Release v0.4.0

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/pull_request_template.md

@@ -0,0 +1,8 @@
+<!-- Add a short description of your contribution here. Skip this if the title is self-explanatory -->
+
+Checklist:
+
+- [ ] I made sure that the CI passed before I ask for a review.
+- [ ] I added a summary of the changes (compared to the last release) in the `CHANGELOG.md`.
+- [ ] If necessary, I made changes to the documentation and/or added new content.
+- [ ] I will remember to squash-and-merge, providing a useful summary of the changes of this PR.

.github/workflows/build_and_test.yaml

@@ -27,11 +27,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        UBUNTU_VERSION: [noble, jammy, focal]
+        UBUNTU_VERSION: [noble, jammy]
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Set up pixi
+        uses: prefix-dev/[email protected]
+
       - name: Generate build directory
         run: mkdir -p ${{ env.FANS_BUILD_DIR }}
 
@@ -67,10 +70,30 @@ jobs:
 
       - name: Tests
         working-directory: ${{ env.FANS_BUILD_DIR }}
-        run: su -c "ctest" ${{ env.FANS_MPI_USER }}
+        run: |
+          su -c "ctest" ${{ env.FANS_MPI_USER }}
 
       - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} CTest logs
           path: ${{ env.FANS_BUILD_DIR }}/Testing/Temporary/LastTest.log
+
+      # ────────────────────────────────────────────────────────────────
+      # Pytest checks
+      # ────────────────────────────────────────────────────────────────
+      - name: Install Pixi Python deps
+        run: |
+          pixi --version
+          pixi install
+
+      - name: Run pytest checks on HDF5 output
+        run: pixi run test
+
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} PyTest logs
+          path: |
+            **/pytest*.xml
+            **/.pytest_cache

.github/workflows/build_and_test_mac.yaml

@@ -0,0 +1,102 @@
+name: Build and test macOS 15
+# Builds FANS for macOS 15 on Apple Silicon CPU and runs the tests.
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+jobs:
+  build-macos:
+    name: macOS 15
+    runs-on: macos-15
+    env:
+      FANS_BUILD_DIR: build
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install FANS dependencies
+        run: |
+          brew install gnu-time cmake gcc@14
+          brew install open-mpi --build-from-source --cc=gcc-14
+          brew install hdf5-mpi --build-from-source --cc=gcc-14
+          brew install fftw eigen
+
+      - name: Set up pixi
+        uses: prefix-dev/[email protected]
+
+      - name: Generate build directory
+        run: mkdir -p ${{ env.FANS_BUILD_DIR }}
+
+      - name: Configure
+        working-directory: ${{ env.FANS_BUILD_DIR }}
+        env:
+          CC: gcc-14
+          CXX: g++-14
+          MPICC: mpicc
+          MPICXX: mpicxx
+        run: |
+          cmake --version
+          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=ON ..
+
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: macOS 15 CMakeCache
+          path: ${{ env.FANS_BUILD_DIR }}/CMakeCache.txt
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: macOS 15 CMakeLogs
+          path: '${{ env.FANS_BUILD_DIR }}/CMakeFiles/*.log'
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: macOS 15 CompileCommands
+          path: ${{ env.FANS_BUILD_DIR }}/compile_commands.json
+
+      - name: Compile
+        working-directory: ${{ env.FANS_BUILD_DIR }}
+        run:
+          cmake --build . -j $(nproc) || cmake --build . -j1
+
+      - name: Tests
+        working-directory: ${{ env.FANS_BUILD_DIR }}
+        env:
+          CTEST_OUTPUT_ON_FAILURE: 1
+        run: ctest
+
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: macOS 15 CTest logs
+          path: ${{ env.FANS_BUILD_DIR }}/Testing/Temporary/LastTest.log
+
+      # ────────────────────────────────────────────────────────────────
+      # Pytest checks
+      # ────────────────────────────────────────────────────────────────
+      - name: Install Pixi Python deps
+        run: |
+          pixi --version
+          pixi install
+
+      - name: Run pytest checks on HDF5 output
+        run: pixi run test
+
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} PyTest logs
+          path: |
+            **/pytest*.xml
+            **/.pytest_cache

.github/workflows/docker.yaml

@@ -6,7 +6,7 @@ jobs:
   build-and-push:
     strategy:
       matrix:
-        ubuntu-version: [noble, jammy, focal]
+        ubuntu-version: [noble, jammy]
 
     runs-on: ubuntu-latest
 

.github/workflows/test_pyfans.yaml

@@ -0,0 +1,56 @@
+name: Test PyFans
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  test-pyfans:
+    runs-on: ubuntu-latest
+    container: unistuttgartdae/fans-ci:noble
+    defaults:
+      run:
+        shell: "bash --login -eo pipefail {0}"
+    env:
+      FANS_BUILD_DIR: build
+      FANS_MPI_USER: fans
+    steps:
+
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Generate build directory
+      run: mkdir -p ${{ env.FANS_BUILD_DIR }}
+
+    - name: Install dependencies
+      run: |
+        apt update
+        apt install -y wget python3-venv
+
+    - name: Install preCICE
+      run: |
+        wget https://github.com/precice/precice/releases/download/v3.2.0/libprecice3_3.2.0_noble.deb
+        apt install -y ./libprecice3_3.2.0_noble.deb
+
+    - name: Install the Micro Manager
+      run: |
+        python3 -m venv .venv
+        . .venv/bin/activate
+        pip install micro-manager-precice
+
+    - name: Configure
+      working-directory: ${{ env.FANS_BUILD_DIR }}
+      run: |
+        cmake .. -DFANS_LIBRARY_FOR_MICRO_MANAGER=ON
+        make
+
+    - name: Run a dummy macro-micro coupling test
+      run: |
+        . .venv/bin/activate
+        cd test/test_pyfans
+        python3 macro-cube.py & micro-manager-precice micro-manager-config.json

.gitignore

@@ -198,10 +198,15 @@ test/input_files/**/*.json
 **/scratch/
 
 # Test microstructure files
-!sphere.h5
+!sphere32.h5
 
 # Test input files
 !test_LinearElastic.json
 !test_LinearThermal.json
 !test_PseudoPlastic.json
 !test_J2Plasticity.json
+!test_MixedBCs.json
+
+# pixi environments
+.pixi
+*.egg-info

CHANGELOG.md

@@ -1,5 +1,21 @@
 # FANS Changelog
 
+## v0.4.0
+
+- Support compilaion on MacOS X via conda-forge https://github.com/DataAnalyticsEngineering/FANS/pull/59
+- Add support for macroscale mixed stress-strain boundary conditions https://github.com/DataAnalyticsEngineering/FANS/pull/58
+- Add grain boundary diffusion material model for polycrystals https://github.com/DataAnalyticsEngineering/FANS/pull/52
+- Add a pixi environment for the FANS_dashboard and some tests https://github.com/DataAnalyticsEngineering/FANS/pull/55
+- Remove MPI initialization from pyFANS and add an integration test for it https://github.com/DataAnalyticsEngineering/FANS/pull/46
+- Native support for MacOS https://github.com/DataAnalyticsEngineering/FANS/pull/25
+- Remove Ubuntu 20.04 from testing and Docker support https://github.com/DataAnalyticsEngineering/FANS/pull/51
+- Add support for `--version` command line argument for checking the version of FANS
+- Modify way to provide micro structure in JSON input https://github.com/DataAnalyticsEngineering/FANS/pull/43
+- Add conda package for FANS https://github.com/DataAnalyticsEngineering/FANS/pull/39
+- Introduce system for checking compiler flags: `avx2` & `fma` https://github.com/DataAnalyticsEngineering/FANS/pull/34
+- Add `results_prefix` field in the JSON input https://github.com/DataAnalyticsEngineering/FANS/pull/36
+- Build FANS as a library to be coupled to a macro-scale simulation via preCICE and the Micro Manager https://github.com/DataAnalyticsEngineering/FANS/pull/23
+
 ## v0.3.0
 
 - Added Linear thermal and mechanical triclinic material models https://github.com/DataAnalyticsEngineering/FANS/pull/32

CMakeLists.txt

@@ -1,11 +1,11 @@
-cmake_minimum_required(VERSION 3.0...3.28)
+cmake_minimum_required(VERSION 3.21)
 
 # ##############################################################################
 # GENERAL SETTINGS
 # ##############################################################################
 
 project(FANS
-        VERSION 0.3.0
+        VERSION 0.4.0
         LANGUAGES C CXX
 )
 
@@ -17,7 +17,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 
 # with -fno-implicit-templates I get linker errors when using std:: stuff
 # TODO: should be developer specific, by using e.g. CMake Presets
-set(CMAKE_CXX_FLAGS "-fmax-errors=1 -O3")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
 set(CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH})
 
 # IPO
@@ -54,9 +54,12 @@ set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # From https://stackoverflow.com/questions/73248130/how-to-avoid-the-removal-of-the-rpath-during-cmake-install-step
-
 # Set RPATH to be relative and honor user overrides, whether at the command line or FetchContent
-set(RPATH_BASE "$ORIGIN")
+if(APPLE)
+        set(RPATH_BASE "@loader_path")
+else()
+        set(RPATH_BASE "$ORIGIN")
+endif()
 file(RELATIVE_PATH REL_PATH_LIB
         "/${CMAKE_INSTALL_BINDIR}/"
         "/${CMAKE_INSTALL_LIBDIR}/")
@@ -81,12 +84,21 @@ find_package(HDF5 REQUIRED COMPONENTS CXX)
 
 find_package(Eigen3 REQUIRED)
 
-find_package(OpenMP REQUIRED)
-
 find_package(MPI REQUIRED)
 
 find_package(FFTW3 REQUIRED COMPONENTS DOUBLE MPI)
 
+option(FANS_LIBRARY_FOR_MICRO_MANAGER "Building FANS as a library to be used by the Micro Manager." OFF)
+
+if (FANS_LIBRARY_FOR_MICRO_MANAGER)
+    include(FetchContent)
+    FetchContent_Declare(
+        pybind11 GIT_REPOSITORY https://github.com/pybind/pybind11.git
+        GIT_TAG v2.12.0
+    )
+    FetchContent_MakeAvailable(pybind11)
+endif()
+
 # ##############################################################################
 # TARGETS
 # ##############################################################################
@@ -100,7 +112,7 @@ endif ()
 add_library(FANS::FANS ALIAS FANS_FANS)
 
 if (CMAKE_SYSTEM_PROCESSOR MATCHES "arm|aarch64")
-    target_compile_options(FANS_FANS PUBLIC -march=armv8-a+simd+fp+crypto)
+
 elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64")
     target_compile_options(FANS_FANS PUBLIC -mavx2 -mfma)
 endif ()
@@ -115,6 +127,10 @@ add_custom_command(
         COMMENT "Create a symlink for FANS executable to ${CMAKE_CURRENT_SOURCE_DIR}/test/"
 )
 
+if (FANS_LIBRARY_FOR_MICRO_MANAGER)
+    add_subdirectory(pyfans)
+endif ()
+
 # ##############################################################################
 # HEADERS
 # ##############################################################################
@@ -132,13 +148,23 @@ set_property(TARGET FANS_FANS PROPERTY PUBLIC_HEADER
         include/solverFP.h
         include/solver.h
         include/setup.h
+        include/mixedBCs.h
 
         include/material_models/LinearThermal.h
+        include/material_models/GBDiffusion.h
+
         include/material_models/LinearElastic.h
         include/material_models/PseudoPlastic.h
         include/material_models/J2Plasticity.h
 )
 
+# version.h is generated and added to the build include directory
+configure_file(
+    "${PROJECT_SOURCE_DIR}/include/version.h.in"
+    "${PROJECT_BINARY_DIR}/include/version.h" @ONLY
+)
+target_include_directories(FANS_main PRIVATE "${PROJECT_BINARY_DIR}/include")
+
 # ##############################################################################
 # SOURCES
 # ##############################################################################
@@ -175,9 +201,6 @@ target_compile_definitions(FANS_FANS PUBLIC ${FFTW3_DEFINITIONS})
 
 target_link_libraries(FANS_FANS PUBLIC Eigen3::Eigen)
 
-target_link_libraries(FANS_FANS PUBLIC OpenMP::OpenMP_CXX)
-
-
 target_link_libraries(FANS_main PRIVATE FANS::FANS)
 
 # ##############################################################################