temp

.clang-tidy

@@ -9,15 +9,19 @@ Checks: >
   cppcoreguidelines-*,
   -cppcoreguidelines-avoid-const-or-ref-data-members,
   -cppcoreguidelines-non-private-member-variables-in-classes,
+  -cppcoreguidelines-avoid-magic-numbers,
   hicpp-*,
   misc-*,
   -misc-non-private-member-variables-in-classes,
   modernize-*,
   -modernize-use-trailing-return-type,
+  -modernize-pass-by-value,
   mpi-*,
   performance-*,
   readability-*,
   -readability-else-after-return,
   -readability-identifier-length,
+  -readability-magic-numbers,
+  -readability-convert-member-functions-to-static,
 
 WarningsAsErrors: '*'

.github/workflows/linux.yml

@@ -7,7 +7,6 @@ on:
   pull_request:
     branches:
       - master
-      - devel
     types:
       - opened
       - reopened

.gitignore

@@ -59,6 +59,7 @@ main
 #Output files
 applications/*/*.vtk
 *.vtu
+*.pvtu
 *.vts
 *.frt
 integratedFields.txt

applications/main.cc

@@ -5,8 +5,8 @@
 #include "core/variableAttributes.h"
 #include "equations.cc"
 
-#include <core/ParseCommandLineOpts.h>
 #include <core/inputFileReader.h>
+#include <core/parse_cmd_options.h>
 #include <core/variableAttributeLoader.h>
 
 // Header file for postprocessing that may or may not exist
@@ -38,7 +38,7 @@ main(int argc, char **argv)
   std::string parameters_filename;
   try
     {
-      ParseCommandLineOpts cli_options(argc, argv);
+      parseCMDOptions cli_options(argc, argv);
       parameters_filename = cli_options.getParametersFilename();
     }
   catch (const char *msg)

applications/multigrid_test/CMakeLists.txt

@@ -0,0 +1,33 @@
+##
+#  CMake script for the PRISMS-PF applications
+#  Adapted from the ASPECT CMake file
+##
+
+cmake_minimum_required(VERSION 3.3.0)
+
+include(${CMAKE_SOURCE_DIR}/../../cmake/setup_application.cmake)
+
+project(myapp)
+
+# Set location of files
+include_directories(${CMAKE_SOURCE_DIR}/../../include)
+include_directories(${CMAKE_SOURCE_DIR}/../../src)
+include_directories(${CMAKE_SOURCE_DIR})
+
+# Set the location of the main.cc file
+set(TARGET_SRC "${CMAKE_SOURCE_DIR}/main.cc" "${CMAKE_SOURCE_DIR}/equations.cc" "${CMAKE_SOURCE_DIR}/ICs_and_BCs.cc")
+
+# Set targets & link libraries for the build type
+if(${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 ${CMAKE_SOURCE_DIR}/../../libprisms-pf-debug.a)
+endif()
+
+if(${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)
+endif()

applications/multigrid_test/ICs_and_BCs.cc

@@ -0,0 +1,24 @@
+#include <cmath>
+#include <config.h>
+#include <core/boundary_conditions/nonuniform_dirichlet.h>
+
+template <int dim>
+void
+customNonuniformDirichlet<dim>::set_nonuniform_dirichlet(
+  [[maybe_unused]] const uint               &index,
+  [[maybe_unused]] const uint               &boundary_id,
+  [[maybe_unused]] const uint               &component,
+  [[maybe_unused]] const dealii::Point<dim> &point,
+  [[maybe_unused]] double                   &scalar_value,
+  [[maybe_unused]] double                   &vector_component_value) const
+{
+  if (index == 0)
+    {
+      if (boundary_id == 0 || boundary_id == 1)
+        {
+          scalar_value = std::sin(point[1] * M_PI);
+        }
+    }
+}
+
+INSTANTIATE_UNI_TEMPLATE(customNonuniformDirichlet)

applications/multigrid_test/custom_pde.h

@@ -0,0 +1,68 @@
+#ifndef CUSTOM_PDE_H_
+#define CUSTOM_PDE_H_
+
+#include <core/matrix_free_operator.h>
+#include <core/user_inputs/user_input_parameters.h>
+#include <core/variable_attributes.h>
+
+using namespace dealii;
+
+/**
+ * \brief This is a derived class of `matrixFreeOperator` where the user implements their
+ * PDEs.
+ *
+ * \tparam dim The number of dimensions in the problem.
+ * \tparam degree The polynomial degree of the shape functions.
+ * \tparam number Datatype to use. Either double or float.
+ */
+template <int dim, int degree, typename number>
+class customPDE : public matrixFreeOperator<dim, degree, number>
+{
+public:
+  using scalarValue = dealii::VectorizedArray<number>;
+  using scalarGrad  = dealii::Tensor<1, dim, dealii::VectorizedArray<number>>;
+  using scalarHess  = dealii::Tensor<2, dim, dealii::VectorizedArray<number>>;
+  using vectorValue = dealii::Tensor<1, dim, dealii::VectorizedArray<number>>;
+  using vectorGrad  = dealii::Tensor<2, dim, dealii::VectorizedArray<number>>;
+  using vectorHess  = dealii::Tensor<3, dim, dealii::VectorizedArray<number>>;
+
+  /**
+   * \brief Constructor.
+   */
+  customPDE(const userInputParameters<dim> &_user_inputs)
+    : matrixFreeOperator<dim, degree, number>(_user_inputs.var_attributes)
+    , user_inputs(_user_inputs)
+  {}
+
+private:
+  /**
+   * \brief User-implemented class for the RHS of explicit equations.
+   */
+  void
+  compute_explicit_RHS(variableContainer<dim, degree, number> &variable_list,
+                       const dealii::Point<dim, dealii::VectorizedArray<number>>
+                         &q_point_loc) const override;
+
+  /**
+   * \brief User-implemented class for the RHS of nonexplicit equations.
+   */
+  void
+  compute_nonexplicit_RHS(variableContainer<dim, degree, number> &variable_list,
+                          const dealii::Point<dim, dealii::VectorizedArray<number>>
+                            &q_point_loc) const override;
+
+  /**
+   * \brief User-implemented class for the LHS of nonexplicit equations.
+   */
+  void
+  compute_nonexplicit_LHS(variableContainer<dim, degree, number> &variable_list,
+                          const dealii::Point<dim, dealii::VectorizedArray<number>>
+                            &q_point_loc) const override;
+
+  /**
+   * \brief The userinputs.
+   */
+  const userInputParameters<dim> &user_inputs;
+};
+
+#endif

applications/multigrid_test/equations.cc

@@ -0,0 +1,53 @@
+#include "custom_pde.h"
+
+#include <config.h>
+#include <core/type_enums.h>
+#include <core/variable_attribute_loader.h>
+
+void
+customAttributeLoader::loadVariableAttributes()
+{
+  set_variable_name(0, "phi");
+  set_variable_type(0, SCALAR);
+  set_variable_equation_type(0, TIME_INDEPENDENT);
+
+  set_dependencies_value_term_RHS(0, "");
+  set_dependencies_gradient_term_RHS(0, "grad(phi)");
+  set_dependencies_value_term_LHS(0, "");
+  set_dependencies_gradient_term_LHS(0, "grad(change(phi))");
+}
+
+void
+customAttributeLoader::loadPostProcessorVariableAttributes()
+{}
+
+template <int dim, int degree, typename number>
+void
+customPDE<dim, degree, number>::compute_explicit_RHS(
+  [[maybe_unused]] variableContainer<dim, degree, number>    &variable_list,
+  [[maybe_unused]] const Point<dim, VectorizedArray<number>> &q_point_loc) const
+{}
+
+template <int dim, int degree, typename number>
+void
+customPDE<dim, degree, number>::compute_nonexplicit_RHS(
+  [[maybe_unused]] variableContainer<dim, degree, number>    &variable_list,
+  [[maybe_unused]] const Point<dim, VectorizedArray<number>> &q_point_loc) const
+{
+  scalarGrad phix = variable_list.get_scalar_gradient(0);
+
+  variable_list.set_scalar_gradient_term(0, -phix);
+}
+
+template <int dim, int degree, typename number>
+void
+customPDE<dim, degree, number>::compute_nonexplicit_LHS(
+  [[maybe_unused]] variableContainer<dim, degree, number>    &variable_list,
+  [[maybe_unused]] const Point<dim, VectorizedArray<number>> &q_point_loc) const
+{
+  scalarGrad change_phix = variable_list.get_scalar_gradient(0, CHANGE);
+
+  variable_list.set_scalar_gradient_term(0, change_phix, CHANGE);
+}
+
+INSTANTIATE_TRI_TEMPLATE(customPDE)