Merge pull request boutproject#2042 from boutproject/physics-model-mesh

Add PhysicsModel::mesh/dump members
mikekryjak · May 29, 2020 · c5d712a · c5d712a
2 parents 63b2c9d + e74fd7d
commit c5d712a
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Showing 60 changed files with 171 additions and 98 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,12 @@
 - The `MUMPS` Laplacian inversion wrapper has been removed. It is still possible
   to use `MUMPS` for Laplacian inversions through the `PETSc`
   wrapper. [\#2018](https://github.com/boutproject/BOUT-dev/pull/2018)
+- The `using namespace bout::globals` statement has been removed from
+  `physics_model.hxx`, and `PhysicsModel` has gained public `mesh` and
+  `dump` members. Custom `main`s, free functions and legacy models
+  will need to be updated to either use `bout::globals::mesh` or
+  `Field::getMesh()` in free
+  functions. [\#2042](https://github.com/boutproject/BOUT-dev/pull/2042)
 
 
 ## [v4.3.1](https://github.com/boutproject/BOUT-dev/tree/v4.3.1) (2020-03-27)

diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx
@@ -17,6 +17,9 @@
 #include <math.h>
 #include <msg_stack.hxx>
 
+using bout::globals::dump;
+using bout::globals::mesh;
+
 BoutReal n0_height, n0_ave, n0_width, n0_center,
     n0_bottom_x; // the total height, average width and center of profile of N0
 BoutReal Tconst; // the ampitude of congstant temperature

diff --git a/examples/IMEX/advection-reaction/split_operator.cxx b/examples/IMEX/advection-reaction/split_operator.cxx
@@ -56,7 +56,7 @@ int physics_init(bool UNUSED(restarting)) {
 
 int physics_run(BoutReal UNUSED(time)) {
   // Need communication
-  mesh->communicate(U);
+  U.getMesh()->communicate(U);
 
   // Form of advection operator for reduced MHD type models
   ddt(U) = -bracket(phi, U, BRACKET_SIMPLE);

diff --git a/examples/advdiff2/init.cxx b/examples/advdiff2/init.cxx
@@ -3,6 +3,7 @@
 #include <boutmain.hxx>
 #include "globals.hxx"
 
+using bout::globals::mesh;
 
 int physics_init(bool restarting)
 {

diff --git a/examples/advdiff2/run.cxx b/examples/advdiff2/run.cxx
@@ -2,10 +2,9 @@
 #include <derivs.hxx>
 #include "globals.hxx"
 
-
 int physics_run(BoutReal UNUSED(t)) {
   // Run communications
-  mesh->communicate(V);
+  V.getMesh()->communicate(V);
 
   //ddt(V) = D2DX2(V) + 0.5*DDX(V) + D2DY2(V);
   ddt(V) = DDX(V);

diff --git a/examples/bout_runners_example/diffusion_3D.cxx b/examples/bout_runners_example/diffusion_3D.cxx
@@ -7,6 +7,8 @@
 // Gives PI and TWOPI
 #include <bout/constants.hxx>
 
+using bout::globals::mesh;
+
 // Global variable initialization
 // ############################################################################
 Field3D n;               // Evolved variable

diff --git a/examples/conduction-snb/conduction-snb.cxx b/examples/conduction-snb/conduction-snb.cxx
@@ -14,7 +14,7 @@ int main(int argc, char** argv) {
   Field3D Ne = opt["Ne"].doc("Electron density in m^-3").as<Field3D>();
   Field3D Te = opt["Te"].doc("Electron temperature in eV").as<Field3D>();
 
-  mesh->communicate(Ne, Te);
+  bout::globals::mesh->communicate(Ne, Te);
 
   // Calculate divergence of heat flux
   HeatFluxSNB snb;
@@ -23,7 +23,7 @@ int main(int argc, char** argv) {
 
   // Save to the output
   SAVE_ONCE(Ne, Te, Div_Q, Div_Q_SH);
-  dump.write();
+  bout::globals::dump.write();
 
   BoutFinalise();
   return 0;

diff --git a/examples/constraints/laplace-dae/laplace_dae.cxx b/examples/constraints/laplace-dae/laplace_dae.cxx
@@ -17,6 +17,8 @@ Field3D phibdry; // Used for calculating error in the boundary
 
 bool constraint;
 
+using bout::globals::mesh;
+
 std::unique_ptr<Laplacian> phiSolver{nullptr}; ///< Inverts a Laplacian to get phi from U
 
 // Preconditioner

diff --git a/examples/finite-volume/test/finite_volume.cxx b/examples/finite-volume/test/finite_volume.cxx
@@ -7,9 +7,9 @@ int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
   Field3D f = 0.0;
-  
-  mesh->communicate(f);
-  
+
+  f.getMesh()->communicate(f);
+
   Field3D g = FV::D4DY4_Index(f);
 
   BoutFinalise();

diff --git a/examples/laplace-petsc3d/test-laplace3d.cxx b/examples/laplace-petsc3d/test-laplace3d.cxx
@@ -54,6 +54,7 @@ int main(int argc, char** argv) {
   ///////////////////////////////////////////////////////////////////////////////////////
 
   Field3D f, rhs;
+  auto* mesh = f.getMesh();
   mesh->get(rhs, "rhs");
 
   // initial profile of f only used to set boundary values
@@ -153,7 +154,7 @@ int main(int argc, char** argv) {
   BoutReal error_max = max(abs(error), true);
 
   SAVE_ONCE(f, rhs, rhs_check, error, error_max);
-  dump.write();
+  bout::globals::dump.write();
 
   laplace_solver.reset(nullptr);
   BoutFinalise();

diff --git a/examples/laplacexy/laplace_perp/test.cxx b/examples/laplacexy/laplace_perp/test.cxx
@@ -4,6 +4,8 @@
 #include <derivs.hxx>
 #include <field_factory.hxx>
 
+using bout::globals::mesh;
+
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
@@ -61,8 +63,8 @@ int main(int argc, char** argv) {
 
   // Write fields to output
   SAVE_ONCE3(input, solved, result);
-  dump.write();
-  
+  bout::globals::dump.write();
+
   BoutFinalise();
   return 0;
 }

diff --git a/examples/laplacexy/simple/test-laplacexy.cxx b/examples/laplacexy/simple/test-laplacexy.cxx
@@ -7,19 +7,20 @@ int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
   /// Create a LaplaceXY object
-  LaplaceXY laplacexy(mesh);
-  
+  LaplaceXY laplacexy(bout::globals::mesh);
+
   /// Generate rhs function
-  Field2D rhs = FieldFactory::get()->create2D("laplacexy:rhs", Options::getRoot(), mesh);
-
+  Field2D rhs = FieldFactory::get()->create2D("laplacexy:rhs", Options::getRoot(),
+                                              bout::globals::mesh);
+
   /// Solution
   Field2D x = 0.0;
 
   x = laplacexy.solve(rhs, x);
 
   SAVE_ONCE2(rhs, x);
-  dump.write();  // Save output file
-  
+  bout::globals::dump.write(); // Save output file
+
   BoutFinalise();
   return 0;
 }

diff --git a/examples/performance/bracket/bracket.cxx b/examples/performance/bracket/bracket.cxx
@@ -21,6 +21,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using bout::globals::mesh;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)                                                   \
   {                                                                                      \

diff --git a/examples/performance/communications/communications.cxx b/examples/performance/communications/communications.cxx
@@ -12,7 +12,7 @@ int main(int argc, char** argv) {
 
   Timer timer("comms");
   for (int i = 0; i < iterations; ++i) {
-    mesh->communicate(f);
+    f.getMesh()->communicate(f);
   }
   BoutReal run_length = timer.getTime();
 

diff --git a/examples/performance/ddx/ddx.cxx b/examples/performance/ddx/ddx.cxx
@@ -19,6 +19,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using bout::globals::mesh;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)                                                   \
   {                                                                                      \

diff --git a/examples/performance/ddy/ddy.cxx b/examples/performance/ddy/ddy.cxx
@@ -19,6 +19,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using bout::globals::mesh;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)                                                   \
   {                                                                                      \

diff --git a/examples/performance/ddz/ddz.cxx b/examples/performance/ddz/ddz.cxx
@@ -19,6 +19,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using bout::globals::mesh;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)                                                   \
   {                                                                                      \

diff --git a/examples/performance/iterator-offsets/iterator-offsets.cxx b/examples/performance/iterator-offsets/iterator-offsets.cxx
@@ -18,6 +18,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using bout::globals::mesh;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)                                                   \
   {                                                                                      \

diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx
@@ -18,6 +18,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using bout::globals::mesh;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)		\
   {__VA_ARGS__								\

diff --git a/examples/performance/laplace/laplace.cxx b/examples/performance/laplace/laplace.cxx
@@ -43,7 +43,7 @@ int main(int argc, char **argv) {
   ConditionalOutput time_output(Output::getInstance());
   time_output.enable(true);
 
-  FieldFactory f{mesh};
+  FieldFactory f{bout::globals::mesh};
 
   Field3D input = f.create3D("(1-gauss(x-0.5,0.2))*gauss(y-pi)*gauss(z-pi)");
   Field2D a = f.create2D("gauss(x) * sin(y)");
@@ -167,8 +167,8 @@ int main(int argc, char **argv) {
   );
 
   // Write and close the output file
-  dump.write();
-  dump.close();
+  bout::globals::dump.write();
+  bout::globals::dump.close();
 
   MPI_Barrier(BoutComm::get()); // Wait for all processors to write data
 

diff --git a/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx b/examples/performance/tuning_regionblocksize/tuning_regionblocksize.cxx
@@ -19,6 +19,7 @@
 using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
 using Duration = std::chrono::duration<double>;
 using namespace std::chrono;
+using namespace bout::globals;
 
 #define ITERATOR_TEST_BLOCK(NAME, ...)                                                   \
   {                                                                                      \

diff --git a/examples/preconditioning/wave/test_precon.cxx b/examples/preconditioning/wave/test_precon.cxx
@@ -35,8 +35,8 @@ int physics_init(bool UNUSED(restarting)) {
 }
 
 int physics_run(BoutReal UNUSED(t)) {
-  mesh->communicate(u,v);
-  
+  u.getMesh()->communicate(u, v);
+
   ddt(u) = Grad_par(v);
   ddt(v) = Grad_par(u);
 
@@ -53,6 +53,8 @@ int physics_run(BoutReal UNUSED(t)) {
  * 
  *********************************************************/
 int precon(BoutReal UNUSED(t), BoutReal gamma, BoutReal UNUSED(delta)) {
+  auto* mesh = u.getMesh();
+
   // Communicate vector to be inverted
   mesh->communicate(ddt(u), ddt(v));
 
@@ -94,6 +96,8 @@ int precon(BoutReal UNUSED(t), BoutReal gamma, BoutReal UNUSED(delta)) {
  *********************************************************/
 
 int jacobian(BoutReal UNUSED(t)) {
+  auto* mesh = u.getMesh();
+
   mesh->communicate(ddt(u), ddt(v));
   Field3D utmp = Grad_par(ddt(v)); // Shouldn't overwrite ddt(u) before using it
   ddt(v) = Grad_par(ddt(u));

diff --git a/examples/staggered_grid/test_staggered.cxx b/examples/staggered_grid/test_staggered.cxx
@@ -4,9 +4,10 @@
 
 #include <bout.hxx>
 #include <boutmain.hxx>
-
 #include <derivs.hxx>
 
+using bout::globals::mesh;
+
 Field3D n, v;
 CELL_LOC maybe_ylow{CELL_CENTRE};
 

diff --git a/include/bout.hxx b/include/bout.hxx
@@ -54,13 +54,6 @@
 #include "bout/solver.hxx"
 #include "bout/version.hxx"
 
-#ifndef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS
-// Include using statement by default in user code.
-// Macro allows us to include bout.hxx or physicsmodel.hxx without the using
-// statement in library code.
-using namespace bout::globals;
-#endif // BOUT_NO_USING_NAMESPACE_BOUTGLOBALS
-
 // BOUT++ main functions
 
 /*!

diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
@@ -45,6 +45,8 @@ class PhysicsModel;
 #include "utils.hxx"
 #include "bout/macro_for_each.hxx"
 
+class Mesh;
+
 /*!
   Base class for physics models
  */
@@ -57,6 +59,9 @@ public:
 
   virtual ~PhysicsModel() = default;
 
+  Mesh* mesh{nullptr};
+  Datafile& dump;
+
   /*!
    * Initialse the model, calling the init() and postInit() methods
    *

diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
@@ -34,7 +34,8 @@
 
 #include <bout/mesh.hxx>
 
-PhysicsModel::PhysicsModel() : modelMonitor(this) {
+PhysicsModel::PhysicsModel()
+    : mesh(bout::globals::mesh), dump(bout::globals::dump), modelMonitor(this) {
 
   // Set up restart file
   restart = Datafile(Options::getRoot()->getSection("restart"));

diff --git a/tests/MMS/diffusion/diffusion.cxx b/tests/MMS/diffusion/diffusion.cxx
@@ -7,6 +7,8 @@
 #include <bout/constants.hxx>
 #include <unused.hxx>
 
+using bout::globals::mesh;
+
 void solution(Field3D &f, BoutReal t, BoutReal D);
 class ErrorMonitor: public Monitor{
 public:

diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -5,6 +5,8 @@
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
+  using bout::globals::mesh;
+
   Field3D input{FieldFactory::get()->create3D("input", Options::getRoot(), mesh)};
   Field3D solution{FieldFactory::get()->create3D("solution", Options::getRoot(), mesh)};
 
@@ -22,7 +24,7 @@ int main(int argc, char** argv) {
     SAVE_ONCE2(input.ynext(-slice), input.ynext(slice));
   }
 
-  dump.write();
+  bout::globals::dump.write();
 
   BoutFinalise();
 }
diff --git a/tests/integrated/test-attribs/test-attribs.cxx b/tests/integrated/test-attribs/test-attribs.cxx
@@ -6,9 +6,9 @@ int main(int argc, char** argv) {
   Field3D a = 0.0;
 
   SAVE_ONCE(a);
-  dump.setAttribute("a", "meta", "something useful");
-  dump.setAttribute("g12", "value", 42);
-  dump.write();
+  bout::globals::dump.setAttribute("a", "meta", "something useful");
+  bout::globals::dump.setAttribute("g12", "value", 42);
+  bout::globals::dump.write();
 
   BoutFinalise();
   return 0;

diff --git a/tests/integrated/test-communications/test-communications.cxx b/tests/integrated/test-communications/test-communications.cxx
@@ -3,6 +3,8 @@
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
+  using bout::globals::mesh;
+
   Field3D f = -1.;
 
   // fill non-guard cells:
@@ -80,8 +82,8 @@ int main(int argc, char** argv) {
   // communicate f to fill guard cells
   mesh->communicate(f);
 
-  dump.add(f, "f", true);
-  dump.write();
+  bout::globals::dump.add(f, "f", true);
+  bout::globals::dump.write();
 
   BoutFinalise();
 }