Update version.h

.github/workflows/build_test_cmake.yml

@@ -27,7 +27,7 @@ jobs:
             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 "
@@ -43,7 +43,7 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           submodules: recursive
 

.github/workflows/build_test_makefile.yml

@@ -16,7 +16,7 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-${{ matrix.tag }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Build
         run: |
           export I_MPI_CXX=icpx

.github/workflows/coverage.yml

@@ -12,7 +12,7 @@ jobs:
     container: ghcr.io/deepmodeling/abacus-gnu
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Install Requirements for Coverage Testing
         run: |
           apt update && apt install -y lcov gpg curl jq ca-certificates

.github/workflows/cuda.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           submodules: recursive
 

.github/workflows/devcontainer.yml

@@ -17,7 +17,7 @@ jobs:
         dockerfile: ["gnu","intel","cuda"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Docker meta
         id: meta

.github/workflows/doxygen.yml

@@ -30,7 +30,7 @@ jobs:
     if: github.repository_owner == 'deepmodeling'
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - 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@v5
       - name: Building
         run: |
           cmake -B build -DENABLE_ASAN=1 -DENABLE_MLALGO=1 -DENABLE_LIBXC=1

.github/workflows/performance.yml

@@ -14,7 +14,7 @@ jobs:
     timeout-minutes: 2880
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - 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@v5
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
             python-version: 3.8
       - name: Build Pyabacus

.github/workflows/test.yml

@@ -17,11 +17,17 @@ jobs:
       volumes:
         - /tmp/ccache:/github/home/.ccache
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v5
         with:
-          submodules: recursive
           fetch-depth: 0
+          # We will handle submodules manually after fixing ownership
+          submodules: 'false'
+
+      - name: Take ownership of the workspace and update submodules
+        run: |
+          sudo chown -R $(whoami) .
+          git submodule update --init --recursive
 
       - name: Install CI tools
         run: |
@@ -126,12 +132,12 @@ jobs:
         run: |
           cmake --build build --target test ARGS="-V --timeout 1700 -R 03_NAO_multik"
 
-      - name: 04_LJ_DP Test
+      - name: 04_FF Test
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -R 04_LJ_DP"
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 04_FF"
 
       - name: 05_rtTDDFT Test
         env:
@@ -180,4 +186,4 @@ jobs:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_LJ_DP|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|source_psi|MODULE_RI'"
+          cmake --build build --target test ARGS="-V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_FF|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|source_psi|MODULE_RI'"

.github/workflows/version_check.yml

@@ -7,7 +7,7 @@ jobs:
   validate_version:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0  # Fetch complete git history for version comparison
 
@@ -25,15 +25,15 @@ jobs:
       # Validate version.h matches the release tag
       - name: Assert version increment
         run: |
-          CODE_VERSION=$(grep -oP '#define\s+VERSION\s+"\K\d+(\.\d+){2,3}' source/source_main/version.h)
+          CODE_VERSION=$(grep -oP '#define\s+VERSION\s+"\Kv?\d+(\.\d+){2,3}' source/source_main/version.h)
 
           if [[ -z "$CODE_VERSION" ]]; then
             echo "::error::Failed to extract version from source/source_main/version.h"
             exit 1
           fi
 
           # Verify that the version in version.h matches the tag
-          if [[ "${{ steps.versions.outputs.current_tag }}" != "v${CODE_VERSION}" ]]; then
+          if [[ "${{ steps.versions.outputs.current_tag }}" != "${CODE_VERSION}" ]]; then
             echo "::error::Version mismatch: tag=${{ steps.versions.outputs.current_tag }} ≠ code=${CODE_VERSION}"
             exit 1
           fi

.gitignore

@@ -23,4 +23,5 @@ __pycache__
 abacus.json
 *.npy
 toolchain/install/
-toolchain/abacus_env.sh
+toolchain/abacus_env.sh
+.trae

CMakeLists.txt

@@ -253,9 +253,6 @@ if(ENABLE_LCAO)
     add_compile_definitions(__PEXSI)
     set(CMAKE_CXX_STANDARD 14)
   endif()
-  if(OLD_GINT)
-    add_compile_definitions(__OLD_GINT)
-  endif()
 else()
   set(ENABLE_MLALGO OFF)
   set(ENABLE_LIBRI OFF)
@@ -287,12 +284,8 @@ if (USE_SW)
   set(SW ON)
   include_directories(${SW_MATH}/include)
   include_directories(${SW_FFT}/include)
-  
+
   target_link_libraries(${ABACUS_BIN_NAME} ${SW_FFT}/lib/libfftw3.a)
-  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswfft.a)
-  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswscalapack.a)
-  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswlapack.a)
-  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswblas.a)
 endif()
 
 find_package(Threads REQUIRED)
@@ -373,6 +366,7 @@ if(USE_CUDA)
   if(USE_CUDA)
     add_compile_definitions(__CUDA)
     add_compile_definitions(__UT_USE_CUDA)
+    target_compile_definitions(${ABACUS_BIN_NAME} PRIVATE __USE_NVTX)
     if (CMAKE_BUILD_TYPE STREQUAL "Debug")
       set(CMAKE_CUDA_FLAGS_DEBUG "${CMAKE_CUDA_FLAGS_DEBUG} -g -G" CACHE STRING "CUDA flags for debug build" FORCE)
     endif()
@@ -468,20 +462,21 @@ if(MKLROOT)
   find_package(MKL REQUIRED)
   add_definitions(-D__MKL)
   include_directories(${MKL_INCLUDE} ${MKL_INCLUDE}/fftw)
-  list(APPEND math_libs MKL::MKL MKL::MKL_SCALAPACK)
+  list(APPEND math_libs MKL::MKL)
   if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
     list(APPEND math_libs ifcore)
   endif()
-elseif(USE_SW)
-   list(APPEND math_libs gfortran)
-  # SW architecture can only use its own math library
-else()
+elseif(NOT USE_SW)
   find_package(FFTW3 REQUIRED)
   find_package(Lapack REQUIRED)
   include_directories(${FFTW3_INCLUDE_DIRS})
   list(APPEND math_libs FFTW3::FFTW3 LAPACK::LAPACK BLAS::BLAS)
+if(USE_DSP)
+  target_link_libraries(${ABACUS_BIN_NAME} ${SCALAPACK_LIBRARY_DIR})
+else()
   find_package(ScaLAPACK REQUIRED)
   list(APPEND math_libs ScaLAPACK::ScaLAPACK)
+endif()
   if(USE_OPENMP)
     list(APPEND math_libs FFTW3::FFTW3_OMP)
   endif()
@@ -520,7 +515,7 @@ if(ENABLE_MLALGO)
     include_directories(${libnpy_INCLUDE_DIR})
   endif()
   include_directories(${libnpy_SOURCE_DIR}/include)
-  
+
   add_compile_definitions(__MLALGO)
 endif()
 
@@ -560,7 +555,7 @@ if (ENABLE_CNPY)
     include_directories(${cnpy_INCLUDE_DIR})
   endif()
   include_directories(${cnpy_SOURCE_DIR})
-  
+
   # find ZLIB and link
   find_package(ZLIB REQUIRED)
   target_link_libraries(${ABACUS_BIN_NAME} cnpy ZLIB::ZLIB)
@@ -649,6 +644,15 @@ if(DEFINED DeePMD_DIR)
   endif()
 endif()
 
+if(DEFINED NEP_DIR)
+  find_package(NEP REQUIRED)
+
+  if(NEP_FOUND)
+    add_compile_definitions(__NEP)
+    target_link_libraries(${ABACUS_BIN_NAME} NEP::nep)
+  endif()
+endif()
+
 if(DEFINED TensorFlow_DIR)
   find_package(TensorFlow REQUIRED)
   include_directories(${TensorFlow_DIR}/include)
@@ -785,11 +789,22 @@ if(ENABLE_RAPIDJSON)
   target_link_libraries(${ABACUS_BIN_NAME} json_output)
 endif()
 
+if (USE_SW)
+  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswfft.a)
+  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswscalapack.a)
+  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswlapack.a)
+  target_link_libraries(${ABACUS_BIN_NAME} ${SW_MATH}/libswblas.a)
+  list(APPEND math_libs gfortran)
+endif()
+
+list(APPEND math_libs m)
+target_link_libraries(${ABACUS_BIN_NAME} ${math_libs})
+
 install(PROGRAMS ${ABACUS_BIN_PATH}
         TYPE BIN
         # DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
 
 if(ENABLE_COVERAGE)
   coverage_evaluate()
-endif()
+endif()