Merge pull request #247 from landinjm/update_automatic_test_script

Update automatic test script

tests/automatic_tests/CHAC_anisotropyRegularized/CMakeLists.txt

@@ -0,0 +1,76 @@
+##
+#  CMake script for the PRISMS-PF applications:
+##
+
+
+# Required cmake version. This should be inline with what is required 
+# for the dealii installation.
+CMAKE_MINIMUM_REQUIRED(VERSION 3.1.0)
+
+# Find deal.II installation
+FIND_PACKAGE(deal.II 9.2.0 REQUIRED
+	HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR})
+
+# Check to make sure deal.II is configured with p4est
+IF(NOT ${DEAL_II_WITH_P4EST})
+  MESSAGE(FATAL_ERROR "\n"
+    "*** deal.II was not installed with p4est. ***\n\n"
+    "The p4est library is a mandatory prerequisite for PRISMS-PF. Please consult the \n"
+    "user guide to confirm that deal.II and p4est were installed and configured correctly."
+    )
+ENDIF()
+
+DEAL_II_INITIALIZE_CACHED_VARIABLES()
+
+# Set up the debug, release, and run targets
+ADD_CUSTOM_TARGET(debug
+  COMMAND +env ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR}
+  COMMAND +env ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
+  COMMENT "Switch CMAKE_BUILD_TYPE to Debug"
+  )
+
+ADD_CUSTOM_TARGET(release
+  COMMAND +env ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR}
+  COMMAND +env ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
+  COMMENT "Switch CMAKE_BUILD_TYPE to Release"
+  )
+
+ADD_CUSTOM_TARGET(run COMMAND main
+  COMMENT "Run with ${CMAKE_BUILD_TYPE} configuration"
+  )
+
+PROJECT(myapp)
+if (${CMAKE_BUILD_TYPE} MATCHES DebugRelease)
+	SET(CMAKE_BUILD_TYPE Debug)
+endif()
+
+# Check if postprocess.cc and nucleation.cc exist and set preprocessor variables
+if (EXISTS "postprocess.cc")
+	add_definitions(-DPOSTPROCESS_FILE_EXISTS)
+endif()
+if (EXISTS "nucleation.cc")
+	add_definitions(-DNUCLEATION_FILE_EXISTS)
+endif()
+
+ADD_EXECUTABLE(main main.cc )
+
+DEAL_II_SETUP_TARGET(main)
+
+set(cmd "cmake")
+set(arg "CMakeLists.txt")
+set(dir ${PROJECT_SOURCE_DIR}/../../..)
+EXECUTE_PROCESS(COMMAND ${cmd} ${arg}
+		WORKING_DIRECTORY ${dir})
+
+set(cmd "make")
+
+EXECUTE_PROCESS(COMMAND ${cmd}
+		WORKING_DIRECTORY ${dir})
+
+if (${CMAKE_BUILD_TYPE} STREQUAL "Release")
+	TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../../libprisms_pf.a)
+elseif(${CMAKE_BUILD_TYPE} STREQUAL "DebugRelease")
+	TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../../libprisms_pf.a)
+else()
+	TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../../libprisms_pf_debug.a)
+endif()

tests/automatic_tests/CHAC_anisotropyRegularized/ICs_and_BCs.cc

@@ -0,0 +1,80 @@
+// ===========================================================================
+// 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
+
+  double r = 0.0;
+
+  if (index == 0)
+    {
+      r = 0.0;
+      for (unsigned int dir = 0; dir < dim; dir++)
+        {
+          r += (p[dir] - userInputs.domain_size[dir] / 2.0) *
+               (p[dir] - userInputs.domain_size[dir] / 2.0);
+        }
+      r         = std::sqrt(r);
+      double n  = 0.5 * (1.0 - std::tanh((r - userInputs.domain_size[0] / 4.0) / 4.0));
+      scalar_IC = 0.082 * 16.0 / (userInputs.domain_size[0] / 4.0) +
+                  (3.0 * n * n - 2.0 * n * n * n);
+    }
+  else if (index == 1)
+    {
+      r = 0.0;
+      for (unsigned int dir = 0; dir < dim; dir++)
+        {
+          r += (p[dir] - userInputs.domain_size[dir] / 2.0) *
+               (p[dir] - userInputs.domain_size[dir] / 2.0);
+        }
+      r         = std::sqrt(r);
+      scalar_IC = 0.5 * (1.0 - std::tanh((r - userInputs.domain_size[0] / 4.0) / 4.0));
+    }
+  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).
+
+  // -------------------------------------------------------------------------
+}

tests/automatic_tests/CHAC_anisotropyRegularized/customPDE.h

@@ -0,0 +1,92 @@
+#include "../../../include/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 "../../../include/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]] Point<dim, VectorizedArray<double>> q_point_loc) 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;
+
+  // 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;
+
+// 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)
+    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 MnV      = userInputs.get_model_constant_double("MnV");
+  double epsilonM = userInputs.get_model_constant_double("epsilonM");
+  double delta2   = userInputs.get_model_constant_double("delta2");
+
+  // ================================================================
+};