Update ABACUS from deepmodeling

.github/workflows/ase_plugin_test.yml

@@ -0,0 +1,66 @@
+name: Atomic Simulation Environment (ASE) Plugin Test
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    name: abacuslite
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/deepmodeling/abacus-gnu
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        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: 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}
+          rm -rf build
+          cmake -B build
+          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

@@ -17,17 +17,17 @@ jobs:
             name: "Build with Intel toolchain"
 
           - tag: gnu
-            build_args: "-DENABLE_LIBXC=1 -DDENABLE_MLALGO=1 -DENABLE_LIBRI=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
             name: "Build extra components with GNU toolchain"
           - tag: intel
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_PEXSI=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda
             build_args: "-DUSE_CUDA=1"
             name: "Build with CUDA support"
           - tag: gnu
-            build_args: "-DENABLE_LCAO=OFF"
+            build_args: "-DENABLE_LCAO=0"
             name: "Build without LCAO"
           - tag: gnu
             build_args: "-DUSE_ELPA=0 "
@@ -43,12 +43,17 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: recursive
 
       - name: Build
         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}
+          rm -rf build
           cmake -B build ${{ matrix.build_args }}
           cmake --build build -j2

.github/workflows/build_test_makefile.yml

@@ -16,10 +16,12 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - 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 +4,87 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - 'v*'
+    - 'v*'
 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@v6
+      with:
+        submodules: recursive
+
+    - name: Install Perl Dependencies and Coverage Tools
+      run: |
+        apt update && apt install -y curl jq ca-certificates python3-pip
+        apt install -y lcov perl-modules
+        apt install -y libcapture-tiny-perl libdatetime-perl libjson-perl libperlio-gzip-perl
+        lcov --version
+
+    - name: Building with Coverage
+      run: |
+        rm -rf build/
+        rm -f CMakeCache.txt
+
+        mkdir -p build
+        chmod -R 755 build/
+
+        cmake -B build \
+          -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@v5
+      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

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: recursive
 
@@ -30,9 +30,10 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y ccache
 
-      - name: Build
+      - name: Configure & Build
         run: |
           nvidia-smi
+          rm -rf build
           cmake -B build -DUSE_CUDA=ON -DBUILD_TESTING=ON
           cmake --build build -j4
           cmake --install build

.github/workflows/devcontainer.yml

@@ -1,6 +1,7 @@
 name: Container
 
 on:
+  create:
   push:
     branches:
       - develop
@@ -16,12 +17,18 @@ jobs:
       matrix:
         dockerfile: ["gnu","intel","cuda"]
     steps:
+      - name: Force Clean Workspace
+        run: |
+          sudo chattr -i -R ${{ github.workspace }} 2>/dev/null || true
+          sudo chown -R $USER:$USER ${{ github.workspace }}
+          sudo find ${{ github.workspace }} -mindepth 1 -delete
+
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Docker meta
         id: meta
-        uses: docker/metadata-action@v5
+        uses: docker/metadata-action@v6
         with:
           images: |
             ghcr.io/deepmodeling/abacus-${{ matrix.dockerfile }}
@@ -30,26 +37,31 @@ jobs:
             type=semver,pattern={{version}},enable=${{ github.ref_type == 'tag' }}
             type=raw,value=latest
 
+      - name: Fix Docker Directory Permissions
+        run: |
+          sudo mkdir -p /home/runner/.docker
+          sudo chown -R $USER:$USER /home/runner/.docker
+
       - name: Setup Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Login to Aliyun Registry
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           registry: dp-harbor-registry.us-east-1.cr.aliyuncs.com
             # AliCloud automatically mirrors to registry.dp.tech
           username: ${{ secrets.DP_HARBOR_USERNAME }}
           password: ${{ secrets.DP_HARBOR_PASSWORD }}
 
       - name: Build and Push Container
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         with:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/doxygen.yml

@@ -30,7 +30,7 @@ jobs:
     if: github.repository_owner == 'deepmodeling'
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Install Doxygen
         run: sudo apt-get install doxygen graphviz -y
@@ -48,7 +48,7 @@ jobs:
         uses: actions/configure-pages@v5
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
         with:
           path: './doxygen/html'
 

.github/workflows/dynamic.yml

@@ -13,7 +13,7 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-gnu
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Building
         run: |
           cmake -B build -DENABLE_ASAN=1 -DENABLE_MLALGO=1 -DENABLE_LIBXC=1
@@ -24,7 +24,7 @@ jobs:
           cd tests/integrate
           bash Autotest.sh -n 2 -s true
       - name: Publish Report to Dashboard
-        uses: crazy-max/ghaction-github-pages@v4
+        uses: crazy-max/ghaction-github-pages@v5
         if: ${{ ! cancelled() }}
         with:
           target_branch: dashboard

.github/workflows/performance.yml

@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 2880
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Install Requirements
         run: |
           apt install -y time

.github/workflows/pytest.yml

@@ -11,9 +11,9 @@ jobs:
       image: ghcr.io/deepmodeling/abacus-gnu
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
             python-version: 3.8
       - name: Build Pyabacus