Merge

Author: Flying-dragon-boxing

.github/workflows/build_test_cmake.yml

@@ -17,7 +17,7 @@ jobs:
             name: "Build with Intel toolchain"
 
           - tag: gnu
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=1 -DENABLE_LIBRI=1 -DENABLE_PAW=1"
+            build_args: "-DENABLE_LIBXC=1 -DENABLE_DEEPKS=1 -DENABLE_MLKEDF=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"

.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_PAW=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
+          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 --build build -j`nproc`
           cmake --install build
       - name: Testing

.github/workflows/cuda.yml

@@ -37,7 +37,27 @@ jobs:
           cmake --build build -j4
           cmake --install build
 
-      - name: Test
+      - name: Test 11_PW_GPU
         run: |
-          cd tests/integrate
-          bash Autotest.sh -n 2 -f CASES_GPU.txt
+          cd tests/11_PW_GPU
+          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+
+      - name: Test 12_NAO_Gamma_GPU
+        run: |
+          cd tests/12_NAO_Gamma_GPU
+          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+
+      - name: Test 13_NAO_multik_GPU
+        run: |
+          cd tests/13_NAO_multik_GPU
+          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+
+      - name: Test 15_rtTDDFT_GPU
+        run: |
+          cd tests/15_rtTDDFT_GPU
+          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+
+      - name: Test 16_SDFT_GPU
+        run: |
+          cd tests/16_SDFT_GPU
+          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt

.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_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_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.
@@ -48,9 +48,136 @@ jobs:
         run: |
           cmake --build build -j8
           cmake --install build
-      - name: Test
+
+      - name: Integrated Tests Preparation
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R integrated_test"
+
+      - name: Module_Base Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_BASE"
+      
+      - name: Module_IO Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_IO"
+
+      - name: Module_HSolver Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_HSOLVER"
+      
+      - name: Module_Cell Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_CELL"
+      
+      - name: Module_MD Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_MD"
+      
+      - name: Module_Psi Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_PSI"
+      
+      - name: Module_RI Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R MODULE_RI"
+
+      - name: 01_PW Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 01_PW"
+
+      - name: 02_NAO_Gamma Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 02_NAO_Gamma"
+
+      - name: 03_NAO_multik Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 03_NAO_multik"
+
+      - name: 04_LJ_DP Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 04_LJ_DP"
+
+      - name: 05_rtTDDFT Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 05_rtTDDFT"
+
+      - name: 06_SDFT Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 06_SDFT"
+
+      - name: 07_OFDFT Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 07_OFDFT"
+
+      - name: 08_EXX Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 08_EXX"
+
+      - name: 09_DeePKS Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 09_DeePKS"
+
+      - name: 10_others Test
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          cmake --build build --target test ARGS="-V --timeout 1700 -R 10_others"
+
+      - name: Other Unittests
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          cmake --build build --target test ARGS="-V --timeout 1700"
+          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|MODULE_PSI|MODULE_RI'"

.gitignore

@@ -17,9 +17,10 @@ STRU_READIN_ADJUST.cif
 build
 dist
 .idea
-toolchain.tar.gz
 time.json
 *.pyc
 __pycache__
 abacus.json
-*.npy
+*.npy
+toolchain/install/
+toolchain/abacus_env.sh

CMakeLists.txt

@@ -10,39 +10,43 @@ project(
   HOMEPAGE_URL "https://github.com/deepmodeling/abacus-develop"
   LANGUAGES CXX)
 
-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)
-option(USE_ROCM "Enable support to ROCm." OFF)
-option(USE_OPENMP "Enable OpenMP in ABACUS." ON)
+option(ENABLE_MPI "Enable MPI" ON)
+option(USE_OPENMP "Enable OpenMP" ON)
+option(USE_CUDA "Enable CUDA" OFF)
+option(USE_CUDA_MPI "Enable CUDA-aware MPI" OFF)
+option(USE_CUDA_ON_DCU "Enable CUDA on DCU" OFF)
+option(USE_ROCM "Enable ROCm" OFF)
+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_LCAO "Enable LCAO algorithm" ON)
+option(USE_ELPA "Enable ELPA for LCAO" ON)
+option(ENABLE_LIBRI "Enable LibRI for hybrid functional" OFF)
+option(ENABLE_LIBCOMM "Enable LibComm" OFF)
+option(ENABLE_PEXSI "Enable PEXSI for LCAO" OFF)
+
+option(BUILD_TESTING "Build unittests" OFF)
+option(DEBUG_INFO "Print message to debug" OFF)
 option(ENABLE_ASAN "Enable AddressSanitizer" OFF)
-option(BUILD_TESTING "Build ABACUS unit tests" OFF)
-option(INFO "Enable gathering of math library information" OFF)
-option(ENABLE_COVERAGE "Enable coverage build." OFF)
-option(ENABLE_LIBRI "Enable EXX with LibRI." OFF)
-option(ENABLE_LIBCOMM "Enable communicate with LibComm." OFF)
-option(ENABLE_PAW "Enable PAW calculation" OFF)
-option(ENABLE_MPI "Enable compilation with or without MPI." ON)
-option(USE_ELPA "Enable ELPA" ON)
-option(USE_ABACUS_LIBM "Build libmath from source to speed up." OFF)
+option(INFO "Enable gathering math library information" OFF)
+option(ENABLE_COVERAGE "Enable coverage build" OFF)
 option(GIT_SUBMODULE "Check submodules during build" ON)
-option(DEBUG_INFO "Print message for developers to debug." OFF)
+
 # Do not enable it if generated code will run on different CPUs
 option(ENABLE_NATIVE_OPTIMIZATION
        "Enable compilation optimization for the native machine's CPU type" OFF)
+
 option(COMMIT_INFO "Print commit information in log" ON)
-option(ENABLE_FFT_TWO_CENTER "Enable FFT-based two-center integral method." ON)
-option(ENABLE_GOOGLEBENCH "Enable GOOGLE-benchmark usage." OFF)
-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)
+option(ENABLE_FFT_TWO_CENTER "Enable FFT-based two-center integral method" ON)
+option(ENABLE_GOOGLEBENCH "Enable GOOGLE-benchmark usage" OFF)
+option(ENABLE_RAPIDJSON "Enable rapid-json usage" OFF)
+option(ENABLE_CNPY "Enable cnpy usage" OFF)
+option(ENABLE_CUSOLVERMP "Enable cusolvermp" OFF)
 
 # enable json support
 if(ENABLE_RAPIDJSON)
@@ -108,11 +112,13 @@ You can install Git first and reinstall abacus.")
   endif()
 endif()
 
+# Serial version of ABACUS will not use ELPA
 if(NOT ENABLE_MPI)
   set(USE_ELPA OFF)
   set(ENABLE_DEEPKS OFF)
 endif()
 
+# Different exe files of ABACUS
 if(ENABLE_LCAO AND ENABLE_MPI)
   set(ABACUS_BIN_NAME abacus)
 elseif(NOT ENABLE_LCAO AND ENABLE_MPI)
@@ -123,6 +129,7 @@ elseif(ENABLE_LCAO AND NOT ENABLE_MPI)
   set(ABACUS_BIN_NAME abacus_serial)
 endif()
 
+# Use DSP hardware
 if (USE_DSP)
   set(USE_ELPA OFF)
   set(ENABLE_LCAO OFF)
@@ -181,6 +188,7 @@ find_program(CCACHE ccache)
 if(CCACHE)
   set(CMAKE_CXX_COMPILER_LAUNCHER ${CCACHE} ${CMAKE_CXX_COMPILER_LAUNCHER})
   set(CMAKE_C_COMPILER_LAUNCHER ${CCACHE} ${CMAKE_C_COMPILER_LAUNCHER})
+  set(CMAKE_CUDA_COMPILER_LAUNCHER ${CCACHE} ${CMAKE_CUDA_COMPILER_LAUNCHER})
 endif()
 
 # Choose build type from: Debug Release RelWithDebInfo MinSizeRel Select
@@ -206,7 +214,7 @@ if(CMAKE_CXX_COMPILER_ID MATCHES Intel)
   add_compile_options(-fp-model=strict)
   set(USE_ABACUS_LIBM OFF) # Force turn off USE_ABACUS_LIBM on Intel Compiler
   set(CMAKE_CXX_FLAGS
-      "${CMAKE_CXX_FLAGS} -Wno-write-strings -Wno-tautological-constant-compare"
+      "${CMAKE_CXX_FLAGS} -Wno-write-strings "
   )
 endif()
 
@@ -261,6 +269,7 @@ 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})
@@ -352,9 +361,19 @@ if(USE_CUDA)
     endif()
     if (ENABLE_CUSOLVERMP)
       add_compile_definitions(__CUSOLVERMP)
+      find_library(CAL_LIBRARY
+          NAMES cal
+          PATHS ${CAL_CUSOLVERMP_PATH}
+          NO_DEFAULT_PATH
+      )
+      find_library(CUSOLVERMP_LIBRARY
+          NAMES cusolverMp
+          PATHS ${CAL_CUSOLVERMP_PATH}
+          NO_DEFAULT_PATH
+      )
       target_link_libraries(${ABACUS_BIN_NAME}
-          cal
-          cusolverMp
+          ${CAL_LIBRARY}
+          ${CUSOLVERMP_LIBRARY}
       )
     endif()
   endif()
@@ -591,18 +610,7 @@ if(ENABLE_LIBCOMM)
   include_directories(${LIBCOMM_DIR}/include)
 endif()
 
-if(ENABLE_PAW)
-  if(LIBPAW_DIR)
-    add_subdirectory(${LIBPAW_DIR})
-  elseif(GIT_SUBMODULE)
-    git_submodule_update()
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/deps/libpaw_interface)
-  else()
-    message(FATAL_ERROR "Must provide LIBPAW_DIR for PAW related features.")
-  endif()
-  target_link_libraries(${ABACUS_BIN_NAME} paw)
-  add_compile_definitions(USE_PAW)
-endif()
+
 
 list(APPEND math_libs m)
 target_link_libraries(${ABACUS_BIN_NAME} ${math_libs})
@@ -778,4 +786,4 @@ install(PROGRAMS ${ABACUS_BIN_PATH}
 
 if(ENABLE_COVERAGE)
   coverage_evaluate()
-endif()
+endif()

Dockerfile.intel

@@ -44,6 +44,9 @@ RUN source /opt/intel/oneapi/setvars.sh && \
     ln -s /usr/local/include/elpa_openmp-$ELPA_VER/elpa /usr/local/include/ && \
     cd /tmp && rm -rf elpa-$ELPA_VER
 
+RUN cd /tmp && git clone https://github.com/Tencent/rapidjson.git && cp -r rapidjson/include/rapidjson /usr/include/ \
+    && rm -rf rapidjson
+
 RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip \
         --no-check-certificate --quiet -O libtorch.zip && \
     unzip -q libtorch.zip -d /opt  && rm libtorch.zip

README.md

@@ -12,7 +12,7 @@
 
 # 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, DeePTB etc.) in molecular and material simulations.
+ABACUS (**A**tomic-orbital **B**ased **A**b-initio **C**omputation at **US**tc) 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 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/).