Merge branch 'develop' into feature/macOS_M1_support

Author: IshaanDesai

.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/clang-format-check.yml

@@ -0,0 +1,37 @@
+name: Test PyFans
+
+on: [push, pull_request]
+
+jobs:
+  pyfans-run-test:
+    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 cmake make g++ python3 python3-numpy python3.12-dev
+
+    - name: Configure
+      working-directory: ${{ env.FANS_BUILD_DIR }}
+      run: |
+        cmake .. -DFANS_LIBRARY_FOR_MICRO_MANAGER=ON
+        make
+
+    - name: Run FANS as a library via a Python script
+      run: |
+        cd test/test_pyfans
+        python3 run_fans_as_library.py

.github/workflows/test_pyfans.yaml

@@ -198,7 +198,7 @@ test/input_files/**/*.json
 **/scratch/
 
 # Test microstructure files
-!sphere.h5
+!sphere32.h5
 
 # Test input files
 !test_LinearElastic.json

.gitignore

@@ -16,8 +16,9 @@ repos:
     - id: black
 # clang-format for C/C++ formatting
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v8.0.1
+    rev: v19.1.2
     hooks:
     -   id: clang-format
         args: ['--style=file']
         exclude: "include/json.hpp"
+        types_or: [c++]

.pre-commit-config.yaml

@@ -1,5 +1,18 @@
 # FANS Changelog
 
+## latest
+
+- 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
+- Added API to get homogenized stress and homogenized tangent https://github.com/DataAnalyticsEngineering/FANS/pull/31
+
 ## v0.2.0
 
 - Add integration tests https://github.com/DataAnalyticsEngineering/FANS/pull/20

CHANGELOG.md

@@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.0...3.28)
 # ##############################################################################
 
 project(FANS
-        VERSION 0.2.0
+        VERSION 0.3.0
         LANGUAGES C CXX
 )
 
@@ -92,6 +92,17 @@ 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
 # ##############################################################################
@@ -107,8 +118,36 @@ 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 ()
+    # Detecting if there is avx2 and fma support on linux
+    # Deteced together, because these flags were introduced by Intel Haskell 4th. Gen
+    # Distinguishing between mac/linux because lscpu is used, which is not supported on mac.
+    if (CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+        # macOS: Assume AVX2 and FMA are supported as per requirement
+        message(STATUS "Assuming AVX2 and FMA support on macOS; using -mavx2 and -mfma.")
+        target_compile_options(FANS_FANS PUBLIC -mavx2 -mfma)
+    elseif (CMAKE_SYSTEM_NAME STREQUAL "Linux")
+        # Linux: Check for AVX2 support using lscpu
+        execute_process(COMMAND lscpu OUTPUT_VARIABLE LSCPU_OUTPUT ERROR_QUIET)
+
+        # Default to AVX; enable AVX2 if supported by hardware
+        set(FANS_USE_AVX2 FALSE)
+        if (LSCPU_OUTPUT MATCHES "avx2")
+            set(FANS_USE_AVX2 TRUE)
+        endif()
+
+        # Apply compiler options based on hardware detection
+        if (FANS_USE_AVX2)
+            message(STATUS "AVX2 and FMA supported by hardware; using -mavx2 and -mfma.")
+            target_compile_options(FANS_FANS PUBLIC -mavx2 -mfma)
+        else()
+            message(WARNING "AVX2 and FMA not supported by hardware; falling back to AVX.")
+            target_compile_options(FANS_FANS PUBLIC -mavx)
+        endif()
+    else()
+        message(WARNING "Unsupported system for AVX2 detection; defaulting to -mavx.")
+        target_compile_options(FANS_FANS PUBLIC -mavx)
+    endif()
+endif()
 
 add_executable(FANS_main)
 add_custom_command(
@@ -120,6 +159,10 @@ 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
 # ##############################################################################
@@ -138,8 +181,8 @@ set_property(TARGET FANS_FANS PROPERTY PUBLIC_HEADER
         include/solver.h
         include/setup.h
 
-        include/material_models/LinearThermalIsotropic.h
-        include/material_models/LinearElasticIsotropic.h
+        include/material_models/LinearThermal.h
+        include/material_models/LinearElastic.h
         include/material_models/PseudoPlastic.h
         include/material_models/J2Plasticity.h
 )