[WIP] Refactor PDE operator for multigrid

.clang-tidy

@@ -9,6 +9,7 @@ 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,
@@ -19,5 +20,6 @@ Checks: >
   readability-*,
   -readability-else-after-return,
   -readability-identifier-length,
+  -readability-magic-numbers,
 
 WarningsAsErrors: '*'

.github/workflows/clang-tidy.yml

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

.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 +1,157 @@
+##
+#  CMake script for the PRISMS-PF applications
+#  Adapted from the ASPECT CMake file
+##
+
+cmake_minimum_required(VERSION 3.3.0)
+
+project(myapp)
+
+message(STATUS "")
+message(STATUS "=========================================================")
+message(STATUS "Configuring PRISMS-PF application")
+message(STATUS "=========================================================")
+message(STATUS "")
+
+# Setup the build type (debug, release, debugrelease)
+if("${CMAKE_BUILD_TYPE}" STREQUAL "")
+  set(CMAKE_BUILD_TYPE "DebugRelease" 
+      CACHE STRING
+      "Choose the type of build, options are: Debug, Release and DebugRelease."
+      FORCE)
+endif()
+
+# Convert build type into the debug and release builds, which may or may 
+# not be built.
+if("${CMAKE_BUILD_TYPE}" STREQUAL "Release" OR
+   "${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR
+   "${CMAKE_BUILD_TYPE}" STREQUAL "DebugRelease" )
+  message(STATUS "Setting up PRISMS-PF application for ${CMAKE_BUILD_TYPE} mode.")
+else()
+  message(FATAL_ERROR
+    "CMAKE_BUILD_TYPE must either be 'Release', 'Debug', or 'DebugRelease', but is set to '${CMAKE_BUILD_TYPE}'.")
+endif()
+
+if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR 
+   "${CMAKE_BUILD_TYPE}" STREQUAL "DebugRelease")
+  set(PRISMS_PF_BUILD_DEBUG "ON")
+else()
+  set(PRISMS_PF_BUILD_DEBUG "OFF")
+endif()
+
+if("${CMAKE_BUILD_TYPE}" STREQUAL "Release" OR 
+   "${CMAKE_BUILD_TYPE}" STREQUAL "DebugRelease")
+  set(PRISMS_PF_BUILD_RELEASE "ON")
+else()
+  set(PRISMS_PF_BUILD_RELEASE "OFF")
+endif()
+
+# Find deal.II installation
+find_package(deal.II 9.6.0 QUIET
+	HINTS ${DEAL_II_DIR} $ENV{DEAL_II_DIR}
+  )
+if(NOT ${deal.II_FOUND})
+  message(FATAL_ERROR "\n*** Could not find a recent version of deal.II. ***\n"
+  "You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake "
+  "or set an environment variable \"DEAL_II_DIR\" that contains a path to a "
+  "recent version of deal.II."
+  )
+endif()
+
+message(STATUS "Found deal.II version ${DEAL_II_PACKAGE_VERSION} at '${deal.II_DIR}'")
+
+set(DEALII_INSTALL_VALID ON)
+
+if(NOT DEAL_II_WITH_P4EST)
+    message(SEND_ERROR
+      "\n**deal.II was built without support for p4est!\n"
+      )
+    set(DEALII_INSTALL_VALID OFF)
+endif()
+
+if(NOT DEALII_INSTALL_VALID)
+  message(FATAL_ERROR
+    "\nPRISMS-PF requires a deal.II installation with certain features enabled!\n"
+    )
+endif()
+
+deal_ii_initialize_cached_variables()
+
+# Make and ninja build options
+if(CMAKE_GENERATOR MATCHES "Ninja")
+  set(_make_command "$ ninja")
+else()
+  set(_make_command " $ make")
+endif()
+
+# Debug and release targets
+if(${DEAL_II_BUILD_TYPE} MATCHES "DebugRelease")
+  add_custom_target(release
+    COMMAND ${CMAKE_COMMAND} -D CMAKE_BUILD_TYPE=Release .
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Release mode. Now recompile with: ${_make_command}"
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    VERBATIM
+    COMMENT "switching to RELEASE mode..."
+  )
+
+  add_custom_target(debug
+    COMMAND ${CMAKE_COMMAND} -D CMAKE_BUILD_TYPE=Debug .
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Debug mode. Now recompile with: ${_make_command}"
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    VERBATIM
+    COMMENT "switching to DEBUG mode..."
+  )
+
+  add_custom_target(debugrelease
+    COMMAND ${CMAKE_COMMAND} -D CMAKE_BUILD_TYPE=DebugRelease .
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Debug and Release mode. Now recompile with: ${_make_command}"
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    VERBATIM
+    COMMENT "switching to DEBUG/RELEASE mode..."
+  )
+endif()
+
+# Add distclean target to clean build
+add_custom_target(distclean
+  COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target clean
+  COMMAND ${CMAKE_COMMAND} -E remove_directory CMakeFiles
+  COMMAND ${CMAKE_COMMAND} -E remove
+    CMakeCache.txt cmake_install.cmake Makefile
+    build.ninja rules.ninja .ninja_deps .ninja_log
+  COMMENT "distclean invoked"
+  )
+
+# Set location of files
+include_directories(${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")
+
+# Check if there has been updates to main library
+set(dir ${PROJECT_SOURCE_DIR}/../..)
+EXECUTE_PROCESS(COMMAND "rm" "CMakeCache.txt" WORKING_DIRECTORY ${dir})
+EXECUTE_PROCESS(COMMAND "cmake" "CMakeLists.txt" WORKING_DIRECTORY ${dir})
+EXECUTE_PROCESS(COMMAND "make" WORKING_DIRECTORY ${dir})
+
+# Set targets & link libraries for the build type
+if(${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/custom_pde.h

@@ -0,0 +1,57 @@
+#ifndef CUSTOM_PDE_H_
+#define CUSTOM_PDE_H_
+
+#include <core/matrix_free_operator.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 = VectorizedArray<number>;
+  using scalarGrad  = Tensor<1, dim, VectorizedArray<number>>;
+  using scalarHess  = Tensor<2, dim, VectorizedArray<number>>;
+  using vectorValue = Tensor<1, dim, VectorizedArray<number>>;
+  using vectorGrad  = Tensor<2, dim, VectorizedArray<number>>;
+  using vectorHess  = Tensor<3, dim, VectorizedArray<number>>;
+
+  /**
+   * \brief Constructor.
+   */
+  customPDE() = default;
+
+  /**
+   * \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;
+};
+
+#endif

applications/multigrid_test/equations.cc

@@ -0,0 +1,48 @@
+#include "custom_pde.h"
+
+#include <config.h>
+#include <core/variableAttributeLoader.h>
+
+void
+customAttributeLoader::loadVariableAttributes()
+{
+  set_variable_name(0, "phi");
+  set_variable_type(0, SCALAR);
+  set_variable_equation_type(0, EXPLICIT_TIME_DEPENDENT);
+
+  set_dependencies_value_term_RHS(0, "");
+  set_dependencies_gradient_term_RHS(0, "");
+}
+
+void
+customAttributeLoader::loadPostProcessorVariableAttributes()
+{}
+
+template <int dim, int degree, typename number>
+void
+customPDE<dim, degree, number>::compute_explicit_RHS(
+  variableContainer<dim, degree, number>    &variable_list,
+  const Point<dim, VectorizedArray<number>> &q_point_loc) const
+{}
+
+template <int dim, int degree, typename number>
+void
+customPDE<dim, degree, number>::compute_nonexplicit_RHS(
+  variableContainer<dim, degree, number>    &variable_list,
+  const Point<dim, VectorizedArray<number>> &q_point_loc) const
+{
+  scalarGrad phi = variable_list.get_scalar_gradient(0);
+
+  scalarValue coefficient = 1.0 / (0.05 + 2.0 * q_point_loc.square());
+
+  variable_list.set_scalar_gradient_term(0, phi * coefficient);
+}
+
+template <int dim, int degree, typename number>
+void
+customPDE<dim, degree, number>::compute_nonexplicit_LHS(
+  variableContainer<dim, degree, number>    &variable_list,
+  const Point<dim, VectorizedArray<number>> &q_point_loc) const
+{}
+
+INSTANTIATE_TRI_TEMPLATE(customPDE)

applications/multigrid_test/main.cc

@@ -0,0 +1,38 @@
+#include "custom_pde.h"
+
+#include <core/temp_test.h>
+
+int
+main(int argc, char *argv[])
+{
+  try
+    {
+      Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1);
+
+      LaplaceProblem<dimension> laplace_problem;
+      laplace_problem.run();
+    }
+  catch (std::exception &exc)
+    {
+      std::cerr << '\n'
+                << '\n'
+                << "----------------------------------------------------" << '\n';
+      std::cerr << "Exception on processing: " << '\n'
+                << exc.what() << '\n'
+                << "Aborting!" << '\n'
+                << "----------------------------------------------------" << '\n';
+      return 1;
+    }
+  catch (...)
+    {
+      std::cerr << '\n'
+                << '\n'
+                << "----------------------------------------------------" << '\n';
+      std::cerr << "Unknown exception!" << '\n'
+                << "Aborting!" << '\n'
+                << "----------------------------------------------------" << '\n';
+      return 1;
+    }
+
+  return 0;
+}

automatic_tests/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)