updating the main CMakeLists

.gitignore

@@ -1,6 +1,9 @@
 # Build folder
 build/*
 
+# Config header
+include/config.h
+
 # VS Code
 *.vscode/*
 
@@ -42,28 +45,30 @@ compile_commands.json
 *.pbs
 
 #Output files
-*vtk
-*vtu
-*vts
-*frt
+*.vtk
+*.vtu
+*.vts
+*.frt
 
 #Temporary files
 *~
 *#
 *.#
 *.btr
-freeEnergy.txt
-integratedFields.txt
 .*vtu*
+
+# Visit log
 visitlog.py
 
-#CMAKE files
+#CMake files
 *.cmake
 CMakeCache.txt
 CMakeFiles/
 Makefile
+.ninja*
+build.ninja
 main
-*#main*
+*main*
 
 #Tex files
 *.aux
@@ -100,18 +105,17 @@ DoxygenWarningLog.txt
 *.project
 *.cproject
 *.DS_Store
-freeEnergy.txt
-output.txt
 
 # Output files
 integratedFields.txt
+output.txt
+error.txt
 
 # Checkpoint/restart files
 restart*
 restart.mesh
+restart.mesh.old
 restart.mesh.info
 restart.mesh.info.old
-restart.mesh.old
-restart.resume.z
 restart.time.info
 restart.time.info.old

CMakeLists.txt

@@ -1,66 +1,253 @@
 ##
-#  CMake script for the PRISMS-PF applications:
+#  CMake for the PRISMS-PF applications:
+#  Adapated from the ASPECT CMake file
 ##
 
-CMAKE_MINIMUM_REQUIRED(VERSION 3.1.0)
+cmake_minimum_required(VERSION 3.1.0)
+
+project(prisms_pf)
+
+file(STRINGS "${CMAKE_SOURCE_DIR}/VERSION" PRISMS_PF_VERSION LIMIT_COUNT 1)
+
+message(STATUS "")
+message(STATUS "=========================================================")
+message(STATUS "Configuring PRISMS-PF v${PRISMS_PF_VERSION}")
+message(STATUS "=========================================================")
+message(STATUS "")
+
+# =========================================================
+# Some basic bookkeeping
+# =========================================================
+
+# Check that a prior CMakeCache is not located in the build directory
+if(EXISTS ${CMAKE_SOURCE_DIR}/CMakeCache.txt)
+  message(FATAL_ERROR "Detected the file:\n"
+  "${CMAKE_SOURCE_DIR}/CMakeCache.txt\n"
+  "in your source directory, which may be leftover from prior builds. " 
+  "Please delete the file before running cmake again.")
+endif()
+
+# 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 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()
+
+# =========================================================
+# External libraries
+# =========================================================
+
+message(STATUS "")
+message(STATUS "=========================================================")
+message(STATUS "Configuring external libraries")
+message(STATUS "=========================================================")
+message(STATUS "")
 
 # Find deal.II installation
-find_package(deal.II 9.2.0 QUIET REQUIRED
-	HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR})
-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"
+find_package(deal.II 9.2.0 QUIET
+	HINTS ${DEAL_II_DIR} $ENV{DEAL_II_DIR}
   )
-
-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"
+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()
 
-ADD_CUSTOM_TARGET(run COMMAND main
-  COMMENT "Run with ${CMAKE_BUILD_TYPE} configuration"
-)
+message(STATUS "Found deal.II version ${DEAL_II_PACKAGE_VERSION} at '${deal.II_DIR}'")
 
+set(DEALII_INSTALL_VALID ON)
 
-# Set up the paths to the library files
-include_directories(include)
+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()
 
-file(GLOB headers include/*.h)
-file(GLOB matrixfree_sources src/matrixfree/*.cc)
-file(GLOB userinputparameters_sources src/userInputParameters/*.cc)
-file(GLOB solverparameters_sources src/SolverParameters/*.cc)
-file(GLOB equationdependencyparser_sources src/EquationDependencyParser/*.cc)
-file(GLOB floodfiller_sources src/FloodFiller/*.cc)
-file(GLOB orderparameterremapper_sources src/OrderParameterRemapper/*.cc)
-file(GLOB simplifiedgrainrepresentation_sources src/SimplifiedGrainRepresentation/*.cc)
+deal_ii_initialize_cached_variables()
 
-# Add main project
-PROJECT(prisms_pf)
-set(CMAKE_BUILD_TYPE Release)
+# Create compile_commands.json
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+set(FORCE_COLORED_OUTPUT ON CACHE BOOL "Forces colored output when compiling with gcc and clang.")
+
+# =========================================================
+# Configure PRISMS-PF Targets
+# =========================================================
+
+message(STATUS "")
+message(STATUS "=========================================================")
+message(STATUS "Configuring PRISMS-PF build targets")
+message(STATUS "=========================================================")
+message(STATUS "")
 
-# Append extra flags for the GNU compiler to suppress some warnings
-if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-  set(DEAL_II_CXX_FLAGS_DEBUG "${DEAL_II_CXX_FLAGS_DEBUG} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
-  set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
+# Generate config.h to enable and disable certain features within the source code.
+set(PRISMS_PF_SOURCE_DIR ${CMAKE_SOURCE_DIR})
+
+configure_file(
+  ${CMAKE_SOURCE_DIR}/include/config.h.in
+  ${CMAKE_BINARY_DIR}/include/config.h
+  )
+
+# Collect source files
+file(GLOB_RECURSE PRISMS_PF_SOURCE_FILES "src/*.cc" "include/*.h")
+file(GLOB_RECURSE PRISMS_PF_UNIT_TEST_FILES "unit_tests/*.cc" "contrib/catch/catch.hpp")
+
+# Setup include directories
+include_directories(BEFORE ${CMAKE_BINARY_DIR}/include include)
+include_directories(AFTER contrib/catch)
+
+# Test stuff goes here
+
+# Make and ninja build options
+if(CMAKE_GENERATOR MATCHES "Ninja")
+  set(_make_command "$ ninja")
+else()
+  set(_make_command " $ make")
 endif()
 
-ADD_LIBRARY(${PROJECT_NAME} ${matrixfree_sources} ${userinputparameters_sources} ${solverparameters_sources} ${equationdependencyparser_sources} ${floodfiller_sources} ${orderparameterremapper_sources} ${simplifiedgrainrepresentation_sources} src/utilities/sortIndexEntryPairList.cc src/variableAttributeLoader/variableAttributeLoader.cc src/utilities/vectorBCFunction.cc src/inputFileReader/inputFileReader.cc src/parallelNucleationList/parallelNucleationList.cc src/variableContainer/variableContainer.cc)
-DEAL_II_SETUP_TARGET(${PROJECT_NAME})
+# 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()
 
-PROJECT(prisms_pf_debug)
-SET(CMAKE_BUILD_TYPE Debug)
+# 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"
+  )
+
+
+file(WRITE ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake
+"message(
+\"###
+#
+#  Project ${TARGET_EXE} set up with  ${DEAL_II_PACKAGE_NAME}-${DEAL_II_PACKAGE_VERSION}  found at
+#      ${DEAL_II_PATH}
+#
+#  CMAKE_BUILD_TYPE:          ${CMAKE_BUILD_TYPE}
+#
+#  You can now run
+#      ${_make_command}                - to compile and link ${TARGET_EXE}
+#      ${_make_command} debug          - to switch the build type to 'Debug'
+#      ${_make_command} release        - to switch the build type to 'Release'
+#      ${_make_command} debugrelease   - to switch the build type to compile both
+#      ${_make_command} clean          - to remove the generated executable as well as
+#                               all intermediate compilation files
+#      ${_make_command} distclean      - to clean the directory from all generated
+#                               files (includes clean, runclean and the removal
+#                               of the generated build system)
+#      ${_make_command} info           - to view this message again
+\")")
+
+add_custom_target(info
+  COMMAND ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/print_usage.cmake
+  )
+
+if (${FORCE_COLORED_OUTPUT})
+  if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER MATCHES "AppleClang")
+    string(APPEND DEAL_II_CXX_FLAGS_DEBUG " -fcolor-diagnostics")
+    string(APPEND DEAL_II_CXX_FLAGS_RELEASE " -fcolor-diagnostics")
+  elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+    string(APPEND DEAL_II_CXX_FLAGS_DEBUG " -fdiagnostics-color=always")
+    string(APPEND DEAL_II_CXX_FLAGS_RELEASE " -fdiagnostics-color=always")
+  endif()
+endif()
+
+# deal.II versions >=9.5 disable deprecation warnings in user code. Enable
+# the warnings again by removing the flag that disables them.
+string(REPLACE "-Wno-deprecated-declarations" "" DEAL_II_WARNING_FLAGS "${DEAL_II_WARNING_FLAGS}")
+
+# Set additional compiler flags
+set(PRISMS_PF_ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CMAKE_CXX_FLAGS applied after the deal.II options.")
+
+if(NOT PRISMS_PF_ADDITIONAL_CXX_FLAGS STREQUAL "")
+  message(STATUS "Appending PRISMS_PF_ADDITIONAL_CXX_FLAGS: '${PRISMS_PF_ADDITIONAL_CXX_FLAGS}':")
+  string(APPEND DEAL_II_CXX_FLAGS_DEBUG " ${PRISMS_PF_ADDITIONAL_CXX_FLAGS}")
+  string(APPEND DEAL_II_CXX_FLAGS_RELEASE " ${PRISMS_PF_ADDITIONAL_CXX_FLAGS}")
+  message(STATUS "  DEAL_II_WARNING_FLAGS: ${DEAL_II_WARNING_FLAGS}")
+  message(STATUS "  DEAL_II_CXX_FLAGS_DEBUG: ${DEAL_II_CXX_FLAGS_DEBUG}")
+  message(STATUS "  DEAL_II_CXX_FLAGS_RELEASE: ${DEAL_II_CXX_FLAGS_RELEASE}")
+endif()
 
-# Append extra flags for the GNU compiler to suppress some warnings
-if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-  set(DEAL_II_CXX_FLAGS_DEBUG "${DEAL_II_CXX_FLAGS_DEBUG} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
-  set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
+if(${PRISMS_PF_BUILD_DEBUG} STREQUAL "ON")
+  set(LIBRARY_NAME_DEBUG "prisms_pf_debug")
+  add_library(${LIBRARY_NAME_DEBUG} STATIC ${PRISMS_PF_SOURCE_FILES})
+  set_property(TARGET ${LIBRARY_NAME_DEBUG} PROPERTY OUTPUT_NAME prisms-pf-debug)
+  target_include_directories(${LIBRARY_NAME_DEBUG} PRIVATE ${CMAKE_BINARY_DIR}/include include)
+  deal_ii_setup_target(${LIBRARY_NAME_DEBUG} DEBUG)
 endif()
 
-ADD_LIBRARY(${PROJECT_NAME} ${matrixfree_sources} ${userinputparameters_sources} ${solverparameters_sources} ${equationdependencyparser_sources} ${floodfiller_sources} ${orderparameterremapper_sources} ${simplifiedgrainrepresentation_sources} src/utilities/sortIndexEntryPairList.cc src/variableAttributeLoader/variableAttributeLoader.cc src/utilities/vectorBCFunction.cc src/inputFileReader/inputFileReader.cc src/parallelNucleationList/parallelNucleationList.cc src/variableContainer/variableContainer.cc)
-DEAL_II_SETUP_TARGET(${PROJECT_NAME})
+if(${PRISMS_PF_BUILD_RELEASE} STREQUAL "ON")
+  set(LIBRARY_NAME_RELEASE "prisms_pf_release")
+  add_library(${LIBRARY_NAME_RELEASE} STATIC ${PRISMS_PF_SOURCE_FILES})
+  set_property(TARGET ${LIBRARY_NAME_RELEASE} PROPERTY OUTPUT_NAME prisms-pf-release)
+  target_include_directories(${LIBRARY_NAME_RELEASE} PRIVATE ${CMAKE_BINARY_DIR}/include include)
+  deal_ii_setup_target(${LIBRARY_NAME_RELEASE} RELEASE)
+endif()