Merge pull request #280 from prisms-center/development

2.4 Release

.clang-tidy

@@ -0,0 +1,12 @@
+# Setting file for clang-tidy
+
+Checks: >
+  -*,
+  boost-*,
+  modernize-*,
+  -modernize-avoid-c-arrays,
+  -modernize-use-trailing-return-type,
+  mpi-*,
+  performance-*
+
+WarningsAsErrors: '*'

.github/workflows/clang-format.yml

@@ -0,0 +1,33 @@
+name: Clang-Format Check
+
+on: 
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+      - development
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request'}}
+
+permissions:
+  contents: read
+
+jobs:
+  clang-format-check:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 30
+
+    - name: Run Clang-Format
+      uses: jidicula/[email protected]
+      with:
+        clang-format-version: '16'

.github/workflows/linux.yml

@@ -0,0 +1,52 @@
+name: CI-Linux
+
+on: 
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+      - development
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+    paths-ignore:
+      - 'applications/**'
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request'}}
+
+permissions:
+  contents: read
+
+jobs:
+  CI-Linux:
+    runs-on: [ubuntu-22.04]
+    timeout-minutes: 120
+
+    container:
+      image: dealii/dealii:v9.6.0-jammy
+      options: --user root
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Compile PRISMS-PF
+        run: |
+          cmake .
+          make -j $(nproc)
+
+      - name: Run PRISMS-PF tests
+        timeout-minutes: 60
+        run: |
+          export OMPI_ALLOW_RUN_AS_ROOT=1
+          export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+          cd tests/automatic_tests
+          python3 run_automatic_tests.py
+

.gitignore

@@ -1,3 +1,19 @@
+# Build folder
+build/*
+
+# VS Code
+.vscode/*
+
+# Python virtual environments
+.venv/*
+*.venv/
+
+# clangd
+.clangd
+
+# misc
+compile_commands.json
+
 # Compiled Object files
 *.slo
 *.lo
@@ -19,6 +35,7 @@
 *.exe
 *.out
 *.app
+*.pbs
 
 #Output files
 *vtk
@@ -82,10 +99,11 @@ DoxygenWarningLog.txt
 freeEnergy.txt
 output.txt
 
-restart*
+# Output files
 integratedFields.txt
 
 # Checkpoint/restart files
+restart*
 restart.mesh
 restart.mesh.info
 restart.mesh.info.old

CMakeLists.txt

@@ -2,12 +2,11 @@
 #  CMake script for the PRISMS-PF applications:
 ##
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.1.0)
 
 # Find deal.II installation
-FIND_PACKAGE(deal.II 8.3.0 REQUIRED
+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
@@ -25,38 +24,30 @@ ADD_CUSTOM_TARGET(release
 
 ADD_CUSTOM_TARGET(run COMMAND main
   COMMENT "Run with ${CMAKE_BUILD_TYPE} configuration"
-  )
+)
 
 
 # Set up the paths to the library files
-INCLUDE_DIRECTORIES(include)
-
-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)
-
-
+include_directories(include)
+
+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)
+
+# Add main project
 PROJECT(prisms_pf)
-SET(CMAKE_BUILD_TYPE Release)
+set(CMAKE_BUILD_TYPE Release)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 # 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-unused-parameter -Wno-extra")
-        #set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-unused-parameter -Wno-extra")
-        set(DEAL_II_CXX_FLAGS_DEBUG "${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 "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
-        #set(CMAKE_CXX_FLAGS "-Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
+  set(DEAL_II_CXX_FLAGS_DEBUG "${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")
 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)
@@ -67,11 +58,8 @@ SET(CMAKE_BUILD_TYPE Debug)
 
 # 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-unused-parameter -Wno-extra")
-        #set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-unused-parameter -Wno-extra")
-        set(DEAL_II_CXX_FLAGS_DEBUG "${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 "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
-        #set(CMAKE_CXX_FLAGS "-Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
+  set(DEAL_II_CXX_FLAGS_DEBUG "${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")
 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)

README.md

@@ -1,6 +1,9 @@
 ![](logo_v2.png)
 
-[![Build Status](https://travis-ci.org/prisms-center/phaseField.svg?branch=master)](https://travis-ci.org/prisms-center/phaseField)
+[![GitHub Linux](https://github.com/prisms-center/phaseField/actions/workflows/linux.yml/badge.svg)](https://github.com/prisms-center/phaseField/actions/workflows/linux.yml)
+[![Clang-Format](https://github.com/prisms-center/phaseField/actions/workflows/clang-format.yml/badge.svg)](https://github.com/prisms-center/phaseField/actions/workflows/clang-format.yml)
+
+
 [![License: LGPL v2.1](https://img.shields.io/badge/License-lgpl-blue.svg)](https://www.gnu.org/licenses/lgpl-2.1)
 [![DOI](https://zenodo.org/badge/22602327.svg)](https://zenodo.org/badge/latestdoi/22602327)
 

applications/CHAC_anisotropy/CMakeLists.txt

@@ -2,80 +2,67 @@
 #  CMake script for the PRISMS-PF applications:
 ##
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
+cmake_minimum_required(VERSION 3.1.0)
+project(myapp)
 
 # Find deal.II installation
-FIND_PACKAGE(deal.II 9.2.0 REQUIRED
+find_package(deal.II 9.2.0 QUIET 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()
+if(NOT ${DEAL_II_WITH_P4EST})
+  message(FATAL_ERROR "deal.II must be installed with p4est.")
+endif()
 
 DEAL_II_INITIALIZE_CACHED_VARIABLES()
 
+# Set default build type
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Debug CACHE STRING "Build type" FORCE)
+endif()
+
 # Set up the debug, release, and run targets
-ADD_CUSTOM_TARGET(debug
+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
+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
+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 postprocess.cc and nucleation.cc if they exist
+if(EXISTS "postprocess.cc")
 	add_definitions(-DPOSTPROCESS_FILE_EXISTS)
 endif()
-if (EXISTS "nucleation.cc")
+if(EXISTS "nucleation.cc")
 	add_definitions(-DNUCLEATION_FILE_EXISTS)
 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-unused-parameter -Wno-extra")
-        set(DEAL_II_CXX_FLAGS_RELEASE "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-uninitialized -Wno-unused-parameter -Wno-extra")
-        #set(DEAL_II_CXX_FLAGS_DEBUG "${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 "${DEAL_II_CXX_FLAGS_RELEASE} -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable")
-#endif()
-
-ADD_EXECUTABLE(main main.cc )
+# Set location of files
+include_directories(${CMAKE_SOURCE_DIR}/../../include)
+include_directories(${CMAKE_SOURCE_DIR}/../../src)
+include_directories(${CMAKE_SOURCE_DIR})
 
-DEAL_II_SETUP_TARGET(main)
+# Set the location of the main.cc file
+set(MAIN "${CMAKE_SOURCE_DIR}/../main.cc")
 
-set(cmd "cmake")
-set(arg "CMakeLists.txt")
-set(dir ${PROJECT_SOURCE_DIR}/../..)
-EXECUTE_PROCESS(COMMAND ${cmd} ${arg}
-		WORKING_DIRECTORY ${dir})
+# Add main.cc for executable target
+add_executable(main ${MAIN})
 
-set(cmd "make")
-
-EXECUTE_PROCESS(COMMAND ${cmd}
-		WORKING_DIRECTORY ${dir})
+# deal.II linker
+DEAL_II_SETUP_TARGET(main)
 
+# Link libraries for the build type
 if (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-	TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../libprisms_pf.a)
+	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)
+  target_link_libraries(main ${CMAKE_SOURCE_DIR}/../../libprisms_pf.a)
 else()
-	TARGET_LINK_LIBRARIES(main ${CMAKE_SOURCE_DIR}/../../libprisms_pf_debug.a)
+  target_link_libraries(main ${CMAKE_SOURCE_DIR}/../../libprisms_pf_debug.a)
 endif()