Merge branch 'develop' into io_libxc_2

Conflicts:
	docs/advanced/input_files/input-main.md

Author: PeizeLin

.github/workflows/build_test_cmake.yml

@@ -17,10 +17,10 @@ jobs:
             name: "Build with Intel toolchain"
 
           - tag: gnu
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1"
+            build_args: "-DENABLE_LIBXC=1 -DDENABLE_MLALGO=1 -DENABLE_LIBRI=1"
             name: "Build extra components with GNU toolchain"
           - tag: intel
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda

.github/workflows/coverage.yml

@@ -18,7 +18,7 @@ jobs:
           apt update && apt install -y lcov gpg curl jq ca-certificates
       - name: Building
         run: |
-          cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
+          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

.github/workflows/dynamic.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@v4
       - name: Building
         run: |
-          cmake -B build -DENABLE_ASAN=1 -DENABLE_DEEPKS=1 -DENABLE_LIBXC=1
+          cmake -B build -DENABLE_ASAN=1 -DENABLE_MLALGO=1 -DENABLE_LIBXC=1
           cmake --build build -j8
           cmake --install build
       - name: Testing

.github/workflows/test.yml

@@ -31,7 +31,7 @@ jobs:
 
       - name: Configure
         run: |
-          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_MLKEDF=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DENABLE_FLOAT_FFTW=ON
+          cmake -B build -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DENABLE_FLOAT_FFTW=ON
 
 # Temporarily removed because no one maintains this now.
 # And it will break the CI test workflow.

.github/workflows/version_check.yml

@@ -0,0 +1,45 @@
+name: Version Check
+on:
+  release:
+    types: [published]
+
+jobs:
+  validate_version:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch complete git history for version comparison
+
+      # Extract last two tags for version comparison
+      - name: Get version history
+        id: versions
+        run: |
+          # Get previous tag (skip current tag)
+          PREV_TAG=$(git describe --tags --abbrev=0 $(git rev-list --tags --skip=1 --max-count=1))
+          # Current tag being published (extracted from GITHUB_REF)
+          CURRENT_TAG=${GITHUB_REF#refs/tags/}
+          echo "prev_tag=${PREV_TAG}" >> $GITHUB_OUTPUT
+          echo "current_tag=${CURRENT_TAG}" >> $GITHUB_OUTPUT
+
+      # Validate version.h matches the release tag
+      - name: Assert version increment
+        run: |
+          CODE_VERSION=$(grep -oP '#define\s+VERSION\s+"\K\d+(\.\d+){2,3}' source/version.h)
+
+          if [[ -z "$CODE_VERSION" ]]; then
+            echo "::error::Failed to extract version from source/version.h"
+            exit 1
+          fi
+
+          # Verify that the version in version.h matches the tag
+          if [[ "${{ steps.versions.outputs.current_tag }}" != "v${CODE_VERSION}" ]]; then
+            echo "::error::Version mismatch: tag=${{ steps.versions.outputs.current_tag }} ≠ code=${CODE_VERSION}"
+            exit 1
+          fi
+
+          # Ensure the version has been incremented
+          if [[ "${{ steps.versions.outputs.prev_tag}}" == "${{ steps.versions.outputs.current_tag }}" ]]; then
+            echo "::error::Version unchanged: ${{ steps.versions.outputs.current_tag }}"
+            exit 1
+          fi

CMakeLists.txt

@@ -21,8 +21,11 @@ option(USE_DSP "Enable DSP" OFF)
 option(USE_ABACUS_LIBM "Build libmath from source to speed up" OFF)
 option(ENABLE_LIBXC "Enable using the LibXC package" OFF)
 option(ENABLE_FLOAT_FFTW "Enable using single-precision FFTW library." OFF)
-option(ENABLE_DEEPKS "Enable the DeePKS algorithm" OFF)
-option(ENABLE_MLKEDF "Enable the Machine-Learning-based KEDF for OFDFT" OFF)
+
+# option(ENABLE_DEEPKS "Enable the DeePKS algorithm" OFF)
+# option(ENABLE_MLKEDF "Enable the Machine-Learning-based KEDF for OFDFT" OFF)
+
+option(ENABLE_MLALGO "Enable the machine learning algorithms" OFF)
 
 option(ENABLE_LCAO "Enable LCAO algorithm" ON)
 option(USE_ELPA "Enable ELPA for LCAO" ON)
@@ -115,7 +118,7 @@ endif()
 # Serial version of ABACUS will not use ELPA
 if(NOT ENABLE_MPI)
   set(USE_ELPA OFF)
-  set(ENABLE_DEEPKS OFF)
+  set(ENABLE_MLALGO OFF)
 endif()
 
 # Different exe files of ABACUS
@@ -253,7 +256,7 @@ if(ENABLE_LCAO)
     add_compile_definitions(__NEW_GINT)
   endif()
 else()
-  set(ENABLE_DEEPKS OFF)
+  set(ENABLE_MLALGO OFF)
   set(ENABLE_LIBRI OFF)
 endif()
 
@@ -480,8 +483,9 @@ if(ENABLE_FLOAT_FFTW)
   add_definitions(-D__ENABLE_FLOAT_FFTW)
 endif()
 
-if(ENABLE_DEEPKS)
-  target_link_libraries(${ABACUS_BIN_NAME} deepks)
+if(ENABLE_MLALGO)
+  target_link_libraries(${ABACUS_BIN_NAME} deepks) # deepks
+  target_link_libraries(${ABACUS_BIN_NAME} hamilt_mlkedf) # mlkedf
 
   find_path(libnpy_SOURCE_DIR npy.hpp HINTS ${libnpy_INCLUDE_DIR})
   if(NOT libnpy_SOURCE_DIR)
@@ -496,32 +500,14 @@ if(ENABLE_DEEPKS)
     include_directories(${libnpy_INCLUDE_DIR})
   endif()
   include_directories(${libnpy_SOURCE_DIR}/include)
-  add_compile_definitions(__DEEPKS)
-endif()
-
-if(ENABLE_MLKEDF)
-  target_link_libraries(${ABACUS_BIN_NAME} hamilt_mlkedf)
-
-  find_path(libnpy_SOURCE_DIR npy.hpp HINTS ${libnpy_INCLUDE_DIR})
-  if(NOT libnpy_SOURCE_DIR)
-    include(FetchContent)
-    FetchContent_Declare(
-      libnpy
-      GIT_REPOSITORY https://github.com/llohse/libnpy.git
-      GIT_SHALLOW TRUE
-      GIT_PROGRESS TRUE)
-    FetchContent_MakeAvailable(libnpy)
-  else()
-    include_directories(${libnpy_INCLUDE_DIR})
-  endif()
-  include_directories(${libnpy_SOURCE_DIR}/include)
-  add_compile_definitions(__MLKEDF)
+  
+  add_compile_definitions(__MLALGO)
 endif()
 
 # Torch uses outdated components to detect CUDA arch, causing failure on
 # latest CUDA kits. Set CMake variable TORCH_CUDA_ARCH_LIST in the form of
 # "major.minor" if required.
-if(ENABLE_DEEPKS OR ENABLE_MLKEDF OR DEFINED Torch_DIR)
+if(ENABLE_MLALGO OR DEFINED Torch_DIR)
   find_package(Torch REQUIRED)
   if(NOT Torch_VERSION VERSION_LESS "2.1.0")
     set_if_higher(CMAKE_CXX_STANDARD 17)

Dockerfile.gnu

@@ -34,7 +34,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
+    cmake -B build -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build

Dockerfile.intel

@@ -58,7 +58,7 @@ ADD https://api.github.com/repos/deepmodeling/abacus-develop/git/refs/heads/deve
 RUN source /opt/intel/oneapi/setvars.sh && \
     git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \
-    cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
+    cmake -B build -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_RAPIDJSON=ON && \
     cmake --build build -j`nproc` && \
     cmake --install build && \
     rm -rf build && \

conda/meta.yaml

@@ -26,7 +26,7 @@ build:
   skip: true  # [not linux]
   script: |
     export CMAKE_PREFIX_PATH=`python -c "import torch;print(torch.__path__[0])"`/share/cmake:$CMAKE_PREFIX_PATH
-    cmake -B conda_build ${CMAKE_ARGS} -DCMAKE_BUILD_TYPE=Release -DENABLE_DEEPKS=1 -DENABLE_LIBXC=1
+    cmake -B conda_build ${CMAKE_ARGS} -DCMAKE_BUILD_TYPE=Release -DENABLE_MLALGO=1 -DENABLE_LIBXC=1
     cmake --build conda_build -j`nproc`
     cmake --install conda_build
   # ${CMAKE_ARGS} applys restrictions for CMake to search libs under conda building env.

docs/advanced/elec_properties/density_matrix.md

@@ -1,8 +1,8 @@
 # Extracting Density Matrices
 
-ABACUS can output the density matrix by adding the keyword "[out_dm](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-dm)" in INPUT file:
+ABACUS can output the density matrix by adding the keyword "[out_dmk](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-dm)" in INPUT file:
 ```
-out_dm             1
+out_dmk    1
 ```
 After finishing the calculation, the information of the density matrix is stroed in files `OUT.${suffix}/SPIN${spin}_DM`, which looks like:
 ```
@@ -37,4 +37,4 @@ The following line is dimension of the density matrix, and the rest lines are th
 
 The examples can be found in [examples/density_matrix](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/density_matrix)
 
-- Note: now this function is valid only for LCAO gamma only calcualtion.
+- Note: now this function is valid only for LCAO gamma only calcualtion.