muGrid 0.90.1__tar.gz

mugrid-0.90.1/.clang-format

@@ -0,0 +1,7 @@
+AccessModifierOffset: -1
+SpacesBeforeTrailingComments: 2
+NamespaceIndentation: All
+SortIncludes: false
+SortUsingDeclarations: false
+PointerAlignment: Middle
+AlwaysBreakTemplateDeclarations: true

mugrid-0.90.1/.gitattributes

@@ -0,0 +1,3 @@
+# Tags in this file will be replaced during git archive. git archive is used
+# by meson to create source packages.
+discover_version.py export-subst

mugrid-0.90.1/.github/install_netcdf4.sh

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+if [ -z "$HOMEBREW_REPOSITORY" ]; then
+    INSTALL_PREFIX=/usr/local
+else
+    brew install pkg-config
+    INSTALL_PREFIX=$HOMEBREW_REPOSITORY
+    export PKG_CONFIG_PATH
+fi
+printenv
+curl -L https://download.gnome.org/sources/libxml2/2.12/libxml2-2.12.7.tar.xz | tar -Jx
+cd libxml2-2.12.7
+./configure --without-lzma --without-python --enable-static --disable-shared --with-pic --prefix=$INSTALL_PREFIX
+make
+make install
+cd ..
+curl -L https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz | tar -zx
+cd netcdf-c-4.9.2
+./configure --disable-hdf5 --disable-byterange --enable-static --disable-shared --with-pic --prefix=$INSTALL_PREFIX
+make
+make install

mugrid-0.90.1/.github/workflows/publish.yml

@@ -0,0 +1,49 @@
+name: Publish
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Installing Python
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y \
+            python3-dev \
+            python3-pip \
+            python3-venv \
+            meson \
+            ninja-build
+          python3 -m venv ../venv
+          source ../venv/bin/activate
+          pip install build
+
+      - name: Build source package
+        run: |
+          source ../venv/bin/activate
+          python3 -m build . -s
+
+      - name: Test installation of source package
+        run: |
+          source ../venv/bin/activate
+          pip install dist/*.tar.gz
+
+      - name: Publish package on PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+

mugrid-0.90.1/.github/workflows/ubuntu.yml

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+name: Tests
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+  schedule:
+    - cron: "0 2 * * 5"  
+jobs:
+  tests:
+    runs-on: ubuntu-22.04
+    timeout-minutes: 45
+
+    strategy:
+      matrix:
+        mpi: ['no', 'yes']
+        compiler: ['gcc', 'clang']
+        python-version: ['3.8', '3.9', '3.10', '3.11' , '3.12']
+        numpy-version: ['<2.0.0']
+        mpi4py-version: ['==3.1.6']
+        exclude:
+          - mpi: 'yes'
+            compiler: 'clang'
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -qy
+          if [ "${{ matrix.compiler }}" == "clang" ]; then
+            sudo apt-get install -y clang
+          fi
+          python3 -m venv venv
+          source venv/bin/activate
+          python3 -m pip install --upgrade pip
+          # Install numpy
+          pip install -v "numpy${{ matrix.numpy-version }}"
+          if [ "${{ matrix.mpi }}" == "yes" ]; then
+            sudo apt-get install -y \
+              ninja-build \
+              libboost-test-dev \
+              openmpi-bin \
+              libopenmpi-dev \
+              libpnetcdf-dev
+            # Install mpi4py
+            echo "Installing mpi4py${{ matrix.mpi4py-version }}"
+            CC=mpicc python3 -m pip install -v \
+              --no-binary mpi4py \
+              "mpi4py${{ matrix.mpi4py-version }}"
+          else
+            sudo apt-get install -y \
+              ninja-build \
+              libboost-test-dev \
+              libnetcdf-dev
+          fi
+          python3 -m pip install build meson
+          python3 -m pip list
+
+      - name: Compile with Meson
+        run: |
+          if [ "${{ matrix.compiler }}" == "clang" ]; then
+            export CC=clang
+            export CXX=clang++
+          fi
+          source venv/bin/activate
+          meson setup builddir
+          cd builddir
+          meson compile
+
+      - name: Run tests
+        run: |
+          source venv/bin/activate
+          cd builddir
+          meson test -v
+
+      - name: Test installation of Python extension module
+        run: |
+          source venv/bin/activate
+          python3 -m pip install .

mugrid-0.90.1/.github/workflows/wheels.yml

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+name: Wheels
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  build_wheels:
+    name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    strategy:
+      matrix:
+        buildplat:
+        - [ubuntu-22.04, manylinux, x86_64]
+        # - [ubuntu-22.04, manylinux, aarch64]
+        - [macos-14, macosx, arm64]
+        # - [macos-14, macosx, x86_64]
+        # - [windows-2019, win, AMD64]
+        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+      fail-fast: false
+
+    env:
+      IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.8'
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.18.1
+        env:
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_BEFORE_ALL: bash .github/install_netcdf4.sh
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_ENVIRONMENT_MACOS: PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/opt/homebrew/lib/pkgconfig
+          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
+          CIBW_TEST_COMMAND: python3 -c "import muGrid; print(muGrid.__version__); from _muGrid import FileIONetCDF"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
+          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
+
+      - name: Check tag
+        id: check-tag
+        run: |
+          if [[ ${{ github.ref }} =~ ^refs/tags/[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+              echo ::set-output name=match::true
+          fi
+        shell: bash
+
+      - name: Deploy to PyPI
+        if: steps.check-tag.outputs.match == 'true'
+        run: |
+          pip install twine
+          twine upload wheelhouse/*.whl
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        shell: bash

mugrid-0.90.1/.gitignore

@@ -0,0 +1,12 @@
+/build/CMake*
+*~
+/build/*
+/build-o3/
+/build*
+/cmake-build-*
+
+*.pyc
+
+.vscode
+.idea
+.ccls-cache

mugrid-0.90.1/.gitmodules

@@ -0,0 +1,11 @@
+[submodule "external/pybind11"]
+	path = external/pybind11
+	url = https://github.com/pybind/pybind11.git
+	branch = stable
+[submodule "external/eigen3"]
+	path = external/eigen3
+	url = https://gitlab.com/libeigen/eigen.git
+	branch = 3.4
+[submodule "external/cork"]
+	path = external/cork
+	url = https://github.com/pastewka/cork

mugrid-0.90.1/CHANGELOG.md

@@ -0,0 +1,249 @@
+Change log for µSpectre
+=======================
+
+0.90.0 (not yet released)
+-------------------------
+
+- Split code into three repositories: muGrid, muFFT and 
+
+0.27.0 (30Jan2024)
+------------------
+
+- muSpectre: Sensitivity analysis for 3D problems
+- Fixing meson-python to >= 0.15.0
+- Updated Eigen3 to v3.4 and pybind11 to v2.11
+
+0.26.4 (04Oct2023)
+------------------
+
+- Fixing meson-python to 0.13.2 because of a bug in 0.14.0
+
+0.26.3 (16Jul2023)
+------------------
+
+- Same as 0.26.2 (debugging CI)
+
+0.26.2 (10Jul2023)
+------------------
+
+- Same as 0.26.1, fixed deployment procedure
+
+0.26.1 (08Jul2023)
+------------------
+
+- macOS wheels
+
+0.26.0 (31Mar2023)
+------------------
+
+- MPI parallelization of sensitivity analysis
+- Wheels for Python 3.11
+
+0.25.2 (14Jan2023)
+------------------
+
+- Fixed macOS build
+
+0.25.1 (28Dec2022)
+------------------
+
+- Same as 0.25.0, changed CI configuration for automatic deployment to PyPI
+
+0.25.0 (28Dec2022)
+------------------
+
+- muSpectre is now distributed with Linux wheels (basic configuration only)
+- muFFT: Added PocketFFT engine (that does not require external dependencies)
+- Added Meson build files (Python package now exclusively build using Meson)
+- Defaulted again to autodetecting MPI
+
+0.24.0 (22Nov2022)
+------------------
+
+- muFFT: Changed Python install procedure; default to no MPI and MPI now needs
+  to be explicitly enabled
+
+0.23.1 (24Mar2022)
+------------------
+- muSpectre: A bug fixed in the call of the constructor of FieldCollection
+- muFFT: Fixed `pip install muFFT` on macOS
+
+
+0.23.0 (15Oct2021)
+------------------
+- muSpectre: making vector operation methods in solver classed with communicating inside them
+- muSpectre: added logical reduction on was_last_step_nonlinear evaluation in CellData 
+
+
+0.22.0 (24Sep2021)
+------------------
+- muSpectre: mean stress control bugs resolved
+- muSpectre: mean stress control is now usable in MPI
+- muSpectre: examples using mean stress control added
+
+
+0.21.0 (26Aug2021)
+------------------
+- CI: Refactoring of the CI with addition of coverage and ccache
+
+
+0.20.2 (04Aug2021)
+------------------
+- muSpectre: deleted an unnecssary parameter from write_2d_class function in iinear_finite_elements.py
+
+
+0.20.1 (03Aug2021)
+------------------
+- muSpectre: improve write_2d and write_3d functions, 2D stencil for hexagonal grid
+
+
+0.20.0 (15Jul2021)
+------------------
+- muSpectre: capability to apply mean stress (instead of mean strain added)
+
+
+0.19.2 (28Jun2021)
+------------------
+- muGrid: correct bugs in the FileIONetCDF
+
+
+0.19.1 (23Jun2021)
+------------------
+- muSpectre: Fixed a minor array reshape bug in the tutorial_example_new.py that was jeopardizing the output stress plot
+
+
+0.19.0 (16Jun2021)
+------------------
+- muSpectre: added material_dunnat_tc (bilinear elastic- linear strain softening with tensile-compressive wiegthed norm as strain measure)
+- muSpectre: added material_dunnat_t (bilinear elastic- linear strain softening with maiximum tensile principal strain as strain measure)
+
+
+0.18.2 (10Jun2021)
+------------------
+- muSpectre: Small bugfix and addition of regularization for slightly non-pd Hessians in phase field fracture material
+- muGrid: Added functions for reporting version
+- muGrid: Added global attributes to FileIONetCDF
+
+0.18.1 (02Jun2021)
+------------------
+- muSpectre: Fix, changed the reset criterion for gradient orthogonality in
+  FEM trust region precondtioned Krylov solvers
+- muSpectre: Fix, added calling clear_was_last_step_nonlinear in
+  fem_newton_trust_region_pc solver
+- muSpectre: Fixed get_complemented_positions
+- muFFT: Fixed large transforms
+- muFFT: Fixed segfault when input buffer had wrong shape
+
+
+0.18.0 (10May2021)
+------------------
+- muSpectre: Added trust fem region solver + ability to handle precondtioner
+- muSpectre: re-organized the krylov solver hierarchy to circumvent diamond
+  inheritance by introducing KrylovSolverXXXTraits classes
+
+
+0.17.0 (24Apr2021)
+------------------
+- muSpectre: Added trust region solver class and a simplistic damage material
+- muSpectre: physics have their specific name that might be used later for outputs
+- muSpectre: trsut region krylov solver has different resetart strategies available
+- muSpectre: gradient integration for solver class + cell data is now available
+
+
+0.16.0 (31Mar2021)
+------------------
+
+- µSpectre: The ProjectionGradient works for vectorial and rank-two-tensor
+  gradient fields and replaces ProjectionFiniteStrainFast
+- µSpectre: The SolverNewtonCG can now handle scalar problems (e.g., diffusion
+  equation, heat equation, etc.)
+- clang: No more warnings are emitted during compilation
+
+
+0.15.1 (30Mar2021)
+------------------
+
+- muSpectre: Added material for phase field fracture simulations
+- muGrid: Fix support for fields with >= 2^32 elements
+
+
+0.15.0 (12Mar2021)
+------------------
+
+- muSpectre: All projection operators now have a gradient argument and can
+  work with discrete derivatives
+- muSpectre: Projection classes now have an `integrate` method that
+  reconstructs the node positions
+- muSpectre: Added `linear_finite_elements` to stencil database
+- muSpectre: Enabled even number of grid points for discrete stencils
+- muFFT: PFFT engine works with pencil decomposition
+- all: Fixed installation via CMake and `make install`
+- all: Fixed cross platform install of NetCDF I/O
+
+
+0.14.0 (04Feb2021)
+------------------
+
+- muFFT: implement serial wrapper to FFTW hcfft
+
+
+0.13.0 (28Jan2021)
+------------------
+
+- muSpectre: CellData and Solver classes for multiphysics calculations
+- muSpectre: Sensitivity analysis
+- Bug fix (muFFT): Handle cases where MPI processes have no grid points
+
+
+0.12.0 (19Nov2020)
+------------------
+
+- muGrid: Parallel I/O via NetCDF
+- muFFT: Derivatives in 1D
+- muFFT: Second derivatives
+
+
+0.11.0 (07Sep20)
+----------------
+
+- Trust-Region Newton-CG solver for nonlinear problems with instabilities
+- Updated Eigen archive URL which broke installation via pip
+
+
+0.10.0 (22Jul2020)
+------------------
+- Support for more flexible strideste in fields: full column-major, row-major and
+  strided pixels portion (#103)
+- User control over buffer copies in muFFT with option to avoid them completely 
+- Gradient integration for multiple quadrature points
+
+
+0.9.3 (28Jun2020)
+-----------------
+- Bug fix: Packaging with sdist did not remove dirty flag which lead to a
+  broken PyPI package
+
+
+0.9.2 (28Jun2020)
+-----------------
+- Bug fix: operator= of TypedFieldBase passed wrong strides during strided
+  copy; this broke the MPI-parallel FFTW forward transform (#130)
+
+
+0.9.1 (17Jun2020)
+-----------------
+- Bug fix: Packaging with sdist only included FFT engines present during
+  the packaging process
+
+
+0.9.0 (17Jun2020)
+-----------------
+- Initial release of µSpectre
+  * FFT based micromechanical homogeneization
+  * Arbitrary constitutive laws in small and finite strain
+  * Krylov and Newton solver suite
+  * MPI parallelization
+- Initial release of µFFT
+  * Generic wrapper for MPI-parallel FFT libraries
+- Initial release of µGrid
+  * Generic library for managing regular grids

mugrid-0.90.1/CPPLINT.cfg

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+set noparent
+headers=hh
+filter=-build/include,-readability/alt_tokens,-runtime/references
+filter=-legal/copyright,-runtime/indentation_namespace,-build/c++11
+#filter=-readability/namespace,-whitespace/comments