Merge branch 'deepmodeling:develop' into feature

Author: ErjieWu

.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

@@ -25,10 +25,10 @@ jobs:
       # Validate version.h matches the release tag
       - name: Assert version increment
         run: |
-          CODE_VERSION=$(grep -oP '#define\s+VERSION\s+"\K\d+(\.\d+){2,3}' source/version.h)
+          CODE_VERSION=$(grep -oP '#define\s+VERSION\s+"\K\d+(\.\d+){2,3}' source/source_main/version.h)
 
           if [[ -z "$CODE_VERSION" ]]; then
-            echo "::error::Failed to extract version from source/version.h"
+            echo "::error::Failed to extract version from source/source_main/version.h"
             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
@@ -164,12 +167,12 @@ set(ABACUS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/source)
 set(ABACUS_TEST_DIR ${CMAKE_CURRENT_SOURCE_DIR}/tests)
 set(ABACUS_BIN_PATH ${CMAKE_CURRENT_BINARY_DIR}/${ABACUS_BIN_NAME})
 include_directories(${ABACUS_SOURCE_DIR})
-include_directories(${ABACUS_SOURCE_DIR}/module_base/module_container)
+include_directories(${ABACUS_SOURCE_DIR}/source_base/module_container)
 
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-add_executable(${ABACUS_BIN_NAME} source/main.cpp)
+add_executable(${ABACUS_BIN_NAME} source/source_main/main.cpp)
 if(ENABLE_COVERAGE)
   add_coverage(${ABACUS_BIN_NAME})
 endif()
@@ -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/CONTRIBUTING.md

@@ -39,7 +39,7 @@ The source code of ABACUS is based on several modules. Under the ABACUS root dir
 For those who are interested in the source code, the following figure shows the structure of the source code.
 
 ```text
-|-- module_base                 A basic module including
+|-- source_base                 A basic module including
 |   |                           (1) Mathematical library interface functions: BLAS, LAPACK, Scalapack;
 |   |                           (2) Custom data classes: matrix, vector definitions and related functions;
 |   |                           (3) Parallelization functions: MPI, OpenMP;
@@ -57,7 +57,7 @@ For those who are interested in the source code, the following figure shows the
 |-- module_elecstate            The module for defining the electronic state and its operations.
 |   |-- module_charge           The module for calculating the charge density, charge mixing
 |   |-- potentials              The module for calculating the potentials, including Hartree, exchange-correlation, local pseudopotential, etc.
-|-- module_esolver              The module defining task-specific driver of corresponding workflow for evaluating energies, forces, etc., including lj, dp, ks, sdft, ofdft, etc.
+|-- source_esolver              The module defining task-specific driver of corresponding workflow for evaluating energies, forces, etc., including lj, dp, ks, sdft, ofdft, etc.
 |   |                           TDDFT, Orbital-free DFT, etc.
 |-- module_hamilt_general       The module for defining general Hamiltonian that can be used both in PW and LCAO calculations.
 |   |-- module_ewald            The module for calculating the Ewald summation.
@@ -77,7 +77,7 @@ For those who are interested in the source code, the following figure shows the
 |   |-- hamilt_pwdft            The module for defining the Hamiltonian in PW-DFT calculations.
 |   |   |-- operator_pw         The module for defining the operators in PW-DFT calculations.
 |   `-- hamilt_stodft           The module for defining the Hamiltonian in STODFT calculations.
-|-- module_hsolver              The module for solving the Hamiltonian with different diagonalization methods, including CG, Davidson in PW
+|-- source_hsolver              The module for solving the Hamiltonian with different diagonalization methods, including CG, Davidson in PW
 |   |                           calculations, and scalapack and genelpa in LCAO calculations.
 |-- module_io                   The module for reading of INPUT files and output properties including band structure, density of states, charge density, etc.
 |-- module_md                   The module for performing molecular dynamics.
@@ -183,7 +183,7 @@ pre-commit install
 
 ## Adding a unit test
 
-We use [GoogleTest](https://github.com/google/googletest) as our test framework. Write your test under the corresponding module folder at `abacus-develop/tests`, then append the test to `tests/CMakeLists.txt`. If there are currently no unit tests provided for the module, do as follows. `module_base` provides a simple demonstration.
+We use [GoogleTest](https://github.com/google/googletest) as our test framework. Write your test under the corresponding module folder at `abacus-develop/tests`, then append the test to `tests/CMakeLists.txt`. If there are currently no unit tests provided for the module, do as follows. `source_base` provides a simple demonstration.
 
 - Add a folder named `test` under the module.
 - Append the content below to `CMakeLists.txt` of the module: