Merge branch 'develop' into updatebfgstrad

Author: 19hello

.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

@@ -15,7 +15,7 @@ jobs:
         uses: actions/checkout@v4
       - name: Install Requirements for Coverage Testing
         run: |
-          apt update && apt install -y lcov gpg
+          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_PAW=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
@@ -27,8 +27,10 @@ jobs:
         run: |
           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

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)
@@ -41,6 +42,7 @@ 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)
@@ -131,6 +133,10 @@ 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)
@@ -235,6 +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)
@@ -253,8 +262,12 @@ if(ENABLE_MPI)
 endif()
 
 if (USE_DSP)
-  target_link_libraries(${ABACUS_BIN_NAME} ${DIR_MTBLAS_LIBRARY})
   add_compile_definitions(__DSP)
+  target_link_libraries(${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)
@@ -425,10 +438,8 @@ else()
   find_package(Lapack REQUIRED)
   include_directories(${FFTW3_INCLUDE_DIRS})
   list(APPEND math_libs FFTW3::FFTW3 LAPACK::LAPACK BLAS::BLAS)
-
   find_package(ScaLAPACK REQUIRED)
   list(APPEND math_libs ScaLAPACK::ScaLAPACK)
-
   if(USE_OPENMP)
     list(APPEND math_libs FFTW3::FFTW3_OMP)
   endif()
@@ -469,10 +480,29 @@ 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 DEFINED Torch_DIR)
+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)

cmake/FindMKL.cmake

@@ -83,7 +83,7 @@ endif()
 endif() # MKL::MKL
 
 # For compatibility with legacy libpaw_interface CMakeLists.txt
-if(TARGET MKL::MKL)
+if(TARGET MKL::MKL AND NOT TARGET IntelMKL::MKL)
   add_library(IntelMKL::MKL ALIAS MKL::MKL)
 endif()
 

docs/CITATIONS.md

@@ -33,3 +33,9 @@ The following references are required to be cited when using ABACUS. Specificall
     Peize Lin, Xinguo Ren, and Lixin He. "Efficient Hybrid Density Functional Calculations for Large Periodic Systems Using Numerical Atomic Orbitals." Journal of Chemical Theory and Computation 2021, 17(1), 222–239.
 
     Peize Lin, Xinguo Ren, and Lixin He. "Accuracy of Localized Resolution of the Identity in Periodic Hybrid Functional Calculations with Numerical Atomic Orbitals." Journal of Physical Chemistry Letters 2020, 11, 3082-3088.
+
+- **If ML-KEDF is used:**
+
+    Sun, Liang, and Mohan Chen. "Machine learning based nonlocal kinetic energy density functional for simple metals and alloys." Physical Review B 109.11 (2024): 115135.
+
+    Sun, Liang, and Mohan Chen. "Multi-channel machine learning based nonlocal kinetic energy density functional for semiconductors." Electronic Structure 6.4 (2024): 045006.