From 2ff41ff1f3255272303f4189c0b80c3c7e746b85 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 7 Jun 2024 12:07:57 +0100
Subject: [PATCH 01/13] Add missing argument in call to
 writeDefaultOutputFile().

---
 examples/conduction-snb/conduction-snb.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/conduction-snb/conduction-snb.cxx b/examples/conduction-snb/conduction-snb.cxx
index a5ff7fd804..bc036dede2 100644
--- a/examples/conduction-snb/conduction-snb.cxx
+++ b/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;

From e86a7cb09468514cd5fc8df64083505c4504c050 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 7 Jun 2024 13:07:43 +0100
Subject: [PATCH 02/13] fci-wave example needs to include
 "bout/parallel_boundary_region.hxx".

---
 examples/fci-wave/fci-wave.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index 2fd383ed3f..028fe35e8f 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -1,4 +1,5 @@
 
+#include "bout/parallel_boundary_region.hxx"
 #include "bout/physicsmodel.hxx"
 
 class FCIwave : public PhysicsModel {

From e4faaa8ffb6ee700330e23fcfeb2584af728e566 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 7 Jun 2024 13:46:33 +0100
Subject: [PATCH 03/13] Add missing argument in call to
 writeDefaultOutputFile().

---
 examples/laplacexy/laplace_perp/test.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/laplacexy/laplace_perp/test.cxx b/examples/laplacexy/laplace_perp/test.cxx
index 7881f4ab82..1312b005da 100644
--- a/examples/laplacexy/laplace_perp/test.cxx
+++ b/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;

From 55d887c4a648808cd61c6ed5e58144266c679ef8 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 7 Jun 2024 15:30:49 +0100
Subject: [PATCH 04/13] Remove 'shim' header file - options_netcdf.hxx no
 longer exists.

---
 include/options_netcdf.hxx | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 include/options_netcdf.hxx

diff --git a/include/options_netcdf.hxx b/include/options_netcdf.hxx
deleted file mode 100644
index c0d14c536a..0000000000
--- a/include/options_netcdf.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#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"

From 926b9b090a6b3714518031f148c22fa5f565224b Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 10 Jun 2024 11:47:44 +0100
Subject: [PATCH 05/13] Use OptionsIOFactory instead of OptionsNetCDF for
 output_file.

---
 examples/subsampling/monitor.cxx | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/examples/subsampling/monitor.cxx b/examples/subsampling/monitor.cxx
index 981ff8b235..6f6d9a0109 100644
--- a/examples/subsampling/monitor.cxx
+++ b/examples/subsampling/monitor.cxx
@@ -16,10 +16,7 @@ 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::OptionsIOFactory::getInstance().createOutput()) {}
 
   int call(Solver*, BoutReal _time, int, int) override {
     // This method writes all the diagnostics to a unique file
@@ -31,7 +28,7 @@ class Monitor1dDump : public Monitor {
         output[item.name].attributes["time_dimension"] = "t";
       }
     }
-    output_file.write(output);
+//    output_file.write(output);
 
     return 0;
   }
@@ -48,7 +45,7 @@ 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

From 9b401b51a7665f6cfd3c08aeae412da74e12074f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 22 Aug 2024 17:14:02 +0100
Subject: [PATCH 06/13] Fix "Use OptionsIOFactory instead of OptionsNetCDF for
 output_file".

---
 examples/subsampling/monitor.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/examples/subsampling/monitor.cxx b/examples/subsampling/monitor.cxx
index 6f6d9a0109..917159eb5c 100644
--- a/examples/subsampling/monitor.cxx
+++ b/examples/subsampling/monitor.cxx
@@ -16,7 +16,9 @@ class Monitor1dDump : public Monitor {
 public:
   Monitor1dDump(BoutReal timestep, std::string section_name)
       : Monitor(timestep),
-        output_file(bout::OptionsIOFactory::getInstance().createOutput()) {}
+        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

From 1c5387cee213101f3adaa756bf2c276c2698c2a0 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 10 Jun 2024 11:47:44 +0100
Subject: [PATCH 07/13] Use reference to Options (not a copy). Required since
 changes in branch next-options-nocopy.

---
 examples/dalf3/dalf3.cxx                                    | 4 ++--
 examples/laplacexy/alfven-wave/alfven.cxx                   | 2 +-
 examples/performance/bracket/bracket.cxx                    | 2 +-
 examples/performance/ddx/ddx.cxx                            | 2 +-
 examples/performance/ddy/ddy.cxx                            | 2 +-
 examples/performance/ddz/ddz.cxx                            | 2 +-
 examples/performance/iterator-offsets/iterator-offsets.cxx  | 2 +-
 examples/performance/iterator/iterator.cxx                  | 2 +-
 examples/performance/laplace/laplace.cxx                    | 2 +-
 .../tuning_regionblocksize/tuning_regionblocksize.cxx       | 2 +-
 manual/sphinx/user_docs/physics_models.rst                  | 6 +++---
 src/bout++.cxx                                              | 2 +-
 12 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx
index acc40aca9b..56df163165 100644
--- a/examples/dalf3/dalf3.cxx
+++ b/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);
diff --git a/examples/laplacexy/alfven-wave/alfven.cxx b/examples/laplacexy/alfven-wave/alfven.cxx
index e7a945b3f4..a4248afcf7 100644
--- a/examples/laplacexy/alfven-wave/alfven.cxx
+++ b/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]
diff --git a/examples/performance/bracket/bracket.cxx b/examples/performance/bracket/bracket.cxx
index 1b4efa49aa..53ee66f4e2 100644
--- a/examples/performance/bracket/bracket.cxx
+++ b/examples/performance/bracket/bracket.cxx
@@ -40,7 +40,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   // Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["performance"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
diff --git a/examples/performance/ddx/ddx.cxx b/examples/performance/ddx/ddx.cxx
index 3e4a7803f6..8c21aefed9 100644
--- a/examples/performance/ddx/ddx.cxx
+++ b/examples/performance/ddx/ddx.cxx
@@ -43,7 +43,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
diff --git a/examples/performance/ddy/ddy.cxx b/examples/performance/ddy/ddy.cxx
index a11e1d52bc..e3a61ad6e2 100644
--- a/examples/performance/ddy/ddy.cxx
+++ b/examples/performance/ddy/ddy.cxx
@@ -43,7 +43,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
diff --git a/examples/performance/ddz/ddz.cxx b/examples/performance/ddz/ddz.cxx
index 8a7262b1cb..b68690822b 100644
--- a/examples/performance/ddz/ddz.cxx
+++ b/examples/performance/ddz/ddz.cxx
@@ -43,7 +43,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
diff --git a/examples/performance/iterator-offsets/iterator-offsets.cxx b/examples/performance/iterator-offsets/iterator-offsets.cxx
index 2376b63578..4e12b10187 100644
--- a/examples/performance/iterator-offsets/iterator-offsets.cxx
+++ b/examples/performance/iterator-offsets/iterator-offsets.cxx
@@ -42,7 +42,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx
index af1163d927..227c691f45 100644
--- a/examples/performance/iterator/iterator.cxx
+++ b/examples/performance/iterator/iterator.cxx
@@ -37,7 +37,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   //Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
diff --git a/examples/performance/laplace/laplace.cxx b/examples/performance/laplace/laplace.cxx
index 1ebbfb7583..01c4d2564e 100644
--- a/examples/performance/laplace/laplace.cxx
+++ b/examples/performance/laplace/laplace.cxx
@@ -39,7 +39,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   // Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["LaplaceTest"];
   int NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(1000);
 
diff --git a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
index 521ffede74..d47b3737d1 100644
--- a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
+++ b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
@@ -39,7 +39,7 @@ int main(int argc, char** argv) {
   std::vector<Duration> times;
 
   // Get options root
-  auto globalOptions = Options::root();
+  auto& globalOptions = Options::root();
   auto modelOpts = globalOptions["tuningRegionBlockSize"];
   const int NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   const int numSteps = modelOpts["numSteps"].withDefault(16);
diff --git a/manual/sphinx/user_docs/physics_models.rst b/manual/sphinx/user_docs/physics_models.rst
index 7c8735f636..aae4edbb3d 100644
--- a/manual/sphinx/user_docs/physics_models.rst
+++ b/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);
         ...
diff --git a/src/bout++.cxx b/src/bout++.cxx
index ff25b1163e..e77592c0c1 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -189,7 +189,7 @@ int BoutInitialise(int& argc, char**& argv) {
     // when checking for unused options. They normally _do_ get used,
     // but it's possible that only happens in BoutFinalise, which is
     // too late for that check.
-    const auto datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
+    const auto& datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
     [[maybe_unused]] const auto optionfile =
         Options::root()["optionfile"].withDefault<std::string>(args.opt_file);
     const auto settingsfile =

From eecc8135cf9e4086a3ef5143341aa4410ef51924 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@users.noreply.github.com>
Date: Fri, 23 Aug 2024 15:29:30 +0000
Subject: [PATCH 08/13] Apply clang-format changes

---
 src/bout++.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/bout++.cxx b/src/bout++.cxx
index e77592c0c1..489e54faaa 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -189,7 +189,8 @@ int BoutInitialise(int& argc, char**& argv) {
     // when checking for unused options. They normally _do_ get used,
     // but it's possible that only happens in BoutFinalise, which is
     // too late for that check.
-    const auto& datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
+    const auto& datadir =
+        Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
     [[maybe_unused]] const auto optionfile =
         Options::root()["optionfile"].withDefault<std::string>(args.opt_file);
     const auto settingsfile =

From d72d11c0bead0ef1e776b3a86894cd09dee4c36d Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 16 Sep 2024 12:16:23 +0100
Subject: [PATCH 09/13] Fix examples/fci-wave (BoundaryRegionPar no longer has
 public fields x, y, z).

---
 examples/fci-wave/fci-wave.cxx | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index 028fe35e8f..794be1c96f 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -32,9 +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());
       }
     }
 
@@ -132,16 +132,16 @@ 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());
       }
     }
 

From bfee7aec453c2998d3976378adf3f5ddba5f59a0 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 16 Sep 2024 12:23:10 +0100
Subject: [PATCH 10/13] Uncomment output_file->write(output) in
 examples/subsampling/monitor.cxx

---
 examples/subsampling/monitor.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/subsampling/monitor.cxx b/examples/subsampling/monitor.cxx
index 917159eb5c..788853a595 100644
--- a/examples/subsampling/monitor.cxx
+++ b/examples/subsampling/monitor.cxx
@@ -30,7 +30,7 @@ class Monitor1dDump : public Monitor {
         output[item.name].attributes["time_dimension"] = "t";
       }
     }
-//    output_file.write(output);
+    output_file->write(output);
 
     return 0;
   }

From 8e0d6e6c03c1e92d42dc5908860e1a8b6864d10a Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 16 Sep 2024 12:23:58 +0100
Subject: [PATCH 11/13] Revert change to reference for 'datadir'.

---
 src/bout++.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bout++.cxx b/src/bout++.cxx
index 489e54faaa..ef06f4d3d3 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -189,7 +189,7 @@ int BoutInitialise(int& argc, char**& argv) {
     // when checking for unused options. They normally _do_ get used,
     // but it's possible that only happens in BoutFinalise, which is
     // too late for that check.
-    const auto& datadir =
+    const auto datadir =
         Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
     [[maybe_unused]] const auto optionfile =
         Options::root()["optionfile"].withDefault<std::string>(args.opt_file);

From 6120ef28ff27959f361d05e0c589e45d0a78633f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 16 Sep 2024 12:45:29 +0100
Subject: [PATCH 12/13] Apply clang-format changes

---
 examples/fci-wave/fci-wave.cxx | 11 ++++++++---
 src/bout++.cxx                 |  3 +--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index 794be1c96f..9f8bb18b8f 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -132,16 +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->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) + n(reg->ind().x(), reg->ind().y(), reg->ind().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->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) + v(reg->ind().x(), reg->ind().y(), reg->ind().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->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->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());
+            2. * n_b * v_b * v_b
+            - momflux(reg->ind().x(), reg->ind().y(), reg->ind().z());
       }
     }
 
diff --git a/src/bout++.cxx b/src/bout++.cxx
index ef06f4d3d3..ff25b1163e 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -189,8 +189,7 @@ int BoutInitialise(int& argc, char**& argv) {
     // when checking for unused options. They normally _do_ get used,
     // but it's possible that only happens in BoutFinalise, which is
     // too late for that check.
-    const auto datadir =
-        Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
+    const auto datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
     [[maybe_unused]] const auto optionfile =
         Options::root()["optionfile"].withDefault<std::string>(args.opt_file);
     const auto settingsfile =

From e78374bd20199cccdf3b96f71889f99c0b5ce045 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 16 Sep 2024 14:13:07 +0100
Subject: [PATCH 13/13] Fix "call to deleted constructor of 'Options'
 [clang-diagnostic-error]"

Use reference to Options (not a copy). Required since changes in branch next-options-nocopy.
---
 examples/performance/bracket/bracket.cxx                        | 2 +-
 examples/performance/ddx/ddx.cxx                                | 2 +-
 examples/performance/ddy/ddy.cxx                                | 2 +-
 examples/performance/ddz/ddz.cxx                                | 2 +-
 examples/performance/iterator-offsets/iterator-offsets.cxx      | 2 +-
 examples/performance/iterator/iterator.cxx                      | 2 +-
 examples/performance/laplace/laplace.cxx                        | 2 +-
 .../tuning_regionblocksize/tuning_regionblocksize.cxx           | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/examples/performance/bracket/bracket.cxx b/examples/performance/bracket/bracket.cxx
index 53ee66f4e2..50012510ff 100644
--- a/examples/performance/bracket/bracket.cxx
+++ b/examples/performance/bracket/bracket.cxx
@@ -41,7 +41,7 @@ int main(int argc, char** argv) {
 
   // Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["performance"];
+  auto& modelOpts = globalOptions["performance"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader, do2D3D, do3D3D;
diff --git a/examples/performance/ddx/ddx.cxx b/examples/performance/ddx/ddx.cxx
index 8c21aefed9..b0bad711e6 100644
--- a/examples/performance/ddx/ddx.cxx
+++ b/examples/performance/ddx/ddx.cxx
@@ -44,7 +44,7 @@ int main(int argc, char** argv) {
 
   //Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;
diff --git a/examples/performance/ddy/ddy.cxx b/examples/performance/ddy/ddy.cxx
index e3a61ad6e2..4c9a336c8c 100644
--- a/examples/performance/ddy/ddy.cxx
+++ b/examples/performance/ddy/ddy.cxx
@@ -44,7 +44,7 @@ int main(int argc, char** argv) {
 
   //Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;
diff --git a/examples/performance/ddz/ddz.cxx b/examples/performance/ddz/ddz.cxx
index b68690822b..5d3bf2c961 100644
--- a/examples/performance/ddz/ddz.cxx
+++ b/examples/performance/ddz/ddz.cxx
@@ -44,7 +44,7 @@ int main(int argc, char** argv) {
 
   //Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;
diff --git a/examples/performance/iterator-offsets/iterator-offsets.cxx b/examples/performance/iterator-offsets/iterator-offsets.cxx
index 4e12b10187..455df38ea5 100644
--- a/examples/performance/iterator-offsets/iterator-offsets.cxx
+++ b/examples/performance/iterator-offsets/iterator-offsets.cxx
@@ -43,7 +43,7 @@ int main(int argc, char** argv) {
 
   //Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;
diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx
index 227c691f45..7a29b00298 100644
--- a/examples/performance/iterator/iterator.cxx
+++ b/examples/performance/iterator/iterator.cxx
@@ -38,7 +38,7 @@ int main(int argc, char** argv) {
 
   //Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["performanceIterator"];
+  auto& modelOpts = globalOptions["performanceIterator"];
   int NUM_LOOPS;
   NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   bool profileMode, includeHeader;
diff --git a/examples/performance/laplace/laplace.cxx b/examples/performance/laplace/laplace.cxx
index 01c4d2564e..20da9311ad 100644
--- a/examples/performance/laplace/laplace.cxx
+++ b/examples/performance/laplace/laplace.cxx
@@ -40,7 +40,7 @@ int main(int argc, char** argv) {
 
   // Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["LaplaceTest"];
+  auto& modelOpts = globalOptions["LaplaceTest"];
   int NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(1000);
 
   ConditionalOutput time_output(Output::getInstance());
diff --git a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
index d47b3737d1..cfa7617e64 100644
--- a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
+++ b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
@@ -40,7 +40,7 @@ int main(int argc, char** argv) {
 
   // Get options root
   auto& globalOptions = Options::root();
-  auto modelOpts = globalOptions["tuningRegionBlockSize"];
+  auto& modelOpts = globalOptions["tuningRegionBlockSize"];
   const int NUM_LOOPS = modelOpts["NUM_LOOPS"].withDefault(100);
   const int numSteps = modelOpts["numSteps"].withDefault(16);