC(rhs, b_in, indexer->getRegionInnerX(), getInnerBoundaryFlags(), x0); + setBC(rhs, b_in, indexer->getRegionOuterX(), getOuterBoundaryFlags(), x0); setBC(rhs, b_in, indexer->getRegionLowerY(), lower_boundary_flags, x0); setBC(rhs, b_in, indexer->getRegionUpperY(), upper_boundary_flags, x0); From 85c8673010bce9a018fb5d80f6b1983b7319eb76 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 24 May 2024 09:27:01 +0100 Subject: [PATCH 372/412] Replace VLAs with `std::vector` Also add an assert to keep static analysis happy, otherwise it might decide `ny` is negative :shrug: --- .../laplace/impls/cyclic/cyclic_laplace.cxx | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx index a9bf0536ca..5ce4e540b7 100644 --- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx +++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx @@ -33,11 +33,13 @@ * */ -#include "cyclic_laplace.hxx" -#include "bout/build_config.hxx" +#include "bout/build_defines.hxx" #if not BOUT_USE_METRIC_3D +#include "cyclic_laplace.hxx" +#include "bout/assert.hxx" +#include "bout/bout_types.hxx" #include #include #include @@ -47,7 +49,7 @@ #include #include -#include "cyclic_laplace.hxx" +#include LaplaceCyclic::LaplaceCyclic(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED(solver)) @@ -348,6 +350,9 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { const int nsys = nmode * ny; // Number of systems of equations to solve const int nxny = nx * ny; // Number of points in X-Y + // This is just to silence static analysis + ASSERT0(ny > 0); + auto a3D = Matrix(nsys, nx); auto b3D = Matrix(nsys, nx); auto c3D = Matrix(nsys, nx); @@ -496,9 +501,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { if (localmesh->periodicX) { // Subtract X average of kz=0 mode - BoutReal local[ny + 1]; + std::vector local(ny + 1, 0.0); for (int y = 0; y < ny; y++) { - local[y] = 0.0; for (int ix = xs; ix <= xe; ix++) { local[y] += xcmplx3D(y * nmode, ix - xs).real(); } @@ -506,8 +510,9 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) { local[ny] = static_cast(xe - xs + 1); // Global reduce - BoutReal global[ny + 1]; - MPI_Allreduce(local, global, ny + 1, MPI_DOUBLE, MPI_SUM, localmesh->getXcomm()); + std::vector global(ny + 1, 0.0); + MPI_Allreduce(local.data(), global.data(), ny + 1, MPI_DOUBLE, MPI_SUM, + localmesh->getXcomm()); // Subtract average from kz=0 modes for (int y = 0; y < ny; y++) { BoutReal avg = global[y] / global[ny]; From 365790dfc6497a25f5ff3b106fe1bba5d394c71d Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 24 May 2024 09:56:24 +0100 Subject: [PATCH 373/412] Replace raw `new` with `Array` This also fixes a crash in `clang-tidy` from adjusting the `alldata` pointer in the dtor --- src/invert/laplace/impls/spt/spt.cxx | 26 ++++++++++---------------- src/invert/laplace/impls/spt/spt.hxx | 17 +++++++---------- 2 files changed, 17 insertions(+), 26 deletions(-) diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx index 2426b362f6..2e4c844c94 100644 --- a/src/invert/laplace/impls/spt/spt.cxx +++ b/src/invert/laplace/impls/spt/spt.cxx @@ -65,10 +65,9 @@ LaplaceSPT::LaplaceSPT(Options* opt, const CELL_LOC loc, Mesh* mesh_in, ye = localmesh->LocalNy - 1; // Contains upper boundary } - alldata = new SPT_data[ye - ys + 1]; - alldata -= ys; // Re-number indices to start at ys + alldata.reallocate(ye - ys + 1); for (int jy = ys; jy <= ye; jy++) { - alldata[jy].comm_tag = SPT_DATA + jy; // Give each one a different tag + alldata[jy - ys].comm_tag = SPT_DATA + jy; // Give each one a different tag } // Temporary array for taking FFTs @@ -76,11 +75,6 @@ LaplaceSPT::LaplaceSPT(Options* opt, const CELL_LOC loc, Mesh* mesh_in, dc1d.reallocate(ncz / 2 + 1); } -LaplaceSPT::~LaplaceSPT() { - alldata += ys; // Return to index from 0 - delete[] alldata; -} - FieldPerp LaplaceSPT::solve(const FieldPerp& b) { return solve(b, b); } FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) { @@ -141,29 +135,29 @@ Field3D LaplaceSPT::solve(const Field3D& b) { for (int jy = ys; jy <= ye; jy++) { // And start another one going - start(sliceXZ(b, jy), alldata[jy]); + start(sliceXZ(b, jy), alldata[jy - ys]); // Move each calculation along one processor for (int jy2 = ys; jy2 < jy; jy2++) { - next(alldata[jy2]); + next(alldata[jy2 - ys]); } } bool running = true; - do { + while (running) { // Move each calculation along until the last one is finished - for (int jy = ys; jy <= ye; jy++) { - running = next(alldata[jy]) == 0; + for (auto& data : alldata) { + running = next(data) == 0; } - } while (running); + } FieldPerp xperp(localmesh); xperp.setLocation(location); xperp.allocate(); // All calculations finished. Get result - for (int jy = ys; jy <= ye; jy++) { - finish(alldata[jy], xperp); + for (auto& data : alldata) { + finish(data, xperp); x = xperp; } diff --git a/src/invert/laplace/impls/spt/spt.hxx b/src/invert/laplace/impls/spt/spt.hxx index c6aa8fd404..a9d5b2583f 100644 --- a/src/invert/laplace/impls/spt/spt.hxx +++ b/src/invert/laplace/impls/spt/spt.hxx @@ -69,7 +69,6 @@ class LaplaceSPT : public Laplacian { public: LaplaceSPT(Options* opt = nullptr, const CELL_LOC = CELL_CENTRE, Mesh* mesh_in = nullptr, Solver* solver = nullptr); - ~LaplaceSPT(); using Laplacian::setCoefA; void setCoefA(const Field2D& val) override { @@ -106,17 +105,15 @@ public: Field3D solve(const Field3D& b, const Field3D& x0) override; private: - enum { SPT_DATA = 1123 }; ///< 'magic' number for SPT MPI messages + constexpr static int SPT_DATA = 1123; ///< 'magic' number for SPT MPI messages Field2D Acoef, Ccoef, Dcoef; /// Data structure for SPT algorithm struct SPT_data { - SPT_data() : comm_tag(SPT_DATA) {} void allocate(int mm, int nx); // Allocates memory - ~SPT_data(){}; // Free memory - int jy; ///< Y index + int jy = 0; ///< Y index Matrix bk; ///< b vector in Fourier space Matrix xk; @@ -125,19 +122,19 @@ private: Matrix avec, bvec, cvec; ///< Diagonal bands of matrix - int proc; // Which processor has this reached? - int dir; // Which direction is it going? + int proc = 0; // Which processor has this reached? + int dir = 1; // Which direction is it going? - comm_handle recv_handle; // Handle for receives + comm_handle recv_handle = nullptr; // Handle for receives - int comm_tag; // Tag for communication + int comm_tag = SPT_DATA; // Tag for communication Array buffer; }; int ys, ye; // Range of Y indices SPT_data slicedata; // Used to solve for a single FieldPerp - SPT_data* alldata; // Used to solve a Field3D + Array alldata; // Used to solve a Field3D Array dc1d; ///< 1D in Z for taking FFTs From 0ac1e5fc9b7d11df7a9d85720255369fb1106093 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 28 May 2024 11:53:24 +0100 Subject: [PATCH 374/412] Don't set deprecated 4th order flag in PETSc laplace test --- tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx index bfd394194f..6929a58542 100644 --- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx @@ -325,7 +325,6 @@ int main(int argc, char** argv) { invert_4th->setInnerBoundaryFlags(INVERT_AC_GRAD); invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setGlobalFlags(INVERT_4TH_ORDER); invert_4th->setCoefA(a1); invert_4th->setCoefC(c1); invert_4th->setCoefD(d1); @@ -702,7 +701,6 @@ int main(int argc, char** argv) { BoutReal max_error6; //Output of test invert_4th->setInnerBoundaryFlags(INVERT_AC_GRAD); invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setGlobalFlags(INVERT_4TH_ORDER); invert_4th->setCoefA(a5); invert_4th->setCoefC(c5); invert_4th->setCoefD(d5); From ae643d8bd6ac1245a0bbd54517be3f9de69b3793 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 28 May 2024 13:39:45 +0100 Subject: [PATCH 375/412] Fix PETSc stack trace issue --- src/invert/laplace/impls/petsc/petsc_laplace.cxx | 1 + 1 file changed, 1 insertion(+) diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx index c5a81b03d6..fd326d1a3c 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx @@ -50,6 +50,7 @@ static PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) { int ierr; + PetscFunctionBegin; // Get the context LaplacePetsc* s; From aadb9d644df473758cacdc67c2935ef498f9026c Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 28 May 2024 13:40:41 +0100 Subject: [PATCH 376/412] Fix some clang-tidy issues with PETSc laplace preconditioner PETSc does a bunch of things wrong, so forces us to do a bunch of things wrong. There isn't actually a way of calling `PCShellGetContext` that keeps clang-tidy happy, I think mostly because it should take `void**` and instead takes `void*` --- include/bout/petsclib.hxx | 2 +- src/invert/laplace/impls/petsc/petsc_laplace.cxx | 11 +++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index 35334ce773..2008671286 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -59,7 +59,7 @@ class Options; // means we _must_ `#include` this header _before_ any PETSc header! #define PETSC_HAVE_BROKEN_RECURSIVE_MACRO -#include +#include // IWYU pragma: export #include #include "bout/boutexception.hxx" diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx index fd326d1a3c..de9ef05025 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx @@ -32,6 +32,7 @@ #include #include #include +#include #include #include @@ -49,15 +50,13 @@ #define KSP_PREONLY "preonly" static PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) { - int ierr; - PetscFunctionBegin; + PetscFunctionBegin; // NOLINT - // Get the context - LaplacePetsc* s; - ierr = PCShellGetContext(pc, reinterpret_cast(&s)); + LaplacePetsc* laplace = nullptr; + const int ierr = PCShellGetContext(pc, reinterpret_cast(&laplace)); // NOLINT CHKERRQ(ierr); - PetscFunctionReturn(s->precon(x, y)); + PetscFunctionReturn(laplace->precon(x, y)); // NOLINT } LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, From 232c3c51b75ad8015923c8c4ad802e2bad8bbdaf Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 28 May 2024 13:54:51 +0100 Subject: [PATCH 377/412] Tidy up test-petsc-laplace --- .../test-petsc_laplace/test_petsc_laplace.cxx | 323 +++++++----------- 1 file changed, 125 insertions(+), 198 deletions(-) diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx index 6929a58542..222f1e6886 100644 --- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx @@ -23,10 +23,10 @@ * **************************************************************************/ +#include "bout/bout_types.hxx" #include -#include -// #include #include +#include #include #include #include @@ -43,11 +43,17 @@ int main(int argc, char** argv) { auto invert_4th = Laplacian::create(options); // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d - Field3D f1, a1, b1, c1, d1, sol1; - BoutReal p, q; //Use to set parameters in constructing trial functions - Field3D error1, - absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) - BoutReal max_error1; //Output of test + Field3D f1; + Field3D a1; + Field3D b1; + Field3D c1; + Field3D d1; + Field3D sol1; + BoutReal p; + BoutReal q; //Use to set parameters in constructing trial functions + Field3D error1; + Field3D absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) + BoutReal max_error1 = -1; //Output of test using bout::globals::mesh; @@ -56,7 +62,7 @@ int main(int argc, char** argv) { BoutReal nx = mesh->GlobalNx - 2 * mesh->xstart - 1; BoutReal nz = mesh->GlobalNz; - //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + ///////////////////////////////////////////////////// // Test 1: Gaussian x-profiles, 2nd order Krylov p = 0.39503274; q = 0.20974396; @@ -64,20 +70,16 @@ int main(int argc, char** argv) { for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { for (int jy = 0; jy < mesh->LocalNy; jy++) { for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - f1(jx, jy, jz) = - 0. + exp(-(100. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-100. * pow(-p, 2)) * x - + (-p * exp(-100. * pow(-p, 2)) - - (1 - p) * exp(-100. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-( - 1. - - cos(2. * PI - * (z - q)))) //make the gradients zero at both x-boundaries - ; + const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + f1(jx, jy, jz) = 0. + exp(-(100. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-100. * pow(-p, 2)) * x + + (-p * exp(-100. * pow(-p, 2)) + - (1 - p) * exp(-100. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); ASSERT0(finite(f1(jx, jy, jz))); } } @@ -86,20 +88,17 @@ int main(int argc, char** argv) { for (int jx = mesh->xstart - 1; jx >= 0; jx--) { for (int jy = 0; jy < mesh->LocalNy; jy++) { for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - f1(jx, jy, jz) = - 0. + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-60. * pow(-p, 2)) * x - + (-p * exp(-60. * pow(-p, 2)) - - (1 - p) * exp(-60. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-( - 1. - - cos( - 2. * PI - * (z - q)))); //make the gradients zero at both x-boundaries + const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + f1(jx, jy, jz) = 0. + + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-60. * pow(-p, 2)) * x + + (-p * exp(-60. * pow(-p, 2)) + - (1 - p) * exp(-60. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); ASSERT0(finite(f1(jx, jy, jz))); } } @@ -109,20 +108,17 @@ int main(int argc, char** argv) { for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { for (int jy = 0; jy < mesh->LocalNy; jy++) { for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - f1(jx, jy, jz) = - 0. + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-60. * pow(-p, 2)) * x - + (-p * exp(-60. * pow(-p, 2)) - - (1 - p) * exp(-60. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-( - 1. - - cos( - 2. * PI - * (z - q)))); //make the gradients zero at both x-boundaries + const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + f1(jx, jy, jz) = 0. + + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-60. * pow(-p, 2)) * x + + (-p * exp(-60. * pow(-p, 2)) + - (1 - p) * exp(-60. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); ASSERT0(finite(f1(jx, jy, jz))); } } @@ -152,7 +148,6 @@ int main(int argc, char** argv) { BoutReal z = BoutReal(jz) / nz; d1(jx, jy, jz) = 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); - // d1(jx, jy, jz) = d1(jx+1, jy, jz); } } } @@ -165,7 +160,6 @@ int main(int argc, char** argv) { BoutReal z = BoutReal(jz) / nz; d1(jx, jy, jz) = 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); - // d1(jx, jy, jz) = d1(jx-1, jy, jz); } } } @@ -192,7 +186,6 @@ int main(int argc, char** argv) { BoutReal z = BoutReal(jz) / nz; c1(jx, jy, jz) = 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); - // c1(jx, jy, jz) = c1(jx+1, jy, jz); } } } @@ -205,7 +198,6 @@ int main(int argc, char** argv) { BoutReal z = BoutReal(jz) / nz; c1(jx, jy, jz) = 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); - // c1(jx, jy, jz) = c1(jx-1, jy, jz); } } } @@ -232,7 +224,6 @@ int main(int argc, char** argv) { BoutReal z = BoutReal(jz) / nz; a1(jx, jy, jz) = -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); - // a1(jx, jy, jz) = a1(jx+1, jy, jz); } } } @@ -245,7 +236,6 @@ int main(int argc, char** argv) { BoutReal z = BoutReal(jz) / nz; a1(jx, jy, jz) = -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); - // a1(jx, jy, jz) = a1(jx-1, jy, jz); } } } @@ -291,19 +281,13 @@ int main(int argc, char** argv) { sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); error1 = (f1 - sol1) / f1; absolute_error1 = f1 - sol1; - // max_error1 = max_error_at_ystart(abs(error1)); max_error1 = max_error_at_ystart(abs(absolute_error1)); } catch (BoutException& err) { - output << "BoutException occured in invert->solve(b1): " << err.what() << endl; - max_error1 = -1; + output.write("BoutException occured in invert->solve(b1): {}\n", err.what()); } - output << endl << "Test 1: PETSc 2nd order" << endl; - // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); @@ -333,19 +317,13 @@ int main(int argc, char** argv) { sol2 = invert_4th->solve(sliceXZ(b1, mesh->ystart)); error2 = (f1 - sol2) / f1; absolute_error2 = f1 - sol2; - // max_error2 = max_error_at_ystart(abs(error2)); max_error2 = max_error_at_ystart(abs(absolute_error2)); } catch (BoutException& err) { - output << "BoutException occured in invert->solve(b1): " << err.what() << endl; - max_error2 = -1; + output.write("BoutException occured in invert->solve(b1): {}\n", err.what()); } - output << endl << "Test 2: PETSc 4th order" << endl; - // output<<"Time to set up is "<firstX()) { for (int jx = mesh->xstart - 1; jx >= 0; jx--) { for (int jy = 0; jy < mesh->LocalNy; jy++) { @@ -398,19 +374,13 @@ int main(int argc, char** argv) { sol3 = invert->solve(sliceXZ(b3, mesh->ystart)); error3 = (f1 - sol3) / f1; absolute_error3 = f1 - sol3; - // max_error3 = max_error_at_ystart(abs(error3)); max_error3 = max_error_at_ystart(abs(absolute_error3)); } catch (BoutException& err) { - output << "BoutException occured in invert->solve(b3): " << err.what() << endl; - max_error3 = -1; + output.write("BoutException occured in invert->solve(b3): {}\n", err.what()); } - output << endl << "Test 3: with coefficients constant in z, PETSc 2nd order" << endl; - // output<<"Time to set up is "<getSection("SPT"); + Options* SPT_options = Options::getRoot()->getSection("SPT"); auto invert_SPT = Laplacian::create(SPT_options); invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD); invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); @@ -434,15 +403,10 @@ int main(int argc, char** argv) { sol4 = invert_SPT->solve(sliceXZ(b3, mesh->ystart)); error4 = (f1 - sol4) / f1; absolute_error4 = f1 - sol4; - // max_error4 = max_error_at_ystart(abs(error4)); - max_error4 = max_error_at_ystart(abs(absolute_error4)); + const BoutReal max_error4 = max_error_at_ystart(abs(absolute_error4)); - output << endl << "Test 4: with coefficients constant in z, default solver" << endl; - // output<<"Time to set up is "<xstart; jx <= mesh->xend; jx++) { for (int jy = 0; jy < mesh->LocalNy; jy++) { for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - f5(jx, jy, jz) = - 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-50. * pow(-p, 2)) * x - + (-p * exp(-50. * pow(-p, 2)) - - (1 - p) * exp(-50. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-( - 1. - - cos(2. * PI - * (z - q)))) //make the gradients zero at both x-boundaries - ; + const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + f5(jx, jy, jz) = 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } @@ -490,18 +450,15 @@ int main(int argc, char** argv) { for (int jz = 0; jz < mesh->LocalNz; jz++) { BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; BoutReal z = BoutReal(jz) / nz; - f5(jx, jy, jz) = - 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-50. * pow(-p, 2)) * x - + (-p * exp(-50. * pow(-p, 2)) - - (1 - p) * exp(-50. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-( - 1. - - cos( - 2. * PI - * (z - q)))); //make the gradients zero at both x-boundaries + //make the gradients zero at both x-boundaries + f5(jx, jy, jz) = 0. + + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } @@ -512,18 +469,15 @@ int main(int argc, char** argv) { for (int jz = 0; jz < mesh->LocalNz; jz++) { BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; BoutReal z = BoutReal(jz) / nz; - f5(jx, jy, jz) = - 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-50. * pow(-p, 2)) * x - + (-p * exp(-50. * pow(-p, 2)) - - (1 - p) * exp(-50. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-( - 1. - - cos( - 2. * PI - * (z - q)))); //make the gradients zero at both x-boundaries + //make the gradients zero at both x-boundaries + f5(jx, jy, jz) = 0. + + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } @@ -669,19 +623,13 @@ int main(int argc, char** argv) { sol5 = invert->solve(sliceXZ(b5, mesh->ystart)); error5 = (f5 - sol5) / f5; absolute_error5 = f5 - sol5; - // max_error5 = max_error_at_ystart(abs(error5)); max_error5 = max_error_at_ystart(abs(absolute_error5)); } catch (BoutException& err) { - output << "BoutException occured in invert->solve(b5): " << err.what() << endl; - max_error5 = -1; + output.write("BoutException occured in invert->solve(b5): {}\n", err.what()); } - output << endl << "Test 5: different profiles, PETSc 2nd order" << endl; - // output<<"Time to set up is "<setInnerBoundaryFlags(INVERT_AC_GRAD); invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); invert_4th->setCoefA(a5); @@ -709,22 +657,16 @@ int main(int argc, char** argv) { sol6 = invert_4th->solve(sliceXZ(b5, mesh->ystart)); error6 = (f5 - sol6) / f5; absolute_error6 = f5 - sol6; - // max_error6 = max_error_at_ystart(abs(error6)); max_error6 = max_error_at_ystart(abs(absolute_error6)); } catch (BoutException& err) { - output - << "BoutException occured in invert->solve(b6): Laplacian inversion failed to " - "converge (probably)" - << endl; - max_error6 = -1; + output.write( + "BoutException occured in invert->solve(b6): Laplacian inversion failed to " + "converge (probably): {}\n", + err.what()); } - output << endl << "Test 6: different profiles, PETSc 4th order" << endl; - // output<<"Time to set up is "<solve(sliceXZ(b7, mesh->ystart)); error7 = (f5 - sol7) / f5; absolute_error7 = f5 - sol7; - // max_error7 = max_error_at_ystart(abs(error7)); max_error7 = max_error_at_ystart(abs(absolute_error7)); } catch (BoutException& err) { - output << "BoutException occured in invert->solve(b7): " << err.what() << endl; - max_error7 = -1; + output.write("BoutException occured in invert->solve(b7): {}\n", err.what()); } - output - << endl - << "Test 7: different profiles, with coefficients constant in z, PETSc 2nd order" - << endl; - // output<<"Time to set up is "<solve(sliceXZ(b7, mesh->ystart)); error8 = (f5 - sol8) / f5; absolute_error8 = f5 - sol8; - // max_error8 = max_error_at_ystart(abs(error8)); - max_error8 = max_error_at_ystart(abs(absolute_error8)); - - output - << endl - << "Test 8: different profiles, with coefficients constant in z, default solver" - << endl; - // output<<"Time to set up is "< Date: Tue, 28 May 2024 14:34:06 +0100 Subject: [PATCH 378/412] Pull out helper functions for PETSc laplace tests --- .../test-petsc_laplace/test_petsc_laplace.cxx | 454 +++++------------- 1 file changed, 122 insertions(+), 332 deletions(-) diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx index 222f1e6886..aab3fe61c0 100644 --- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx @@ -23,15 +23,68 @@ * **************************************************************************/ +#include "bout/bout.hxx" #include "bout/bout_types.hxx" -#include -#include -#include -#include -#include +#include "bout/boutexception.hxx" +#include "bout/constants.hxx" +#include "bout/field2d.hxx" +#include "bout/field3d.hxx" +#include "bout/invert_laplace.hxx" +#include "bout/options.hxx" +#include "bout/output.hxx" +#include "bout/traits.hxx" + +#include "fmt/core.h" + #include +#include BoutReal max_error_at_ystart(const Field3D& error); +void apply_flat_boundary(Field3D& bcoef); + +template +void check_laplace(int test_num, std::string_view test_name, Laplacian& invert, + int inner_flags, int outer_flags, const T& acoef, const T& ccoef, + const T& dcoef, const U& bcoef, const Field3D& field, int ystart, + Options& dump) { + static_assert(bout::utils::is_Field_v, "check_laplace requires Field2D or Field3D"); + static_assert(bout::utils::is_Field_v, "check_laplace requires Field2D or Field3D"); + + invert.setInnerBoundaryFlags(inner_flags); + invert.setOuterBoundaryFlags(outer_flags); + invert.setCoefA(acoef); + invert.setCoefC(ccoef); + invert.setCoefD(dcoef); + + checkData(bcoef); + + Field3D sol; + Field3D error; + Field3D abs_error; + BoutReal max_error = -1; + + try { + sol = invert.solve(sliceXZ(bcoef, ystart)); + error = (field - sol) / field; + abs_error = field - sol; + max_error = max_error_at_ystart(abs(abs_error)); + } catch (BoutException& err) { + output.write("BoutException occured in invert->solve(b1): {}\n", err.what()); + } + + output.write("\nTest {}: {}\n", test_num, test_name); + output.write("Magnitude of maximum absolute error is {}\n", max_error); + + dump[fmt::format("a{}", test_num)] = acoef; + dump[fmt::format("b{}", test_num)] = bcoef; + dump[fmt::format("c{}", test_num)] = ccoef; + dump[fmt::format("d{}", test_num)] = dcoef; + dump[fmt::format("f{}", test_num)] = field; + dump[fmt::format("sol{}", test_num)] = sol; + dump[fmt::format("error{}", test_num)] = error; + dump[fmt::format("absolute_error{}", test_num)] = abs_error; + dump[fmt::format("max_error{}", test_num)] = max_error; +} int main(int argc, char** argv) { @@ -42,25 +95,22 @@ int main(int argc, char** argv) { options = Options::getRoot()->getSection("petsc4th"); auto invert_4th = Laplacian::create(options); + Options dump; + // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d Field3D f1; Field3D a1; - Field3D b1; Field3D c1; Field3D d1; - Field3D sol1; BoutReal p; BoutReal q; //Use to set parameters in constructing trial functions - Field3D error1; - Field3D absolute_error1; //Absolute value of relative error: abs( (f1-sol1)/f1 ) - BoutReal max_error1 = -1; //Output of test using bout::globals::mesh; // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z. // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point - BoutReal nx = mesh->GlobalNx - 2 * mesh->xstart - 1; - BoutReal nz = mesh->GlobalNz; + const BoutReal nx = mesh->GlobalNx - 2 * mesh->xstart - 1; + const BoutReal nz = mesh->GlobalNz; ///////////////////////////////////////////////////// // Test 1: Gaussian x-profiles, 2nd order Krylov @@ -248,182 +298,41 @@ int main(int argc, char** argv) { mesh->communicate(f1, a1, c1, d1); - b1 = d1 * Delp2(f1) + Grad_perp(c1) * Grad_perp(f1) / c1 + a1 * f1; - - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b1(jx, jy, jz) = b1(jx + 1, jy, jz); - } - } - } - } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b1(jx, jy, jz) = b1(jx - 1, jy, jz); - } - } - } - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a1); - invert->setCoefC(c1); - invert->setCoefD(d1); - - checkData(b1); - - try { - sol1 = invert->solve(sliceXZ(b1, mesh->ystart)); - error1 = (f1 - sol1) / f1; - absolute_error1 = f1 - sol1; - max_error1 = max_error_at_ystart(abs(absolute_error1)); - } catch (BoutException& err) { - output.write("BoutException occured in invert->solve(b1): {}\n", err.what()); - } + Field3D b1 = d1 * Delp2(f1) + Grad_perp(c1) * Grad_perp(f1) / c1 + a1 * f1; + apply_flat_boundary(b1); - output.write("\nTest 1: PETSc 2nd order\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error1); - - Options dump; - dump["a1"] = a1; - dump["b1"] = b1; - dump["c1"] = c1; - dump["d1"] = d1; - dump["f1"] = f1; - dump["sol1"] = sol1; - dump["error1"] = error1; - dump["absolute_error1"] = absolute_error1; - dump["max_error1"] = max_error1; + int test_num = 0; + check_laplace(++test_num, "PETSc 2nd order", *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a1, c1, + d1, b1, f1, mesh->ystart, dump); ///////////////////////////////////////////////// // Test 2: Gaussian x-profiles, 4th order Krylov - Field3D sol2; - Field3D error2; - Field3D absolute_error2; //Absolute value of relative error: abs( (f3-sol3)/f3 ) - BoutReal max_error2 = -1; //Output of test - - invert_4th->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setCoefA(a1); - invert_4th->setCoefC(c1); - invert_4th->setCoefD(d1); - - try { - sol2 = invert_4th->solve(sliceXZ(b1, mesh->ystart)); - error2 = (f1 - sol2) / f1; - absolute_error2 = f1 - sol2; - max_error2 = max_error_at_ystart(abs(absolute_error2)); - } catch (BoutException& err) { - output.write("BoutException occured in invert->solve(b1): {}\n", err.what()); - } - - output.write("\nTest 2: PETSc 4th order\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error2); - dump["a2"] = a1; - dump["b2"] = b1; - dump["c2"] = c1; - dump["d2"] = d1; - dump["f2"] = f1; - dump["sol2"] = sol2; - dump["error2"] = error2; - dump["absolute_error2"] = absolute_error2; - dump["max_error2"] = max_error2; + check_laplace(++test_num, "PETSc 4th order", *invert_4th, INVERT_AC_GRAD, INVERT_AC_GRAD, a1, + c1, d1, b1, f1, mesh->ystart, dump); //////////////////////////////////////////////////////////////////////////////////////// // Test 3+4: Gaussian x-profiles, z-independent coefficients and compare with SPT method - Field3D sol3, sol4; - Field3D error3, absolute_error3, error4, absolute_error4; - BoutReal max_error3 = -1; - Field2D a3 = DC(a1); - Field2D c3 = DC(c1); - Field2D d3 = DC(d1); + const Field2D a3 = DC(a1); + const Field2D c3 = DC(c1); + const Field2D d3 = DC(d1); Field3D b3 = d3 * Delp2(f1) + Grad_perp(c3) * Grad_perp(f1) / c3 + a3 * f1; - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b3(jx, jy, jz) = b3(jx + 1, jy, jz); - } - } - } - } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b3(jx, jy, jz) = b3(jx - 1, jy, jz); - } - } - } - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a3); - invert->setCoefC(c3); - invert->setCoefD(d3); - - try { - sol3 = invert->solve(sliceXZ(b3, mesh->ystart)); - error3 = (f1 - sol3) / f1; - absolute_error3 = f1 - sol3; - max_error3 = max_error_at_ystart(abs(absolute_error3)); - } catch (BoutException& err) { - output.write("BoutException occured in invert->solve(b3): {}\n", err.what()); - } + apply_flat_boundary(b3); - output.write("\nTest 3: with coefficients constant in z, PETSc 2nd order\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error3); - - dump["a3"] = a3; - dump["b3"] = b3; - dump["c3"] = c3; - dump["d3"] = d3; - dump["f3"] = f1; - dump["sol3"] = sol3; - dump["error3"] = error3; - dump["absolute_error3"] = absolute_error3; - dump["max_error3"] = max_error3; + check_laplace(++test_num, "with coefficients constant in z, PETSc 2nd order", *invert, + INVERT_AC_GRAD, INVERT_AC_GRAD, a3, c3, d3, b3, f1, mesh->ystart, dump); Options* SPT_options = Options::getRoot()->getSection("SPT"); auto invert_SPT = Laplacian::create(SPT_options); - invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); - invert_SPT->setCoefA(a3); - invert_SPT->setCoefC(c3); - invert_SPT->setCoefD(d3); - - sol4 = invert_SPT->solve(sliceXZ(b3, mesh->ystart)); - error4 = (f1 - sol4) / f1; - absolute_error4 = f1 - sol4; - const BoutReal max_error4 = max_error_at_ystart(abs(absolute_error4)); - - output.write("\nTest 4: with coefficients constant in z, default solver\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error4); - - dump["a4"] = a3; - dump["b4"] = b3; - dump["c4"] = c3; - dump["d4"] = d3; - dump["f4"] = f1; - dump["sol4"] = sol4; - dump["error4"] = error4; - dump["absolute_error4"] = absolute_error4; - dump["max_error4"] = max_error4; - - //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + check_laplace(++test_num, "with coefficients constant in z, default solver", *invert_SPT, + INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a3, c3, d3, b3, f1, + mesh->ystart, dump); + + ////////////////////////////////////////////// // Test 5: Cosine x-profiles, 2nd order Krylov - Field3D f5, a5, b5, c5, d5, sol5; - Field3D error5; - Field3D absolute_error5; //Absolute value of relative error: abs( (f5-sol5)/f5 ) - BoutReal max_error5 = -1; //Output of test + Field3D f5, a5, c5, d5; p = 0.623901; q = 0.01209489; @@ -593,175 +502,34 @@ int main(int argc, char** argv) { f5.applyBoundary("neumann"); mesh->communicate(f5, a5, c5, d5); - b5 = d5 * Delp2(f5) + Grad_perp(c5) * Grad_perp(f5) / c5 + a5 * f5; - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b5(jx, jy, jz) = b5(jx + 1, jy, jz); - } - } - } - } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b5(jx, jy, jz) = b5(jx - 1, jy, jz); - } - } - } - } - - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a5); - invert->setCoefC(c5); - invert->setCoefD(d5); - - try { - sol5 = invert->solve(sliceXZ(b5, mesh->ystart)); - error5 = (f5 - sol5) / f5; - absolute_error5 = f5 - sol5; - max_error5 = max_error_at_ystart(abs(absolute_error5)); - } catch (BoutException& err) { - output.write("BoutException occured in invert->solve(b5): {}\n", err.what()); - } + Field3D b5 = d5 * Delp2(f5) + Grad_perp(c5) * Grad_perp(f5) / c5 + a5 * f5; + apply_flat_boundary(b5); - output.write("\nTest 5: different profiles, PETSc 2nd order\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error5); - - dump["a5"] = a5; - dump["b5"] = b5; - dump["c5"] = c5; - dump["d5"] = d5; - dump["f5"] = f5; - dump["sol5"] = sol5; - dump["error5"] = error5; - dump["absolute_error5"] = absolute_error5; - dump["max_error5"] = max_error5; + check_laplace(++test_num, "different profiles, PETSc 2nd order", *invert, INVERT_AC_GRAD, + INVERT_AC_GRAD, a5, c5, d5, b5, f5, mesh->ystart, dump); ////////////////////////////////////////////// // Test 6: Cosine x-profiles, 4th order Krylov - Field3D sol6; - Field3D error6; - Field3D absolute_error6; //Absolute value of relative error: abs( (f5-sol5)/f5 ) - BoutReal max_error6 = -1; //Output of test - invert_4th->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert_4th->setCoefA(a5); - invert_4th->setCoefC(c5); - invert_4th->setCoefD(d5); - - try { - sol6 = invert_4th->solve(sliceXZ(b5, mesh->ystart)); - error6 = (f5 - sol6) / f5; - absolute_error6 = f5 - sol6; - max_error6 = max_error_at_ystart(abs(absolute_error6)); - } catch (BoutException& err) { - output.write( - "BoutException occured in invert->solve(b6): Laplacian inversion failed to " - "converge (probably): {}\n", - err.what()); - } - - output.write("\nTest 6: different profiles, PETSc 4th order\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error6); - dump["a6"] = a5; - dump["b6"] = b5; - dump["c6"] = c5; - dump["d6"] = d5; - dump["f6"] = f5; - dump["sol6"] = sol6; - dump["error6"] = error6; - dump["absolute_error6"] = absolute_error6; - dump["max_error6"] = max_error6; + check_laplace(++test_num, "different profiles, PETSc 4th order", *invert_4th, INVERT_AC_GRAD, + INVERT_AC_GRAD, a5, c5, d5, b5, f5, mesh->ystart, dump); ////////////////////////////////////////////////////////////////////////////////////// // Test 7+8: Cosine x-profiles, z-independent coefficients and compare with SPT method - Field2D a7, c7, d7; - Field3D b7; - Field3D sol7, sol8; - Field3D error7, absolute_error7, error8, absolute_error8; - BoutReal max_error7 = -1; - - a7 = DC(a5); - c7 = DC(c5); - d7 = DC(d5); - b7 = d7 * Delp2(f5) + Grad_perp(c7) * Grad_perp(f5) / c7 + a7 * f5; - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b7(jx, jy, jz) = b7(jx + 1, jy, jz); - } - } - } - } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - b7(jx, jy, jz) = b7(jx - 1, jy, jz); - } - } - } - } - invert->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert->setOuterBoundaryFlags(INVERT_AC_GRAD); - invert->setCoefA(a7); - invert->setCoefC(c7); - invert->setCoefD(d7); - - try { - sol7 = invert->solve(sliceXZ(b7, mesh->ystart)); - error7 = (f5 - sol7) / f5; - absolute_error7 = f5 - sol7; - max_error7 = max_error_at_ystart(abs(absolute_error7)); - } catch (BoutException& err) { - output.write("BoutException occured in invert->solve(b7): {}\n", err.what()); - } + const Field2D a7 = DC(a5); + const Field2D c7 = DC(c5); + const Field2D d7 = DC(d5); + Field3D b7 = d7 * Delp2(f5) + Grad_perp(c7) * Grad_perp(f5) / c7 + a7 * f5; + apply_flat_boundary(b7); + + check_laplace(++test_num, "different profiles, with coefficients constant in z, PETSc 2nd order", + *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a7, c7, d7, b7, f5, mesh->ystart, dump); - output.write( - "Test 7: different profiles, with coefficients constant in z, PETSc 2nd order\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error7); - - dump["a7"] = a7; - dump["b7"] = b7; - dump["c7"] = c7; - dump["d7"] = d7; - dump["f7"] = f5; - dump["sol7"] = sol7; - dump["error7"] = error7; - dump["absolute_error7"] = absolute_error7; - dump["max_error7"] = max_error7; - - invert_SPT->setInnerBoundaryFlags(INVERT_AC_GRAD); - invert_SPT->setOuterBoundaryFlags(INVERT_AC_GRAD | INVERT_DC_GRAD); - invert_SPT->setCoefA(a7); - invert_SPT->setCoefC(c7); - invert_SPT->setCoefD(d7); - - sol8 = invert_SPT->solve(sliceXZ(b7, mesh->ystart)); - error8 = (f5 - sol8) / f5; - absolute_error8 = f5 - sol8; - const BoutReal max_error8 = max_error_at_ystart(abs(absolute_error8)); - - output.write( - "Test 8: different profiles, with coefficients constant in z, default solver\n"); - output.write("Magnitude of maximum absolute error is {}\n", max_error8); - - dump["a8"] = a7; - dump["b8"] = b7; - dump["c8"] = c7; - dump["d8"] = d7; - dump["f8"] = f5; - dump["sol8"] = sol8; - dump["error8"] = error8; - dump["absolute_error8"] = absolute_error8; - dump["max_error8"] = max_error8; + check_laplace(++test_num, + "different profiles, with coefficients constant in z, default solver", + *invert_SPT, INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a7, c7, + d7, b7, f5, mesh->ystart, dump); // Write and close the output file bout::writeDefaultOutputFile(dump); @@ -793,3 +561,25 @@ BoutReal max_error_at_ystart(const Field3D& error) { return max_error; } + +void apply_flat_boundary(Field3D& bcoef) { + const Mesh& mesh = *bcoef.getMesh(); + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + bcoef(jx, jy, jz) = bcoef(jx + 1, jy, jz); + } + } + } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + bcoef(jx, jy, jz) = bcoef(jx - 1, jy, jz); + } + } + } + } +} From 61f1d82c5e17bf284a4c398d547fe5ee52b79d13 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 28 May 2024 15:09:59 +0100 Subject: [PATCH 379/412] Move field initialisation to separate functions for petsc test --- .../test-petsc_laplace/test_petsc_laplace.cxx | 850 ++++++++++-------- 1 file changed, 467 insertions(+), 383 deletions(-) diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx index aab3fe61c0..1e3cdde310 100644 --- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx +++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx @@ -23,18 +23,21 @@ * **************************************************************************/ -#include "bout/bout.hxx" +#include "bout/bout.hxx" // NOLINT #include "bout/bout_types.hxx" #include "bout/boutexception.hxx" #include "bout/constants.hxx" +#include "bout/difops.hxx" #include "bout/field2d.hxx" #include "bout/field3d.hxx" #include "bout/invert_laplace.hxx" #include "bout/options.hxx" +#include "bout/options_io.hxx" #include "bout/output.hxx" #include "bout/traits.hxx" #include "fmt/core.h" +#include #include #include @@ -86,6 +89,25 @@ void check_laplace(int test_num, std::string_view test_name, Laplacian& invert, dump[fmt::format("max_error{}", test_num)] = max_error; } +template +Field3D forward_laplace(const Field3D& field, const T& acoef, const T& ccoef, + const T& dcoef) { + auto bcoef = + dcoef * Delp2(field) + Grad_perp(ccoef) * Grad_perp(field) / ccoef + acoef * field; + apply_flat_boundary(bcoef); + return bcoef; +} + +Field3D generate_f1(const Mesh& mesh); +Field3D generate_a1(const Mesh& mesh); +Field3D generate_c1(const Mesh& mesh); +Field3D generate_d1(const Mesh& mesh); + +Field3D generate_f5(const Mesh& mesh); +Field3D generate_a5(const Mesh& mesh); +Field3D generate_c5(const Mesh& mesh); +Field3D generate_d5(const Mesh& mesh); + int main(int argc, char** argv) { BoutInitialise(argc, argv); @@ -98,488 +120,550 @@ int main(int argc, char** argv) { Options dump; // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d - Field3D f1; - Field3D a1; - Field3D c1; - Field3D d1; - BoutReal p; - BoutReal q; //Use to set parameters in constructing trial functions - using bout::globals::mesh; // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z. // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point - const BoutReal nx = mesh->GlobalNx - 2 * mesh->xstart - 1; - const BoutReal nz = mesh->GlobalNz; ///////////////////////////////////////////////////// // Test 1: Gaussian x-profiles, 2nd order Krylov - p = 0.39503274; - q = 0.20974396; - f1.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - const BoutReal z = BoutReal(jz) / nz; - //make the gradients zero at both x-boundaries - f1(jx, jy, jz) = 0. + exp(-(100. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-100. * pow(-p, 2)) * x - + (-p * exp(-100. * pow(-p, 2)) - - (1 - p) * exp(-100. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-(1. - cos(2. * PI * (z - q)))); - ASSERT0(finite(f1(jx, jy, jz))); + Field3D f_1 = generate_f1(*mesh); + Field3D a_1 = generate_a1(*mesh); + Field3D c_1 = generate_c1(*mesh); + Field3D d_1 = generate_d1(*mesh); + + mesh->communicate(f_1, a_1, c_1, d_1); + + const Field3D b_1 = forward_laplace(f_1, a_1, c_1, d_1); + + int test_num = 0; + check_laplace(++test_num, "PETSc 2nd order", *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, + a_1, c_1, d_1, b_1, f_1, mesh->ystart, dump); + + ///////////////////////////////////////////////// + // Test 2: Gaussian x-profiles, 4th order Krylov + + check_laplace(++test_num, "PETSc 4th order", *invert_4th, INVERT_AC_GRAD, + INVERT_AC_GRAD, a_1, c_1, d_1, b_1, f_1, mesh->ystart, dump); + + //////////////////////////////////////////////////////////////////////////////////////// + // Test 3+4: Gaussian x-profiles, z-independent coefficients and compare with SPT method + + const Field2D a_3 = DC(a_1); + const Field2D c_3 = DC(c_1); + const Field2D d_3 = DC(d_1); + const Field3D b_3 = forward_laplace(f_1, a_3, c_3, d_3); + + check_laplace(++test_num, "with coefficients constant in z, PETSc 2nd order", *invert, + INVERT_AC_GRAD, INVERT_AC_GRAD, a_3, c_3, d_3, b_3, f_1, mesh->ystart, + dump); + + Options* SPT_options = Options::getRoot()->getSection("SPT"); + auto invert_SPT = Laplacian::create(SPT_options); + + check_laplace(++test_num, "with coefficients constant in z, default solver", + *invert_SPT, INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a_3, c_3, + d_3, b_3, f_1, mesh->ystart, dump); + + ////////////////////////////////////////////// + // Test 5: Cosine x-profiles, 2nd order Krylov + Field3D f_5 = generate_f5(*mesh); + Field3D a_5 = generate_a5(*mesh); + Field3D c_5 = generate_c5(*mesh); + Field3D d_5 = generate_d5(*mesh); + + mesh->communicate(f_5, a_5, c_5, d_5); + + const Field3D b_5 = forward_laplace(f_5, a_5, c_5, d_5); + + check_laplace(++test_num, "different profiles, PETSc 2nd order", *invert, + INVERT_AC_GRAD, INVERT_AC_GRAD, a_5, c_5, d_5, b_5, f_5, mesh->ystart, + dump); + + ////////////////////////////////////////////// + // Test 6: Cosine x-profiles, 4th order Krylov + + check_laplace(++test_num, "different profiles, PETSc 4th order", *invert_4th, + INVERT_AC_GRAD, INVERT_AC_GRAD, a_5, c_5, d_5, b_5, f_5, mesh->ystart, + dump); + + ////////////////////////////////////////////////////////////////////////////////////// + // Test 7+8: Cosine x-profiles, z-independent coefficients and compare with SPT method + + const Field2D a_7 = DC(a_5); + const Field2D c_7 = DC(c_5); + const Field2D d_7 = DC(d_5); + const Field3D b_7 = forward_laplace(f_5, a_7, c_7, d_7); + + check_laplace(++test_num, + "different profiles, with coefficients constant in z, PETSc 2nd order", + *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a_7, c_7, d_7, b_7, f_5, + mesh->ystart, dump); + + check_laplace(++test_num, + "different profiles, with coefficients constant in z, default solver", + *invert_SPT, INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a_7, c_7, + d_7, b_7, f_5, mesh->ystart, dump); + + // Write and close the output file + bout::writeDefaultOutputFile(dump); + + MPI_Barrier(BoutComm::get()); // Wait for all processors to write data + } + + bout::checkForUnusedOptions(); + + BoutFinalise(); + return 0; +} + +BoutReal max_error_at_ystart(const Field3D& error) { + const auto* mesh = error.getMesh(); + BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0); + + for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { + for (int jz = 0; jz < mesh->LocalNz; jz++) { + if (local_max_error < error(jx, mesh->ystart, jz)) { + local_max_error = error(jx, mesh->ystart, jz); + } + } + } + + BoutReal max_error = BoutNaN; + + MPI_Allreduce(&local_max_error, &max_error, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get()); + + return max_error; +} + +void apply_flat_boundary(Field3D& bcoef) { + const Mesh& mesh = *bcoef.getMesh(); + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + bcoef(jx, jy, jz) = bcoef(jx + 1, jy, jz); } } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - const BoutReal z = BoutReal(jz) / nz; - //make the gradients zero at both x-boundaries - f1(jx, jy, jz) = 0. - + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-60. * pow(-p, 2)) * x - + (-p * exp(-60. * pow(-p, 2)) - - (1 - p) * exp(-60. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-(1. - cos(2. * PI * (z - q)))); - ASSERT0(finite(f1(jx, jy, jz))); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + bcoef(jx, jy, jz) = bcoef(jx - 1, jy, jz); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - const BoutReal z = BoutReal(jz) / nz; - //make the gradients zero at both x-boundaries - f1(jx, jy, jz) = 0. - + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + } +} + +Field3D generate_f1(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + + constexpr BoutReal p = 0.39503274; // NOLINT + constexpr BoutReal q = 0.20974396; // NOLINT + + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + result(jx, jy, jz) = 0. + + exp(-(100. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - 50. - * (2. * p * exp(-60. * pow(-p, 2)) * x - + (-p * exp(-60. * pow(-p, 2)) - - (1 - p) * exp(-60. * pow(1 - p, 2))) + * (2. * p * exp(-100. * pow(-p, 2)) * x + + (-p * exp(-100. * pow(-p, 2)) + - (1 - p) * exp(-100. * pow(1 - p, 2))) * pow(x, 2)) * exp(-(1. - cos(2. * PI * (z - q)))); - ASSERT0(finite(f1(jx, jy, jz))); - } - } } } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; - f1.applyBoundary("neumann"); - - p = 0.512547; - q = 0.30908712; - d1.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - d1(jx, jy, jz) = - 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); - } - } - } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - d1(jx, jy, jz) = - 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); - } + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + result(jx, jy, jz) = 0. + + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-60. * pow(-p, 2)) * x + + (-p * exp(-60. * pow(-p, 2)) + - (1 - p) * exp(-60. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - d1(jx, jy, jz) = - 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + result(jx, jy, jz) = 0. + + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-60. * pow(-p, 2)) * x + + (-p * exp(-60. * pow(-p, 2)) + - (1 - p) * exp(-60. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } + } - p = 0.18439023; - q = 0.401089473; - c1.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - c1(jx, jy, jz) = - 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); - } + checkData(result); + result.applyBoundary("neumann"); + return result; +} + +Field3D generate_d1(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + + constexpr BoutReal p = 0.512547; // NOLINT + constexpr BoutReal q = 0.30908712; // NOLINT + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - c1(jx, jy, jz) = - 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); - } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - c1(jx, jy, jz) = - 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.); } } } + } + checkData(result); + return result; +} - p = 0.612547; - q = 0.30908712; - a1.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - a1(jx, jy, jz) = - -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); - } +Field3D generate_c1(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + + constexpr BoutReal p = 0.18439023; // NOLINT + constexpr BoutReal q = 0.401089473; // NOLINT + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - a1(jx, jy, jz) = - -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); - } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - a1(jx, jy, jz) = - -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.); } } } + } - checkData(f1); - checkData(a1); - checkData(c1); - checkData(d1); - - mesh->communicate(f1, a1, c1, d1); - - Field3D b1 = d1 * Delp2(f1) + Grad_perp(c1) * Grad_perp(f1) / c1 + a1 * f1; - apply_flat_boundary(b1); - - int test_num = 0; - check_laplace(++test_num, "PETSc 2nd order", *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a1, c1, - d1, b1, f1, mesh->ystart, dump); - - ///////////////////////////////////////////////// - // Test 2: Gaussian x-profiles, 4th order Krylov - - check_laplace(++test_num, "PETSc 4th order", *invert_4th, INVERT_AC_GRAD, INVERT_AC_GRAD, a1, - c1, d1, b1, f1, mesh->ystart, dump); - - //////////////////////////////////////////////////////////////////////////////////////// - // Test 3+4: Gaussian x-profiles, z-independent coefficients and compare with SPT method - - const Field2D a3 = DC(a1); - const Field2D c3 = DC(c1); - const Field2D d3 = DC(d1); - Field3D b3 = d3 * Delp2(f1) + Grad_perp(c3) * Grad_perp(f1) / c3 + a3 * f1; - apply_flat_boundary(b3); - - check_laplace(++test_num, "with coefficients constant in z, PETSc 2nd order", *invert, - INVERT_AC_GRAD, INVERT_AC_GRAD, a3, c3, d3, b3, f1, mesh->ystart, dump); - - Options* SPT_options = Options::getRoot()->getSection("SPT"); - auto invert_SPT = Laplacian::create(SPT_options); - - check_laplace(++test_num, "with coefficients constant in z, default solver", *invert_SPT, - INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a3, c3, d3, b3, f1, - mesh->ystart, dump); + checkData(result); + return result; +} - ////////////////////////////////////////////// - // Test 5: Cosine x-profiles, 2nd order Krylov - Field3D f5, a5, c5, d5; - - p = 0.623901; - q = 0.01209489; - f5.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - const BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - const BoutReal z = BoutReal(jz) / nz; - //make the gradients zero at both x-boundaries - f5(jx, jy, jz) = 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-50. * pow(-p, 2)) * x - + (-p * exp(-50. * pow(-p, 2)) - - (1 - p) * exp(-50. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-(1. - cos(2. * PI * (z - q)))); - } +Field3D generate_a1(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + + constexpr BoutReal p = 0.612547; // NOLINT + constexpr BoutReal q = 0.30908712; // NOLINT + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - //make the gradients zero at both x-boundaries - f5(jx, jy, jz) = 0. - + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-50. * pow(-p, 2)) * x - + (-p * exp(-50. * pow(-p, 2)) - - (1 - p) * exp(-50. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-(1. - cos(2. * PI * (z - q)))); - } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - //make the gradients zero at both x-boundaries - f5(jx, jy, jz) = 0. - + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) - - 50. - * (2. * p * exp(-50. * pow(-p, 2)) * x - + (-p * exp(-50. * pow(-p, 2)) - - (1 - p) * exp(-50. * pow(1 - p, 2))) - * pow(x, 2)) - * exp(-(1. - cos(2. * PI * (z - q)))); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.); } } } + } - p = 0.63298589; - q = 0.889237890; - d5.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - d5(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); - } + checkData(result); + return result; +} + +Field3D generate_f5(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + constexpr BoutReal p = 0.623901; // NOLINT + constexpr BoutReal q = 0.01209489; // NOLINT + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + result(jx, jy, jz) = + 0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - d5(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); - } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + result(jx, jy, jz) = 0. + + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - d5(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + //make the gradients zero at both x-boundaries + result(jx, jy, jz) = 0. + + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q)))) + - 50. + * (2. * p * exp(-50. * pow(-p, 2)) * x + + (-p * exp(-50. * pow(-p, 2)) + - (1 - p) * exp(-50. * pow(1 - p, 2))) + * pow(x, 2)) + * exp(-(1. - cos(2. * PI * (z - q)))); } } } + } + result.applyBoundary("neumann"); + checkData(result); + return result; +} - p = 0.160983834; - q = 0.73050121087; - c5.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - c5(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); - } +Field3D generate_d5(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + constexpr BoutReal p = 0.63298589; // NOLINT + constexpr BoutReal q = 0.889237890; // NOLINT + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - c5(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); - } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - c5(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.); } } } + } + checkData(result); + return result; +} - p = 0.5378950; - q = 0.2805870; - a5.allocate(); - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - a5(jx, jy, jz) = -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); - } +Field3D generate_c5(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + constexpr BoutReal p = 0.160983834; // NOLINT + constexpr BoutReal q = 0.73050121087; // NOLINT + + Field3D result; + + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); } } - if (mesh->firstX()) { - for (int jx = mesh->xstart - 1; jx >= 0; jx--) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - a5(jx, jy, jz) = - -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); - } + } + if (mesh.firstX()) { + for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); } } } - if (mesh->lastX()) { - for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) { - for (int jy = 0; jy < mesh->LocalNy; jy++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx; - BoutReal z = BoutReal(jz) / nz; - a5(jx, jy, jz) = - -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); - } + } + if (mesh.lastX()) { + for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.); } } } - - f5.applyBoundary("neumann"); - mesh->communicate(f5, a5, c5, d5); - - Field3D b5 = d5 * Delp2(f5) + Grad_perp(c5) * Grad_perp(f5) / c5 + a5 * f5; - apply_flat_boundary(b5); - - check_laplace(++test_num, "different profiles, PETSc 2nd order", *invert, INVERT_AC_GRAD, - INVERT_AC_GRAD, a5, c5, d5, b5, f5, mesh->ystart, dump); - - ////////////////////////////////////////////// - // Test 6: Cosine x-profiles, 4th order Krylov - - check_laplace(++test_num, "different profiles, PETSc 4th order", *invert_4th, INVERT_AC_GRAD, - INVERT_AC_GRAD, a5, c5, d5, b5, f5, mesh->ystart, dump); - - ////////////////////////////////////////////////////////////////////////////////////// - // Test 7+8: Cosine x-profiles, z-independent coefficients and compare with SPT method - - const Field2D a7 = DC(a5); - const Field2D c7 = DC(c5); - const Field2D d7 = DC(d5); - Field3D b7 = d7 * Delp2(f5) + Grad_perp(c7) * Grad_perp(f5) / c7 + a7 * f5; - apply_flat_boundary(b7); - - check_laplace(++test_num, "different profiles, with coefficients constant in z, PETSc 2nd order", - *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a7, c7, d7, b7, f5, mesh->ystart, dump); - - check_laplace(++test_num, - "different profiles, with coefficients constant in z, default solver", - *invert_SPT, INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a7, c7, - d7, b7, f5, mesh->ystart, dump); - - // Write and close the output file - bout::writeDefaultOutputFile(dump); - - MPI_Barrier(BoutComm::get()); // Wait for all processors to write data } - - bout::checkForUnusedOptions(); - - BoutFinalise(); - return 0; + checkData(result); + return result; } -BoutReal max_error_at_ystart(const Field3D& error) { - const auto* mesh = error.getMesh(); - BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0); - - for (int jx = mesh->xstart; jx <= mesh->xend; jx++) { - for (int jz = 0; jz < mesh->LocalNz; jz++) { - if (local_max_error < error(jx, mesh->ystart, jz)) { - local_max_error = error(jx, mesh->ystart, jz); +Field3D generate_a5(const Mesh& mesh) { + const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1; + const BoutReal nz = mesh.GlobalNz; + constexpr BoutReal p = 0.5378950; // NOLINT + constexpr BoutReal q = 0.2805870; // NOLINT + Field3D result; + result.allocate(); + for (int jx = mesh.xstart; jx <= mesh.xend; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; + for (int jy = 0; jy < mesh.LocalNy; jy++) { + for (int jz = 0; jz < mesh.LocalNz; jz++) { + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); } } } - - BoutReal max_error = BoutNaN; - - MPI_Allreduce(&local_max_error, &max_error, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get()); - - return max_error; -} - -void apply_flat_boundary(Field3D& bcoef) { - const Mesh& mesh = *bcoef.getMesh(); if (mesh.firstX()) { for (int jx = mesh.xstart - 1; jx >= 0; jx--) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; for (int jy = 0; jy < mesh.LocalNy; jy++) { for (int jz = 0; jz < mesh.LocalNz; jz++) { - bcoef(jx, jy, jz) = bcoef(jx + 1, jy, jz); + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); } } } } if (mesh.lastX()) { for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) { + const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx; for (int jy = 0; jy < mesh.LocalNy; jy++) { for (int jz = 0; jz < mesh.LocalNz; jz++) { - bcoef(jx, jy, jz) = bcoef(jx - 1, jy, jz); + const BoutReal z = BoutReal(jz) / nz; + result(jx, jy, jz) = + -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.); } } } } + checkData(result); + return result; } From f9269930f18e37e7622b5770c4406f1a09417a7c Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Tue, 28 May 2024 16:38:47 +0100 Subject: [PATCH 380/412] Reduce duplicated flag checking in `LaplacePetsc` --- .../laplace/impls/petsc/petsc_laplace.cxx | 67 +++++++------------ .../laplace/impls/petsc/petsc_laplace.hxx | 9 +-- 2 files changed, 31 insertions(+), 45 deletions(-) diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx index de9ef05025..f06f4c7de6 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx @@ -23,7 +23,8 @@ * along with BOUT++. If not, see . * **************************************************************************/ -#include "bout/build_config.hxx" + +#include "bout/build_defines.hxx" #if BOUT_HAS_PETSC @@ -32,6 +33,7 @@ #include #include #include +#include #include #include #include @@ -79,28 +81,9 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in, } #if CHECK > 0 - // These are the implemented flags - implemented_flags = INVERT_START_NEW; - implemented_boundary_flags = INVERT_AC_GRAD + INVERT_SET + INVERT_RHS; // Checking flags are set to something which is not implemented - // This is done binary (which is possible as each flag is a power of 2) - if (isGlobalFlagSet(~implemented_flags)) { - if (isGlobalFlagSet(INVERT_4TH_ORDER)) { - output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " - "setting INVERT_4TH_ORDER flag" - << endl; - } - throw BoutException("Attempted to set Laplacian inversion flag that is not " - "implemented in petsc_laplace.cxx"); - } - if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); - } - if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); - } + checkFlags(); + if (localmesh->periodicX) { throw BoutException("LaplacePetsc does not work with periodicity in the x direction " "(localmesh->PeriodicX == true). Change boundary conditions or " @@ -360,25 +343,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) { ASSERT1(x0.getLocation() == location); #if CHECK > 0 - // Checking flags are set to something which is not implemented (see - // constructor for details) - if (isGlobalFlagSet(~implemented_flags)) { - if (isGlobalFlagSet(INVERT_4TH_ORDER)) { - output << "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " - "setting INVERT_4TH_ORDER flag" - << endl; - } - throw BoutException("Attempted to set Laplacian inversion flag that is not " - "implemented in petsc_laplace.cxx"); - } - if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); - } - if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) { - throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " - "implemented in petsc_laplace.cxx"); - } + checkFlags(); #endif int y = b.getIndex(); // Get the Y index @@ -1194,4 +1159,24 @@ int LaplacePetsc::precon(Vec x, Vec y) { return 0; } +void LaplacePetsc::checkFlags() { + if (isGlobalFlagSet(~implemented_flags)) { + if (isGlobalFlagSet(INVERT_4TH_ORDER)) { + output_error.write( + "For PETSc based Laplacian inverter, use 'fourth_order=true' instead of " + "setting INVERT_4TH_ORDER flag\n"); + } + throw BoutException("Attempted to set Laplacian inversion flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (isInnerBoundaryFlagSet(~implemented_boundary_flags)) { + throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } + if (isOuterBoundaryFlagSet(~implemented_boundary_flags)) { + throw BoutException("Attempted to set Laplacian inversion boundary flag that is not " + "implemented in petsc_laplace.cxx"); + } +} + #endif // BOUT_HAS_PETSC_3_3 diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx index 011f8971df..55482644be 100644 --- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx +++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx @@ -254,10 +254,11 @@ private: void vecToField(Vec x, FieldPerp& f); // Copy a vector into a fieldperp void fieldToVec(const FieldPerp& f, Vec x); // Copy a fieldperp into a vector -#if CHECK > 0 - int implemented_flags; - int implemented_boundary_flags; -#endif + static constexpr int implemented_flags = INVERT_START_NEW; + static constexpr int implemented_boundary_flags = + INVERT_AC_GRAD | INVERT_SET | INVERT_RHS; + + void checkFlags(); }; #endif //BOUT_HAS_PETSC From c2855aa19200f171f92896586f83f5346432402e Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 30 May 2024 18:02:43 +0100 Subject: [PATCH 381/412] Remove some deprecated includes in boutmesh --- src/mesh/impls/bout/boutmesh.cxx | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx index 684c8afc40..16061cd47e 100644 --- a/src/mesh/impls/bout/boutmesh.cxx +++ b/src/mesh/impls/bout/boutmesh.cxx @@ -49,9 +49,6 @@ #include #include -#include "boundary_region.hxx" -#include "parallel_boundary_region.hxx" - #include #include #include From c67ffef332b1fd86df58876d36326b44ae812994 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 30 May 2024 18:03:07 +0100 Subject: [PATCH 382/412] Enclose some macro arguments in parentheses This silences `bugprone-macro-parentheses` clang-tidy warning --- include/bout/region.hxx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 5e2eb9c1a2..0378dc1dc0 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -117,14 +117,14 @@ class BoutMask; // #define BOUT_FOR_SERIAL(index, region) \ - for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend(); \ + for (auto block = (region).getBlocks().cbegin(), end = (region).getBlocks().cend(); \ block < end; ++block) \ for (auto index = block->first; index < block->second; ++index) #if BOUT_USE_OPENMP #define BOUT_FOR_OMP(index, region, omp_pragmas) \ BOUT_OMP_PERF(omp_pragmas) \ - for (auto block = region.getBlocks().cbegin(); block < region.getBlocks().cend(); \ + for (auto block = (region).getBlocks().cbegin(); block < (region).getBlocks().cend(); \ ++block) \ for (auto index = block->first; index < block->second; ++index) #else @@ -133,10 +133,10 @@ class BoutMask; #endif #define BOUT_FOR(index, region) \ - BOUT_FOR_OMP(index, region, parallel for schedule(BOUT_OPENMP_SCHEDULE)) + BOUT_FOR_OMP(index, (region), parallel for schedule(BOUT_OPENMP_SCHEDULE)) #define BOUT_FOR_INNER(index, region) \ - BOUT_FOR_OMP(index, region, for schedule(BOUT_OPENMP_SCHEDULE) nowait) + BOUT_FOR_OMP(index, (region), for schedule(BOUT_OPENMP_SCHEDULE) nowait) // NOLINTEND(cppcoreguidelines-macro-usage,bugprone-macro-parentheses) enum class IND_TYPE { IND_3D = 0, IND_2D = 1, IND_PERP = 2 }; From b1606af6febf64bea07f7b316bd6c3b525a1179c Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Thu, 30 May 2024 18:03:48 +0100 Subject: [PATCH 383/412] Try to convince IWYU/clang-include-cleaner to use top-level headers Rather than always wanting to include petsc subheaders directly, or a bunch of our headers instead of just using `bout.hxx` --- include/bout/bout.hxx | 2 ++ include/bout/petsclib.hxx | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/include/bout/bout.hxx b/include/bout/bout.hxx index d929a19c2f..09433bcc3b 100644 --- a/include/bout/bout.hxx +++ b/include/bout/bout.hxx @@ -34,6 +34,7 @@ #ifndef BOUT_H #define BOUT_H +// IWYU pragma: begin_keep, begin_export #include "bout/build_config.hxx" #include "bout/boutcomm.hxx" @@ -53,6 +54,7 @@ #include "bout/vector3d.hxx" #include "bout/version.hxx" #include "bout/where.hxx" +// IWYU pragma: end_keep, end_export // BOUT++ main functions diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx index 35334ce773..2008671286 100644 --- a/include/bout/petsclib.hxx +++ b/include/bout/petsclib.hxx @@ -59,7 +59,7 @@ class Options; // means we _must_ `#include` this header _before_ any PETSc header! #define PETSC_HAVE_BROKEN_RECURSIVE_MACRO -#include +#include // IWYU pragma: export #include #include "bout/boutexception.hxx" From 533e446f684305351a9a0318f617e162bd9a497f Mon Sep 17 00:00:00 2001 From: ZedThree Date: Thu, 30 May 2024 17:10:26 +0000 Subject: [PATCH 384/412] Apply clang-format changes --- include/bout/region.hxx | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/include/bout/region.hxx b/include/bout/region.hxx index 0378dc1dc0..4649b680eb 100644 --- a/include/bout/region.hxx +++ b/include/bout/region.hxx @@ -116,16 +116,16 @@ class BoutMask; /// } // -#define BOUT_FOR_SERIAL(index, region) \ +#define BOUT_FOR_SERIAL(index, region) \ for (auto block = (region).getBlocks().cbegin(), end = (region).getBlocks().cend(); \ - block < end; ++block) \ + block < end; ++block) \ for (auto index = block->first; index < block->second; ++index) #if BOUT_USE_OPENMP -#define BOUT_FOR_OMP(index, region, omp_pragmas) \ - BOUT_OMP_PERF(omp_pragmas) \ +#define BOUT_FOR_OMP(index, region, omp_pragmas) \ + BOUT_OMP_PERF(omp_pragmas) \ for (auto block = (region).getBlocks().cbegin(); block < (region).getBlocks().cend(); \ - ++block) \ + ++block) \ for (auto index = block->first; index < block->second; ++index) #else // No OpenMP, so fall back to slightly more efficient serial form From a6aa83507b12e775ad11dfb2c328c8de2609562f Mon Sep 17 00:00:00 2001 From: David Bold Date: Tue, 4 Jun 2024 16:18:19 +0200 Subject: [PATCH 385/412] Update MPCDF instructions --- bin/bout-build-deps.sh | 12 ++++++------ manual/sphinx/user_docs/advanced_install.rst | 15 +++++++-------- 2 files changed, 13 insertions(+), 14 deletions(-) diff --git a/bin/bout-build-deps.sh b/bin/bout-build-deps.sh index 19e3b2a0d3..25b50e0948 100755 --- a/bin/bout-build-deps.sh +++ b/bin/bout-build-deps.sh @@ -286,17 +286,17 @@ set -x ## Setup folders and links setup ## Build and install hdf5 -hdf5 +test $NO_HDF5 || hdf5 ## Build and install netcdf -netcdf +test $NO_NETCDF || netcdf ## Build and install C++ interface for netcdf -nccxx +test $NO_NCXX || nccxx ## Build and install FFTW -fftw +test $NO_FFTW || fftw ## Build and install Sundials -sundials +test $NO_SUNDIALS || sundials ## Build and install PETSc -petsc +test $NO_PETSC || petsc ## Download BOUT++ submodules submod # Install python packages diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst index 57ac5f8e3f..048a26a6e3 100644 --- a/manual/sphinx/user_docs/advanced_install.rst +++ b/manual/sphinx/user_docs/advanced_install.rst @@ -145,13 +145,12 @@ where ```` is the path to the build directory MPCDF HPC Systems ~~~~~~~~~~~~~~~~~ +After cloning BOUT-dev and checking out the branch you want (e.g. db-outer), run: .. code-block:: bash - module purge # or at least onload intel and impi and mkl - module load gcc/10 cmake/3.18 openmpi/4 - # ensure python3 is >= python3.6 - skip if you have a newer python3 loaded - mkdir -p $HOME/bin ; test -e $HOME/bin/python3 || ln -s $(which python3.6) $HOME/bin/python3 - BUILD=/ptmp/$USER/bout-deps bin/bout-build-deps.sh + module purge # or at least onload intel + module load gcc/13 anaconda/3/2021.11 impi/2021.9 hdf5-serial/1.12.2 mkl/2022.0 netcdf-serial/4.8.1 fftw-mpi/3.3.10 + BUILD=/ptmp/$USER/bout-deps NO_HDF5=1 NO_NETCDF=1 NO_FFTW=1 bin/bout-build-deps.sh and follow the instructions for configuring BOUT++. To enable openMP for a production run use: @@ -159,11 +158,11 @@ for a production run use: .. code-block:: bash module load bout-dep - cmake .. -DBOUT_USE_NETCDF=ON -DnetCDF_ROOT=$BOUT_DEP -DnetCDFCxx_ROOT=$BOUT_DEP \ + cmake .. -DBOUT_USE_NETCDF=ON -DnetCDFCxx_ROOT=$BOUT_DEP \ -DBOUT_USE_PETSC=ON -DPETSC_DIR=$BOUT_DEP \ - -DBOUT_USE_FFTW=ON -DFFTW_ROOT=$BOUT_DEP \ + -DBOUT_USE_FFTW=ON \ -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=$BOUT_DEP \ - -DBOUT_ENABLE_OPENMP=ON \ + -DBOUT_ENABLE_OPENMP=OFF \ -DCMAKE_BUILD_TYPE=Release From 77103c2463af2031b24ee2555586a6c89ede4190 Mon Sep 17 00:00:00 2001 From: David Bold Date: Wed, 5 Jun 2024 12:00:52 +0200 Subject: [PATCH 386/412] Fix netcdf-cxx4 url --- bin/bout-build-deps.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/bout-build-deps.sh b/bin/bout-build-deps.sh index 25b50e0948..6acd3d82bf 100755 --- a/bin/bout-build-deps.sh +++ b/bin/bout-build-deps.sh @@ -98,7 +98,7 @@ netcdf() { nccxx() { cd $BUILD - wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx4-$NCCXXVER.tar.gz || : + wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/4.3.1/netcdf-cxx4-$NCCXXVER.tar.gz || : tar -xf netcdf-cxx4-$NCCXXVER.tar.gz cd netcdf-cxx4-$NCCXXVER CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib/" ./configure --prefix=$PREFIX $NCCXXFLAGS From d67016ad5f43e0ea15f4fc002c87dcac74cc56b3 Mon Sep 17 00:00:00 2001 From: David Bold Date: Mon, 10 Jun 2024 10:12:31 +0200 Subject: [PATCH 387/412] Fix URL thanks @ZedThree for noticing --- bin/bout-build-deps.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/bout-build-deps.sh b/bin/bout-build-deps.sh index 6acd3d82bf..d96d500dc9 100755 --- a/bin/bout-build-deps.sh +++ b/bin/bout-build-deps.sh @@ -98,7 +98,7 @@ netcdf() { nccxx() { cd $BUILD - wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/4.3.1/netcdf-cxx4-$NCCXXVER.tar.gz || : + wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/$NCCXXVER/netcdf-cxx4-$NCCXXVER.tar.gz || : tar -xf netcdf-cxx4-$NCCXXVER.tar.gz cd netcdf-cxx4-$NCCXXVER CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib/" ./configure --prefix=$PREFIX $NCCXXFLAGS From b98253066e1a7d4a0eacf68218236c30751cdb72 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 10 Jun 2024 18:17:15 -0700 Subject: [PATCH 388/412] Fix version checking for SUNDIALS --- cmake/SetupBOUTThirdParty.cmake | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 127fbda765..dc11ba29cb 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -297,7 +297,11 @@ if (BOUT_USE_SUNDIALS) FetchContent_MakeAvailable(sundials) message(STATUS "SUNDIALS done configuring") else() - find_package(SUNDIALS 4 REQUIRED) + ENABLE_LANGUAGE(C) + find_package(SUNDIALS REQUIRED) + if (SUNDIALS_VERSION VERSION_LESS 4.0.0) + message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.") + endif() endif() target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel) target_link_libraries(bout++ PUBLIC SUNDIALS::cvode) From 505f2b3190a71d9adbee63d029929915e776b44b Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Mon, 17 Jun 2024 16:03:34 +0100 Subject: [PATCH 389/412] Fix docstrings for Laplacian flag getters [skip ci] Co-authored-by: David Bold --- include/bout/invert_laplace.hxx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx index b1ff84782f..0b416d4aab 100644 --- a/include/bout/invert_laplace.hxx +++ b/include/bout/invert_laplace.hxx @@ -324,10 +324,10 @@ protected: } /// Return true if \p flag is set for the inner boundary condition - /// on the inner processor(s) + /// and this is the first proc in X direction bool isInnerBoundaryFlagSetOnFirstX(int flag) const; /// Return true if \p flag is set for the outer boundary condition - /// on the outer processor(s) + /// and this the last proc in X direction bool isOuterBoundaryFlagSetOnLastX(int flag) const; void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, dcomplex& c, From e916f2ee8857e70c3cc99292d54691f8486a3945 Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Wed, 19 Jun 2024 09:46:10 +0100 Subject: [PATCH 390/412] CMake: Use lowercase command --- cmake/SetupBOUTThirdParty.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index dc11ba29cb..9c49fe6fdc 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -297,7 +297,7 @@ if (BOUT_USE_SUNDIALS) FetchContent_MakeAvailable(sundials) message(STATUS "SUNDIALS done configuring") else() - ENABLE_LANGUAGE(C) + enable_language(C) find_package(SUNDIALS REQUIRED) if (SUNDIALS_VERSION VERSION_LESS 4.0.0) message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.") From c37218e60f5ceb1a461bb5935351b56686e1ffac Mon Sep 17 00:00:00 2001 From: Peter Hill Date: Fri, 21 Jun 2024 10:11:08 +0100 Subject: [PATCH 391/412] CI: Bump python dependencies Mostly need to ensure we have a compatible NumPy version --- requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/requirements.txt b/requirements.txt index 75358b10db..dcbe5cef5c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,8 +1,8 @@ -Jinja2>=2.11.3 -numpy>=1.14.1 -scipy>=1.0.0 -netcdf4~=1.6.0 -matplotlib>=2.0.0 +Jinja2~=3.1.0 +numpy~=2.0.0 +scipy>=1.11.0 +netcdf4~=1.7.1 +matplotlib>=3.7.0 Cython~=3.0.0 boututils~=0.2.1 boutdata~=0.2.1 From b704bbdd4ad3a8f0daaf2380f20f2066403e0198 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Fri, 21 Jun 2024 15:39:49 -0500 Subject: [PATCH 392/412] solver:explicit issue is resolved --- src/solver/impls/arkode/arkode.cxx | 213 +++++++++++++++-------------- 1 file changed, 110 insertions(+), 103 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index bc3be6f80a..62020c1f5e 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -195,30 +195,29 @@ int ArkodeSolver::init() { // Put the variables into uvec save_vars(N_VGetArrayPointer(uvec)); - ASSERT1(solve_explicit or solve_implicit); + ASSERT1(imex or solve_explicit or solve_implicit); - const auto& explicit_rhs = [this]() { - if (imex) { - return arkode_rhs_explicit; - } else { - return solve_explicit ? arkode_rhs : nullptr; - } - }(); - const auto& implicit_rhs = [this]() { - if (imex) { - return arkode_rhs_implicit; - } else { - return solve_implicit ? arkode_rhs : nullptr; - } - }(); - - arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, explicit_rhs, implicit_rhs, - simtime, uvec); + if(imex or (solve_explicit and solve_implicit)) + { + imex = true; + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, + simtime, uvec); + } + else if (solve_explicit) + { + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, + simtime, uvec); + } + else + { + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_rhs, + simtime, uvec); + } if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); - } + } - if (imex and solve_explicit and solve_implicit) { + if (imex) { output_info.write("\tUsing ARKode ImEx solver \n"); if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImEx failed\n"); @@ -372,91 +371,94 @@ int ArkodeSolver::init() { } } - if (fixed_point) { - output.write("\tUsing accelerated fixed point solver\n"); - nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); - if (nonlinear_solver == nullptr) { - throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); - } - if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { - throw BoutException("ARKStepSetNonlinearSolver failed\n"); - } - } else { - output.write("\tUsing Newton iteration\n"); - - const auto prectype = - use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; - sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); - if (sun_solver == nullptr) { - throw BoutException("Creating SUNDIALS linear solver failed\n"); - } - if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { - throw BoutException("ARKStepSetLinearSolver failed\n"); - } + if (imex or solve_implicit) + { + if (fixed_point) { + output.write("\tUsing accelerated fixed point solver\n"); + nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); + if (nonlinear_solver == nullptr) { + throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); + } + if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { + throw BoutException("ARKStepSetNonlinearSolver failed\n"); + } + } else { + output.write("\tUsing Newton iteration\n"); - /// Set Preconditioner - if (use_precon) { - if (hasPreconditioner()) { - output.write("\tUsing user-supplied preconditioner\n"); + const auto prectype = + use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); + if (sun_solver == nullptr) { + throw BoutException("Creating SUNDIALS linear solver failed\n"); + } + if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetLinearSolver failed\n"); + } - if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) { - throw BoutException("ARKStepSetPreconditioner failed\n"); + /// Set Preconditioner + if (use_precon) { + if (hasPreconditioner()) { + output.write("\tUsing user-supplied preconditioner\n"); + + if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetPreconditioner failed\n"); + } + } else { + output.write("\tUsing BBD preconditioner\n"); + + /// Get options + // Compute band_width_default from actually added fields, to allow for multiple + // Mesh objects + // + // Previous implementation was equivalent to: + // int MXSUB = mesh->xend - mesh->xstart + 1; + // int band_width_default = n3Dvars()*(MXSUB+2); + const int band_width_default = std::accumulate( + begin(f3d), end(f3d), 0, [](int acc, const VarStr& fvar) { + Mesh* localmesh = fvar.var->getMesh(); + return acc + localmesh->xend - localmesh->xstart + 3; + }); + + const auto mudq = (*options)["mudq"] + .doc("Upper half-bandwidth to be used in the difference " + "quotient Jacobian approximation") + .withDefault(band_width_default); + const auto mldq = (*options)["mldq"] + .doc("Lower half-bandwidth to be used in the difference " + "quotient Jacobian approximation") + .withDefault(band_width_default); + const auto mukeep = (*options)["mukeep"] + .doc("Upper half-bandwidth of the retained banded " + "approximate Jacobian block") + .withDefault(n3Dvars() + n2Dvars()); + const auto mlkeep = (*options)["mlkeep"] + .doc("Lower half-bandwidth of the retained banded " + "approximate Jacobian block") + .withDefault(n3Dvars() + n2Dvars()); + + if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, + arkode_bbd_rhs, nullptr) + != ARKLS_SUCCESS) { + throw BoutException("ARKBBDPrecInit failed\n"); + } } } else { - output.write("\tUsing BBD preconditioner\n"); - - /// Get options - // Compute band_width_default from actually added fields, to allow for multiple - // Mesh objects - // - // Previous implementation was equivalent to: - // int MXSUB = mesh->xend - mesh->xstart + 1; - // int band_width_default = n3Dvars()*(MXSUB+2); - const int band_width_default = std::accumulate( - begin(f3d), end(f3d), 0, [](int acc, const VarStr& fvar) { - Mesh* localmesh = fvar.var->getMesh(); - return acc + localmesh->xend - localmesh->xstart + 3; - }); - - const auto mudq = (*options)["mudq"] - .doc("Upper half-bandwidth to be used in the difference " - "quotient Jacobian approximation") - .withDefault(band_width_default); - const auto mldq = (*options)["mldq"] - .doc("Lower half-bandwidth to be used in the difference " - "quotient Jacobian approximation") - .withDefault(band_width_default); - const auto mukeep = (*options)["mukeep"] - .doc("Upper half-bandwidth of the retained banded " - "approximate Jacobian block") - .withDefault(n3Dvars() + n2Dvars()); - const auto mlkeep = (*options)["mlkeep"] - .doc("Lower half-bandwidth of the retained banded " - "approximate Jacobian block") - .withDefault(n3Dvars() + n2Dvars()); - - if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, - arkode_bbd_rhs, nullptr) - != ARKLS_SUCCESS) { - throw BoutException("ARKBBDPrecInit failed\n"); - } + // Not using preconditioning + output.write("\tNo preconditioning\n"); } - } else { - // Not using preconditioning - output.write("\tNo preconditioning\n"); } - } - - /// Set Jacobian-vector multiplication function - if (use_jacobian and hasJacobian()) { - output.write("\tUsing user-supplied Jacobian function\n"); + /// Set Jacobian-vector multiplication function + + if (use_jacobian and hasJacobian()) { + output.write("\tUsing user-supplied Jacobian function\n"); - if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { - throw BoutException("ARKStepSetJacTimes failed\n"); - } - } else { + if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetJacTimes failed\n"); + } + } else { output.write("\tUsing difference quotient approximation for Jacobian\n"); + } } if (optimize) { @@ -499,24 +501,29 @@ int ArkodeSolver::run() { ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); nfe_evals = int(temp_long_int); nfi_evals = int(temp_long_int2); - ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); - nniters = int(temp_long_int); - ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); - npevals = int(temp_long_int); - ARKStepGetNumLinIters(arkode_mem, &temp_long_int); - nliters = int(temp_long_int); + if(imex or solve_implicit) + { + ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); + nniters = int(temp_long_int); + ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); + npevals = int(temp_long_int); + ARKStepGetNumLinIters(arkode_mem, &temp_long_int); + nliters = int(temp_long_int); + } if (diagnose) { output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, " "npevals {:d}, nliters {:d}\n", nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters); - + if(imex or solve_implicit) + { output.write(" -> Newton iterations per step: {:e}\n", static_cast(nniters) / static_cast(nsteps)); output.write(" -> Linear iterations per Newton iteration: {:e}\n", static_cast(nliters) / static_cast(nniters)); output.write(" -> Preconditioner evaluations per Newton: {:e}\n", static_cast(npevals) / static_cast(nniters)); + } } if (call_monitors(simtime, i, getNumberOutputSteps())) { From 1083271f748fd02d91886df583a7420d9b74c879 Mon Sep 17 00:00:00 2001 From: maggul Date: Mon, 24 Jun 2024 10:58:04 -0500 Subject: [PATCH 393/412] Imex issue is resolved --- src/solver/impls/arkode/arkode.cxx | 226 +++++++++++++++-------------- 1 file changed, 117 insertions(+), 109 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index bc3be6f80a..579c525bcd 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -195,30 +195,29 @@ int ArkodeSolver::init() { // Put the variables into uvec save_vars(N_VGetArrayPointer(uvec)); - ASSERT1(solve_explicit or solve_implicit); + ASSERT1(imex or solve_explicit or solve_implicit); - const auto& explicit_rhs = [this]() { - if (imex) { - return arkode_rhs_explicit; - } else { - return solve_explicit ? arkode_rhs : nullptr; - } - }(); - const auto& implicit_rhs = [this]() { - if (imex) { - return arkode_rhs_implicit; - } else { - return solve_implicit ? arkode_rhs : nullptr; - } - }(); - - arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, explicit_rhs, implicit_rhs, - simtime, uvec); + if(imex or (solve_explicit and solve_implicit)) + { + imex = true; + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, + simtime, uvec); + } + else if (solve_explicit) + { + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, + simtime, uvec); + } + else + { + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_rhs, + simtime, uvec); + } if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); - } + } - if (imex and solve_explicit and solve_implicit) { + if (imex) { output_info.write("\tUsing ARKode ImEx solver \n"); if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImEx failed\n"); @@ -372,91 +371,94 @@ int ArkodeSolver::init() { } } - if (fixed_point) { - output.write("\tUsing accelerated fixed point solver\n"); - nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); - if (nonlinear_solver == nullptr) { - throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); - } - if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { - throw BoutException("ARKStepSetNonlinearSolver failed\n"); - } - } else { - output.write("\tUsing Newton iteration\n"); - - const auto prectype = - use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; - sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); - if (sun_solver == nullptr) { - throw BoutException("Creating SUNDIALS linear solver failed\n"); - } - if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { - throw BoutException("ARKStepSetLinearSolver failed\n"); - } + if (imex or solve_implicit) + { + if (fixed_point) { + output.write("\tUsing accelerated fixed point solver\n"); + nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); + if (nonlinear_solver == nullptr) { + throw BoutException("Creating SUNDIALS fixed point nonlinear solver failed\n"); + } + if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { + throw BoutException("ARKStepSetNonlinearSolver failed\n"); + } + } else { + output.write("\tUsing Newton iteration\n"); - /// Set Preconditioner - if (use_precon) { - if (hasPreconditioner()) { - output.write("\tUsing user-supplied preconditioner\n"); + const auto prectype = + use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE; + sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl); + if (sun_solver == nullptr) { + throw BoutException("Creating SUNDIALS linear solver failed\n"); + } + if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetLinearSolver failed\n"); + } - if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) { - throw BoutException("ARKStepSetPreconditioner failed\n"); + /// Set Preconditioner + if (use_precon) { + if (hasPreconditioner()) { + output.write("\tUsing user-supplied preconditioner\n"); + + if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetPreconditioner failed\n"); + } + } else { + output.write("\tUsing BBD preconditioner\n"); + + /// Get options + // Compute band_width_default from actually added fields, to allow for multiple + // Mesh objects + // + // Previous implementation was equivalent to: + // int MXSUB = mesh->xend - mesh->xstart + 1; + // int band_width_default = n3Dvars()*(MXSUB+2); + const int band_width_default = std::accumulate( + begin(f3d), end(f3d), 0, [](int acc, const VarStr& fvar) { + Mesh* localmesh = fvar.var->getMesh(); + return acc + localmesh->xend - localmesh->xstart + 3; + }); + + const auto mudq = (*options)["mudq"] + .doc("Upper half-bandwidth to be used in the difference " + "quotient Jacobian approximation") + .withDefault(band_width_default); + const auto mldq = (*options)["mldq"] + .doc("Lower half-bandwidth to be used in the difference " + "quotient Jacobian approximation") + .withDefault(band_width_default); + const auto mukeep = (*options)["mukeep"] + .doc("Upper half-bandwidth of the retained banded " + "approximate Jacobian block") + .withDefault(n3Dvars() + n2Dvars()); + const auto mlkeep = (*options)["mlkeep"] + .doc("Lower half-bandwidth of the retained banded " + "approximate Jacobian block") + .withDefault(n3Dvars() + n2Dvars()); + + if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, + arkode_bbd_rhs, nullptr) + != ARKLS_SUCCESS) { + throw BoutException("ARKBBDPrecInit failed\n"); + } } } else { - output.write("\tUsing BBD preconditioner\n"); - - /// Get options - // Compute band_width_default from actually added fields, to allow for multiple - // Mesh objects - // - // Previous implementation was equivalent to: - // int MXSUB = mesh->xend - mesh->xstart + 1; - // int band_width_default = n3Dvars()*(MXSUB+2); - const int band_width_default = std::accumulate( - begin(f3d), end(f3d), 0, [](int acc, const VarStr& fvar) { - Mesh* localmesh = fvar.var->getMesh(); - return acc + localmesh->xend - localmesh->xstart + 3; - }); - - const auto mudq = (*options)["mudq"] - .doc("Upper half-bandwidth to be used in the difference " - "quotient Jacobian approximation") - .withDefault(band_width_default); - const auto mldq = (*options)["mldq"] - .doc("Lower half-bandwidth to be used in the difference " - "quotient Jacobian approximation") - .withDefault(band_width_default); - const auto mukeep = (*options)["mukeep"] - .doc("Upper half-bandwidth of the retained banded " - "approximate Jacobian block") - .withDefault(n3Dvars() + n2Dvars()); - const auto mlkeep = (*options)["mlkeep"] - .doc("Lower half-bandwidth of the retained banded " - "approximate Jacobian block") - .withDefault(n3Dvars() + n2Dvars()); - - if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0, - arkode_bbd_rhs, nullptr) - != ARKLS_SUCCESS) { - throw BoutException("ARKBBDPrecInit failed\n"); - } + // Not using preconditioning + output.write("\tNo preconditioning\n"); } - } else { - // Not using preconditioning - output.write("\tNo preconditioning\n"); } - } - /// Set Jacobian-vector multiplication function + /// Set Jacobian-vector multiplication function + + if (use_jacobian and hasJacobian()) { + output.write("\tUsing user-supplied Jacobian function\n"); - if (use_jacobian and hasJacobian()) { - output.write("\tUsing user-supplied Jacobian function\n"); - - if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { - throw BoutException("ARKStepSetJacTimes failed\n"); - } - } else { + if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { + throw BoutException("ARKStepSetJacTimes failed\n"); + } + } else { output.write("\tUsing difference quotient approximation for Jacobian\n"); + } } if (optimize) { @@ -499,24 +501,29 @@ int ArkodeSolver::run() { ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); nfe_evals = int(temp_long_int); nfi_evals = int(temp_long_int2); - ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); - nniters = int(temp_long_int); - ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); - npevals = int(temp_long_int); - ARKStepGetNumLinIters(arkode_mem, &temp_long_int); - nliters = int(temp_long_int); + if(imex or solve_implicit) + { + ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); + nniters = int(temp_long_int); + ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); + npevals = int(temp_long_int); + ARKStepGetNumLinIters(arkode_mem, &temp_long_int); + nliters = int(temp_long_int); + } if (diagnose) { output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, " "npevals {:d}, nliters {:d}\n", nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters); - - output.write(" -> Newton iterations per step: {:e}\n", - static_cast(nniters) / static_cast(nsteps)); - output.write(" -> Linear iterations per Newton iteration: {:e}\n", - static_cast(nliters) / static_cast(nniters)); - output.write(" -> Preconditioner evaluations per Newton: {:e}\n", - static_cast(npevals) / static_cast(nniters)); + if(imex or solve_implicit) + { + output.write(" -> Newton iterations per step: {:e}\n", + static_cast(nniters) / static_cast(nsteps)); + output.write(" -> Linear iterations per Newton iteration: {:e}\n", + static_cast(nliters) / static_cast(nniters)); + output.write(" -> Preconditioner evaluations per Newton: {:e}\n", + static_cast(npevals) / static_cast(nniters)); + } } if (call_monitors(simtime, i, getNumberOutputSteps())) { @@ -816,3 +823,4 @@ void ArkodeSolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_ } #endif + From 2875347b6f006678750123035390997ac58302df Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 25 Jun 2024 14:23:29 -0700 Subject: [PATCH 394/412] CVODE solver: Pass linear flag to rhs() Uses CVodeSetNlsRhsFn to set different callback functions for linear and nonlinear solves. Both callbacks end up calling the same user rhs() function, but with a boolean argument that differs. --- src/solver/impls/cvode/cvode.cxx | 38 ++++++++++++++++++++++++-------- src/solver/impls/cvode/cvode.hxx | 4 ++-- 2 files changed, 31 insertions(+), 11 deletions(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 22f7f154f7..fd7547c8e8 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -3,9 +3,9 @@ * * ************************************************************************** - * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu + * Copyright 2010-2024 BOUT++ contributors * - * Contact: Ben Dudson, bd512@york.ac.uk + * Contact: Ben Dudson, dudson2@llnl.gov * * This file is part of BOUT++. * @@ -59,7 +59,8 @@ BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative, // NOLINTBEGIN(readability-identifier-length) namespace { -int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); +int cvode_linear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); +int cvode_nonlinear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data); int cvode_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du, void* user_data); @@ -216,7 +217,7 @@ int CvodeSolver::init() { throw BoutException("CVodeSetUserData failed\n"); } - if (CVodeInit(cvode_mem, cvode_rhs, simtime, uvec) != CV_SUCCESS) { + if (CVodeInit(cvode_mem, cvode_linear_rhs, simtime, uvec) != CV_SUCCESS) { throw BoutException("CVodeInit failed\n"); } @@ -385,6 +386,9 @@ int CvodeSolver::init() { } } + // Set the RHS function to be used in the nonlinear solver + CVodeSetNlsRhsFn(cvode_mem, cvode_nonlinear_rhs); + // Set internal tolerance factors if (CVodeSetNonlinConvCoef(cvode_mem, cvode_nonlinear_convergence_coef) != CV_SUCCESS) { throw BoutException("CVodeSetNonlinConvCoef failed\n"); @@ -573,7 +577,7 @@ BoutReal CvodeSolver::run(BoutReal tout) { * RHS function du = F(t, u) **************************************************************************/ -void CvodeSolver::rhs(BoutReal t, BoutReal* udata, BoutReal* dudata) { +void CvodeSolver::rhs(BoutReal t, BoutReal* udata, BoutReal* dudata, bool linear) { TRACE("Running RHS: CvodeSolver::res({})", t); // Load state from udata @@ -584,7 +588,7 @@ void CvodeSolver::rhs(BoutReal t, BoutReal* udata, BoutReal* dudata) { CVodeGetLastStep(cvode_mem, &hcur); // Call RHS function - run_rhs(t); + run_rhs(t, linear); // Save derivatives to dudata save_derivs(dudata); @@ -655,7 +659,23 @@ void CvodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jv // NOLINTBEGIN(readability-identifier-length) namespace { -int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { +int cvode_linear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { + + BoutReal* udata = N_VGetArrayPointer(u); + BoutReal* dudata = N_VGetArrayPointer(du); + + auto* s = static_cast(user_data); + + // Calculate RHS function + try { + s->rhs(t, udata, dudata, true); + } catch (BoutRhsFail& error) { + return 1; + } + return 0; +} + +int cvode_nonlinear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { BoutReal* udata = N_VGetArrayPointer(u); BoutReal* dudata = N_VGetArrayPointer(du); @@ -664,7 +684,7 @@ int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { // Calculate RHS function try { - s->rhs(t, udata, dudata); + s->rhs(t, udata, dudata, false); } catch (BoutRhsFail& error) { return 1; } @@ -674,7 +694,7 @@ int cvode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) { /// RHS function for BBD preconditioner int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du, void* user_data) { - return cvode_rhs(t, u, du, user_data); + return cvode_linear_rhs(t, u, du, user_data); } /// Preconditioner function diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx index 89c3a613a8..9d318f3aee 100644 --- a/src/solver/impls/cvode/cvode.hxx +++ b/src/solver/impls/cvode/cvode.hxx @@ -68,8 +68,8 @@ public: void resetInternalFields() override; - // These functions used internally (but need to be public) - void rhs(BoutReal t, BoutReal* udata, BoutReal* dudata); + // These functions are used internally (but need to be public) + void rhs(BoutReal t, BoutReal* udata, BoutReal* dudata, bool linear); void pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec, BoutReal* zvec); void jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata); From e443df6f77fc9e3daed1e245004ddf52544e391f Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 26 Jun 2024 11:27:46 -0700 Subject: [PATCH 395/412] Add CVODE version guard The function CVodeSetNlsRhsFn is only available from major version 6 onwards. --- src/solver/impls/cvode/cvode.cxx | 9 +++++++++ src/solver/impls/cvode/cvode.hxx | 2 +- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index fd7547c8e8..1fca765687 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -217,9 +217,16 @@ int CvodeSolver::init() { throw BoutException("CVodeSetUserData failed\n"); } +#if SUNDIALS_VERSION_MAJOR >= 6 + // Set the default RHS to linear, then pass nonlinear rhs to NL solver if (CVodeInit(cvode_mem, cvode_linear_rhs, simtime, uvec) != CV_SUCCESS) { throw BoutException("CVodeInit failed\n"); } +#else + if (CVodeInit(cvode_mem, cvode_nonlinear_rhs, simtime, uvec) != CV_SUCCESS) { + throw BoutException("CVodeInit failed\n"); + } +#endif if (max_order > 0) { if (CVodeSetMaxOrd(cvode_mem, max_order) != CV_SUCCESS) { @@ -386,8 +393,10 @@ int CvodeSolver::init() { } } +#if SUNDIALS_VERSION_MAJOR >= 6 // Set the RHS function to be used in the nonlinear solver CVodeSetNlsRhsFn(cvode_mem, cvode_nonlinear_rhs); +#endif // Set internal tolerance factors if (CVodeSetNonlinConvCoef(cvode_mem, cvode_nonlinear_convergence_coef) != CV_SUCCESS) { diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx index 9d318f3aee..04db7427ab 100644 --- a/src/solver/impls/cvode/cvode.hxx +++ b/src/solver/impls/cvode/cvode.hxx @@ -138,7 +138,7 @@ private: int nonlin_fails{0}; int stab_lims{0}; - bool cvode_initialised = false; + bool cvode_initialised {false}; void set_vector_option_values(BoutReal* option_data, std::vector& f2dtols, std::vector& f3dtols); From 5d87ce20675a816bd489794174e2b355162b72e8 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Wed, 26 Jun 2024 13:00:19 -0700 Subject: [PATCH 396/412] Solver: Ensure nonlinear RHS called first I think this is probably already the case, but this ensures that the nonlinear RHS is called first to evaluate all coefficients. --- include/bout/solver.hxx | 2 ++ src/solver/solver.cxx | 6 ++++++ 2 files changed, 8 insertions(+) diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx index 896ce62965..47fef7ce73 100644 --- a/include/bout/solver.hxx +++ b/include/bout/solver.hxx @@ -429,6 +429,8 @@ protected: bool has_constraints{false}; /// Has init been called yet? bool initialised{false}; + /// If calling user RHS for the first time + bool first_rhs_call{true}; /// Current simulation time BoutReal simtime{0.0}; diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx index 1b7ec1fd74..8a75ff43a4 100644 --- a/src/solver/solver.cxx +++ b/src/solver/solver.cxx @@ -1364,6 +1364,12 @@ int Solver::run_rhs(BoutReal t, bool linear) { Timer timer("rhs"); + if (first_rhs_call) { + // Ensure that nonlinear terms are calculated on first call + linear = false; + first_rhs_call = false; + } + if (model->splitOperator()) { // Run both parts From f009116a0bf29312d599c7d3bb769003e0a3c6ea Mon Sep 17 00:00:00 2001 From: bendudson Date: Wed, 26 Jun 2024 20:02:54 +0000 Subject: [PATCH 397/412] Apply clang-format changes --- src/solver/impls/cvode/cvode.hxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx index 04db7427ab..d44fcf2335 100644 --- a/src/solver/impls/cvode/cvode.hxx +++ b/src/solver/impls/cvode/cvode.hxx @@ -138,7 +138,7 @@ private: int nonlin_fails{0}; int stab_lims{0}; - bool cvode_initialised {false}; + bool cvode_initialised{false}; void set_vector_option_values(BoutReal* option_data, std::vector& f2dtols, std::vector& f3dtols); From 9638740c3d387d97c8ec60acf4960ab149fcb4cd Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Wed, 24 Jul 2024 10:37:08 -0700 Subject: [PATCH 398/412] Add mxorder option back, now deprecated --- src/solver/impls/cvode/cvode.cxx | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx index 22f7f154f7..04d9a529b7 100644 --- a/src/solver/impls/cvode/cvode.cxx +++ b/src/solver/impls/cvode/cvode.cxx @@ -220,6 +220,13 @@ int CvodeSolver::init() { throw BoutException("CVodeInit failed\n"); } + if (mxorder > 0) { + output_warn << "WARNING: Option 'mxorder' is deprecated. Please use " + "'cvode_max_order' instead\n"; + if (CVodeSetMaxOrd(cvode_mem, mxorder) != CV_SUCCESS) { + throw BoutException("CVodeSetMaxOrder failed\n"); + } + } if (max_order > 0) { if (CVodeSetMaxOrd(cvode_mem, max_order) != CV_SUCCESS) { throw BoutException("CVodeSetMaxOrder failed\n"); From 4e3e4cc73d42ec39806439098a770c47bbf6db53 Mon Sep 17 00:00:00 2001 From: Kefu Chai Date: Sun, 14 Jul 2024 09:50:10 +0800 Subject: [PATCH 399/412] mark fmt::format() const MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit fmt v11 preserves and enforces the constness of the formatted argument. without this change, the tree fails to build with fmt v11, like: ``` In file included from /usr/include/fmt/format.h:41, from /usr/include/fmt/core.h:5, from /builddir/build/BUILD/bout++-5.1.0-build/BOUT++-v5.1.0/include/bout/sys/expressionparser.hxx:33: /usr/include/fmt/base.h: In instantiation of ‘static void fmt::v11::detail::value::format_custom_arg(void*, typename Context::parse_context_type&, Context&) [with T = Options; Formatter = fmt::v11::formatter; Context = fmt::v11::context; typename Context::parse_context_type = fmt::v11::basic_format_parse_context]’: /usr/include/fmt/base.h:1373:19: required from ‘fmt::v11::detail::value::value(T&) [with T = Options; Context = fmt::v11::context]’ 1373 | custom.format = format_custom_arg< | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 1374 | value_type, typename Context::template formatter_type>; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/fmt/base.h:1631:41: required from ‘constexpr fmt::v11::detail::value fmt::v11::detail::make_arg(T&) [with bool PACKED = true; Context = fmt::v11::context; T = Options; typename std::enable_if::type = 0]’ 1631 | return {arg_mapper().map(val)}; | ^ /usr/include/fmt/base.h:2002:74: required from ‘constexpr fmt::v11::detail::format_arg_store fmt::v11::make_format_args(T& ...) [with Context = context; T = {Options}; long unsigned int NUM_ARGS = 1; long unsigned int NUM_NAMED_ARGS = 0; long long unsigned int DESC = 15; typename std::enable_if<(NUM_NAMED_ARGS == 0), int>::type = 0]’ 2002 | return {{detail::make_arg( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2003 | args)...}}; | ~~~~~ /usr/include/fmt/format.h:4357:44: required from ‘std::string fmt::v11::format(format_string, T&& ...) [with T = {Options&}; std::string = std::__cxx11::basic_string; format_string = basic_format_string]’ 4357 | return vformat(fmt, fmt::make_format_args(args...)); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/bout++-5.1.0-build/BOUT++-v5.1.0/src/bout++.cxx:333:27: required from ‘void bout::experimental::printTypeOptions(const std::string&) [with Factory = SolverFactory; std::string = std::__cxx11::basic_string]’ 333 | std::cout << fmt::format("{:id}\n", help_options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.1.0-build/BOUT++-v5.1.0/src/bout++.cxx:355:30: required from ‘void bout::experimental::handleFactoryHelp(const std::string&, int, int, char**, bool) [with Factory = SolverFactory; std::string = std::__cxx11::basic_string]’ 355 | printTypeOptions(argv[i + 1]); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.1.0-build/BOUT++-v5.1.0/src/bout++.cxx:417:37: required from here 417 | handleFactoryHelp(current_arg, i, argc, argv); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/fmt/base.h:1392:29: error: passing ‘const fmt::v11::formatter’ as ‘this’ argument discards qualifiers [-fpermissive] ``` Signed-off-by: Kefu Chai --- include/bout/options.hxx | 2 +- include/bout/output_bout_types.hxx | 2 +- src/sys/options.cxx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/include/bout/options.hxx b/include/bout/options.hxx index a0b745670f..4a32907b17 100644 --- a/include/bout/options.hxx +++ b/include/bout/options.hxx @@ -981,7 +981,7 @@ namespace details { /// avoiding lengthy recompilation if we change it struct OptionsFormatterBase { auto parse(fmt::format_parse_context& ctx) -> fmt::format_parse_context::iterator; - auto format(const Options& options, fmt::format_context& ctx) + auto format(const Options& options, fmt::format_context& ctx) const -> fmt::format_context::iterator; private: diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx index 6b1829b088..b67762521b 100644 --- a/include/bout/output_bout_types.hxx +++ b/include/bout/output_bout_types.hxx @@ -34,7 +34,7 @@ struct fmt::formatter> { // Formats the point p using the parsed format specification (presentation) // stored in this formatter. template - auto format(const SpecificInd& ind, FormatContext& ctx) { + auto format(const SpecificInd& ind, FormatContext& ctx) const { // ctx.out() is an output iterator to write to. if (presentation == 'c') { switch (N) { diff --git a/src/sys/options.cxx b/src/sys/options.cxx index 1d18a0e462..c50d702b4a 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -968,7 +968,7 @@ bout::details::OptionsFormatterBase::parse(fmt::format_parse_context& ctx) { fmt::format_context::iterator bout::details::OptionsFormatterBase::format(const Options& options, - fmt::format_context& ctx) { + fmt::format_context& ctx) const { const auto conditionally_used = [](const Options& option) -> bool { if (not option.hasAttribute(conditionally_used_attribute)) { From 78034d7578ac2a75b302dbdc5ef8e9d7d58cc5ef Mon Sep 17 00:00:00 2001 From: Kefu Chai Date: Sun, 14 Jul 2024 10:55:48 +0800 Subject: [PATCH 400/412] include fmt/ranges.h for using fmt::join() fmt::join() overloads was moved into fmt/ranges.h since fmt v11, so let's include fmt/ranges.h as well. Signed-off-by: Kefu Chai --- src/sys/options.cxx | 1 + 1 file changed, 1 insertion(+) diff --git a/src/sys/options.cxx b/src/sys/options.cxx index c50d702b4a..e2f39542fd 100644 --- a/src/sys/options.cxx +++ b/src/sys/options.cxx @@ -18,6 +18,7 @@ #include #include +#include #include #include From f77fe52d52fc8073e6934bb7bcb3e9e53b76a85c Mon Sep 17 00:00:00 2001 From: maggul Date: Mon, 19 Aug 2024 11:19:30 -0500 Subject: [PATCH 401/412] changed ARKODE config. to use string as the treatment --- cmake/SetupBOUTThirdParty.cmake | 4 +++- src/solver/impls/arkode/arkode.cxx | 34 +++++++++++++++++++----------- src/solver/impls/arkode/arkode.hxx | 2 ++ 3 files changed, 27 insertions(+), 13 deletions(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 127fbda765..4115e1feb9 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -297,7 +297,8 @@ if (BOUT_USE_SUNDIALS) FetchContent_MakeAvailable(sundials) message(STATUS "SUNDIALS done configuring") else() - find_package(SUNDIALS 4 REQUIRED) + enable_language(C) + find_package(SUNDIALS REQUIRED) endif() target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel) target_link_libraries(bout++ PUBLIC SUNDIALS::cvode) @@ -360,3 +361,4 @@ if (BOUT_USE_UUID_SYSTEM_GENERATOR) endif() message(STATUS "UUID_SYSTEM_GENERATOR: ${BOUT_USE_UUID_SYSTEM_GENERATOR}") set(BOUT_HAS_UUID_SYSTEM_GENERATOR ${BOUT_USE_UUID_SYSTEM_GENERATOR}) + diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 579c525bcd..f9b4eb1424 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -74,11 +74,14 @@ ArkodeSolver::ArkodeSolver(Options* opts) mxsteps((*options)["mxstep"] .doc("Maximum number of steps to take between outputs") .withDefault(500)), - imex((*options)["imex"].doc("Use ImEx capability").withDefault(true)), + treatment((*options)["treatment"] + .doc("Use default capability (imex) or provide a specific treatment: implicit or explicit") + .withDefault("")), + imex((*options)["imex"].doc("Use ImEx capability").withDefault(false)), solve_explicit( - (*options)["explicit"].doc("Solve only explicit part").withDefault(true)), + (*options)["explicit"].doc("Solve only explicit part").withDefault(false)), solve_implicit( - (*options)["implicit"].doc("Solve only implicit part").withDefault(true)), + (*options)["implicit"].doc("Solve only implicit part").withDefault(false)), set_linear( (*options)["set_linear"] .doc("Use linear implicit solver (only evaluates jacobian inversion once)") @@ -194,16 +197,23 @@ int ArkodeSolver::init() { // Put the variables into uvec save_vars(N_VGetArrayPointer(uvec)); + + if(treatment == "") + { + if(imex or (solve_explicit and solve_implicit)) {treatment = "imex";} + else if (solve_explicit) {treatment = "explicit";} + else if (solve_implicit) {treatment = "implicit";} + else {treatment = "imex";} + } - ASSERT1(imex or solve_explicit or solve_implicit); + ASSERT1(treatment == "imex" or treatment == "implicit" or treatment == "explicit"); - if(imex or (solve_explicit and solve_implicit)) + if(treatment == "imex") { - imex = true; arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, simtime, uvec); } - else if (solve_explicit) + else if (treatment == "explicit") { arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, simtime, uvec); @@ -217,12 +227,12 @@ int ArkodeSolver::init() { throw BoutException("ARKStepCreate failed\n"); } - if (imex) { + if (treatment == "imex") { output_info.write("\tUsing ARKode ImEx solver \n"); if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImEx failed\n"); } - } else if (solve_explicit) { + } else if (treatment == "explicit") { output_info.write("\tUsing ARKStep Explicit solver \n"); if (ARKStepSetExplicit(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetExplicit failed\n"); @@ -371,7 +381,7 @@ int ArkodeSolver::init() { } } - if (imex or solve_implicit) + if (treatment == "imex" or treatment == "implicit") { if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); @@ -501,7 +511,7 @@ int ArkodeSolver::run() { ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); nfe_evals = int(temp_long_int); nfi_evals = int(temp_long_int2); - if(imex or solve_implicit) + if (treatment == "imex" or treatment == "implicit") { ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); nniters = int(temp_long_int); @@ -515,7 +525,7 @@ int ArkodeSolver::run() { output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, " "npevals {:d}, nliters {:d}\n", nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters); - if(imex or solve_implicit) + if (treatment == "imex" or treatment == "implicit") { output.write(" -> Newton iterations per step: {:e}\n", static_cast(nniters) / static_cast(nsteps)); diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index 08bb3ea729..c86961ab20 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -93,6 +93,8 @@ private: /// Maximum number of steps to take between outputs int mxsteps; + /// Name of the integrator treatment, imex, implicit or explicit + std::string treatment; /// Use ImEx capability bool imex; /// Solve only explicit part From c254cbf582ee7363069e2d8e0ca8371b10593fd4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Mon, 19 Aug 2024 23:41:39 -0500 Subject: [PATCH 402/412] Update src/solver/impls/arkode/arkode.cxx Co-authored-by: Steven Roberts --- src/solver/impls/arkode/arkode.cxx | 1 + 1 file changed, 1 insertion(+) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index f9b4eb1424..f64badfbda 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -77,6 +77,7 @@ ArkodeSolver::ArkodeSolver(Options* opts) treatment((*options)["treatment"] .doc("Use default capability (imex) or provide a specific treatment: implicit or explicit") .withDefault("")), + // TODO: remove imex, explicit, and implicit options. These are deprecated in favor of treatment imex((*options)["imex"].doc("Use ImEx capability").withDefault(false)), solve_explicit( (*options)["explicit"].doc("Solve only explicit part").withDefault(false)), From 5a6bdf756103cfe26f478750cc6d605d86dfe896 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Mon, 19 Aug 2024 23:44:01 -0500 Subject: [PATCH 403/412] Update src/solver/impls/arkode/arkode.cxx Co-authored-by: Steven Roberts --- src/solver/impls/arkode/arkode.cxx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index f64badfbda..1c961d6501 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -199,7 +199,7 @@ int ArkodeSolver::init() { // Put the variables into uvec save_vars(N_VGetArrayPointer(uvec)); - if(treatment == "") + if(treatment.empty()) { if(imex or (solve_explicit and solve_implicit)) {treatment = "imex";} else if (solve_explicit) {treatment = "explicit";} From 8da57ca12c9447feb9f014628823631a1342c9dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Mon, 19 Aug 2024 23:45:55 -0500 Subject: [PATCH 404/412] Update src/solver/impls/arkode/arkode.cxx Co-authored-by: Steven Roberts --- src/solver/impls/arkode/arkode.cxx | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 1c961d6501..76c436a048 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -201,10 +201,9 @@ int ArkodeSolver::init() { if(treatment.empty()) { - if(imex or (solve_explicit and solve_implicit)) {treatment = "imex";} + if(imex or (solve_explicit == solve_implicit)) {treatment = "imex";} else if (solve_explicit) {treatment = "explicit";} - else if (solve_implicit) {treatment = "implicit";} - else {treatment = "imex";} + else {treatment = "implicit";} } ASSERT1(treatment == "imex" or treatment == "implicit" or treatment == "explicit"); From 3d84ffdec8c550487dfb6ae7c109e1c0da743c1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Mon, 19 Aug 2024 23:47:43 -0500 Subject: [PATCH 405/412] Update src/solver/impls/arkode/arkode.cxx Co-authored-by: Steven Roberts --- src/solver/impls/arkode/arkode.cxx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 76c436a048..0e5a57dec0 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -218,10 +218,12 @@ int ArkodeSolver::init() { arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, simtime, uvec); } - else + else if (treatment == "implicit") { arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_rhs, simtime, uvec); + } else { + throw BoutException("Invalid treatment: {}\n", treatment); } if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); From bf94971506cafc805d0a95e329d936569b973e89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Mon, 19 Aug 2024 23:50:55 -0500 Subject: [PATCH 406/412] Removed ASSERT1 --- src/solver/impls/arkode/arkode.cxx | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 0e5a57dec0..6a36659989 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -206,8 +206,6 @@ int ArkodeSolver::init() { else {treatment = "implicit";} } - ASSERT1(treatment == "imex" or treatment == "implicit" or treatment == "explicit"); - if(treatment == "imex") { arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, From fd69cc3f564607ca2a945d57c92085c19ed62722 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mustafa=20A=C4=9Fg=C3=BCl?= <33010171+maggul@users.noreply.github.com> Date: Mon, 19 Aug 2024 23:55:13 -0500 Subject: [PATCH 407/412] Deleted the last line --- cmake/SetupBOUTThirdParty.cmake | 1 - 1 file changed, 1 deletion(-) diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake index 9fa9ac8434..9c49fe6fdc 100644 --- a/cmake/SetupBOUTThirdParty.cmake +++ b/cmake/SetupBOUTThirdParty.cmake @@ -364,4 +364,3 @@ if (BOUT_USE_UUID_SYSTEM_GENERATOR) endif() message(STATUS "UUID_SYSTEM_GENERATOR: ${BOUT_USE_UUID_SYSTEM_GENERATOR}") set(BOUT_HAS_UUID_SYSTEM_GENERATOR ${BOUT_USE_UUID_SYSTEM_GENERATOR}) - From a7d986fcb30140b92063215d8106baed45d98314 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Tue, 20 Aug 2024 09:55:30 -0700 Subject: [PATCH 408/412] arkode solver: Clang format --- src/solver/impls/arkode/arkode.cxx | 72 ++++++++++++++---------------- 1 file changed, 34 insertions(+), 38 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 6a36659989..20c378026f 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -75,14 +75,15 @@ ArkodeSolver::ArkodeSolver(Options* opts) .doc("Maximum number of steps to take between outputs") .withDefault(500)), treatment((*options)["treatment"] - .doc("Use default capability (imex) or provide a specific treatment: implicit or explicit") + .doc("Use default capability (imex) or provide a specific treatment: " + "implicit or explicit") .withDefault("")), // TODO: remove imex, explicit, and implicit options. These are deprecated in favor of treatment imex((*options)["imex"].doc("Use ImEx capability").withDefault(false)), solve_explicit( (*options)["explicit"].doc("Solve only explicit part").withDefault(false)), solve_implicit( - (*options)["implicit"].doc("Solve only implicit part").withDefault(false)), + (*options)["implicit"].doc("Solve only implicit part").withDefault(false)), set_linear( (*options)["set_linear"] .doc("Use linear implicit solver (only evaluates jacobian inversion once)") @@ -198,34 +199,32 @@ int ArkodeSolver::init() { // Put the variables into uvec save_vars(N_VGetArrayPointer(uvec)); - - if(treatment.empty()) - { - if(imex or (solve_explicit == solve_implicit)) {treatment = "imex";} - else if (solve_explicit) {treatment = "explicit";} - else {treatment = "implicit";} - } - - if(treatment == "imex") - { - arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, - simtime, uvec); - } - else if (treatment == "explicit") - { - arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, - simtime, uvec); - } - else if (treatment == "implicit") - { - arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_rhs, - simtime, uvec); + + if (treatment.empty()) { + if (imex or (solve_explicit == solve_implicit)) { + treatment = "imex"; + } else if (solve_explicit) { + treatment = "explicit"; + } else { + treatment = "implicit"; + } + } + + if (treatment == "imex") { + arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, + arkode_rhs_implicit, simtime, uvec); + } else if (treatment == "explicit") { + arkode_mem = + callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, simtime, uvec); + } else if (treatment == "implicit") { + arkode_mem = + callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_rhs, simtime, uvec); } else { throw BoutException("Invalid treatment: {}\n", treatment); } if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); - } + } if (treatment == "imex") { output_info.write("\tUsing ARKode ImEx solver \n"); @@ -381,8 +380,7 @@ int ArkodeSolver::init() { } } - if (treatment == "imex" or treatment == "implicit") - { + if (treatment == "imex" or treatment == "implicit") { if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); @@ -410,7 +408,8 @@ int ArkodeSolver::init() { if (hasPreconditioner()) { output.write("\tUsing user-supplied preconditioner\n"); - if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) { + if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) + != ARKLS_SUCCESS) { throw BoutException("ARKStepSetPreconditioner failed\n"); } } else { @@ -459,7 +458,7 @@ int ArkodeSolver::init() { } /// Set Jacobian-vector multiplication function - + if (use_jacobian and hasJacobian()) { output.write("\tUsing user-supplied Jacobian function\n"); @@ -467,7 +466,7 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetJacTimes failed\n"); } } else { - output.write("\tUsing difference quotient approximation for Jacobian\n"); + output.write("\tUsing difference quotient approximation for Jacobian\n"); } } @@ -511,8 +510,7 @@ int ArkodeSolver::run() { ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); nfe_evals = int(temp_long_int); nfi_evals = int(temp_long_int2); - if (treatment == "imex" or treatment == "implicit") - { + if (treatment == "imex" or treatment == "implicit") { ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); nniters = int(temp_long_int); ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); @@ -525,14 +523,13 @@ int ArkodeSolver::run() { output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, " "npevals {:d}, nliters {:d}\n", nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters); - if (treatment == "imex" or treatment == "implicit") - { + if (treatment == "imex" or treatment == "implicit") { output.write(" -> Newton iterations per step: {:e}\n", - static_cast(nniters) / static_cast(nsteps)); + static_cast(nniters) / static_cast(nsteps)); output.write(" -> Linear iterations per Newton iteration: {:e}\n", - static_cast(nliters) / static_cast(nniters)); + static_cast(nliters) / static_cast(nniters)); output.write(" -> Preconditioner evaluations per Newton: {:e}\n", - static_cast(npevals) / static_cast(nniters)); + static_cast(npevals) / static_cast(nniters)); } } @@ -833,4 +830,3 @@ void ArkodeSolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_ } #endif - From e2f2332639958b0166233692fd5e87f265c964a5 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 22 Aug 2024 10:19:48 -0700 Subject: [PATCH 409/412] Arkode solver: Add treatment enum, remove imex/implicit/explicit - treatment is now an enum, rather than a string. Allowed values are "imex", "explicit" or "implicit" (Lower case in input). - The conversion from string to enum now lists the valid values when a string isn't recognised e.g: ``` Option solver:treatment = Implicit (Command line) Error encountered: Did not find enum Implicit. Valid values: explicit imex implicitStacktrace not enabled. ====== Back trace ====== -> Treatment TreatmentFromString(const std::string &) on line 66 of '/Users/dudson2/code/BOUT-dev/src/solver/impls/arkode/arkode.hxx' ====== Exception thrown ====== Did not find enum Implicit. Valid values: explicit imex implicit ``` - The separate "imex", "implicit" and "explicit" booleans have been removed, all controlled by "treatment" now. --- include/bout/bout_enum_class.hxx | 6 +++- src/solver/impls/arkode/arkode.cxx | 57 +++++++++++++----------------- src/solver/impls/arkode/arkode.hxx | 19 +++++----- 3 files changed, 39 insertions(+), 43 deletions(-) diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx index f8c9e364c5..585e5b020e 100644 --- a/include/bout/bout_enum_class.hxx +++ b/include/bout/bout_enum_class.hxx @@ -86,7 +86,11 @@ BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__)}; \ auto found = fromString_map.find(s); \ if (found == fromString_map.end()) { \ - throw BoutException("Did not find enum {:s}", s); \ + std::string valid_values {}; \ + for (auto const& entry : fromString_map) { \ + valid_values += std::string(" ") + entry.first; \ + } \ + throw BoutException("Did not find enum {:s}. Valid values: {:s}", s, valid_values); \ } \ return found->second; \ } \ diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 20c378026f..9b4b813fe6 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -4,9 +4,7 @@ * NOTE: ARKode is still in beta testing so use with cautious optimism * ************************************************************************** - * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu - * - * Contact: Nick Walkden, nick.walkden@ccfe.ac.uk + * Copyright 2010-2024 BOUT++ contributors * * This file is part of BOUT++. * @@ -32,6 +30,7 @@ #if BOUT_HAS_ARKODE #include "bout/boutcomm.hxx" +#include "bout/bout_enum_class.hxx" #include "bout/boutexception.hxx" #include "bout/field3d.hxx" #include "bout/mesh.hxx" @@ -75,15 +74,9 @@ ArkodeSolver::ArkodeSolver(Options* opts) .doc("Maximum number of steps to take between outputs") .withDefault(500)), treatment((*options)["treatment"] - .doc("Use default capability (imex) or provide a specific treatment: " + .doc("Use default capability (imex) or provide a specific treatment: " "implicit or explicit") - .withDefault("")), - // TODO: remove imex, explicit, and implicit options. These are deprecated in favor of treatment - imex((*options)["imex"].doc("Use ImEx capability").withDefault(false)), - solve_explicit( - (*options)["explicit"].doc("Solve only explicit part").withDefault(false)), - solve_implicit( - (*options)["implicit"].doc("Solve only implicit part").withDefault(false)), + .withDefault(Treatment::IMEX)), set_linear( (*options)["set_linear"] .doc("Use linear implicit solver (only evaluates jacobian inversion once)") @@ -200,47 +193,47 @@ int ArkodeSolver::init() { // Put the variables into uvec save_vars(N_VGetArrayPointer(uvec)); - if (treatment.empty()) { - if (imex or (solve_explicit == solve_implicit)) { - treatment = "imex"; - } else if (solve_explicit) { - treatment = "explicit"; - } else { - treatment = "implicit"; - } - } - - if (treatment == "imex") { + switch (treatment) { + case Treatment::IMEX: arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, simtime, uvec); - } else if (treatment == "explicit") { + break; + case Treatment::Explicit: arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs, nullptr, simtime, uvec); - } else if (treatment == "implicit") { + break; + case Treatment::Implicit: arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_rhs, simtime, uvec); - } else { - throw BoutException("Invalid treatment: {}\n", treatment); + break; + default: + throw BoutException("Invalid treatment: {}\n", toString(treatment)); } if (arkode_mem == nullptr) { throw BoutException("ARKStepCreate failed\n"); } - if (treatment == "imex") { + switch (treatment) { + case Treatment::IMEX: output_info.write("\tUsing ARKode ImEx solver \n"); if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImEx failed\n"); } - } else if (treatment == "explicit") { + break; + case Treatment::Explicit: output_info.write("\tUsing ARKStep Explicit solver \n"); if (ARKStepSetExplicit(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetExplicit failed\n"); } - } else { + break; + case Treatment::Implicit: output_info.write("\tUsing ARKStep Implicit solver \n"); if (ARKStepSetImplicit(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImplicit failed\n"); } + break; + default: + throw BoutException("Invalid treatment: {}\n", toString(treatment)); } // For callbacks, need pointer to solver object @@ -380,7 +373,7 @@ int ArkodeSolver::init() { } } - if (treatment == "imex" or treatment == "implicit") { + if (treatment == Treatment::IMEX or treatment == Treatment::Implicit) { if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); @@ -510,7 +503,7 @@ int ArkodeSolver::run() { ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); nfe_evals = int(temp_long_int); nfi_evals = int(temp_long_int2); - if (treatment == "imex" or treatment == "implicit") { + if (treatment == Treatment::IMEX or treatment == Treatment::Implicit) { ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); nniters = int(temp_long_int); ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); @@ -523,7 +516,7 @@ int ArkodeSolver::run() { output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, " "npevals {:d}, nliters {:d}\n", nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters); - if (treatment == "imex" or treatment == "implicit") { + if (treatment == Treatment::IMEX or treatment == Treatment::Implicit) { output.write(" -> Newton iterations per step: {:e}\n", static_cast(nniters) / static_cast(nsteps)); output.write(" -> Linear iterations per Newton iteration: {:e}\n", diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index c86961ab20..bfda2bed0c 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -5,9 +5,9 @@ * NOTE: Only one solver can currently be compiled in * ************************************************************************** - * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu + * Copyright 2010-2024 BOUT++ contributors * - * Contact: Ben Dudson, bd512@york.ac.uk + * Contact: Ben Dudson, dudson2@llnl.gov * * This file is part of BOUT++. * @@ -41,6 +41,7 @@ RegisterUnavailableSolver #else +#include "bout/bout_enum_class.hxx" #include "bout/bout_types.hxx" #include "bout/sundials_backports.hxx" @@ -60,6 +61,10 @@ namespace { RegisterSolver registersolverarkode("arkode"); } +// enum describing treatment of equations +// Note: Capitalized because `explicit` is a C++ reserved keyword +BOUT_ENUM_CLASS(Treatment, IMEX, Implicit, Explicit); + class ArkodeSolver : public Solver { public: explicit ArkodeSolver(Options* opts = nullptr); @@ -93,14 +98,8 @@ private: /// Maximum number of steps to take between outputs int mxsteps; - /// Name of the integrator treatment, imex, implicit or explicit - std::string treatment; - /// Use ImEx capability - bool imex; - /// Solve only explicit part - bool solve_explicit; - /// Solve only implicit part - bool solve_implicit; + /// Integrator treatment enum: IMEX, Implicit or Explicit + Treatment treatment; /// Use linear implicit solver (only evaluates jacobian inversion once) bool set_linear; /// Solve explicit portion in fixed timestep mode. NOTE: This is not recommended except From 5e6a7d1cb5353bb83a947d4e8aa1827f086e3c12 Mon Sep 17 00:00:00 2001 From: Ben Dudson Date: Thu, 22 Aug 2024 10:42:29 -0700 Subject: [PATCH 410/412] Arkode solver: Change adap_method to an enum class Inputs are now "pid", "pi", "i", etc. rather than 0 .. 5. If an invalid value is used then the valid choices are printed. --- src/solver/impls/arkode/arkode.cxx | 67 ++++++++++++++++++++---------- src/solver/impls/arkode/arkode.hxx | 16 ++++--- 2 files changed, 53 insertions(+), 30 deletions(-) diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx index 9b4b813fe6..440f8f54f1 100644 --- a/src/solver/impls/arkode/arkode.cxx +++ b/src/solver/impls/arkode/arkode.cxx @@ -29,8 +29,8 @@ #if BOUT_HAS_ARKODE -#include "bout/boutcomm.hxx" #include "bout/bout_enum_class.hxx" +#include "bout/boutcomm.hxx" #include "bout/boutexception.hxx" #include "bout/field3d.hxx" #include "bout/mesh.hxx" @@ -74,9 +74,9 @@ ArkodeSolver::ArkodeSolver(Options* opts) .doc("Maximum number of steps to take between outputs") .withDefault(500)), treatment((*options)["treatment"] - .doc("Use default capability (imex) or provide a specific treatment: " + .doc("Use default capability (imex) or provide a specific treatment: " "implicit or explicit") - .withDefault(Treatment::IMEX)), + .withDefault(Treatment::ImEx)), set_linear( (*options)["set_linear"] .doc("Use linear implicit solver (only evaluates jacobian inversion once)") @@ -97,11 +97,11 @@ ArkodeSolver::ArkodeSolver(Options* opts) cfl_frac((*options)["cfl_frac"] .doc("Fraction of the estimated explicitly stable step to use") .withDefault(-1.0)), - adap_method((*options)["adap_method"] - .doc("Set timestep adaptivity function: 0 -> PID adaptivity " - "(default); 1 -> PI; 2 -> I; 3 -> explicit Gustafsson; 4 -> " - "implicit Gustafsson; 5 -> ImEx Gustafsson;") - .withDefault(0)), + adap_method( + (*options)["adap_method"] + .doc("Set timestep adaptivity function: pid, pi, i, explicit_gustafsson, " + "implicit_gustafsson, imex_gustafsson.") + .withDefault(AdapMethod::PID)), abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)), reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)), use_vector_abstol((*options)["use_vector_abstol"] @@ -194,7 +194,7 @@ int ArkodeSolver::init() { save_vars(N_VGetArrayPointer(uvec)); switch (treatment) { - case Treatment::IMEX: + case Treatment::ImEx: arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_explicit, arkode_rhs_implicit, simtime, uvec); break; @@ -214,7 +214,7 @@ int ArkodeSolver::init() { } switch (treatment) { - case Treatment::IMEX: + case Treatment::ImEx: output_info.write("\tUsing ARKode ImEx solver \n"); if (ARKStepSetImEx(arkode_mem) != ARK_SUCCESS) { throw BoutException("ARKStepSetImEx failed\n"); @@ -275,25 +275,24 @@ int ArkodeSolver::init() { #if SUNDIALS_CONTROLLER_SUPPORT switch (adap_method) { - case 0: + case AdapMethod::PID: controller = SUNAdaptController_PID(suncontext); break; - case 1: + case AdapMethod::PI: controller = SUNAdaptController_PI(suncontext); break; - case 2: + case AdapMethod::I: controller = SUNAdaptController_I(suncontext); break; - case 3: + case AdapMethod::Explicit_Gustafsson: controller = SUNAdaptController_ExpGus(suncontext); break; - case 4: + case AdapMethod::Implicit_Gustafsson: controller = SUNAdaptController_ImpGus(suncontext); break; - case 5: + case AdapMethod::ImEx_Gustafsson: controller = SUNAdaptController_ImExGus(suncontext); break; - default: throw BoutException("Invalid adap_method\n"); } @@ -306,7 +305,33 @@ int ArkodeSolver::init() { throw BoutException("ARKStepSetAdaptivityAdjustment failed\n"); } #else - if (ARKStepSetAdaptivityMethod(arkode_mem, adap_method, 1, 1, nullptr) != ARK_SUCCESS) { + int adap_method_int; + // Could cast to underlying integer, but this is more explicit + switch (adap_method) { + case AdapMethod::PID: + adap_method_int = 0; + break; + case AdapMethod::PI: + adap_method_int = 1; + break; + case AdapMethod::I: + adap_method_int = 2; + break; + case AdapMethod::Explicit_Gustafsson: + adap_method_int = 3; + break; + case AdapMethod::Implicit_Gustafsson: + adap_method_int = 4; + break; + case AdapMethod::ImEx_Gustafsson: + adap_method_int = 5; + break; + default: + throw BoutException("Invalid adap_method\n"); + } + + if (ARKStepSetAdaptivityMethod(arkode_mem, adap_method_int, 1, 1, nullptr) + != ARK_SUCCESS) { throw BoutException("ARKStepSetAdaptivityMethod failed\n"); } #endif @@ -373,7 +398,7 @@ int ArkodeSolver::init() { } } - if (treatment == Treatment::IMEX or treatment == Treatment::Implicit) { + if (treatment == Treatment::ImEx or treatment == Treatment::Implicit) { if (fixed_point) { output.write("\tUsing accelerated fixed point solver\n"); nonlinear_solver = callWithSUNContext(SUNNonlinSol_FixedPoint, suncontext, uvec, 3); @@ -503,7 +528,7 @@ int ArkodeSolver::run() { ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); nfe_evals = int(temp_long_int); nfi_evals = int(temp_long_int2); - if (treatment == Treatment::IMEX or treatment == Treatment::Implicit) { + if (treatment == Treatment::ImEx or treatment == Treatment::Implicit) { ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); nniters = int(temp_long_int); ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); @@ -516,7 +541,7 @@ int ArkodeSolver::run() { output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, " "npevals {:d}, nliters {:d}\n", nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters); - if (treatment == Treatment::IMEX or treatment == Treatment::Implicit) { + if (treatment == Treatment::ImEx or treatment == Treatment::Implicit) { output.write(" -> Newton iterations per step: {:e}\n", static_cast(nniters) / static_cast(nsteps)); output.write(" -> Linear iterations per Newton iteration: {:e}\n", diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx index bfda2bed0c..4050ed377f 100644 --- a/src/solver/impls/arkode/arkode.hxx +++ b/src/solver/impls/arkode/arkode.hxx @@ -63,7 +63,11 @@ RegisterSolver registersolverarkode("arkode"); // enum describing treatment of equations // Note: Capitalized because `explicit` is a C++ reserved keyword -BOUT_ENUM_CLASS(Treatment, IMEX, Implicit, Explicit); +BOUT_ENUM_CLASS(Treatment, ImEx, Implicit, Explicit); + +// Adaptivity method +BOUT_ENUM_CLASS(AdapMethod, PID, PI, I, Explicit_Gustafsson, Implicit_Gustafsson, + ImEx_Gustafsson); class ArkodeSolver : public Solver { public: @@ -113,14 +117,8 @@ private: std::string explicit_table; /// Fraction of the estimated explicitly stable step to use BoutReal cfl_frac; - /// Set timestep adaptivity function: - /// - 0: PID adaptivity (default) - /// - 1: PI - /// - 2: I - /// - 3: explicit Gustafsson - /// - 4: implicit Gustafsson - /// - 5: ImEx Gustafsson - int adap_method; + /// Timestep adaptivity function + AdapMethod adap_method; /// Absolute tolerance BoutReal abstol; /// Relative tolerance From 13ef65400fec58c918801df7d40d7028cdddf1d7 Mon Sep 17 00:00:00 2001 From: BS Date: Fri, 23 Aug 2024 15:35:04 +0200 Subject: [PATCH 411/412] Fix typos in laplacian inversion documentation (credit @migmadeira) --- manual/sphinx/user_docs/laplacian.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/manual/sphinx/user_docs/laplacian.rst b/manual/sphinx/user_docs/laplacian.rst index e422fa82bd..5365ba14a7 100644 --- a/manual/sphinx/user_docs/laplacian.rst +++ b/manual/sphinx/user_docs/laplacian.rst @@ -536,7 +536,6 @@ Fourth order approximation &+ c_{i-2,j} f_{i-2,j} + c_{i-2,j+1} f_{i-2,j+1} \\ &+ c_{i-2,j+2} f_{i-2,j+2} + c_{i-1,j-2} f_{i-1,j-2} \\ &+ c_{i-1,j-1} f_{i-1,j-1} + c_{i-1,j} f_{i-1,j} \\ - &+ c_{i-1,j-1} f_{i-1,j-1} + c_{i-1,j} f_{i-1,j} \\ &+ c_{i-1,j+1} f_{i-1,j+1} + c_{i-1,j+2} f_{i-1,j+2} \\ &+ c_{i,j-2} f_{i,j-2} + c_{i,j-1} f_{i,j-1} \\ &+ c_{i,j+1} f_{i,j+1} + c_{i,j+2} f_{i,j+2} \\ @@ -573,9 +572,9 @@ Fourth order approximation (9-point stencil) .. math:: \texttt{ddx\_c} = \frac{-\texttt{c2}_{x+2} + 8\texttt{c2}_{x+1} - - 8\texttt{c2}_{x-1} + \texttt{c2}_{x-1} }{ 12\texttt{c1}\text{d}x} \\ + 8\texttt{c2}_{x-1} + \texttt{c2}_{x-2} }{ 12\texttt{c1}\text{d}x} \\ \texttt{ddz\_c} = \frac{-\texttt{c2}_{z+2} + 8\texttt{c2}_{z+1} - - 8\texttt{c2}_{z-1} + \texttt{c2}_{z-1} }{ 12\texttt{c1}\text{d}z} + 8\texttt{c2}_{z-1} + \texttt{c2}_{z-2} }{ 12\texttt{c1}\text{d}z} This gives From 43458ab5d45f8bc42c2677e0124956357c453884 Mon Sep 17 00:00:00 2001 From: Mike Kryjak Date: Wed, 28 Aug 2024 18:12:52 +0100 Subject: [PATCH 412/412] Fix compilation error Prevously this would result in the error "Unknown CMake command "check_c_source_compiles" when compiling Hermes-3 --- cmake/FindPackageMultipass.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/FindPackageMultipass.cmake b/cmake/FindPackageMultipass.cmake index 2452096b56..99bbace448 100644 --- a/cmake/FindPackageMultipass.cmake +++ b/cmake/FindPackageMultipass.cmake @@ -108,7 +108,7 @@ macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs) endmacro (MULTIPASS_C_SOURCE_RUNS) macro (MULTIPASS_SOURCE_COMPILES includes libraries source runs language) - include (Check${language}SourceRuns) + include (Check${language}SourceCompiles) # This is a ridiculous hack. CHECK_${language}_SOURCE_* thinks that if the # *name* of the return variable doesn't change, then the test does # not need to be re-run. We keep an internal count which we