Merge remote-tracking branch 'upstream/develop' into develop

# Conflicts:
#	source/module_psi/psi_initializer.h

Author: Flying-dragon-boxing

.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_LIBRI=1 -DENABLE_PAW=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1 -DENABLE_PAW=1"
             name: "Build extra components with GNU toolchain"
           - tag: intel
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_LIBRI=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda

.github/workflows/coverage.yml

@@ -15,20 +15,22 @@ jobs:
         uses: actions/checkout@v4
       - name: Install Requirements for Coverage Testing
         run: |
-          apt update && apt install -y lcov
+          apt update && apt install -y lcov gpg curl jq ca-certificates
       - name: Building
         run: |
-          cmake -B build -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DBUILD_TESTING=ON -DENABLE_COVERAGE=ON
+          cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_PAW=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"
+          cmake --build build --target test ARGS="-V --timeout 21600" || exit 0
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         if: ${{ ! cancelled() }}
         with:
-          gcov: true
+          fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
+          skip_validation: true
+          verbose: true

.github/workflows/test.yml

@@ -31,15 +31,18 @@ jobs:
 
       - name: Configure
         run: |
-          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_PAW=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1
+          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON -DENABLE_MLKEDF=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_PAW=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1
 
-      - uses: pre-commit/[email protected]
-        with:
-          extra_args:
-            --from-ref ${{ github.event.pull_request.base.sha }}
-              --to-ref ${{ github.event.pull_request.head.sha }}
-        continue-on-error: true
-      - uses: pre-commit-ci/[email protected]
+# Temporarily removed because no one maintains this now.
+# And it will break the CI test workflow.
+
+#      - uses: pre-commit/[email protected]
+#        with:
+#          extra_args:
+#            --from-ref ${{ github.event.pull_request.base.sha }}
+#              --to-ref ${{ github.event.pull_request.head.sha }}
+#        continue-on-error: true
+#      - uses: pre-commit-ci/[email protected]
 
       - name: Build
         run: |

.gitignore

@@ -22,4 +22,4 @@ time.json
 *.pyc
 __pycache__
 abacus.json
-*.npy
+*.npy

.gitmodules

@@ -1,11 +1,3 @@
-[submodule "deps/LibRI"]
-	path = deps/LibRI
-	url = https://github.com/abacusmodeling/LibRI.git
-	branch = master
-[submodule "deps/LibComm"]
-	path = deps/LibComm
-	url = https://github.com/abacusmodeling/LibComm.git
-	branch = master
 [submodule "deps/libpaw_interface"]
 	path = deps/libpaw_interface
 	url = https://github.com/wenfei-li/libpaw_interface

CMakeLists.txt

@@ -12,6 +12,7 @@ project(
 
 option(ENABLE_LCAO "Enable LCAO calculation." ON)
 option(ENABLE_DEEPKS "Enable DeePKS functionality" OFF)
+option(ENABLE_MLKEDF "Enable Machine Learning based KEDF for OFDFT" OFF)
 option(ENABLE_LIBXC "Enable LibXC functionality" OFF)
 option(USE_CUDA "Enable support to CUDA for ABACUS." OFF)
 option(ENABLE_FLOAT_FFTW "Enable support to single precision FFTW library." OFF)
@@ -39,6 +40,9 @@ option(ENABLE_RAPIDJSON "Enable rapid-json usage." OFF)
 option(ENABLE_CNPY "Enable cnpy usage." OFF)
 option(ENABLE_PEXSI "Enable support for PEXSI." OFF)
 option(ENABLE_CUSOLVERMP "Enable cusolvermp." OFF)
+option(USE_DSP "Enable DSP usage." OFF)
+option(USE_CUDA_ON_DCU "Enable CUDA on DCU" OFF)
+option(USE_CUDA_MPI "Enable CUDA-aware MPI" OFF)
 
 # enable json support
 if(ENABLE_RAPIDJSON)
@@ -119,6 +123,20 @@ elseif(ENABLE_LCAO AND NOT ENABLE_MPI)
   set(ABACUS_BIN_NAME abacus_serial)
 endif()
 
+if (USE_DSP)
+  set(USE_ELPA OFF)
+  set(ENABLE_LCAO OFF)
+  set(ABACUS_BIN_NAME abacus_dsp)
+endif()
+
+if (USE_CUDA_ON_DCU)
+  add_compile_definitions(__CUDA_ON_DCU)
+endif()
+
+if (USE_CUDA_MPI)
+  add_compile_definitions(__CUDA_MPI)
+endif()
+
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 if(ENABLE_COVERAGE)
@@ -223,6 +241,9 @@ if(ENABLE_LCAO)
     add_compile_definitions(__PEXSI)
     set(CMAKE_CXX_STANDARD 14)
   endif()
+  if(NEW_GINT)
+    add_compile_definitions(__NEW_GINT)
+  endif()
 else()
   set(ENABLE_DEEPKS OFF)
   set(ENABLE_LIBRI OFF)
@@ -240,6 +261,15 @@ if(ENABLE_MPI)
   list(APPEND math_libs MPI::MPI_CXX)
 endif()
 
+if (USE_DSP)
+  add_compile_definitions(__DSP)
+  target_link_libraries(${ABACUS_BIN_NAME} ${OMPI_LIBRARY1})
+  include_directories(${MTBLAS_FFT_DIR}/libmtblas/include)
+  include_directories(${MT_HOST_DIR}/include)
+  target_link_libraries(${ABACUS_BIN_NAME} ${MT_HOST_DIR}/hthreads/lib/libhthread_device.a)
+  target_link_libraries(${ABACUS_BIN_NAME} ${MT_HOST_DIR}/hthreads/lib/libhthread_host.a)
+endif()
+
 find_package(Threads REQUIRED)
 target_link_libraries(${ABACUS_BIN_NAME} Threads::Threads)
 
@@ -408,12 +438,8 @@ else()
   find_package(Lapack REQUIRED)
   include_directories(${FFTW3_INCLUDE_DIRS})
   list(APPEND math_libs FFTW3::FFTW3 LAPACK::LAPACK BLAS::BLAS)
-
-  if(ENABLE_LCAO)
-    find_package(ScaLAPACK REQUIRED)
-    list(APPEND math_libs ScaLAPACK::ScaLAPACK)
-  endif()
-
+  find_package(ScaLAPACK REQUIRED)
+  list(APPEND math_libs ScaLAPACK::ScaLAPACK)
   if(USE_OPENMP)
     list(APPEND math_libs FFTW3::FFTW3_OMP)
   endif()
@@ -436,22 +462,6 @@ if(ENABLE_FLOAT_FFTW)
 endif()
 
 if(ENABLE_DEEPKS)
-  # 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.
-  find_package(Torch REQUIRED)
-  if(NOT Torch_VERSION VERSION_LESS "2.1.0")
-    set_if_higher(CMAKE_CXX_STANDARD 17)
-  elseif(NOT Torch_VERSION VERSION_LESS "1.5.0")
-    set_if_higher(CMAKE_CXX_STANDARD 14)
-  endif()
-  include_directories(${TORCH_INCLUDE_DIRS})
-  if(MKL_FOUND)
-    list(PREPEND math_libs ${TORCH_LIBRARIES})
-  else()
-    list(APPEND math_libs ${TORCH_LIBRARIES})
-  endif()
-  add_compile_options(${TORCH_CXX_FLAGS})
   target_link_libraries(${ABACUS_BIN_NAME} deepks)
 
   find_path(libnpy_SOURCE_DIR npy.hpp HINTS ${libnpy_INCLUDE_DIR})
@@ -470,6 +480,44 @@ if(ENABLE_DEEPKS)
   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(${libnpy_SOURCE_DIR}/include)
+  add_compile_definitions(__MLKEDF)
+endif()
+
+# Torch uses outdated components to detect CUDA arch, causing failure on
+# latest CUDA kits. Set CMake variable TORCH_CUDA_ARCH_LIST in the form of
+# "major.minor" if required.
+if(ENABLE_DEEPKS OR ENABLE_MLKEDF OR DEFINED Torch_DIR)
+  find_package(Torch REQUIRED)
+  if(NOT Torch_VERSION VERSION_LESS "2.1.0")
+    set_if_higher(CMAKE_CXX_STANDARD 17)
+  elseif(NOT Torch_VERSION VERSION_LESS "1.5.0")
+    set_if_higher(CMAKE_CXX_STANDARD 14)
+  endif()
+  include_directories(${TORCH_INCLUDE_DIRS})
+  if(MKL_FOUND)
+    list(PREPEND math_libs ${TORCH_LIBRARIES})
+  else()
+    list(APPEND math_libs ${TORCH_LIBRARIES})
+  endif()
+  add_compile_options(${TORCH_CXX_FLAGS})
+endif()
+
 if (ENABLE_CNPY)
   find_path(cnpy_SOURCE_DIR
     cnpy.h
@@ -523,13 +571,10 @@ endif()
 if(ENABLE_LIBRI)
   set_if_higher(CMAKE_CXX_STANDARD 14)
   if(LIBRI_DIR)
-    include_directories(${LIBRI_DIR}/include)
-  elseif(GIT_SUBMODULE)
-    git_submodule_update()
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR}/deps/LibRI/include)
   else()
-    message(FATAL_ERROR "Must provide LIBRI_DIR for RI related features.")
+    find_package(LibRI REQUIRED)
   endif()
+  include_directories(${LIBRI_DIR}/include)
   target_link_libraries(${ABACUS_BIN_NAME} ri module_exx_symmetry)
   add_compile_definitions(__EXX EXX_DM=3 EXX_H_COMM=2 TEST_EXX_LCAO=0
                           TEST_EXX_RADIAL=1)
@@ -540,13 +585,10 @@ if(ENABLE_LIBRI OR DEFINED LIBCOMM_DIR)
 endif()
 if(ENABLE_LIBCOMM)
   if(LIBCOMM_DIR)
-    include_directories(${LIBCOMM_DIR}/include)
-  elseif(GIT_SUBMODULE)
-    git_submodule_update()
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR}/deps/LibComm/include)
   else()
-    message(FATAL_ERROR "Must provide LIBCOMM_DIR for RI related features.")
+    find_package(LibComm REQUIRED)
   endif()
+  include_directories(${LIBCOMM_DIR}/include)
 endif()
 
 if(ENABLE_PAW)
@@ -590,13 +632,14 @@ if(DEFINED DeePMD_DIR)
     add_compile_definitions(__DPMDC)
   else()
     target_link_libraries(${ABACUS_BIN_NAME} DeePMD::deepmd_cc)
-    if(NOT DEFINED TensorFlow_DIR)
-      set(TensorFlow_DIR ${DeePMD_DIR})
-    endif()
-    find_package(TensorFlow REQUIRED)
-    if(TensorFlow_FOUND)
-      target_link_libraries(${ABACUS_BIN_NAME} TensorFlow::tensorflow_cc)
-    endif()
+  endif()
+endif()
+
+if(DEFINED TensorFlow_DIR)
+  find_package(TensorFlow REQUIRED)
+  include_directories(${TensorFlow_DIR}/include)
+  if(TensorFlow_FOUND)
+    target_link_libraries(${ABACUS_BIN_NAME} TensorFlow::tensorflow_cc)
   endif()
 endif()
 
@@ -699,22 +742,24 @@ target_link_libraries(
   hamilt_stodft
   psi
   psi_initializer
+  psi_overall_init
   esolver
   vdw
   device
-  container)
+  container
+  dftu
+  deltaspin)
 if(ENABLE_LCAO)
   target_link_libraries(
     ${ABACUS_BIN_NAME}
     hamilt_lcao
     tddft
     orb
     gint
-    dftu
     hcontainer
-    deltaspin
     numerical_atomic_orbitals
-    lr)
+    lr
+    rdmft)
   if(USE_ELPA)
     target_link_libraries(${ABACUS_BIN_NAME} genelpa)
   endif()

README.md

@@ -12,7 +12,9 @@
 
 # About ABACUS
 
-ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is an open-source package based on density functional theory (DFT). The package utilizes both plane wave and numerical atomic basis sets with the usage of norm-conserving pseudopotentials to describe the interactions between nuclear ions and valence electrons. ABACUS supports LDA, GGA, meta-GGA, and hybrid functionals. Apart from single-point calculations, the package allows geometry optimizations and ab-initio molecular dynamics with various ensembles. The package also provides a variety of advanced functionalities for simulating materials, including the DFT+U, VdW corrections, and implicit solvation model, etc. In addition, ABACUS strives to provide a general infrastructure to facilitate the developments and applications of novel machine-learning-assisted DFT methods (DeePKS, DP-GEN, DeepH, etc.) in molecular and material simulations.
+ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is an open-source package based on density functional theory (DFT). The package utilizes both plane wave and numerical atomic basis sets with the usage of norm-conserving pseudopotentials to describe the interactions between nuclear ions and valence electrons. ABACUS supports LDA, GGA, meta-GGA, and hybrid functionals. Apart from single-point calculations, the package allows geometry optimizations and ab-initio molecular dynamics with various ensembles. The package also provides a variety of advanced functionalities for simulating materials, including the DFT+U, VdW corrections, and implicit solvation model, etc. In addition, ABACUS strives to provide a general infrastructure to facilitate the developments and applications of novel machine-learning-assisted DFT methods (DeePKS, DP-GEN, DeepH, DeePTB etc.) in molecular and material simulations.
 
 # Online Documentation
 For detailed documentation, please refer to [our documentation website](https://abacus.deepmodeling.com/).
+
+See our [Github Pages](https://mcresearch.github.io/abacus-user-guide/) for more tutorials and developer guides.

cmake/FindLibComm.cmake

@@ -0,0 +1,30 @@
+###############################################################################
+# - Find LibComm
+# Find the native LibComm files.
+#
+#  LIBCOMM_FOUND - True if LibComm is found.
+#  LIBCOMM_DIR - Where to find LibComm files.
+
+find_path(LIBCOMM_DIR
+    include/Comm/Comm_Tools.h
+    HINTS ${LIBCOMM_DIR}
+    HINTS ${LibComm_DIR}
+    HINTS ${libcomm_DIR}
+)
+
+if(NOT LIBCOMM_DIR)
+    include(FetchContent)
+    FetchContent_Declare(
+        LibComm
+        URL https://github.com/abacusmodeling/LibComm/archive/refs/tags/v0.1.1.tar.gz
+    )
+    FetchContent_Populate(LibComm)
+    set(LIBCOMM_DIR ${libcomm_SOURCE_DIR})
+endif()
+# Handle the QUIET and REQUIRED arguments and
+# set LIBCOMM_FOUND to TRUE if all variables are non-zero.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LibComm DEFAULT_MSG LIBCOMM_DIR)
+
+# Copy the results to the output variables and target.
+mark_as_advanced(LIBCOMM_DIR)

cmake/FindLibRI.cmake

@@ -0,0 +1,30 @@
+###############################################################################
+# - Find LibRI
+# Find the native LibRI files.
+#
+#  LIBRI_FOUND - True if LibRI is found.
+#  LIBRI_DIR - Where to find LibRI files.
+
+find_path(LIBRI_DIR
+    include/RI/version.h
+    HINTS ${LIBRI_DIR}
+    HINTS ${LibRI_DIR}
+    HINTS ${libri_DIR}
+)
+
+if(NOT LIBRI_DIR)
+    include(FetchContent)
+    FetchContent_Declare(
+        LibRI
+        URL https://github.com/abacusmodeling/LibRI/archive/refs/tags/v0.2.1.1.tar.gz
+    )
+    FetchContent_Populate(LibRI)
+    set(LIBRI_DIR ${libri_SOURCE_DIR})
+endif()
+# Handle the QUIET and REQUIRED arguments and
+# set LIBRI_FOUND to TRUE if all variables are non-zero.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LibRI DEFAULT_MSG LIBRI_DIR)
+
+# Copy the results to the output variables and target.
+mark_as_advanced(LIBRI_DIR)