Fix for non-uniform Dirichlet BCs (Issue #406)

.clang-tidy

@@ -9,20 +9,15 @@ 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,
-  -misc-include-cleaner,
   modernize-*,
   -modernize-use-trailing-return-type,
   mpi-*,
   performance-*,
   readability-*,
   -readability-else-after-return,
-  -readability-static-accessed-through-instance,
-  -readability-avoid-const-params-in-decls,
-  -readability-magic-numbers,
   -readability-identifier-length,
 
 WarningsAsErrors: '*'

.github/workflows/clang-format.yml

@@ -7,6 +7,10 @@ on:
   pull_request:
     branches:
       - master
+      - devel
+    paths-ignore:
+      - 'doc/**'
+      - 'contrib/**'
 
 concurrency:
   group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}

.github/workflows/clang-tidy.yml

@@ -7,13 +7,19 @@ on:
   pull_request:
       branches:
         - master
+        - devel
       types:
         - opened
         - reopened
         - synchronize
         - ready_for_review
       paths-ignore:
       - 'applications/**'
+      - 'contrib/**'
+      - 'doc/**'
+      - 'automatic_test/**'
+      - 'tests/**'
+
 
 concurrency:
   group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}

.github/workflows/github-pages.yml

@@ -0,0 +1,48 @@
+name: Publish doc to GitHub pages
+
+on:
+  push:
+    branches:
+      - devel
+
+permissions:
+  contents: write
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request'}}
+
+jobs:
+  docs:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v4
+
+    - name: Setup doxygen
+      run: |
+        sudo apt-get install doxygen
+        sudo apt-get install -y graphviz
+
+    - name: Build doxygen files
+      run: |
+        cd doc/doxygen
+        cmake .
+        make
+
+    - name: Upload folders
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-doc
+        path: doc/doxygen/html/
+
+    - name: Deploy to GitHub pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      if: github.ref == 'refs/heads/devel'
+      with:
+        branch: gh-pages
+        folder: doc/doxygen/html/
+        target-folder: doxygen/
+

.github/workflows/linux.yml

@@ -7,13 +7,16 @@ on:
   pull_request:
     branches:
       - master
+      - devel
     types:
       - opened
       - reopened
       - synchronize
       - ready_for_review
     paths-ignore:
       - 'applications/**'
+      - 'doc/**'
+      - 'contrib/**'
 
 concurrency:
   group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
@@ -40,12 +43,24 @@ jobs:
           cmake .
           make -j $(nproc)
 
-      - name: Run PRISMS-PF tests
+      - name: Run PRISMS-PF unit tests
+        run: |
+          export OMPI_ALLOW_RUN_AS_ROOT=1
+          export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+          cd tests
+          cmake .
+          make -j $(nproc)
+          ctest
+          cd ..
+
+
+      - name: Run PRISMS-PF automatic tests
         timeout-minutes: 60
         run: |
           export OMPI_ALLOW_RUN_AS_ROOT=1
           export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
-          cd tests/automatic_tests
+          cd automatic_tests
           python3 run_automatic_tests.py
 

.gitignore

@@ -3,6 +3,7 @@ build/*
 CMakeFiles/
 CMakeCache.txt
 *.cmake
+!cmake/*.cmake
 Makefile
 .ninja*
 build.ninja
@@ -56,13 +57,14 @@ main-debug
 main
 
 #Output files
-*.vtk
+applications/*/*.vtk
 *.vtu
 *.vts
 *.frt
 integratedFields.txt
 output.txt
 error.txt
+CTestCostData.txt
 
 # Checkpoint/restart files
 restart.*
@@ -113,3 +115,10 @@ DoxygenWarningLog.txt
 *.nav
 *.snm
 *.nlo
+
+# Doxygen
+doc/doxygen/html/*
+doc/doxygen/latex/*
+doc/doxygen/Doxyfile.doc_doxygen
+doc/doxygen/CMakeDoxyfile.in
+doc/doxygen/DoxygenWarningLog.txt

CMakeLists.txt

@@ -3,9 +3,7 @@
 #  Adapted from the ASPECT CMake file
 ##
 
-cmake_minimum_required(VERSION 3.1.0)
-
-project(prisms_pf)
+cmake_minimum_required(VERSION 3.8.0)
 
 file(STRINGS "${CMAKE_SOURCE_DIR}/VERSION" PRISMS_PF_VERSION LIMIT_COUNT 1)
 
@@ -27,6 +25,14 @@ if(EXISTS ${CMAKE_SOURCE_DIR}/CMakeCache.txt)
   "Please delete the file before running cmake again.")
 endif()
 
+# Print the current cmake version
+message(STATUS "CMake version: ${CMAKE_VERSION}")
+
+# Set the standard to C++17
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
 # Setup the build type (debug, release, debugrelease)
 if("${CMAKE_BUILD_TYPE}" STREQUAL "")
   set(CMAKE_BUILD_TYPE "DebugRelease" 
@@ -71,7 +77,7 @@ message(STATUS "=========================================================")
 message(STATUS "")
 
 # Find deal.II installation
-find_package(deal.II 9.2.0 QUIET
+find_package(deal.II 9.5.0 QUIET
 	HINTS ${DEAL_II_DIR} $ENV{DEAL_II_DIR}
   )
 if(NOT ${deal.II_FOUND})
@@ -93,14 +99,56 @@ if(NOT DEAL_II_WITH_P4EST)
     set(DEALII_INSTALL_VALID OFF)
 endif()
 
+if(NOT DEAL_II_WITH_MPI)
+    message(SEND_ERROR
+      "\n**deal.II was built without support for MPI!\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()
 
+# Optional deal.II packages
+set(PRISMS_PF_WITH_ZLIB OFF CACHE BOOL "Whether the user wants to compile PRISMS-PF with deal.II's zlib dependency, or not.")
+message(STATUS "Using PRISMS_PF_WITH_ZLIB = '${PRISMS_PF_WITH_ZLIB}'")
+if(PRISMS_PF_WITH_ZLIB)
+  if(DEAL_II_WITH_ZLIB)
+    message(STATUS "  Found deal.II installation with zlib")
+  else()
+    message(FATAL_ERROR "deal.II installation with zlib not found. Disable PRISMS_PF_WITH_ZLIB or recompile deal.II with zlib.")
+  endif()
+endif()
+
+set(PRISMS_PF_WITH_SUNDIALS OFF CACHE BOOL "Whether the user wants to compile PRISMS-PF with deal.II's SUNDIALS dependency, or not.")
+message(STATUS "Using PRISMS_PF_WITH_SUNDIALS = '${PRISMS_PF_WITH_SUNDIALS}'")
+if(PRISMS_PF_WITH_SUNDIALS)
+  if(DEAL_II_WITH_SUNDIALS)
+    message(STATUS "  Found deal.II installation with SUNDIALS")
+  else()
+    message(FATAL_ERROR "deal.II installation with SUNDIALS not found. Disable PRISMS_PF_WITH_SUNDIALS or recompile deal.II with SUNDIALS.")
+  endif()
+endif()
+
+# Load deal.II cached variables
 deal_ii_initialize_cached_variables()
 
+# Caliper
+set(PRISMS_PF_WITH_CALIPER OFF CACHE BOOL "Whether the user wants to compile PRISMS-PF with the profiling code Caliper, or not.")
+message(STATUS "Using PRISMS_PF_WITH_CALIPER = '${PRISMS_PF_WITH_CALIPER}'")
+if(PRISMS_PF_WITH_CALIPER)
+  find_package(CALIPER)
+  if(${CALIPER_FOUND})
+    include_directories(${CALIPER_INCLUDE_DIR})
+    message(STATUS "  Caliper found at ${CALIPER_DIR}")
+  else()
+    message(FATAL_ERROR "Caliper not found. Disable PRISMS_PF_WITH_CALIPER or specify a hint to your installation directory with CALIPER_DIR")
+  endif()
+endif()
+
 # 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.")
@@ -115,6 +163,8 @@ message(STATUS "Configuring PRISMS-PF build targets")
 message(STATUS "=========================================================")
 message(STATUS "")
 
+project(prisms_pf CXX)
+
 # Generate config.h to enable and disable certain features within the source code.
 set(PRISMS_PF_SOURCE_DIR ${CMAKE_SOURCE_DIR})
 
@@ -124,12 +174,7 @@ configure_file(
   )
 
 # 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)
+add_subdirectory(src)
 
 # Test stuff goes here
 
@@ -250,4 +295,4 @@ if(${PRISMS_PF_BUILD_RELEASE} STREQUAL "ON")
   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()
+endif()

README.md

@@ -44,7 +44,7 @@ For detailed instructions on how to download and use PRISMS-PF, please consult t
 
 ### Install:
 
-Install CMake, p4est, and deal.II (version 9.6 recommended).
+Install CMake, p4est, and deal.II (version 9.6.0 or above required).
 
 Clone the PRISMS-PF GitHub repository and navigate its folder.
 ```bash
@@ -98,7 +98,16 @@ following open source applications:
 
 ## Version information:
 
-This version of the code, v2.4, contains moderate changes from v2.3. It was released in November 2024. See [version_changes.md](version_changes.md) for details.
+This version of the code, v3.0, is still under development. See [version_changes.md](version_changes.md) for details of previous releases.
+
+## Contributors
+Thanks to everyone who has contributed to the project!
+
+<a href="https://github.com/prisms-center/phaseField/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=prisms-center/phaseField" />
+</a>
+
+Made with [contrib.rocks](https://contrib.rocks).
 
 ## License:
 

VERSION

@@ -1 +1 @@
-2.5-pre
+3.0-pre