Merge branch 'prisms-center:master' into master

prisms-center · Nov 2, 2024 · b7d2517 · b7d2517
2 parents 9f272b7 + 4a5742f
commit b7d2517
Show file tree

Hide file tree

Showing 151 changed files with 1,473 additions and 1,584 deletions.
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -26,6 +26,7 @@ permissions:
 jobs:
   CI-Linux:
     runs-on: [ubuntu-22.04]
+    timeout-minutes: 120
 
     container:
       image: dealii/dealii:v9.6.0-jammy
@@ -41,6 +42,7 @@ jobs:
           make -j $(nproc)
 
       - name: Run PRISMS-PF tests
+        timeout-minutes: 60
         run: |
           export OMPI_ALLOW_RUN_AS_ROOT=1
           export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@
 
 ## Version information:
 
-This version of the code, v2.3, contains moderate changes from v2.2. It was released in March 20213. See [version_changes.md](version_changes.md) for details.
+This version of the code, v2.4, contains moderate changes from v2.3. It was released in November 2024. See [version_changes.md](version_changes.md) for details.
 
 ## What is PRISMS-PF?
 

diff --git a/applications/CHAC_anisotropy/CMakeLists.txt b/applications/CHAC_anisotropy/CMakeLists.txt
@@ -49,7 +49,7 @@ include_directories(${CMAKE_SOURCE_DIR}/../../include)
 include_directories(${CMAKE_SOURCE_DIR}/../../src)
 include_directories(${CMAKE_SOURCE_DIR})
 
-# SEt the location of the main.cc file
+# Set the location of the main.cc file
 set(MAIN "${CMAKE_SOURCE_DIR}/../main.cc")
 
 # Add main.cc for executable target

diff --git a/applications/CHAC_anisotropy/customPDE.h b/applications/CHAC_anisotropy/customPDE.h
@@ -38,23 +38,26 @@ class customPDE : public MatrixFreePDE<dim, degree>
   void
   explicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the RHS of the governing equations for all other equations
   // (in equations.h)
   void
   nonExplicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the LHS of the governing equations (in equations.h)
   void
   equationLHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
 // Function to set postprocessing expressions (in postprocess.h)
 #ifdef POSTPROCESS_FILE_EXISTS
@@ -64,8 +67,8 @@ class customPDE : public MatrixFreePDE<dim, degree>
       &variable_list,
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                               &pp_variable_list,
-    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc)
-    const override;
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 #endif
 
 // Function to set the nucleation probability (in nucleation.h)

diff --git a/applications/CHAC_anisotropy/equations.cc b/applications/CHAC_anisotropy/equations.cc
@@ -50,7 +50,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::explicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 
@@ -150,7 +151,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::nonExplicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {}
 
 // =============================================================================================
@@ -172,5 +174,6 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::equationLHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {}
diff --git a/applications/CHAC_anisotropy/postprocess.cc b/applications/CHAC_anisotropy/postprocess.cc
@@ -42,7 +42,8 @@ customPDE<dim, degree>::postProcessedFields(
     &variable_list,
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                             &pp_variable_list,
-  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double>             element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
   // c

diff --git a/applications/CHAC_anisotropyRegularized/CMakeLists.txt b/applications/CHAC_anisotropyRegularized/CMakeLists.txt
@@ -49,7 +49,7 @@ include_directories(${CMAKE_SOURCE_DIR}/../../include)
 include_directories(${CMAKE_SOURCE_DIR}/../../src)
 include_directories(${CMAKE_SOURCE_DIR})
 
-# SEt the location of the main.cc file
+# Set the location of the main.cc file
 set(MAIN "${CMAKE_SOURCE_DIR}/../main.cc")
 
 # Add main.cc for executable target

diff --git a/applications/CHAC_anisotropyRegularized/customPDE.h b/applications/CHAC_anisotropyRegularized/customPDE.h
@@ -38,23 +38,26 @@ class customPDE : public MatrixFreePDE<dim, degree>
   void
   explicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the RHS of the governing equations for all other equations
   // (in equations.h)
   void
   nonExplicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the LHS of the governing equations (in equations.h)
   void
   equationLHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
 // Function to set postprocessing expressions (in postprocess.h)
 #ifdef POSTPROCESS_FILE_EXISTS
@@ -64,8 +67,8 @@ class customPDE : public MatrixFreePDE<dim, degree>
       &variable_list,
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                               &pp_variable_list,
-    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc)
-    const override;
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 #endif
 
 // Function to set the nucleation probability (in nucleation.h)

diff --git a/applications/CHAC_anisotropyRegularized/equations.cc b/applications/CHAC_anisotropyRegularized/equations.cc
@@ -58,7 +58,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::explicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 
@@ -163,7 +164,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::nonExplicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 
@@ -194,5 +196,6 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::equationLHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {}
diff --git a/applications/CHAC_anisotropyRegularized/postprocess.cc b/applications/CHAC_anisotropyRegularized/postprocess.cc
@@ -42,7 +42,8 @@ customPDE<dim, degree>::postProcessedFields(
     &variable_list,
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                             &pp_variable_list,
-  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double>             element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 

diff --git a/applications/CHAC_performance_test/CMakeLists.txt b/applications/CHAC_performance_test/CMakeLists.txt
@@ -49,7 +49,7 @@ include_directories(${CMAKE_SOURCE_DIR}/../../include)
 include_directories(${CMAKE_SOURCE_DIR}/../../src)
 include_directories(${CMAKE_SOURCE_DIR})
 
-# SEt the location of the main.cc file
+# Set the location of the main.cc file
 set(MAIN "${CMAKE_SOURCE_DIR}/../main.cc")
 
 # Add main.cc for executable target

diff --git a/applications/CHAC_performance_test/customPDE.h b/applications/CHAC_performance_test/customPDE.h
@@ -38,23 +38,26 @@ class customPDE : public MatrixFreePDE<dim, degree>
   void
   explicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the RHS of the governing equations for all other equations
   // (in equations.h)
   void
   nonExplicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the LHS of the governing equations (in equations.h)
   void
   equationLHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
 // Function to set postprocessing expressions (in postprocess.h)
 #ifdef POSTPROCESS_FILE_EXISTS
@@ -64,8 +67,8 @@ class customPDE : public MatrixFreePDE<dim, degree>
       &variable_list,
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                               &pp_variable_list,
-    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc)
-    const override;
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 #endif
 
 // Function to set the nucleation probability (in nucleation.h)

diff --git a/applications/CHAC_performance_test/equations.cc b/applications/CHAC_performance_test/equations.cc
@@ -50,7 +50,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::explicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 
@@ -111,7 +112,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::nonExplicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {}
 
 // =============================================================================================
@@ -133,5 +135,6 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::equationLHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {}
diff --git a/applications/CHAC_performance_test/postprocess.cc b/applications/CHAC_performance_test/postprocess.cc
@@ -40,7 +40,8 @@ customPDE<dim, degree>::postProcessedFields(
     &variable_list,
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                             &pp_variable_list,
-  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double>             element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/customPDE.h
@@ -38,23 +38,26 @@ class customPDE : public MatrixFreePDE<dim, degree>
   void
   explicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the RHS of the governing equations for all other equations
   // (in equations.h)
   void
   nonExplicitEquationRHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
   // Function to set the LHS of the governing equations (in equations.h)
   void
   equationLHS(
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
-                                                        &variable_list,
-    [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const override;
+                                                              &variable_list,
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 
 // Function to set postprocessing expressions (in postprocess.h)
 #ifdef POSTPROCESS_FILE_EXISTS
@@ -64,8 +67,8 @@ class customPDE : public MatrixFreePDE<dim, degree>
       &variable_list,
     [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                               &pp_variable_list,
-    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc)
-    const override;
+    [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+    [[maybe_unused]] const VectorizedArray<double> element_volume) const override;
 #endif
 
 // Function to set the nucleation probability (in nucleation.h)

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/equations.cc
@@ -50,7 +50,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::explicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 
@@ -89,7 +90,8 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::nonExplicitEquationRHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---
 
@@ -132,5 +134,6 @@ template <int dim, int degree>
 void
 customPDE<dim, degree>::equationLHS(
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>> &variable_list,
-  [[maybe_unused]] Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>>                q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double> element_volume) const
 {}
diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1a/postprocess.cc
@@ -42,7 +42,8 @@ customPDE<dim, degree>::postProcessedFields(
     &variable_list,
   [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
                                                             &pp_variable_list,
-  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc) const
+  [[maybe_unused]] const Point<dim, VectorizedArray<double>> q_point_loc,
+  [[maybe_unused]] const VectorizedArray<double>             element_volume) const
 {
   // --- Getting the values and derivatives of the model variables ---