Some more examples fixes

examples/conduction-snb/conduction-snb.cxx

@@ -27,7 +27,7 @@ int main(int argc, char** argv) {
   Options::root()["Div_Q"] = Div_Q;
   Options::root()["Div_Q_SH"] = Div_Q_SH;
 
-  bout::writeDefaultOutputFile();
+  bout::writeDefaultOutputFile(opt);
 
   BoutFinalise();
   return 0;

examples/dalf3/dalf3.cxx

@@ -118,8 +118,8 @@ class DALF3 : public PhysicsModel {
     //////////////////////////////////////////////////////////////
     // Options
 
-    auto globalOptions = Options::root();
-    auto options = globalOptions["dalf3"];
+    auto& globalOptions = Options::root();
+    auto& options = globalOptions["dalf3"];
 
     split_n0 = options["split_n0"].withDefault(false);
     estatic = options["estatic"].withDefault(false);

examples/fci-wave/fci-wave.cxx

@@ -1,4 +1,5 @@
 
+#include "bout/parallel_boundary_region.hxx"
 #include "bout/physicsmodel.hxx"
 
 class FCIwave : public PhysicsModel {
@@ -31,9 +32,9 @@ class FCIwave : public PhysicsModel {
       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->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) =
+            f_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z())
+            / B_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z());
       }
     }
 
@@ -131,16 +132,21 @@ class FCIwave : public PhysicsModel {
         // Note: If evolving density, this should interpolate logn
         // but neumann boundaries are used here anyway.
         BoutReal n_b =
-            0.5 * (n_next(reg->x, reg->y + reg->dir, reg->z) + n(reg->x, reg->y, reg->z));
+            0.5
+            * (n_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z())
+               + n(reg->ind().x(), reg->ind().y(), reg->ind().z()));
         // Velocity at the boundary
         BoutReal v_b =
-            0.5 * (v_next(reg->x, reg->y + reg->dir, reg->z) + v(reg->x, reg->y, reg->z));
+            0.5
+            * (v_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z())
+               + v(reg->ind().x(), reg->ind().y(), reg->ind().z()));
 
-        nv_next(reg->x, reg->y + reg->dir, reg->z) =
-            2. * n_b * v_b - nv(reg->x, reg->y, reg->z);
+        nv_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) =
+            2. * n_b * v_b - nv(reg->ind().x(), reg->ind().y(), reg->ind().z());
 
-        momflux_next(reg->x, reg->y + reg->dir, reg->z) =
-            2. * n_b * v_b * v_b - momflux(reg->x, reg->y, reg->z);
+        momflux_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) =
+            2. * n_b * v_b * v_b
+            - momflux(reg->ind().x(), reg->ind().y(), reg->ind().z());
       }
     }
 

examples/laplacexy/alfven-wave/alfven.cxx

@@ -41,7 +41,7 @@ class Alfven : public PhysicsModel {
   int init(bool UNUSED(restarting)) {
 
     // Normalisation
-    auto opt = Options::root()["alfven"];
+    auto& opt = Options::root()["alfven"];
     Tnorm = opt["Tnorm"].withDefault(100);  // Reference temperature [eV]
     Nnorm = opt["Nnorm"].withDefault(1e19); // Reference density [m^-3]
     Bnorm = opt["Bnorm"].withDefault(1.0);  // Reference magnetic field [T]

examples/laplacexy/laplace_perp/test.cxx

@@ -65,7 +65,7 @@ int main(int argc, char** argv) {
   Options::root()["input"] = input;
   Options::root()["solved"] = solved;
 
-  bout::writeDefaultOutputFile();
+  bout::writeDefaultOutputFile(Options::root());
 
   BoutFinalise();
   return 0;

examples/performance/bracket/bracket.cxx

@@ -40,8 +40,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   // Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["performance"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["performance"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader, do2D3D, do3D3D;

examples/performance/ddx/ddx.cxx

@@ -43,8 +43,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;

examples/performance/ddy/ddy.cxx

@@ -43,8 +43,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;

examples/performance/ddz/ddz.cxx

@@ -43,8 +43,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;

examples/performance/iterator-offsets/iterator-offsets.cxx

@@ -42,8 +42,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;

examples/performance/iterator/iterator.cxx

@@ -37,8 +37,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;

examples/performance/laplace/laplace.cxx

@@ -39,8 +39,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   // Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["LaplaceTest"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["LaplaceTest"];
   int NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(1000);
 
   ConditionalOutput time_output(Output::getInstance());

examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx

@@ -39,8 +39,8 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   // Get options root
-  auto globalOptions = Options::root();
-  auto modelOpts = globalOptions["tuningRegionBlockSize"];
+  auto& globalOptions = Options::root();
+  auto& modelOpts = globalOptions["tuningRegionBlockSize"];
   const int NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   const int numSteps = modelOpts["numSteps"].withDefault(16);
 

examples/subsampling/monitor.cxx

@@ -16,10 +16,9 @@ class Monitor1dDump : public Monitor {
 public:
   Monitor1dDump(BoutReal timestep, std::string section_name)
       : Monitor(timestep),
-        output_file(getCustomOutputName(Options::root()[section_name]),
-                    Options::root()[section_name]["append"].withDefault(false)
-                        ? bout::OptionsNetCDF::FileMode::append
-                        : bout::OptionsNetCDF::FileMode::replace) {}
+        output_file(bout::OptionsIO::create(
+            {{"file", getCustomOutputName(Options::root()[section_name])},
+             {"append", Options::root()[section_name]["append"].withDefault(false)}})) {}
 
   int call(Solver*, BoutReal _time, int, int) override {
     // This method writes all the diagnostics to a unique file
@@ -31,7 +30,7 @@ class Monitor1dDump : public Monitor {
         output[item.name].attributes["time_dimension"] = "t";
       }
     }
-    output_file.write(output);
+    output_file->write(output);
 
     return 0;
   }
@@ -48,7 +47,7 @@ class Monitor1dDump : public Monitor {
 
 private:
   bout::DataFileFacade dump;
-  bout::OptionsNetCDF output_file;
+  std::unique_ptr<bout::OptionsIO> output_file;
 };
 
 /// An example of using multiple monitors on different timescales

manual/sphinx/user_docs/physics_models.rst

@@ -161,7 +161,7 @@ During initialisation (the ``init`` function), the conduction example
 first reads an option (lines 21 and 24) from the input settings file
 (``data/BOUT.inp`` by default)::
 
-    auto options = Options::root()["conduction"];
+    auto& options = Options::root()["conduction"];
 
     OPTION(options, chi, 1.0);
 
@@ -500,8 +500,8 @@ object in the initialisation function::
       BoutReal gamma;
 
       int init(bool restarting) override {
-        auto globalOptions = Options::root();
-        auto options = globalOptions["mhd"];
+        auto& globalOptions = Options::root();
+        auto& options = globalOptions["mhd"];
 
         OPTION(options, g, 5.0 / 3.0);
         ...