Docs: suggesting smaller mixing parameters for spin-polarized calculations

.gitattributes

@@ -0,0 +1,12 @@
+# Shell scripts and the bash-parsed integration-test case lists must keep LF
+# endings so they run under bash, including MSYS2/Git-Bash on Windows where
+# core.autocrlf may rewrite them to CRLF (which breaks `#!/bin/bash` and adds
+# stray \r to parsed lines such as the case names in CASES_*.txt).
+*.sh text eol=lf
+CASES_*.txt text eol=lf
+
+.gitattributes export-ignore
+.gitignore export-ignore
+.gitmodules export-ignore
+.pre-commit-config.yaml export-ignore
+.github/ export-ignore

.github/workflows/ase_plugin_test.yml

@@ -0,0 +1,79 @@
+name: Atomic Simulation Environment (ASE) Plugin Test
+
+on:
+  pull_request:
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test:
+    name: abacuslite
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/deepmodeling/abacus-gnu
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v7
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v4
+        with:
+          miniconda-version: 'latest'
+          activate-environment: abacuslite
+          python-version: '3.10'
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          conda install -y pip
+          pip install numpy scipy matplotlib
+
+      - name: Install abacuslite
+        shell: bash -l {0}
+        run: |
+          cd interfaces/ASE_interface
+          pip install .
+
+      - name: Install external tools from toolchain
+        run: |
+          sudo apt update && sudo apt install -y xz-utils ninja-build
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+          ./scripts/stage4/install_stage4.sh
+          cd ..
+
+      - name: Configure & Build ABACUS (GNU)
+        run: |
+          git config --global --add safe.directory `pwd`
+          export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
+          export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
+          export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
+          export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
+          source toolchain/install/setup
+          rm -rf build
+          cmake -B build -G Ninja
+          cmake --build build -j2
+
+      - name: Install and Soft Link ABACUS
+        run: |
+          cmake --install build
+          if [ -f /usr/local/bin/abacus_2p ]; then
+            ln -sf /usr/local/bin/abacus_2p /usr/local/bin/abacus
+          fi
+
+      - name: Run unit tests
+        shell: bash -l {0}
+        run: |
+          cd interfaces/ASE_interface/abacuslite
+          chmod +x xtest.sh
+          ./xtest.sh
+
+      - name: Run integration tests
+        shell: bash -l {0}
+        run: |
+          cd interfaces/ASE_interface/tests
+          chmod +x xtest.sh
+          ./xtest.sh

.github/workflows/build_test_cmake.yml

@@ -3,6 +3,10 @@ on:
   push:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -13,42 +17,64 @@ jobs:
             build_args: ""
             name: "Build with GNU toolchain"
           - tag: intel
+            external_toolchain_args: "--with-intel"
             build_args: ""
             name: "Build with Intel toolchain"
 
           - tag: gnu
-            build_args: "-DENABLE_LIBXC=1 -DDENABLE_MLALGO=1 -DENABLE_LIBRI=1"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_LIBXC=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON"
             name: "Build extra components with GNU toolchain"
           - tag: intel
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
+            external_toolchain_args: "--with-intel"
+            build_args: "-DENABLE_LIBXC=ON -DENABLE_PEXSI=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda
-            build_args: "-DUSE_CUDA=1"
+            external_toolchain_args: ""
+            build_args: "-DUSE_CUDA=ON"
             name: "Build with CUDA support"
           - tag: gnu
+            external_toolchain_args: ""
             build_args: "-DENABLE_LCAO=OFF"
             name: "Build without LCAO"
           - tag: gnu
-            build_args: "-DUSE_ELPA=0 "
+            external_toolchain_args: ""
+            build_args: "-DUSE_ELPA=OFF "
             name: "Build without ELPA"
           - tag: gnu
-            build_args: "-DENABLE_MPI=0"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_MPI=OFF"
             name: "Build without MPI"
           - tag: gnu
-            build_args: "-DENABLE_MPI=0 -DENABLE_LCAO=0"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_MPI=OFF -DENABLE_LCAO=OFF"
             name: "Build without LCAO and MPI"
 
     name: ${{ matrix.name }}
     container: ghcr.io/deepmodeling/abacus-${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           submodules: recursive
 
+      - name: Install external tools from toolchain
+        run: |
+          sudo apt update && sudo apt install -y gfortran ninja-build xz-utils
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run ${{matrix.external_toolchain_args}}
+          ./scripts/stage4/install_stage4.sh
+          cd ..
+
       - name: Build
         run: |
           git config --global --add safe.directory `pwd`
-          cmake -B build ${{ matrix.build_args }}
-          cmake --build build -j2
+          export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
+          export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
+          export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
+          export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
+          source toolchain/install/setup
+          rm -rf build
+          cmake -B build -G Ninja ${{ matrix.build_args }}
+          cmake --build build -j $(nproc)

.github/workflows/build_test_makefile.yml

@@ -3,6 +3,10 @@ on:
   push:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -16,10 +20,12 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Build
         run: |
           export I_MPI_CXX=icpx
+          chmod a+x generate_build_info.sh
           cd source
-          make -j2 ${{ matrix.build_args }}
+          mkdir build && cd build
+          make -f ../Makefile -j2 ${{ matrix.build_args }}
 

.github/workflows/coverage.yml

@@ -4,33 +4,111 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - 'v*'
+    - 'v*'
+
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test-coverage:
     name: Generate Coverage Report
     runs-on: X64
     container: ghcr.io/deepmodeling/abacus-gnu
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Install Requirements for Coverage Testing
-        run: |
-          apt update && apt install -y lcov gpg curl jq ca-certificates
-      - name: Building
-        run: |
-          cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
-          cmake --build build -j`nproc`
-          cmake --install build
-      - name: Testing
-        env:
-          OMP_NUM_THREADS: 1
-        run: |
-          cmake --build build --target test ARGS="-V --timeout 21600" || exit 0
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v5
-        if: ${{ ! cancelled() }}
-        with:
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
-          skip_validation: true
-          verbose: true
+    - name: Checkout
+      uses: actions/checkout@v7
+      with:
+        submodules: recursive
+
+    - name: Install Perl Dependencies and Coverage Tools
+      run: |
+        sudo apt update
+        sudo apt install -y \
+          curl \
+          jq \
+          ca-certificates \
+          python3-pip \
+          xz-utils \
+          ninja-build \
+          lcov \
+          perl-modules \
+          libcapture-tiny-perl \
+          libdatetime-perl \
+          libjson-perl \
+          libperlio-gzip-perl
+        lcov --version
+
+    - name: Install external tools from toolchain
+      run: |
+        cd toolchain
+        ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+        ./scripts/stage4/install_stage4.sh
+        cd ..
+
+    - name: Building with Coverage
+      run: |
+        source toolchain/install/setup
+        rm -rf build/
+        rm -f CMakeCache.txt
+
+        mkdir -p build
+        chmod -R 755 build/
+
+        cmake -B build -G Ninja \
+          -DENABLE_COVERAGE=ON \
+          -DBUILD_TESTING=ON \
+          -DENABLE_MLALGO=ON \
+          -DENABLE_LIBXC=ON \
+          -DENABLE_LIBRI=ON \
+          -DENABLE_GOOGLEBENCH=ON \
+          -DENABLE_RAPIDJSON=ON \
+          -DCMAKE_BUILD_TYPE=Debug \
+          -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage" \
+          -DCMAKE_EXE_LINKER_FLAGS="--coverage"
+        cmake --build build -j`nproc`
+        cmake --install build
+
+    - name: Testing
+      env:
+        OMP_NUM_THREADS: 1
+      run: |
+        chmod -R 755 build/
+        cmake --build build --target test ARGS="-V --timeout 21600" || echo "Some tests failed but continuing for coverage"
+
+    - name: Generate Coverage Data
+      run: |
+        cd build
+
+        lcov --directory . --capture --output-file coverage.info
+
+        lcov --remove coverage.info '/usr/*' '*/test/*' '*/external/*' '*/build/*' --output-file coverage.filtered.info
+
+        genhtml coverage.filtered.info --output-directory coverage-report
+
+        cd ..
+
+    - name: Upload Coverage to Codecov
+      uses: codecov/codecov-action@v7
+      if: ${{ ! cancelled() }}
+      with:
+        fail_ci_if_error: true
+        files: ./build/coverage.xml,./build/coverage.info
+        directory: ./build/
+        flags: unittests
+        name: codecov-umbrella
+        verbose: true
+
+        use_oidc: true
+    - name: Upload Coverage Report Artifact
+      uses: actions/upload-artifact@v7
+      if: always()
+      with:
+        name: coverage-report
+        path: |
+          build/coverage-report/
+          build/coverage.info
+          build/coverage.xml
+        retention-days: 30
+permissions:
+  id-token: write

.github/workflows/cuda.yml

@@ -4,14 +4,18 @@ on:
   workflow_dispatch:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   test:
     name: Test on CUDA Build
-    runs-on: nvidia
+    runs-on: gpu
     if: github.repository_owner == 'deepmodeling'
     container:
       image: ghcr.io/deepmodeling/abacus-cuda
@@ -21,19 +25,28 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           submodules: recursive
 
       - name: Install Ccache
         run: |
           sudo apt-get update
-          sudo apt-get install -y ccache
+          sudo apt-get install -y ccache xz-utils ninja-build
+
+      - name: Install external tools from toolchain
+        run: |
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+          ./scripts/stage4/install_stage4.sh
+          cd ..
 
-      - name: Build
+      - name: Configure & Build
         run: |
           nvidia-smi
-          cmake -B build -DUSE_CUDA=ON -DBUILD_TESTING=ON
+          source toolchain/install/setup
+          rm -rf build
+          cmake -B build -G Ninja -DUSE_CUDA=ON -DBUILD_TESTING=ON -DENABLE_FLOAT_FFTW=ON
           cmake --build build -j4
           cmake --install build