Adding more automatic tests

.github/workflows/linux.yml

@@ -47,6 +47,6 @@ jobs:
           export OMPI_ALLOW_RUN_AS_ROOT=1
           export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
-          cd tests/automatic_tests
+          cd automatic_tests
           python3 run_automatic_tests.py
 

.gitignore

@@ -63,6 +63,7 @@ main
 integratedFields.txt
 output.txt
 error.txt
+CTestCostData.txt
 
 # Checkpoint/restart files
 restart.*

tests/automatic_tests/CHAC_anisotropyRegularized/CMakeLists.txt → automatic_tests/CHAC_anisotropyRegularized/CMakeLists.txt

@@ -136,8 +136,8 @@ if(EXISTS "nucleation.cc")
 endif()
 
 # Set location of files
-include_directories(${CMAKE_SOURCE_DIR}/../../../include)
-include_directories(${CMAKE_SOURCE_DIR}/../../../src)
+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
@@ -154,12 +154,12 @@ if(${PRISMS_PF_BUILD_DEBUG} STREQUAL "ON")
   add_executable(main_debug ${TARGET_SRC})
   set_property(TARGET main_debug PROPERTY OUTPUT_NAME main-debug)
   deal_ii_setup_target(main_debug DEBUG)
-  target_link_libraries(main_debug ${CMAKE_SOURCE_DIR}/../../../libprisms-pf-debug.a)
+  target_link_libraries(main_debug ${CMAKE_SOURCE_DIR}/../../libprisms-pf-debug.a)
 endif()
 
 if(${PRISMS_PF_BUILD_RELEASE} STREQUAL "ON")
   add_executable(main_release ${TARGET_SRC})
   set_property(TARGET main_release PROPERTY OUTPUT_NAME main)
   deal_ii_setup_target(main_release RELEASE)
-  target_link_libraries(main_release ${CMAKE_SOURCE_DIR}/../../../libprisms-pf-release.a)
+  target_link_libraries(main_release ${CMAKE_SOURCE_DIR}/../../libprisms-pf-release.a)
 endif()

automatic_tests/CHAC_anisotropyRegularized/parameters.prm

@@ -0,0 +1,77 @@
+# =================================================================================
+# Set the number of dimensions (2 or 3 for a 2D or 3D calculation)
+# =================================================================================
+set Number of dimensions = 2
+
+# =================================================================================
+# Set the length of the domain in all three dimensions
+# (Domain size Z ignored in 2D)
+# =================================================================================
+set Domain size X = 100
+set Domain size Y = 100
+set Domain size Z = 100
+
+# =================================================================================
+# Set the element parameters
+# =================================================================================
+set Subdivisions X = 1
+set Subdivisions Y = 1
+set Subdivisions Z = 1
+
+set Refine factor = 7
+
+set Element degree = 1
+
+# =================================================================================
+# Set the adaptive mesh refinement parameters
+# =================================================================================
+set Mesh adaptivity = true
+
+set Max refinement level = 7
+set Min refinement level = 4
+
+set Steps between remeshing operations = 1000
+
+subsection Refinement criterion: n
+    set Criterion type = VALUE
+    set Value lower bound = 0.001
+    set Value upper bound = 0.999
+end
+
+# =================================================================================
+# Set the time step parameters
+# =================================================================================
+set Time step = 5.0e-2
+
+set Number of time steps = 5000
+
+# =================================================================================
+# Set the boundary conditions
+# =================================================================================
+set Boundary condition for variable c = NATURAL
+set Boundary condition for variable n = NATURAL
+set Boundary condition for variable biharm = NATURAL
+
+# =================================================================================
+# Set the model constants
+# =================================================================================
+# The CH mobility, McV in equations.h
+set Model constant McV = 1.0, DOUBLE
+
+# The AC mobility, MnV in equations.h
+set Model constant MnV = 0.1, DOUBLE
+
+# Anisotropy parameter
+set Model constant epsilonM = 0.2, DOUBLE
+
+# Regularization parameter
+set Model constant delta2 = 1.0, DOUBLE
+
+# =================================================================================
+# Set the output parameters
+# =================================================================================
+set Output condition = EQUAL_SPACING
+
+set Number of outputs = 10
+
+set Skip print steps = 1000

tests/automatic_tests/coupledCahnHilliardAllenCahn/CMakeLists.txt → automatic_tests/CHiMaD_benchmark6a/CMakeLists.txt

@@ -136,8 +136,8 @@ if(EXISTS "nucleation.cc")
 endif()
 
 # Set location of files
-include_directories(${CMAKE_SOURCE_DIR}/../../../include)
-include_directories(${CMAKE_SOURCE_DIR}/../../../src)
+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
@@ -154,12 +154,12 @@ if(${PRISMS_PF_BUILD_DEBUG} STREQUAL "ON")
   add_executable(main_debug ${TARGET_SRC})
   set_property(TARGET main_debug PROPERTY OUTPUT_NAME main-debug)
   deal_ii_setup_target(main_debug DEBUG)
-  target_link_libraries(main_debug ${CMAKE_SOURCE_DIR}/../../../libprisms-pf-debug.a)
+  target_link_libraries(main_debug ${CMAKE_SOURCE_DIR}/../../libprisms-pf-debug.a)
 endif()
 
 if(${PRISMS_PF_BUILD_RELEASE} STREQUAL "ON")
   add_executable(main_release ${TARGET_SRC})
   set_property(TARGET main_release PROPERTY OUTPUT_NAME main)
   deal_ii_setup_target(main_release RELEASE)
-  target_link_libraries(main_release ${CMAKE_SOURCE_DIR}/../../../libprisms-pf-release.a)
+  target_link_libraries(main_release ${CMAKE_SOURCE_DIR}/../../libprisms-pf-release.a)
 endif()

automatic_tests/CHiMaD_benchmark6a/ICs_and_BCs.cc

@@ -0,0 +1,81 @@
+// ===========================================================================
+// FUNCTION FOR INITIAL CONDITIONS
+// ===========================================================================
+
+template <int dim, int degree>
+void
+customPDE<dim, degree>::setInitialCondition([[maybe_unused]] const Point<dim>  &p,
+                                            [[maybe_unused]] const unsigned int index,
+                                            [[maybe_unused]] double            &scalar_IC,
+                                            [[maybe_unused]] Vector<double>    &vector_IC)
+{
+  // ---------------------------------------------------------------------
+  // ENTER THE INITIAL CONDITIONS HERE
+  // ---------------------------------------------------------------------
+  // Enter the function describing conditions for the fields at point "p".
+  // Use "if" statements to set the initial condition for each variable
+  // according to its variable index
+
+  // The initial condition is a set of overlapping circles/spheres defined
+  // by a hyperbolic tangent function. The center of each circle/sphere is
+  // given by "center" and its radius is given by "radius".
+
+  if (index == 0)
+    {
+      double x  = p[0];
+      double y  = p[1];
+      double c0 = 0.5;
+      double c1 = 0.04;
+
+      double t1 = std::cos(0.2 * x) * std::cos(0.11 * y);
+      double t2 = std::cos(0.13 * x) * std::cos(0.087 * y) * std::cos(0.13 * x) *
+                  std::cos(0.087 * y);
+      double t3 = std::cos(0.025 * x - 0.15 * y) * std::cos(0.07 * x - 0.02 * y);
+
+      scalar_IC = c0 + c1 * (t1 + t2 + t3);
+    }
+  else
+    {
+      scalar_IC = 0.0;
+    }
+
+  // =====================================================================
+}
+
+// ===========================================================================
+// FUNCTION FOR NON-UNIFORM DIRICHLET BOUNDARY CONDITIONS
+// ===========================================================================
+
+template <int dim, int degree>
+void
+customPDE<dim, degree>::setNonUniformDirichletBCs(
+  [[maybe_unused]] const Point<dim>  &p,
+  [[maybe_unused]] const unsigned int index,
+  [[maybe_unused]] const unsigned int direction,
+  [[maybe_unused]] const double       time,
+  [[maybe_unused]] double            &scalar_BC,
+  [[maybe_unused]] Vector<double>    &vector_BC)
+{
+  // --------------------------------------------------------------------------
+  // ENTER THE NON-UNIFORM DIRICHLET BOUNDARY CONDITIONS HERE
+  // --------------------------------------------------------------------------
+  // Enter the function describing conditions for the fields at point "p".
+  // Use "if" statements to set the boundary condition for each variable
+  // according to its variable index. This function can be left blank if there
+  // are no non-uniform Dirichlet boundary conditions. For BCs that change in
+  // time, you can access the current time through the variable "time". The
+  // boundary index can be accessed via the variable "direction", which starts
+  // at zero and uses the same order as the BC specification in parameters.in
+  // (i.e. left = 0, right = 1, bottom = 2, top = 3, front = 4, back = 5).
+
+  if (index == 2)
+    {
+      if (direction == 1)
+        {
+          double y  = p[1];
+          scalar_BC = std::sin(y / 7.0);
+        }
+    }
+
+  // -------------------------------------------------------------------------
+}

automatic_tests/CHiMaD_benchmark6a/customPDE.h

@@ -0,0 +1,98 @@
+#include <core/matrixFreePDE.h>
+
+using namespace dealii;
+
+template <int dim, int degree>
+class customPDE : public MatrixFreePDE<dim, degree>
+{
+public:
+  // Constructor
+  customPDE(userInputParameters<dim> _userInputs)
+    : MatrixFreePDE<dim, degree>(_userInputs)
+    , userInputs(_userInputs) {};
+
+  // Function to set the initial conditions (in ICs_and_BCs.h)
+  void
+  setInitialCondition([[maybe_unused]] const Point<dim>  &p,
+                      [[maybe_unused]] const unsigned int index,
+                      [[maybe_unused]] double            &scalar_IC,
+                      [[maybe_unused]] Vector<double>    &vector_IC) override;
+
+  // Function to set the non-uniform Dirichlet boundary conditions (in
+  // ICs_and_BCs.h)
+  void
+  setNonUniformDirichletBCs([[maybe_unused]] const Point<dim>  &p,
+                            [[maybe_unused]] const unsigned int index,
+                            [[maybe_unused]] const unsigned int direction,
+                            [[maybe_unused]] const double       time,
+                            [[maybe_unused]] double            &scalar_BC,
+                            [[maybe_unused]] Vector<double>    &vector_BC) override;
+
+private:
+#include <core/typeDefs.h>
+
+  const userInputParameters<dim> userInputs;
+
+  // Function to set the RHS of the governing equations for explicit time
+  // dependent equations (in equations.h)
+  void
+  explicitEquationRHS(
+    [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
+                                                              &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]] 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]] 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
+  void
+  postProcessedFields(
+    [[maybe_unused]] const variableContainer<dim, degree, VectorizedArray<double>>
+      &variable_list,
+    [[maybe_unused]] variableContainer<dim, degree, VectorizedArray<double>>
+                                                              &pp_variable_list,
+    [[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)
+#ifdef NUCLEATION_FILE_EXISTS
+  double
+  getNucleationProbability([[maybe_unused]] variableValueContainer variable_value,
+                           [[maybe_unused]] double                 dV) const override;
+#endif
+
+  // ================================================================
+  // Methods specific to this subclass
+  // ================================================================
+
+  // ================================================================
+  // Model constants specific to this subclass
+  // ================================================================
+
+  double McV     = userInputs.get_model_constant_double("McV");
+  double KcV     = userInputs.get_model_constant_double("KcV");
+  double rho     = userInputs.get_model_constant_double("rho");
+  double c_alpha = userInputs.get_model_constant_double("c_alpha");
+  double c_beta  = userInputs.get_model_constant_double("c_beta");
+  double k       = userInputs.get_model_constant_double("k");
+  double epsilon = userInputs.get_model_constant_double("epsilon");
+
+  // ================================================================
+};