diff --git a/.github/workflows/check-vla.yml b/.github/workflows/check-vla.yml new file mode 100644 index 0000000000..26f23cc33f --- /dev/null +++ b/.github/workflows/check-vla.yml @@ -0,0 +1,89 @@ +# GitHub action to build LAMMPS on Linux with gcc and -Werror=vla +name: "Check for Variable Length Arrays" + +on: + push: + branches: + - develop + pull_request: + branches: + - develop + + workflow_dispatch: + +jobs: + build: + name: Build with -Werror=vla + if: ${{ github.repository == 'lammps/lammps' }} + runs-on: ubuntu-latest + env: + CCACHE_DIR: ${{ github.workspace }}/.ccache + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + fetch-depth: 2 + + - name: Install extra packages + run: | + sudo apt-get install -y ccache \ + libeigen3-dev \ + libgsl-dev \ + libcurl4-openssl-dev \ + mold \ + mpi-default-bin \ + mpi-default-dev \ + ninja-build \ + python3-dev + + - name: Create Build Environment + run: mkdir build + + - name: Set up ccache + uses: actions/cache@v4 + with: + path: ${{ env.CCACHE_DIR }} + key: linux-vla-ccache-${{ github.sha }} + restore-keys: linux-vla-ccache- + + - name: Building LAMMPS via CMake + shell: bash + run: | + ccache -z + python3 -m venv linuxenv + source linuxenv/bin/activate + python3 -m pip install numpy + python3 -m pip install pyyaml + cmake -S cmake -B build \ + -C cmake/presets/most.cmake \ + -D CMAKE_CXX_COMPILER=g++ \ + -D CMAKE_C_COMPILER=gcc \ + -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -D CMAKE_C_COMPILER_LAUNCHER=ccache \ + -D CMAKE_BUILD_TYPE=Debug \ + -D CMAKE_CXX_FLAGS_DEBUG="-Og -g -Werror=vla" \ + -D DOWNLOAD_POTENTIALS=off \ + -D BUILD_MPI=on \ + -D BUILD_SHARED_LIBS=off \ + -D BUILD_TOOLS=off \ + -D ENABLE_TESTING=off \ + -D MLIAP_ENABLE_ACE=on \ + -D MLIAP_ENABLE_PYTHON=off \ + -D PKG_AWPMD=on \ + -D PKG_GPU=on \ + -D GPU_API=opencl \ + -D PKG_LATBOLTZ=on \ + -D PKG_MDI=on \ + -D PKG_MANIFOLD=on \ + -D PKG_ML-PACE=on \ + -D PKG_ML-RANN=off \ + -D PKG_MOLFILE=on \ + -D PKG_RHEO=on \ + -D PKG_PTM=on \ + -D PKG_PYTHON=on \ + -D PKG_QTB=on \ + -D PKG_SMTBQ=on \ + -G Ninja + cmake --build build + ccache -s diff --git a/.github/workflows/compile-msvc.yml b/.github/workflows/compile-msvc.yml index 1a0f1ea62f..e384f191e5 100644 --- a/.github/workflows/compile-msvc.yml +++ b/.github/workflows/compile-msvc.yml @@ -1,5 +1,5 @@ # GitHub action to build LAMMPS on Windows with Visual C++ -name: "Native Windows Compilation and Unit Tests" +name: "Windows Unit Tests" on: push: @@ -16,6 +16,8 @@ jobs: name: Windows Compilation Test if: ${{ github.repository == 'lammps/lammps' }} runs-on: windows-latest + env: + CCACHE_DIR: ${{ github.workspace }}/.ccache steps: - name: Checkout repository @@ -23,36 +25,41 @@ jobs: with: fetch-depth: 2 + - name: Enable MSVC++ + uses: lammps/setup-msvc-dev@v3 + with: + arch: x64 + + - name: Install Ccache + run: | + choco install ccache ninja -y + + - name: Set up ccache + uses: actions/cache@v4 + with: + path: ${{ env.CCACHE_DIR }} + key: win-unit-ccache-${{ github.sha }} + restore-keys: win-unit-ccache- + - name: Select Python version uses: actions/setup-python@v5 with: python-version: '3.11' - name: Building LAMMPS via CMake - shell: bash run: | + ccache -z python3 -m pip install numpy python3 -m pip install pyyaml - nuget install MSMPIsdk - nuget install MSMPIDIST - cmake -C cmake/presets/windows.cmake \ - -D DOWNLOAD_POTENTIALS=off \ - -D PKG_PYTHON=on \ - -D WITH_PNG=off \ - -D WITH_JPEG=off \ - -S cmake -B build \ - -D BUILD_SHARED_LIBS=on \ - -D LAMMPS_EXCEPTIONS=on \ - -D ENABLE_TESTING=on - cmake --build build --config Release --parallel 2 + cmake -C cmake\presets\windows.cmake -D CMAKE_CXX_COMPILER=cl -D CMAKE_CXX_COMPILER_LAUNCHER=ccache -D CMAKE_C_COMPILER=cl -D CMAKE_C_COMPILER_LAUNCHER=ccache -D CMAKE_Fortran_COMPILER="" -D DOWNLOAD_POTENTIALS=off -D PKG_PYTHON=on -D WITH_PNG=off -D WITH_JPEG=off -S cmake -B build -D BUILD_SHARED_LIBS=on -D ENABLE_TESTING=on -D CMAKE_BUILD_TYPE=Release -G Ninja + cmake --build build + ccache -s - name: Run LAMMPS executable - shell: bash run: | - ./build/Release/lmp.exe -h - ./build/Release/lmp.exe -in bench/in.lj + build\lmp.exe -h + build\lmp.exe -in bench\in.lj - name: Run Unit Tests working-directory: build - shell: bash - run: ctest -V -C Release -E FixTimestep:python_move_nve + run: ctest -V -E FixTimestep:python_move_nve diff --git a/.github/workflows/unittest-linux.yml b/.github/workflows/unittest-linux.yml new file mode 100644 index 0000000000..366db25a99 --- /dev/null +++ b/.github/workflows/unittest-linux.yml @@ -0,0 +1,82 @@ +# GitHub action to build LAMMPS on Linux and run standard unit tests +name: "Unittest for Linux /w LAMMPS_BIGBIG" + +on: + push: + branches: + - develop + pull_request: + branches: + - develop + + workflow_dispatch: + +jobs: + build: + name: Linux Unit Test + if: ${{ github.repository == 'lammps/lammps' }} + runs-on: ubuntu-latest + env: + CCACHE_DIR: ${{ github.workspace }}/.ccache + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + fetch-depth: 2 + + - name: Install extra packages + run: | + sudo apt-get install -y ccache \ + libeigen3-dev \ + libgsl-dev \ + libcurl4-openssl-dev \ + mold \ + ninja-build \ + python3-dev + + - name: Create Build Environment + run: mkdir build + + - name: Set up ccache + uses: actions/cache@v4 + with: + path: ${{ env.CCACHE_DIR }} + key: linux-unit-ccache-${{ github.sha }} + restore-keys: linux-unit-ccache- + + - name: Building LAMMPS via CMake + shell: bash + run: | + ccache -z + python3 -m venv linuxenv + source linuxenv/bin/activate + python3 -m pip install numpy + python3 -m pip install pyyaml + cmake -S cmake -B build \ + -C cmake/presets/gcc.cmake \ + -C cmake/presets/most.cmake \ + -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \ + -D CMAKE_C_COMPILER_LAUNCHER=ccache \ + -D BUILD_SHARED_LIBS=on \ + -D LAMMPS_SIZES=bigbig \ + -D DOWNLOAD_POTENTIALS=off \ + -D ENABLE_TESTING=on \ + -D MLIAP_ENABLE_ACE=on \ + -D MLIAP_ENABLE_PYTHON=off \ + -D PKG_MANIFOLD=on \ + -D PKG_ML-PACE=on \ + -D PKG_ML-RANN=on \ + -D PKG_RHEO=on \ + -D PKG_PTM=on \ + -D PKG_PYTHON=on \ + -D PKG_QTB=on \ + -D PKG_SMTBQ=on \ + -G Ninja + cmake --build build + ccache -s + + - name: Run Tests + working-directory: build + shell: bash + run: ctest -V diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 723015c1f9..c68a925324 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -474,13 +474,13 @@ if(BUILD_OMP) if(CMAKE_VERSION VERSION_LESS 3.28) get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME) if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC")) - set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp") - set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp") + set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp") + set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp") endif() else() if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") - set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp") - set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp") + set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp") + set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp") endif() endif() endif() @@ -515,14 +515,6 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T endif() endif() -find_package(CURL QUIET COMPONENTS HTTP HTTPS) -option(WITH_CURL "Enable libcurl support" ${CURL_FOUND}) -if(WITH_CURL) - find_package(CURL REQUIRED COMPONENTS HTTP HTTPS) - target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL) - target_link_libraries(lammps PRIVATE CURL::libcurl) -endif() - # tweak jpeg library names to avoid linker errors with MinGW cross-compilation set(JPEG_NAMES libjpeg libjpeg-62) find_package(JPEG QUIET) @@ -580,7 +572,7 @@ else() endif() foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF - PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO) + PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO EXTRA-COMMAND) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() @@ -973,6 +965,9 @@ message(STATUS "<<< Compilers and Flags: >>> C++ Standard: ${CMAKE_CXX_STANDARD} C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} Defines: ${DEFINES}") +if(CMAKE_CXX_COMPILER_LAUNCHER) + message(STATUS " Launcher: ${CMAKE_CXX_COMPILER_LAUNCHER}") +endif() get_target_property(OPTIONS lammps COMPILE_OPTIONS) if(OPTIONS) message(" Options: ${OPTIONS}") @@ -991,6 +986,9 @@ if(_index GREATER -1) Type: ${CMAKE_C_COMPILER_ID} Version: ${CMAKE_C_COMPILER_VERSION} C Flags: ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}") + if(CMAKE_C_COMPILER_LAUNCHER) + message(STATUS " Launcher: ${CMAKE_C_COMPILER_LAUNCHER}") + endif() endif() message(STATUS "<<< Linker flags: >>>") message(STATUS "Executable name: ${LAMMPS_BINARY}") diff --git a/cmake/Modules/Packages/EXTRA-COMMAND.cmake b/cmake/Modules/Packages/EXTRA-COMMAND.cmake new file mode 100644 index 0000000000..13c98bafd3 --- /dev/null +++ b/cmake/Modules/Packages/EXTRA-COMMAND.cmake @@ -0,0 +1,10 @@ +# the geturl command needs libcurl + +find_package(CURL QUIET COMPONENTS HTTP HTTPS) +option(WITH_CURL "Enable libcurl support" ${CURL_FOUND}) +if(WITH_CURL) + find_package(CURL REQUIRED COMPONENTS HTTP HTTPS) + target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL) + target_link_libraries(lammps PRIVATE CURL::libcurl) +endif() + diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 3776d18a3e..bf0a18d324 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -127,7 +127,7 @@ if(PKG_KSPACE) ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package") - set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT) + set(FFT_KOKKOS_VALUES KISS FFTW3 MKL NVPL HIPFFT CUFFT MKL_GPU) set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES}) validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES) string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS) @@ -137,10 +137,8 @@ if(PKG_KSPACE) message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.") elseif(FFT_KOKKOS STREQUAL "KISS") message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.") - target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS) elseif(FFT_KOKKOS STREQUAL "CUFFT") find_package(CUDAToolkit REQUIRED) - target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT) target_link_libraries(lammps PRIVATE CUDA::cufft) endif() elseif(Kokkos_ENABLE_HIP) @@ -152,10 +150,21 @@ if(PKG_KSPACE) elseif(FFT_KOKKOS STREQUAL "HIPFFT") include(DetectHIPInstallation) find_package(hipfft REQUIRED) - target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT) target_link_libraries(lammps PRIVATE hip::hipfft) endif() + elseif(FFT_KOKKOS STREQUAL "MKL_GPU") + if(NOT Kokkos_ENABLE_SYCL) + message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.") + endif() + find_package(MKL REQUIRED) + target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb) + elseif(FFT_KOKKOS STREQUAL "MKL") + find_package(MKL REQUIRED) + elseif(FFT_KOKKOS STREQUAL "NVPL") + find_package(nvpl_fft REQUIRED) + target_link_libraries(lammps PRIVATE nvpl::fftw) endif() + target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${FFT_KOKKOS}) endif() if(PKG_ML-IAP) diff --git a/cmake/Modules/Packages/KSPACE.cmake b/cmake/Modules/Packages/KSPACE.cmake index 1fdd898144..3801140fe0 100644 --- a/cmake/Modules/Packages/KSPACE.cmake +++ b/cmake/Modules/Packages/KSPACE.cmake @@ -10,7 +10,7 @@ if(${FFTW}_FOUND) else() set(FFT "KISS" CACHE STRING "FFT library for KSPACE package") endif() -set(FFT_VALUES KISS FFTW3 MKL) +set(FFT_VALUES KISS FFTW3 MKL NVPL) set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES}) validate_option(FFT FFT_VALUES) string(TOUPPER ${FFT} FFT) @@ -41,6 +41,10 @@ elseif(FFT STREQUAL "MKL") target_compile_definitions(lammps PRIVATE -DFFT_MKL_THREADS) endif() target_link_libraries(lammps PRIVATE MKL::MKL) +elseif(FFT STREQUAL "NVPL") + find_package(nvpl_fft REQUIRED) + target_compile_definitions(lammps PRIVATE -DFFT_NVPL) + target_link_libraries(lammps PRIVATE nvpl::fftw) else() # last option is KISSFFT target_compile_definitions(lammps PRIVATE -DFFT_KISS) diff --git a/cmake/Modules/Packages/PLUMED.cmake b/cmake/Modules/Packages/PLUMED.cmake index 595b6824c1..8dab157a24 100644 --- a/cmake/Modules/Packages/PLUMED.cmake +++ b/cmake/Modules/Packages/PLUMED.cmake @@ -32,9 +32,9 @@ endif() # Note: must also adjust check for supported API versions in # fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y -set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz" +set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz" CACHE STRING "URL for PLUMED tarball") -set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball") +set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball") mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) diff --git a/cmake/presets/kokkos-sycl-intel.cmake b/cmake/presets/kokkos-sycl-intel.cmake new file mode 100644 index 0000000000..3fc75e4b2d --- /dev/null +++ b/cmake/presets/kokkos-sycl-intel.cmake @@ -0,0 +1,18 @@ +# preset that enables KOKKOS and selects SYCL compilation with OpenMP +# enabled as well. Also sets some performance related compiler flags. +set(PKG_KOKKOS ON CACHE BOOL "" FORCE) +set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE) +set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE) +set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "" FORCE) +set(Kokkos_ENABLE_SYCL ON CACHE BOOL "" FORCE) + +# hide deprecation warnings temporarily for stable release +set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE) + +set(CMAKE_CXX_COMPILER icpx CACHE STRING "" FORCE) +set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) +set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE) +# Silence everything +set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE) +set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-max-parallel-link-jobs=32 -fsycl-targets=spir64_gen -Xsycl-target-backend \"-device 12.60.7\" " CACHE STRING "" FORCE) +set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE) diff --git a/cmake/presets/kokkos-sycl.cmake b/cmake/presets/kokkos-sycl-nvidia.cmake similarity index 100% rename from cmake/presets/kokkos-sycl.cmake rename to cmake/presets/kokkos-sycl-nvidia.cmake diff --git a/doc/msi2lmp.1 b/doc/msi2lmp.1 index 5cb0754e4f..075e25e3b9 100644 --- a/doc/msi2lmp.1 +++ b/doc/msi2lmp.1 @@ -1,4 +1,4 @@ -.TH MSI2LMP "1" "v3.9.10" "2023-03-10" +.TH MSI2LMP "1" "v3.9.11" "2024-09-06" .SH NAME .B MSI2LMP \- Converter for Materials Studio files to LAMMPS @@ -101,7 +101,7 @@ msi2lmp decane -c 0 -f oplsaa .SH COPYRIGHT -© 2003--2022 Sandia Corporation +© 2003--2024 Sandia Corporation This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index 9cd938280b..f315569b24 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -630,11 +630,35 @@ The following target are available for both, GNU make and CMake: GitHub command line interface ----------------------------- -GitHub is developing a `tool for the command line -`_ that interacts with the GitHub website via a -command called ``gh``. This can be extremely convenient when working -with a Git repository hosted on GitHub (like LAMMPS). It is thus highly -recommended to install it when doing LAMMPS development. +GitHub has developed a `command line tool `_ +to interact with the GitHub website via a command called ``gh``. +This is extremely convenient when working with a Git repository hosted +on GitHub (like LAMMPS). It is thus highly recommended to install it +when doing LAMMPS development. To use ``gh`` you must be within a git +checkout of a repository and you must obtain an authentication token +to connect your checkout with a GitHub user. This is done with the +command: ``gh auth login`` where you then have to follow the prompts. +Here are some examples: -The capabilities of the ``gh`` command is continually expanding, so -please see the documentation at https://cli.github.com/manual/ +.. list-table:: + :header-rows: 1 + :widths: 34 66 + + * - Command + - Description + * - ``gh pr list`` + - List currently open pull requests + * - ``gh pr checks 404`` + - Shows the status of all checks for pull request #404 + * - ``gh pr view 404`` + - Shows the description and recent comments for pull request #404 + * - ``gh co 404`` + - Check out the branch from pull request #404; set up for pushing changes + * - ``gh issue list`` + - List currently open issues + * - ``gh issue view 430 --comments`` + - Shows the description and all comments for issue #430 + +The capabilities of the ``gh`` command are continually expanding, so +for more details please see the documentation at https://cli.github.com/manual/ +or use ``gh --help`` or ``gh --help`` for embedded help. diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 1dd64b3160..ac7edc7678 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -7,6 +7,8 @@ in addition to .. list-table:: :align: center :header-rows: 1 + :widths: 50 50 + :width: 80% * - CMake build - Traditional make @@ -115,7 +117,7 @@ GPU package To build with this package, you must choose options for precision and which GPU hardware to build for. The GPU package currently supports -three different types of backends: OpenCL, CUDA and HIP. +three different types of back ends: OpenCL, CUDA and HIP. CMake build ^^^^^^^^^^^ @@ -205,7 +207,7 @@ necessary for ``hipcc`` and the linker to work correctly. .. versionadded:: 3Aug2022 Using the CHIP-SPV implementation of HIP is supported. It allows one to -run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use +run HIP code on Intel GPUs via the OpenCL or Level Zero back ends. To use CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022, the use of HIP for Intel GPUs is experimental. You should only use this @@ -751,14 +753,27 @@ This list was last updated for version 4.3.0 of the Kokkos library. platform-appropriate vendor library: rocFFT on AMD GPUs or cuFFT on NVIDIA GPUs. - To simplify compilation, five preset files are included in the + For Intel GPUs using SYCL, set these variables: + + .. code-block:: bash + + -D Kokkos_ARCH_HOSTARCH=yes # HOSTARCH = HOST from list above + -D Kokkos_ARCH_GPUARCH=yes # GPUARCH = GPU from list above + -D Kokkos_ENABLE_SYCL=yes + -D Kokkos_ENABLE_OPENMP=yes + -D FFT_KOKKOS=MKL_GPU + + This will enable FFTs on the GPU using the oneMKL library. + + To simplify compilation, six preset files are included in the ``cmake/presets`` folder, ``kokkos-serial.cmake``, ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``, - ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``. They will enable - the KOKKOS package and enable some hardware choices. For GPU - support those preset files must be customized to match the - hardware used. So to compile with CUDA device parallelization with - some common packages enabled, you can do the following: + ``kokkos-hip.cmake``, ``kokkos-sycl-nvidia.cmake``, and + ``kokkos-sycl-intel.cmake``. They will enable the KOKKOS + package and enable some hardware choices. For GPU support those + preset files must be customized to match the hardware used. So + to compile with CUDA device parallelization with some common + packages enabled, you can do the following: .. code-block:: bash @@ -830,6 +845,18 @@ This list was last updated for version 4.3.0 of the Kokkos library. FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional) FFT_LIB = -lhipfft # link to hipFFT library + For Intel GPUs using SYCL: + + .. code-block:: make + + KOKKOS_DEVICES = SYCL + KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is + # hosting the GPU + # GPUARCH = GPU from list above + FFT_INC = -DFFT_KOKKOS_MKL_GPU # enable use of oneMKL for Intel GPUs (optional) + # link to oneMKL FFT library + FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -mkl_core -ltbb + Advanced KOKKOS compilation settings ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 9d31f6b431..2787560be5 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -67,10 +67,10 @@ libraries and better pipelining for packing and communication. .. code-block:: bash - -D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, - # else KISS - -D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, - # default is KISS + -D FFT=value # FFTW3 or MKL or NVPL or KISS, + # default is FFTW3 if found, else KISS + -D FFT_KOKKOS=value # FFTW3 or MKL or NVPL or KISS or CUFFT + # or HIPFFT or MKL_GPU, default is KISS -D FFT_SINGLE=value # yes or no (default), no = double precision -D FFT_PACK=value # array (default) or pointer or memcpy -D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe @@ -103,6 +103,8 @@ libraries and better pipelining for packing and communication. -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock # heFFTe back end -D Heffte_ROOT=path # path to an existing heFFTe installation + -D nvpl_fft_INCLUDE_DIR=path # path to NVPL FFT include files + -D nvpl_fft_LIBRARY_DIR=path # path to NVPL FFT libraries .. note:: @@ -121,9 +123,10 @@ libraries and better pipelining for packing and communication. .. code-block:: make FFT_INC = -DFFT_ # where is KISS (default), FFTW3, - # FFTW (same as FFTW3), or MKL + # FFTW (same as FFTW3), NVPL, or MKL FFT_INC = -DFFT_KOKKOS_ # where is KISS (default), FFTW3, - # FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT + # FFTW (same as FFTW3), NVPL, MKL, CUFFT, + # HIPFFT, or MKL_GPU FFT_INC = -DFFT_SINGLE # do not specify for double precision FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries @@ -141,6 +144,9 @@ libraries and better pipelining for packing and communication. # cuFFT either precision FFT_LIB = -lcufft + # MKL_GPU either precision + FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -ltbb + # FFTW3 double precision FFT_LIB = -lfftw3 @@ -165,6 +171,10 @@ libraries and better pipelining for packing and communication. # MKL with automatic runtime selection of interface libs FFT_LIB = -lmkl_rt + # threaded NVPL FFT + FFT_LIB = -lnvpl_fftw + + As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if the compiler can find the FFT header and library files in its default search path. You must specify ``FFT_LIB`` @@ -218,10 +228,16 @@ The Intel MKL math library is part of the Intel compiler suite. It can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting above). +The NVIDIA Performance Libraries (NVPL) FFT library is optimized for NVIDIA +Grace Armv9.0 architecture. You can download it from +`https://docs.nvidia.com/nvpl/`_. + The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and AMD's HIP installations, respectively. These FFT libraries require the Kokkos acceleration package to be enabled and the Kokkos back end to be -GPU-resident (i.e., HIP or CUDA). +GPU-resident (i.e., HIP or CUDA). Similarly, GPU offload of FFTs on +Intel GPUs with oneMKL currently requires the Kokkos acceleration +package to be enabled with the SYCL back end. Performing 3d FFTs in parallel can be time-consuming due to data access and required communication. This cost can be reduced by performing diff --git a/doc/src/Developer_write.rst b/doc/src/Developer_write.rst index ef4d06a5f6..54b1b6eb81 100644 --- a/doc/src/Developer_write.rst +++ b/doc/src/Developer_write.rst @@ -12,3 +12,4 @@ details are provided for writing code for LAMMPS. Developer_write_pair Developer_write_fix + Developer_write_command diff --git a/doc/src/Developer_write_command.rst b/doc/src/Developer_write_command.rst new file mode 100644 index 0000000000..16ac2092f6 --- /dev/null +++ b/doc/src/Developer_write_command.rst @@ -0,0 +1,348 @@ +Writing a new command style +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Command styles allow to do system manipulations or interfaces to the +operating system. + +In the text below, we will discuss the implementation of one example. As +shown on the page for :doc:`writing or extending command styles +`, in order to implement a new command style, a new class +must be written that is either directly or indirectly derived from the +``Command`` class. There is just one method that must be implemented: +``Command::command()``. In addition, a custom constructor is needed to get +access to the members of the ``LAMMPS`` class like the ``Error`` class to +print out error messages. The ``Command::command()`` method processes the +arguments passed to the command in the input and executes it. Any other +methods would be for the convenience of implementation of the new command. + +In general, new command styles should be added to the :ref:`EXTRA-COMMAND +package `. If you feel that your contribution should be +added to a different package, please consult with the :doc:`LAMMPS +developers ` first. The contributed code needs to support +the :doc:`traditional GNU make build process ` **and** the +:doc:`CMake build process `. + +---- + +Case 1: Implementing the geturl command +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +In this section, we will describe the procedure of adding a simple command +style to LAMMPS: the :doc:`geturl command ` that allows to download +files directly without having to rely on an external program like "wget" or +"curl". The complete implementation can be found in the files +``src/EXTRA-COMMAND/geturl.cpp`` and ``src/EXTRA-COMMAND/geturl.h`` of the +LAMMPS source code. + +Interfacing the *libcurl* library +""""""""""""""""""""""""""""""""" + +Rather than implementing the various protocols for downloading files, we +rely on an external library: `libcurl library `_. +This requires that the library and its headers are installed. For the +traditional GNU make build system, this simply requires edits to the machine +makefile to add compilation flags like for other libraries. For the CMake +based build system, we need to add some lines to the file +``cmake/Modules/Packages/EXTRA-COMMAND.cmake``: + +.. code-block:: cmake + + find_package(CURL QUIET COMPONENTS HTTP HTTPS) + option(WITH_CURL "Enable libcurl support" ${CURL_FOUND}) + if(WITH_CURL) + find_package(CURL REQUIRED COMPONENTS HTTP HTTPS) + target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL) + target_link_libraries(lammps PRIVATE CURL::libcurl) + endif() + +The first ``find_package()`` command uses a built-in CMake module to find +an existing *libcurl* installation with development headers and support for +using the HTTP and HTTPS protocols. The "QUIET" flag ensures that there is +no screen output and no error if the search fails. The status of the search +is recorded in the "${CURL_FOUND}" variable. That variable sets the default +of the WITH_CURL option, which toggles whether support for *libcurl* is included +or not. + +The second ``find_package()`` uses the "REQUIRED" flag to produce an error +if the WITH_CURL option was set to ``True``, but no suitable *libcurl* +implementation with development support was found. This construct is used +so that the CMake script code inside the ``if(WITH_CURL)`` and ``endif()`` +block can be expanded later to download and compile *libcurl* as part of the +LAMMPS build process, if it is not found locally. The +``target_compile_definitions()`` function added the define ``-DLAMMPS_CURL`` +to the compilation flags when compiling objects for the LAMMPS library. +This allows to always compile the :doc:`geturl command `, but use +pre-processing to compile in the interface to *libcurl* only when it is +present and usable and otherwise stop with an error message about the +unavailability of *libcurl* to execute the functionality of the command. + +Header file +""""""""""" + +The first segment of any LAMMPS source should be the copyright and +license statement. Note the marker in the first line to indicate to +editors like emacs that this file is a C++ source, even though the .h +extension suggests a C source (this is a convention inherited from the +very beginning of the C++ version of LAMMPS). + +.. code-block:: c++ + + /* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +Every command style must be registered in LAMMPS by including the following +lines of code in the second part of the header after the copyright +message and before the include guards for the class definition: + +.. code-block:: c++ + + #ifdef COMMAND_CLASS + // clang-format off + CommandStyle(geturl,GetURL); + // clang-format on + #else + +This block between ``#ifdef COMMAND_CLASS`` and ``#else`` will be +included by the ``Input`` class in ``input.cpp`` to build a map of +"factory functions" that will create an instance of a Command class +and call its ``command()`` method. The map connects the name of the +command ``geturl`` with the name of the class ``GetURL``. During +compilation, LAMMPS constructs a file ``style_command.h`` that contains +``#include`` statements for all "installed" command styles. Before +including ``style_command.h`` into ``input.cpp``, the ``COMMAND_CLASS`` +define is set and the ``CommandStyle(name,class)`` macro defined. The +code of the macro adds the installed command styles to the "factory map" +which enables the ``Input`` to execute the command. + +The list of header files to include in ``style_command.h`` is automatically +updated by the build system if there are new files, so the presence of the +new header file in the ``src/EXTRA-COMMAND`` folder and the enabling of the +EXTRA-COMMAND package will trigger LAMMPS to include the new command style +when it is (re-)compiled. The "// clang-format" format comments are needed +so that running :ref:`clang-format ` on the file will not +insert unwanted blanks which would break the ``CommandStyle`` macro. + +The third part of the header file is the actual class definition of the +``GetURL`` class. This has the custom constructor and the ``command()`` +method implemented by this command style. For the constructor there is +nothing to do but to pass the ``lmp`` pointer to the base class. Since the +``command()`` method is labeled "virtual" in the base class, it must be +given the "override" property. + +.. code-block:: c++ + + #ifndef LMP_GETURL_H + #define LMP_GETURL_H + + #include "command.h" + + namespace LAMMPS_NS { + + class GetURL : public Command { + public: + GetURL(class LAMMPS *lmp) : Command(lmp) {}; + void command(int, char **) override; + }; + } // namespace LAMMPS_NS + #endif + #endif + +The "override" property helps to detect unexpected mismatches because +compilation will stop with an error in case the signature of a function +is changed in the base class without also changing it in all derived +classes. + +Implementation file +""""""""""""""""""" + +We move on to the implementation of the ``GetURL`` class in the +``geturl.cpp`` file. This file also starts with a LAMMPS copyright and +license header. Below that notice is typically the space where comments may +be added with additional information about this specific file, the +author(s), affiliation(s), and email address(es). This way the contributing +author(s) can be easily contacted, when there are questions about the +implementation later. Since the file(s) may be around for a long time, it +is beneficial to use some kind of "permanent" email address, if possible. + +.. code-block:: c++ + + /* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + + /* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + ------------------------------------------------------------------------- */ + + #include "geturl.h" + + #include "comm.h" + #include "error.h" + + #if defined(LAMMPS_CURL) + #include + #endif + + using namespace LAMMPS_NS; + +The second section of the implementation file has various include +statements. The include file for the class header has to come first, then a +couple of LAMMPS classes (sorted alphabetically) followed by the header for +the *libcurl* interface. This is wrapped into an ``#ifdef`` block so that +LAMMPS will compile this file without error when the *libcurl* header is not +available and thus the define not set. The final statement of this segment +imports the ``LAMMPS_NS::`` namespace globally for this file. This way, all +LAMMPS specific functions and classes do not have to be prefixed with +``LAMMPS_NS::``. + +The command() function (required) +""""""""""""""""""""""""""""""""" + +Since the required custom constructor is trivial and implemented in the +header, there is only one function that must be implemented for a command +style and that is the ``command()`` function. + +.. code-block:: c++ + + void GetURL::command(int narg, char **arg) + { + #if !defined(LAMMPS_CURL) + error->all(FLERR, "LAMMPS has not been compiled with libcurl support"); + #else + if (narg < 1) utils::missing_cmd_args(FLERR, "geturl", error); + int verify = 1; + int overwrite = 1; + int verbose = 0; + +This first part also has the ``#ifdef`` block depending on the LAMMPS_CURL +define. This way the command will simply print an error, if *libcurl* is +not available but will not fail to compile. Furthermore, it sets the +defaults for the following optional arguments. + +.. code-block:: c++ + + // process arguments + + std::string url = arg[0]; + + // sanity check + + if ((url.find(':') == std::string::npos) || (url.find('/') == std::string::npos)) + error->all(FLERR, "URL '{}' is not a supported URL", url); + + std::string output = url.substr(url.find_last_of('/') + 1); + if (output.empty()) error->all(FLERR, "URL '{}' must end in a file string", url); + +This block stores the positional, i.e. non-optional argument of the URL to +be downloaded and adds a couple of sanity checks on the string to make sure it is +a valid URL. Also it derives the default name of the output file from the URL. + +.. code-block:: c++ + + int iarg = 1; + while (iarg < narg) { + if (strcmp(arg[iarg], "output") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl output", error); + output = arg[iarg + 1]; + ++iarg; + } else if (strcmp(arg[iarg], "overwrite") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl overwrite", error); + overwrite = utils::logical(FLERR, arg[iarg + 1], false, lmp); + ++iarg; + } else if (strcmp(arg[iarg], "verify") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl verify", error); + verify = utils::logical(FLERR, arg[iarg + 1], false, lmp); + ++iarg; + } else if (strcmp(arg[iarg], "verbose") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl verbose", error); + verbose = utils::logical(FLERR, arg[iarg + 1], false, lmp); + ++iarg; + } else { + error->all(FLERR, "Unknown geturl keyword: {}", arg[iarg]); + } + ++iarg; + } + +This block parses the optional arguments following the URL and stops with an +error if there are arguments missing or an unknown argument is encountered. + +.. code-block:: c++ + + // only download files from rank 0 + + if (comm->me != 0) return; + + if (!overwrite && platform::file_is_readable(output)) return; + + // open output file for writing + + FILE *out = fopen(output.c_str(), "wb"); + if (!out) + error->all(FLERR, "Cannot open output file {} for writing: {}", output, utils::getsyserror()); + +Here all MPI ranks other than 0 will return, so that the URL download will +only happen from a single MPI rank. For that rank the output file is opened +for writing using the C library function ``fopen()``. + +.. code-block:: c++ + + // initialize curl and perform download + + CURL *curl; + curl_global_init(CURL_GLOBAL_DEFAULT); + curl = curl_easy_init(); + if (curl) { + (void) curl_easy_setopt(curl, CURLOPT_URL, url.c_str()); + (void) curl_easy_setopt(curl, CURLOPT_WRITEDATA, (void *) out); + (void) curl_easy_setopt(curl, CURLOPT_FILETIME, 1L); + (void) curl_easy_setopt(curl, CURLOPT_FAILONERROR, 1L); + if (verbose && screen) { + (void) curl_easy_setopt(curl, CURLOPT_VERBOSE, 1L); + (void) curl_easy_setopt(curl, CURLOPT_STDERR, (void *) screen); + } + if (!verify) { + (void) curl_easy_setopt(curl, CURLOPT_SSL_VERIFYPEER, 0L); + (void) curl_easy_setopt(curl, CURLOPT_SSL_VERIFYHOST, 0L); + } + auto res = curl_easy_perform(curl); + if (res != CURLE_OK) { + long response = 0L; + curl_easy_getinfo(curl, CURLINFO_RESPONSE_CODE, &response); + error->one(FLERR, "Download of {} failed with: {} {}", output, curl_easy_strerror(res), + response); + } + curl_easy_cleanup(curl); + +This block now implements the actual URL download with the selected options +via the "easy" interface of *libcurl*. For the details of what these +function calls do, please have a look at the `*libcurl documentation +`_. + + .. code-block:: c++ + + } + curl_global_cleanup(); + fclose(out); + #endif + } + +Finally, the previously opened file is closed and the command is complete. diff --git a/doc/src/Developer_write_pair.rst b/doc/src/Developer_write_pair.rst index 1433effc54..5d5e081042 100644 --- a/doc/src/Developer_write_pair.rst +++ b/doc/src/Developer_write_pair.rst @@ -160,7 +160,7 @@ message and before the include guards for the class definition: #endif -This block of between ``#ifdef PAIR_CLASS`` and ``#else`` will be +This block between ``#ifdef PAIR_CLASS`` and ``#else`` will be included by the ``Force`` class in ``force.cpp`` to build a map of "factory functions" that will create an instance of these classes and return a pointer to it. The map connects the name of the pair style, diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst index 55e5b171a6..43aa519293 100644 --- a/doc/src/Howto_cmake.rst +++ b/doc/src/Howto_cmake.rst @@ -348,7 +348,7 @@ Some common LAMMPS specific variables * - ``FFT`` - select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found) * - ``FFT_KOKKOS`` - - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default) + - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``MKL_GPU``, ``KISS`` (default) * - ``FFT_SINGLE`` - select whether to use single precision FFTs (default: ``off``) * - ``WITH_JPEG`` diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index 5ef3248e1d..645434bbab 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -39,16 +39,18 @@ lammps.lammps * interface modeled after the LAMMPS :ref:`C language library interface API ` * requires knowledge of how LAMMPS internally works (C pointers, etc) * full support for running Python with MPI using `mpi4py `_ +* no overhead from creating a more Python-like interface lammps.PyLammps """"""""""""""" -* higher-level abstraction built on *top* of original :py:class:`ctypes based interface ` +* higher-level abstraction built on *top* of the original :py:class:`ctypes based interface ` * manipulation of Python objects * communication with LAMMPS is hidden from API user * shorter, more concise Python * better IPython integration, designed for quick prototyping * designed for serial execution +* additional overhead from capturing and parsing the LAMMPS screen output Quick Start ----------- diff --git a/doc/src/Library_atoms.rst b/doc/src/Library_atoms.rst index cebd8f0c2e..5ebfe04b37 100644 --- a/doc/src/Library_atoms.rst +++ b/doc/src/Library_atoms.rst @@ -4,6 +4,7 @@ Per-atom properties This section documents the following functions: - :cpp:func:`lammps_extract_atom_datatype` +- :cpp:func:`lammps_extract_atom_size` - :cpp:func:`lammps_extract_atom` ----------------------- @@ -13,6 +14,11 @@ This section documents the following functions: ----------------------- +.. doxygenfunction:: lammps_extract_atom_size + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_extract_atom :project: progguide diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 7e73f23b08..ce19ff9e38 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -18,28 +18,27 @@ Syntax .. code-block:: LAMMPS - pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof + pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutoff * style = *hbond/dreiding/lj* or *hbond/dreiding/morse* -* n = cosine angle periodicity +* N = power of cosine of angle theta (integer) * inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units) * outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units) -* angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor -* interactions (degrees) +* angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor interactions (degrees) Examples """""""" .. code-block:: LAMMPS - pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 + pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90.0 pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 - pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90 - pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 + pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90.0 + pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9.0 11.0 90.0 labelmap atom 1 C 2 O 3 H - pair_coeff C O hbond/dreiding/morse H i 3.88 1.7241379 2.9 2 9 11 90 + pair_coeff C O hbond/dreiding/morse H i 3.88 1.7241379 2.9 2 9.0 11.0 90.0 Description """"""""""" @@ -65,7 +64,8 @@ force field, given by: where :math:`r_{\rm in}` is the inner spline distance cutoff, :math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is -the angle cutoff, and *n* is the cosine periodicity. +the angle cutoff, and :math:`n` is the power of the cosine of the angle +:math:`\theta`. Here, *r* is the radial distance between the donor (D) and acceptor (A) atoms and :math:`\theta` is the bond angle between the acceptor, the @@ -217,7 +217,8 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles do not write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands need to be +These pair styles do not write their information to :doc:`binary restart +files `, so pair_style and pair_coeff commands need to be re-specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index cfbddbe5f6..3a714ffdd6 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -215,7 +215,6 @@ ba Babadi Babaei backcolor -backends Baczewski Bagchi Bagi @@ -1539,6 +1538,7 @@ idx ie ielement ieni +ifdef ifdefs iff ifort @@ -2725,6 +2725,7 @@ OMP oneAPI onebody onelevel +oneMKL oneway onlysalt ons diff --git a/examples/COUPLE/plugin/liblammpsplugin.c b/examples/COUPLE/plugin/liblammpsplugin.c index 50ad2f5192..c8a38c21e4 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.c +++ b/examples/COUPLE/plugin/liblammpsplugin.c @@ -105,6 +105,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(map_atom); ADDSYM(extract_atom_datatype); + ADDSYM(extract_atom_size); ADDSYM(extract_atom); ADDSYM(extract_compute); diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h index 556718816c..b444f75215 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.h +++ b/examples/COUPLE/plugin/liblammpsplugin.h @@ -151,6 +151,7 @@ struct _liblammpsplugin { int (*map_atom)(void *, const void *); int (*extract_atom_datatype)(void *, const char *); + int (*extract_atom_size)(void *, const char *, int); void *(*extract_atom)(void *, const char *); void *(*extract_compute)(void *, const char *, int, int); diff --git a/examples/PACKAGES/pace/plugin/CMakeLists.txt b/examples/PACKAGES/pace/plugin/CMakeLists.txt index 0701a754c4..ede63e3d38 100644 --- a/examples/PACKAGES/pace/plugin/CMakeLists.txt +++ b/examples/PACKAGES/pace/plugin/CMakeLists.txt @@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.16) -project(paceplugin VERSION 1.0 LANGUAGES CXX) +project(paceplugin VERSION 1.1 LANGUAGES CXX) set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}) include(CheckIncludeFileCXX) @@ -15,7 +15,11 @@ include(ML-PACE) ########################## # building the plugins -add_library(paceplugin MODULE paceplugin.cpp ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp) +add_library(paceplugin MODULE paceplugin.cpp + ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp + ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace_extrapolation.cpp + ${LAMMPS_SOURCE_DIR}/ML-PACE/compute_pace.cpp) + target_link_libraries(paceplugin PRIVATE pace) target_link_libraries(paceplugin PRIVATE lammps) target_include_directories(paceplugin PRIVATE ${LAMMPS_SOURCE_DIR}/ML-PACE) diff --git a/examples/PACKAGES/pace/plugin/paceplugin.cpp b/examples/PACKAGES/pace/plugin/paceplugin.cpp index adf1c168f9..f231318d23 100644 --- a/examples/PACKAGES/pace/plugin/paceplugin.cpp +++ b/examples/PACKAGES/pace/plugin/paceplugin.cpp @@ -3,6 +3,8 @@ #include "version.h" #include "pair_pace.h" +#include "pair_pace_extrapolation.h" +#include "compute_pace.h" using namespace LAMMPS_NS; @@ -11,6 +13,16 @@ static Pair *pair_pace_creator(LAMMPS *lmp) return new PairPACE(lmp); } +static Pair *pair_pace_extrapolation_creator(LAMMPS *lmp) +{ + return new PairPACEExtrapolation(lmp); +} + +static Compute *compute_pace_creator(LAMMPS *lmp, int argc, char **argv) +{ + return new ComputePACE(lmp, argc, argv); +} + extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) { lammpsplugin_t plugin; @@ -25,4 +37,24 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_creator; plugin.handle = handle; (*register_plugin)(&plugin, lmp); + + // register pace/extrapolation pair style + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "pace/extrapolation"; + plugin.info = "PACE plugin extrapolation pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_extrapolation_creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); + + // register pace compute style + plugin.version = LAMMPS_VERSION; + plugin.style = "compute"; + plugin.name = "pace"; + plugin.info = "PACE plugin compute style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v2 = (lammpsplugin_factory2 *) &compute_pace_creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); } diff --git a/fortran/lammps.f90 b/fortran/lammps.f90 index 1617891b92..a2f28073e5 100644 --- a/fortran/lammps.f90 +++ b/fortran/lammps.f90 @@ -542,6 +542,14 @@ MODULE LIBLAMMPS INTEGER(c_int) :: lammps_extract_atom_datatype END FUNCTION lammps_extract_atom_datatype + FUNCTION lammps_extract_atom_size(handle, name, dtype) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: handle, name + INTEGER(c_int), INTENT(IN), VALUE :: dtype + INTEGER(c_int) :: lammps_extract_atom_size + END FUNCTION lammps_extract_atom_size + FUNCTION lammps_extract_atom(handle, name) BIND(C) IMPORT :: c_ptr IMPLICIT NONE @@ -1435,7 +1443,7 @@ CONTAINS IF (SIZE_TAGINT == 8) THEN Cptr = C_LOC(id) ELSE - id32 = id + id32 = INT(id, c_int) Cptr = C_LOC(id32) END IF lmp_map_atom_big = lammps_map_atom(self%handle, Cptr) + 1 @@ -1461,43 +1469,35 @@ CONTAINS ntypes = lmp_extract_setting(self, 'ntypes') Cname = f2c_string(name) datatype = lammps_extract_atom_datatype(self%handle, Cname) + nrows = lammps_extract_atom_size(self%handle, Cname, LMP_SIZE_ROWS) + ncols = lammps_extract_atom_size(self%handle, Cname, LMP_SIZE_COLS) Cptr = lammps_extract_atom(self%handle, Cname) CALL lammps_free(Cname) - SELECT CASE (name) - CASE ('mass') - ncols = ntypes + 1 - nrows = 1 - CASE ('x','v','f','mu','omega','torque','angmom') - ncols = nmax - nrows = 3 - CASE DEFAULT - ncols = nmax - nrows = 1 - END SELECT - peratom_data%lammps_instance => self SELECT CASE (datatype) CASE (LAMMPS_INT) peratom_data%datatype = DATA_INT_1D - CALL C_F_POINTER(Cptr, peratom_data%i32_vec, [ncols]) + CALL C_F_POINTER(Cptr, peratom_data%i32_vec, [nrows]) CASE (LAMMPS_INT64) peratom_data%datatype = DATA_INT64_1D - CALL C_F_POINTER(Cptr, peratom_data%i64_vec, [ncols]) + CALL C_F_POINTER(Cptr, peratom_data%i64_vec, [nrows]) CASE (LAMMPS_DOUBLE) peratom_data%datatype = DATA_DOUBLE_1D + ! The mass array is allocated from 0, but only used from 1. We also want to use it from 1. IF (name == 'mass') THEN - CALL C_F_POINTER(Cptr, dummy, [ncols]) + CALL C_F_POINTER(Cptr, dummy, [nrows]) peratom_data%r64_vec(0:) => dummy ELSE - CALL C_F_POINTER(Cptr, peratom_data%r64_vec, [ncols]) + CALL C_F_POINTER(Cptr, peratom_data%r64_vec, [nrows]) END IF CASE (LAMMPS_DOUBLE_2D) peratom_data%datatype = DATA_DOUBLE_2D ! First, we dereference the void** pointer to point to the void* - CALL C_F_POINTER(Cptr, Catomptr, [ncols]) + CALL C_F_POINTER(Cptr, Catomptr, [nrows]) ! Catomptr(1) now points to the first element of the array - CALL C_F_POINTER(Catomptr(1), peratom_data%r64_mat, [nrows,ncols]) + ! rows and columns are swapped in Fortran + CALL C_F_POINTER(Catomptr(1), peratom_data%r64_mat, [ncols,nrows]) CASE (-1) CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & 'per-atom property ' // name // ' not found in extract_setting') @@ -2604,6 +2604,8 @@ CONTAINS TYPE(c_ptr) :: Cid, Ctype, Cx, Cv, Cimage INTEGER(c_int) :: tagint_size, atoms_created + Ctype = c_null_ptr + Cx = c_null_ptr ! type is actually NOT optional, but we can't make id optional without it, ! so we check at run-time IF (.NOT. PRESENT(type)) THEN diff --git a/lib/gpu/Makefile.aurora b/lib/gpu/Makefile.aurora new file mode 100644 index 0000000000..c343e061ee --- /dev/null +++ b/lib/gpu/Makefile.aurora @@ -0,0 +1,31 @@ +# /* ---------------------------------------------------------------------- +# Generic Linux Makefile for OpenCL +# ------------------------------------------------------------------------- */ + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.opencl + +# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi +# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler +# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress +OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device + +# this setting should match LAMMPS Makefile +# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL + +LMP_INC = -DLAMMPS_SMALLBIG + +OCL_INC = -I/opt/intel/oneapi/compiler/latest/linux/include/sycl/ # Path to CL directory +OCL_CPP = mpicxx -cxx=icpx -DCUDA_PROXY $(DEFAULT_DEVICE) -xHost -O2 -ffp-model=fast -qoverride-limits -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC) -DGERYON_NO_PROF +OCL_LINK = -L/opt/intel/oneapi/compiler/latest/linux/lib/ -lOpenCL +OCL_PREC = -D_SINGLE_DOUBLE + +BIN_DIR = ./ +OBJ_DIR = ./ +LIB_DIR = ./ +AR = ar +BSH = /bin/sh + +include Opencl.makefile + diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index 66501a74e9..485845b67a 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -19,7 +19,7 @@ parser = ArgumentParser(prog='Install.py', # Note: must also adjust check for supported API versions in # fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y -version = "2.9.1" +version = "2.9.2" mode = "static" # help message @@ -51,6 +51,7 @@ checksums = { \ '2.8.4' : '9f59c4f9bda86fe5bef19543c295a981', \ '2.9.0' : '661eabeebee05cf84bbf9dc23d7d5f46', \ '2.9.1' : 'c3b2d31479c1e9ce211719d40e9efbd7', \ + '2.9.2' : '04862602a372c1013bdfee2d6d03bace', \ } # parse and process arguments diff --git a/python/lammps/core.py b/python/lammps/core.py index 9e6329fe3c..249b4719e0 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -18,12 +18,21 @@ from __future__ import print_function import os import sys -from ctypes import * # lgtm [py/polluting-import] -from os.path import dirname,abspath,join +from ctypes import CDLL, POINTER, RTLD_GLOBAL, CFUNCTYPE, py_object, byref, cast, sizeof, \ + create_string_buffer, c_int, c_int32, c_int64, c_double, c_void_p, c_char_p, pythonapi, \ + pointer +from os.path import dirname, abspath, join from inspect import getsourcefile -from .constants import * # lgtm [py/polluting-import] -from .data import * # lgtm [py/polluting-import] +from lammps.constants import LAMMPS_AUTODETECT, LAMMPS_STRING, \ + LAMMPS_INT, LAMMPS_INT_2D, LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, \ + LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, \ + LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, \ + LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS, \ + LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING, \ + get_ctypes_int + +from lammps.data import NeighList # ------------------------------------------------------------------------- @@ -318,6 +327,8 @@ class lammps(object): self.lib.lammps_extract_atom.argtypes = [c_void_p, c_char_p] self.lib.lammps_extract_atom_datatype.argtypes = [c_void_p, c_char_p] self.lib.lammps_extract_atom_datatype.restype = c_int + self.lib.lammps_extract_atom_size.argtypes = [c_void_p, c_char_p, c_int] + self.lib.lammps_extract_atom_size.restype = c_int self.lib.lammps_extract_fix.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int, c_int] @@ -1070,31 +1081,59 @@ class lammps(object): else: return None return self.lib.lammps_extract_atom_datatype(self.lmp, newname) + # ------------------------------------------------------------------------- + # extract per-atom info datatype + + def extract_atom_size(self, name, dtype): + """Retrieve per-atom property dimensions from LAMMPS + + This is a wrapper around the :cpp:func:`lammps_extract_atom_size` + function of the C-library interface. Its documentation includes a + list of the supported keywords. + This function returns ``None`` if the keyword is not + recognized. Otherwise it will return an integer value with the size + of the per-atom vector or array. If *name* corresponds to a per-atom + array, the *dtype* keyword must be either LMP_SIZE_ROWS or LMP_SIZE_COLS + from the :ref:`type ` constants defined in the + :py:mod:`lammps` module. The return value is the requested size. + If *name* corresponds to a per-atom vector the *dtype* keyword is ignored. + + :param name: name of the property + :type name: string + :param type: either LMP_SIZE_ROWS or LMP_SIZE_COLS for arrays, otherwise ignored + :type type: int + :return: data type of per-atom property (see :ref:`py_datatype_constants`) + :rtype: int + """ + if name: newname = name.encode() + else: return None + return self.lib.lammps_extract_atom_size(self.lmp, newname, dtype) + # ------------------------------------------------------------------------- # extract per-atom info def extract_atom(self, name, dtype=LAMMPS_AUTODETECT): """Retrieve per-atom properties from LAMMPS - This is a wrapper around the :cpp:func:`lammps_extract_atom` - function of the C-library interface. Its documentation includes a - list of the supported keywords and their data types. - Since Python needs to know the data type to be able to interpret - the result, by default, this function will try to auto-detect the data type - by asking the library. You can also force a specific data type by setting ``dtype`` - to one of the :ref:`data type ` constants defined in the - :py:mod:`lammps` module. - This function returns ``None`` if either the keyword is not - recognized, or an invalid data type constant is used. + This is a wrapper around the :cpp:func:`lammps_extract_atom` function of the + C-library interface. Its documentation includes a list of the supported + keywords and their data types. Since Python needs to know the data type to + be able to interpret the result, by default, this function will try to + auto-detect the data type by asking the library. You can also force a + specific data type by setting ``dtype`` to one of the :ref:`data type + ` constants defined in the :py:mod:`lammps` module. + This function returns ``None`` if either the keyword is not recognized, or + an invalid data type constant is used. .. note:: - While the returned arrays of per-atom data are dimensioned - for the range [0:nmax] - as is the underlying storage - - the data is usually only valid for the range of [0:nlocal], - unless the property of interest is also updated for ghost - atoms. In some cases, this depends on a LAMMPS setting, see - for example :doc:`comm_modify vel yes `. + While the returned vectors or arrays of per-atom data are dimensioned for + the range [0:nmax] - as is the underlying storage - the data is usually + only valid for the range of [0:nlocal], unless the property of interest + is also updated for ghost atoms. In some cases, this depends on a LAMMPS + setting, see for example :doc:`comm_modify vel yes `. + The actual size can be determined by calling + py:meth:`extract_atom_size() `. :param name: name of the property :type name: string @@ -1105,6 +1144,7 @@ class lammps(object): ctypes.POINTER(ctypes.c_int64), ctypes.POINTER(ctypes.POINTER(ctypes.c_int64)), ctypes.POINTER(ctypes.c_double), ctypes.POINTER(ctypes.POINTER(ctypes.c_double)), or NoneType + """ if dtype == LAMMPS_AUTODETECT: dtype = self.extract_atom_datatype(name) @@ -2227,7 +2267,6 @@ class lammps(object): :param caller: reference to some object passed to the callback function :type: object, optional """ - import numpy as np def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr): tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1) @@ -2522,3 +2561,7 @@ class lammps(object): newcomputeid = computeid.encode() idx = self.lib.lammps_find_compute_neighlist(self.lmp, newcomputeid, reqid) return idx + +# Local Variables: +# fill-column: 80 +# End: diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index 9ab7f538de..6e8c7ebcd2 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -16,14 +16,17 @@ # Written by Richard Berger ################################################################################ -import warnings from ctypes import POINTER, c_void_p, c_char_p, c_double, c_int, c_int32, c_int64, cast +from .constants import LAMMPS_AUTODETECT, LAMMPS_INT, LAMMPS_INT_2D, \ + LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, \ + LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, \ + LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, \ + LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS, \ + LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING -from .constants import * # lgtm [py/polluting-import] from .data import NeighList - class numpy_wrapper: """lammps API NumPy Wrapper @@ -54,7 +57,8 @@ class numpy_wrapper: # ------------------------------------------------------------------------- - def extract_atom(self, name, dtype=LAMMPS_AUTODETECT, nelem=LAMMPS_AUTODETECT, dim=LAMMPS_AUTODETECT): + def extract_atom(self, name, dtype=LAMMPS_AUTODETECT, nelem=LAMMPS_AUTODETECT, + dim=LAMMPS_AUTODETECT): """Retrieve per-atom properties from LAMMPS as NumPy arrays This is a wrapper around the :py:meth:`lammps.extract_atom()` method. @@ -63,16 +67,16 @@ class numpy_wrapper: .. note:: - The returned arrays of per-atom data are by default dimensioned - for the range [0:nlocal] since that data is *always* valid. The - underlying storage for the data, however, is typically allocated - for the range of [0:nmax]. Whether there is valid data in the range - [nlocal:nlocal+nghost] depends on whether the property of interest - is also updated for ghost atoms. This is not often the case. In - some cases, it depends on a LAMMPS setting, see for example - :doc:`comm_modify vel yes `. By using the optional - *nelem* parameter the size of the returned NumPy can be overridden. - There is no check whether the number of elements chosen is valid. + The returned vectors or arrays of per-atom data are dimensioned + according to the return value of :py:meth:`lammps.extract_atom_size()`. + Except for the "mass" property, the underlying storage will always be + dimensioned for the range [0:nmax]. The actual usable data may be + only in the range [0:nlocal] or [0:nlocal][0:dim]. Whether there is + valid data in the range [nlocal:nlocal+nghost] or [nlocal:local+nghost][0:dim] + depends on whether the property of interest is also updated for ghost atoms. + Also the value of *dim* depends on the value of *name*. By using the optional + *nelem* and *dim* parameters the dimensions of the returned NumPy array can + be overridden. There is no check whether the number of elements chosen is valid. :param name: name of the property :type name: string @@ -89,21 +93,10 @@ class numpy_wrapper: dtype = self.lmp.extract_atom_datatype(name) if nelem == LAMMPS_AUTODETECT: - if name == "mass": - nelem = self.lmp.extract_global("ntypes") + 1 - else: - nelem = self.lmp.extract_global("nlocal") + nelem = self.lmp.extract_atom_size(name, LMP_SIZE_ROWS) if dim == LAMMPS_AUTODETECT: if dtype in (LAMMPS_INT_2D, LAMMPS_DOUBLE_2D, LAMMPS_INT64_2D): - # TODO add other fields - if name in ("x", "v", "f", "x0","omega", "angmom", "torque", "csforce", "vforce", "vest"): - dim = 3 - elif name == "smd_data_9": - dim = 9 - elif name == "smd_stress": - dim = 6 - else: - dim = 2 + dim = self.lmp.extract_atom_size(name, LMP_SIZE_COLS) else: dim = 1 @@ -119,37 +112,6 @@ class numpy_wrapper: # ------------------------------------------------------------------------- - def extract_atom_iarray(self, name, nelem, dim=1): - warnings.warn("deprecated, use extract_atom instead", DeprecationWarning) - - if name in ['id', 'molecule']: - c_int_type = self.lmp.c_tagint - elif name in ['image']: - c_int_type = self.lmp.c_imageint - else: - c_int_type = c_int - - if dim == 1: - raw_ptr = self.lmp.extract_atom(name, LAMMPS_INT) - else: - raw_ptr = self.lmp.extract_atom(name, LAMMPS_INT_2D) - - return self.iarray(c_int_type, raw_ptr, nelem, dim) - - # ------------------------------------------------------------------------- - - def extract_atom_darray(self, name, nelem, dim=1): - warnings.warn("deprecated, use extract_atom instead", DeprecationWarning) - - if dim == 1: - raw_ptr = self.lmp.extract_atom(name, LAMMPS_DOUBLE) - else: - raw_ptr = self.lmp.extract_atom(name, LAMMPS_DOUBLE_2D) - - return self.darray(raw_ptr, nelem, dim) - - # ------------------------------------------------------------------------- - def extract_compute(self, cid, cstyle, ctype): """Retrieve data from a LAMMPS compute diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index 9087305ba3..1f5a1a0db9 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -27,8 +27,8 @@ import sys import tempfile from collections import namedtuple -from .core import lammps -from .constants import * # lgtm [py/polluting-import] +from lammps.core import lammps +from lammps.constants import LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING # ------------------------------------------------------------------------- diff --git a/src/CG-DNA/atom_vec_oxdna.cpp b/src/CG-DNA/atom_vec_oxdna.cpp index 38f78f94bf..0836e9b47c 100644 --- a/src/CG-DNA/atom_vec_oxdna.cpp +++ b/src/CG-DNA/atom_vec_oxdna.cpp @@ -37,6 +37,7 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp) fields_grow = {"id5p"}; fields_copy = {"id5p"}; fields_border = {"id5p"}; + fields_border_vel = {"id5p"}; fields_exchange = {"id5p"}; fields_restart = {"id5p"}; fields_data_atom = {"id", "type", "x"}; diff --git a/src/DIFFRACTION/compute_saed.cpp b/src/DIFFRACTION/compute_saed.cpp index 1350257910..e2a7bb33d9 100644 --- a/src/DIFFRACTION/compute_saed.cpp +++ b/src/DIFFRACTION/compute_saed.cpp @@ -401,7 +401,7 @@ void ComputeSAED::compute_vector() // Setting up OMP #if defined(_OPENMP) - if (me == 0 && echo) utils::logmesg(lmp," using {}OMP threads\n",comm->nthreads); + if (me == 0 && echo) utils::logmesg(lmp," using {} OMP thread(s)\n",comm->nthreads); #endif if (me == 0 && echo) utils::logmesg(lmp,"\n"); @@ -478,7 +478,7 @@ void ComputeSAED::compute_vector() } } } // End of pragma omp for region - delete [] f; + delete[] f; } auto scratch = new double[2*nRows]; @@ -499,10 +499,10 @@ void ComputeSAED::compute_vector() utils::logmesg(lmp," 100% \nTime elapsed during compute_saed = {:.2f} sec " "using {:.2f} Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0); - delete [] xlocal; - delete [] typelocal; - delete [] scratch; - delete [] Fvec; + delete[] xlocal; + delete[] typelocal; + delete[] scratch; + delete[] Fvec; } /* ---------------------------------------------------------------------- diff --git a/src/DIFFRACTION/compute_xrd.cpp b/src/DIFFRACTION/compute_xrd.cpp index 11e0bb9a9f..a769be7d4f 100644 --- a/src/DIFFRACTION/compute_xrd.cpp +++ b/src/DIFFRACTION/compute_xrd.cpp @@ -332,7 +332,7 @@ void ComputeXRD::compute_array() // Setting up OMP #if defined(_OPENMP) - if ((me == 0) && echo) utils::logmesg(lmp," using {} OMP threads\n",comm->nthreads); + if ((me == 0) && echo) utils::logmesg(lmp," using {} OMP thread(s)\n",comm->nthreads); #endif if ((me == 0) && echo) { @@ -482,7 +482,7 @@ void ComputeXRD::compute_array() } } // End of pragma omp for region } // End of if LP=1 check - delete [] f; + delete[] f; } // End of pragma omp parallel region auto scratch = new double[2*size_array_rows]; @@ -503,10 +503,10 @@ void ComputeXRD::compute_array() utils::logmesg(lmp," 100% \nTime elapsed during compute_xrd = {:.2f} sec " "using {:.2f} Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0); - delete [] scratch; - delete [] Fvec; - delete [] xlocal; - delete [] typelocal; + delete[] scratch; + delete[] Fvec; + delete[] xlocal; + delete[] typelocal; } /* ---------------------------------------------------------------------- diff --git a/src/DIFFRACTION/fix_saed_vtk.cpp b/src/DIFFRACTION/fix_saed_vtk.cpp index b3f6693e9e..693bb925b6 100644 --- a/src/DIFFRACTION/fix_saed_vtk.cpp +++ b/src/DIFFRACTION/fix_saed_vtk.cpp @@ -114,6 +114,7 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) : memory->create(vector_total,nrows,"saed/vtk:vector_total"); vector_flag = 1; + extvector = 0; size_vector = nrows; if (nOutput == 0) { @@ -248,8 +249,8 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) : FixSAEDVTK::~FixSAEDVTK() { - delete [] filename; - delete [] ids; + delete[] filename; + delete[] ids; memory->destroy(vector); memory->destroy(vector_total); if (fp && comm->me == 0) fclose(fp); diff --git a/src/EXTRA-COMMAND/ndx_group.cpp b/src/EXTRA-COMMAND/ndx_group.cpp index c5b0d3cf8a..d006473bb8 100644 --- a/src/EXTRA-COMMAND/ndx_group.cpp +++ b/src/EXTRA-COMMAND/ndx_group.cpp @@ -33,7 +33,8 @@ static std::string find_section(FILE *fp, const std::string &name) { char linebuf[BUFLEN]; - fgets(linebuf, BUFLEN, fp); + if (!fgets(linebuf, BUFLEN, fp)) + throw TokenizerException("Read error", utils::getsyserror()); while (!feof(fp)) { if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) { auto words = Tokenizer(linebuf).as_vector(); diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index 9d5347f173..f4c5fa5028 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -44,12 +44,18 @@ FFT3dKokkos::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int int ngpus = lmp->kokkos->ngpus; ExecutionSpace execution_space = ExecutionSpaceFromDevice::space; -#if defined(FFT_KOKKOS_MKL) +#if defined(FFT_KOKKOS_MKL_GPU) + if (ngpus > 0 && execution_space == Host) + lmp->error->all(FLERR,"Cannot use the MKL library with Kokkos on the host CPUs in a GPU build"); +#elif defined(FFT_KOKKOS_MKL) if (ngpus > 0 && execution_space == Device) lmp->error->all(FLERR,"Cannot use the MKL library with Kokkos on GPUs"); #elif defined(FFT_KOKKOS_FFTW3) if (ngpus > 0 && execution_space == Device) lmp->error->all(FLERR,"Cannot use the FFTW library with Kokkos on GPUs"); +#elif defined(FFT_KOKKOS_NVPL) + if (ngpus > 0 && execution_space == Device) + lmp->error->all(FLERR,"Cannot use the NVPL FFT library with Kokkos on GPUs"); #elif defined(FFT_KOKKOS_CUFFT) if (ngpus > 0 && execution_space == Host) lmp->error->all(FLERR,"Cannot use the cuFFT library with Kokkos on the host CPUs"); @@ -151,7 +157,7 @@ public: KOKKOS_INLINE_FUNCTION void operator() (const int &i) const { -#if defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_CUFFT) || defined(FFT_KOKKOS_HIPFFT) +#if defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_CUFFT) || defined(FFT_KOKKOS_HIPFFT) || defined(FFT_KOKKOS_MKL_GPU) || defined(FFT_KOKKOS_NVPL) FFT_SCALAR* out_ptr = (FFT_SCALAR *)(d_out.data()+i); *(out_ptr++) *= norm; *(out_ptr++) *= norm; @@ -221,12 +227,17 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, total = plan->total1; length = plan->length1; - #if defined(FFT_KOKKOS_MKL) + #if defined(FFT_KOKKOS_MKL_GPU) + if (flag == 1) + oneapi::mkl::dft::compute_forward(*(plan->desc_fast), (FFT_SCALAR*)d_data.data()); + else + oneapi::mkl::dft::compute_backward(*(plan->desc_fast), (FFT_SCALAR*)d_data.data()); + #elif defined(FFT_KOKKOS_MKL) if (flag == 1) DftiComputeForward(plan->handle_fast,d_data.data()); else DftiComputeBackward(plan->handle_fast,d_data.data()); - #elif defined(FFT_KOKKOS_FFTW3) + #elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) if (flag == 1) FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); else @@ -267,12 +278,17 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, total = plan->total2; length = plan->length2; - #if defined(FFT_KOKKOS_MKL) + #if defined(FFT_KOKKOS_MKL_GPU) + if (flag == 1) + oneapi::mkl::dft::compute_forward(*(plan->desc_mid), (FFT_SCALAR*)d_data.data()); + else + oneapi::mkl::dft::compute_backward(*(plan->desc_mid), (FFT_SCALAR*)d_data.data()); + #elif defined(FFT_KOKKOS_MKL) if (flag == 1) DftiComputeForward(plan->handle_mid,d_data.data()); else DftiComputeBackward(plan->handle_mid,d_data.data()); - #elif defined(FFT_KOKKOS_FFTW3) + #elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) if (flag == 1) FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); else @@ -311,12 +327,17 @@ void FFT3dKokkos::fft_3d_kokkos(typename FFT_AT::t_FFT_DATA_1d d_in, total = plan->total3; length = plan->length3; - #if defined(FFT_KOKKOS_MKL) + #if defined(FFT_KOKKOS_MKL_GPU) + if (flag == 1) + oneapi::mkl::dft::compute_forward(*(plan->desc_slow), (FFT_SCALAR*)d_data.data()); + else + oneapi::mkl::dft::compute_backward(*(plan->desc_slow), (FFT_SCALAR*)d_data.data()); + #elif defined(FFT_KOKKOS_MKL) if (flag == 1) DftiComputeForward(plan->handle_slow,d_data.data()); else DftiComputeBackward(plan->handle_slow,d_data.data()); - #elif defined(FFT_KOKKOS_FFTW3) + #elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) if (flag == 1) FFTW_API(execute_dft)(plan->plan_slow_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); else @@ -610,7 +631,28 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl // system specific pre-computation of 1d FFT coeffs // and scaling normalization -#if defined(FFT_KOKKOS_MKL) +#if defined(FFT_KOKKOS_MKL_GPU) + sycl::queue queue = LMPDeviceType().sycl_queue(); + + plan->desc_fast = new descriptor_t (nfast); + plan->desc_fast->set_value(oneapi::mkl::dft::config_param::NUMBER_OF_TRANSFORMS, plan->total1/nfast); + plan->desc_fast->set_value(oneapi::mkl::dft::config_param::FWD_DISTANCE, plan->length1); + plan->desc_fast->set_value(oneapi::mkl::dft::config_param::BWD_DISTANCE, plan->length1); + plan->desc_fast->commit(queue); + + plan->desc_mid = new descriptor_t (nmid); + plan->desc_mid->set_value(oneapi::mkl::dft::config_param::NUMBER_OF_TRANSFORMS, plan->total2/nmid); + plan->desc_mid->set_value(oneapi::mkl::dft::config_param::FWD_DISTANCE, plan->length2); + plan->desc_mid->set_value(oneapi::mkl::dft::config_param::BWD_DISTANCE, plan->length2); + plan->desc_mid->commit(queue); + + plan->desc_slow = new descriptor_t (nslow); + plan->desc_slow->set_value(oneapi::mkl::dft::config_param::NUMBER_OF_TRANSFORMS, plan->total3/nslow); + plan->desc_slow->set_value(oneapi::mkl::dft::config_param::FWD_DISTANCE, plan->length3); + plan->desc_slow->set_value(oneapi::mkl::dft::config_param::BWD_DISTANCE, plan->length3); + plan->desc_slow->commit(queue); + +#elif defined(FFT_KOKKOS_MKL) DftiCreateDescriptor( &(plan->handle_fast), FFT_KOKKOS_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nfast); DftiSetValue(plan->handle_fast, DFTI_NUMBER_OF_TRANSFORMS, @@ -647,7 +689,7 @@ struct fft_plan_3d_kokkos* FFT3dKokkos::fft_3d_create_pl #endif DftiCommitDescriptor(plan->handle_slow); -#elif defined(FFT_KOKKOS_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) #if defined (FFT_KOKKOS_FFTW_THREADS) if (nthreads > 1) { @@ -782,11 +824,15 @@ void FFT3dKokkos::fft_3d_destroy_plan_kokkos(struct fft_plan_3d_kokk if (plan->mid2_plan) remapKK->remap_3d_destroy_plan_kokkos(plan->mid2_plan); if (plan->post_plan) remapKK->remap_3d_destroy_plan_kokkos(plan->post_plan); -#if defined(FFT_KOKKOS_MKL) +#if defined(FFT_KOKKOS_MKL_GPU) + delete plan->desc_fast; + delete plan->desc_mid; + delete plan->desc_slow; +#elif defined(FFT_KOKKOS_MKL) DftiFreeDescriptor(&(plan->handle_fast)); DftiFreeDescriptor(&(plan->handle_mid)); DftiFreeDescriptor(&(plan->handle_slow)); -#elif defined(FFT_KOKKOS_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) FFTW_API(destroy_plan)(plan->plan_slow_forward); FFTW_API(destroy_plan)(plan->plan_slow_backward); FFTW_API(destroy_plan)(plan->plan_mid_forward); @@ -857,7 +903,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ // fftw3 and Dfti in MKL encode the number of transforms // into the plan, so we cannot operate on a smaller data set -#if defined(FFT_KOKKOS_MKL) || defined(FFT_KOKKOS_FFTW3) +#if defined(FFT_KOKKOS_MKL_GPU) || defined(FFT_KOKKOS_MKL) || defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) if ((total1 > nsize) || (total2 > nsize) || (total3 > nsize)) return; #endif @@ -868,7 +914,17 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ // perform 1d FFTs in each of 3 dimensions // data is just an array of 0.0 -#if defined(FFT_KOKKOS_MKL) +#if defined(FFT_KOKKOS_MKL_GPU) + if (flag == -1) { + oneapi::mkl::dft::compute_forward(*(plan->desc_fast), (FFT_SCALAR*)d_data.data()); + oneapi::mkl::dft::compute_forward(*(plan->desc_mid), (FFT_SCALAR*)d_data.data()); + oneapi::mkl::dft::compute_forward(*(plan->desc_slow), (FFT_SCALAR*)d_data.data()); + } else { + oneapi::mkl::dft::compute_backward(*(plan->desc_fast), (FFT_SCALAR*)d_data.data()); + oneapi::mkl::dft::compute_backward(*(plan->desc_mid), (FFT_SCALAR*)d_data.data()); + oneapi::mkl::dft::compute_backward(*(plan->desc_slow), (FFT_SCALAR*)d_data.data()); + } +#elif defined(FFT_KOKKOS_MKL) if (flag == -1) { DftiComputeForward(plan->handle_fast,d_data.data()); DftiComputeForward(plan->handle_mid,d_data.data()); @@ -878,7 +934,7 @@ void FFT3dKokkos::fft_3d_1d_only_kokkos(typename FFT_AT::t_FFT_DATA_ DftiComputeBackward(plan->handle_mid,d_data.data()); DftiComputeBackward(plan->handle_slow,d_data.data()); } -#elif defined(FFT_KOKKOS_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) if (flag == -1) { FFTW_API(execute_dft)(plan->plan_fast_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); FFTW_API(execute_dft)(plan->plan_mid_forward,(FFT_KOKKOS_DATA*)d_data.data(),(FFT_KOKKOS_DATA*)d_data.data()); diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index 48b0fd76de..ae7ef3a6d2 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -21,6 +21,14 @@ namespace LAMMPS_NS { +#if defined(FFT_KOKKOS_MKL_GPU) +#ifdef FFT_SINGLE + typedef oneapi::mkl::dft::descriptor descriptor_t; +#else + typedef oneapi::mkl::dft::descriptor descriptor_t; +#endif +#endif + // ------------------------------------------------------------------------- // plan for how to perform a 3d FFT @@ -45,11 +53,15 @@ struct fft_plan_3d_kokkos { double norm; // normalization factor for rescaling // system specific 1d FFT info -#if defined(FFT_KOKKOS_MKL) +#if defined(FFT_KOKKOS_MKL_GPU) + descriptor_t *desc_fast; + descriptor_t *desc_mid; + descriptor_t *desc_slow; +#elif defined(FFT_KOKKOS_MKL) DFTI_DESCRIPTOR *handle_fast; DFTI_DESCRIPTOR *handle_mid; DFTI_DESCRIPTOR *handle_slow; -#elif defined(FFT_KOKKOS_FFTW3) +#elif defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) FFTW_API(plan) plan_fast_forward; FFTW_API(plan) plan_fast_backward; FFTW_API(plan) plan_mid_forward; diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index 0cb59f49cb..be6c8c199d 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -36,8 +36,8 @@ # endif #endif -// with KOKKOS in CUDA or HIP mode we can only have -// CUFFT/HIPFFT or KISS, thus undefine all other +// with KOKKOS in CUDA, HIP, or SYCL mode we can only have +// CUFFT/HIPFFT/MKL_GPU or KISS, thus undefine all other // FFTs here #ifdef KOKKOS_ENABLE_CUDA @@ -60,12 +60,28 @@ # if defined(FFT_KOKKOS_FFTW3) # undef FFT_KOKKOS_FFTW3 # endif +# if defined(FFT_KOKKOS_NVPL) +# undef FFT_KOKKOS_NVPL +# endif # if defined(FFT_KOKKOS_MKL) # undef FFT_KOKKOS_MKL # endif # if !defined(FFT_KOKKOS_HIPFFT) && !defined(FFT_KOKKOS_KISS) # define FFT_KOKKOS_KISS # endif +#elif defined(KOKKOS_ENABLE_SYCL) +# if defined(FFT_KOKKOS_FFTW) +# undef FFT_KOKKOS_FFTW +# endif +# if defined(FFT_KOKKOS_FFTW3) +# undef FFT_KOKKOS_FFTW3 +# endif +# if defined(FFT_KOKKOS_MKL) +# undef FFT_KOKKOS_MKL +# endif +# if !defined(FFT_KOKKOS_MKL_GPU) && !defined(FFT_KOKKOS_KISS) +# define FFT_KOKKOS_KISS +# endif #else # if defined(FFT_KOKKOS_CUFFT) # error "Must enable CUDA with KOKKOS to use -DFFT_KOKKOS_CUFFT" @@ -73,6 +89,9 @@ # if defined(FFT_KOKKOS_HIPFFT) # error "Must enable HIP with KOKKOS to use -DFFT_KOKKOS_HIPFFT" # endif +# if defined(FFT_KOKKOS_MKL_GPU) +# error "Must enable SYCL with KOKKOS to use -DFFT_KOKKOS_MKL_GPU" +# endif #endif // set strings for library info output @@ -85,12 +104,27 @@ #define LMP_FFT_KOKKOS_LIB "FFTW3" #elif defined(FFT_KOKKOS_MKL) #define LMP_FFT_KOKKOS_LIB "MKL FFT" +#elif defined(FFT_KOKKOS_MKL_GPU) +#define LMP_FFT_KOKKOS_LIB "MKL_GPU FFT" +#elif defined(FFT_KOKKOS_NVPL) +#define LMP_FFT_KOKKOS_LIB "NVPL FFT" #else #define LMP_FFT_KOKKOS_LIB "KISS FFT" #endif -#if defined(FFT_KOKKOS_MKL) +#if defined(FFT_KOKKOS_MKL_GPU) + #include "CL/sycl.hpp" + #include "oneapi/mkl/dfti.hpp" + #include "mkl.h" + #if defined(FFT_SINGLE) + typedef std::complex FFT_KOKKOS_DATA; + #define FFT_KOKKOS_MKL_PREC DFTI_SINGLE + #else + typedef std::complex FFT_KOKKOS_DATA; + #define FFT_KOKKOS_MKL_PREC DFTI_DOUBLE + #endif +#elif defined(FFT_KOKKOS_MKL) #include "mkl_dfti.h" #if defined(FFT_SINGLE) typedef float _Complex FFT_KOKKOS_DATA; @@ -108,6 +142,15 @@ typedef fftw_complex FFT_KOKKOS_DATA; #define FFTW_API(function) fftw_ ## function #endif +#elif defined(FFT_KOKKOS_NVPL) + #include "nvpl_fftw.h" + #if defined(FFT_SINGLE) + typedef fftwf_complex FFT_KOKKOS_DATA; + #define FFTW_API(function) fftwf_ ## function + #else + typedef fftw_complex FFT_KOKKOS_DATA; + #define FFTW_API(function) fftw_ ## function + #endif #elif defined(FFT_KOKKOS_CUFFT) #include "cufft.h" #if defined(FFT_SINGLE) @@ -146,7 +189,7 @@ #endif // (double[2]*) is not a 1D pointer -#if defined(FFT_KOKKOS_FFTW3) +#if defined(FFT_KOKKOS_FFTW3) || defined(FFT_KOKKOS_NVPL) typedef FFT_SCALAR* FFT_KOKKOS_DATA_POINTER; #else typedef FFT_KOKKOS_DATA* FFT_KOKKOS_DATA_POINTER; diff --git a/src/KOKKOS/fix_shake_kokkos.cpp b/src/KOKKOS/fix_shake_kokkos.cpp index b25e2dad59..47f932d8f2 100644 --- a/src/KOKKOS/fix_shake_kokkos.cpp +++ b/src/KOKKOS/fix_shake_kokkos.cpp @@ -172,7 +172,6 @@ void FixShakeKokkos::init() k_angle_distance.sync(); } - /* ---------------------------------------------------------------------- run setup for minimization. ------------------------------------------------------------------------- */ diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 8019925c6f..b3edb0e6a0 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -149,6 +149,14 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) set_flag = 1; } } + if ((str = getenv("PALS_LOCAL_RANKID"))) { + if (ngpus > 0) { + int local_rank = atoi(str); + device = local_rank % ngpus; + if (device >= skip_gpu) device++; + set_flag = 1; + } + } if (ngpus > 1 && !set_flag) error->all(FLERR,"Could not determine local MPI rank for multiple " diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 7f0eb5c105..e9061dd7a3 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -341,17 +341,17 @@ public: // define precision // handle global precision, force, energy, positions, kspace separately -#ifndef PRECISION -#define PRECISION 2 +#ifndef LMP_PRECISION +#define LMP_PRECISION 2 #endif -#if PRECISION==1 +#if LMP_PRECISION==1 typedef float LMP_FLOAT; #else typedef double LMP_FLOAT; #endif #ifndef PREC_FORCE -#define PREC_FORCE PRECISION +#define PREC_FORCE LMP_PRECISION #endif #if PREC_FORCE==1 @@ -361,7 +361,7 @@ typedef double F_FLOAT; #endif #ifndef PREC_ENERGY -#define PREC_ENERGY PRECISION +#define PREC_ENERGY LMP_PRECISION #endif #if PREC_ENERGY==1 @@ -521,7 +521,7 @@ struct BinOp3DLAMMPS { }; #ifndef PREC_POS -#define PREC_POS PRECISION +#define PREC_POS LMP_PRECISION #endif #if PREC_POS==1 @@ -531,7 +531,7 @@ typedef double X_FLOAT; #endif #ifndef PREC_VELOCITIES -#define PREC_VELOCITIES PRECISION +#define PREC_VELOCITIES LMP_PRECISION #endif #if PREC_VELOCITIES==1 diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 858df5df6c..d839362aa5 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -162,8 +162,10 @@ void VerletKokkos::setup(int flag) lmp->kokkos->auto_sync = 0; modify->setup(vflag); - output->setup(flag); lmp->kokkos->auto_sync = 1; + + atomKK->sync(Host,ALL_MASK); + output->setup(flag); update->setupflag = 0; } @@ -252,6 +254,7 @@ void VerletKokkos::setup_minimal(int flag) lmp->kokkos->auto_sync = 0; modify->setup(vflag); lmp->kokkos->auto_sync = 1; + update->setupflag = 0; } diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index a9956f4397..9ee798b50d 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -72,14 +72,14 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) { FFT_SCALAR norm; -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) FFT_SCALAR *out_ptr; #endif FFT_DATA *data,*copy; // system specific constants -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) FFTW_API(plan) theplan; #else // nothing to do for other FFTs @@ -105,7 +105,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) DftiComputeForward(plan->handle_fast,data); else DftiComputeBackward(plan->handle_fast,data); -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) if (flag == 1) theplan=plan->plan_fast_forward; else @@ -139,7 +139,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) DftiComputeForward(plan->handle_mid,data); else DftiComputeBackward(plan->handle_mid,data); -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) if (flag == 1) theplan=plan->plan_mid_forward; else @@ -173,7 +173,7 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) DftiComputeForward(plan->handle_slow,data); else DftiComputeBackward(plan->handle_slow,data); -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) if (flag == 1) theplan=plan->plan_slow_forward; else @@ -203,11 +203,11 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) if (flag == -1 && plan->scaled) { norm = plan->norm; const int num = plan->normnum; -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) out_ptr = (FFT_SCALAR *)out; #endif for (int i = 0; i < num; i++) { -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) *(out_ptr++) *= norm; *(out_ptr++) *= norm; #elif defined(FFT_MKL) @@ -515,7 +515,7 @@ struct fft_plan_3d *fft_3d_create_plan( #endif DftiCommitDescriptor(plan->handle_slow); -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) #if defined(FFT_FFTW_THREADS) if (nthreads > 1) { FFTW_API(init_threads)(); @@ -613,7 +613,7 @@ void fft_3d_destroy_plan(struct fft_plan_3d *plan) DftiFreeDescriptor(&(plan->handle_fast)); DftiFreeDescriptor(&(plan->handle_mid)); DftiFreeDescriptor(&(plan->handle_slow)); -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) FFTW_API(destroy_plan)(plan->plan_slow_forward); FFTW_API(destroy_plan)(plan->plan_slow_backward); FFTW_API(destroy_plan)(plan->plan_mid_forward); @@ -714,7 +714,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan) { int i,num; FFT_SCALAR norm; -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) FFT_SCALAR *data_ptr; #endif @@ -733,7 +733,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan) // fftw3 and Dfti in MKL encode the number of transforms // into the plan, so we cannot operate on a smaller data set -#if defined(FFT_MKL) || defined(FFT_FFTW3) +#if defined(FFT_MKL) || defined(FFT_FFTW3) || defined(FFT_NVPL) if ((total1 > nsize) || (total2 > nsize) || (total3 > nsize)) return; #endif @@ -754,7 +754,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan) DftiComputeBackward(plan->handle_mid,data); DftiComputeBackward(plan->handle_slow,data); } -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) FFTW_API(plan) theplan; if (flag == 1) theplan=plan->plan_fast_forward; @@ -795,11 +795,11 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan) if (flag == -1 && plan->scaled) { norm = plan->norm; num = MIN(plan->normnum,nsize); -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) data_ptr = (FFT_SCALAR *)data; #endif for (i = 0; i < num; i++) { -#if defined(FFT_FFTW3) +#if defined(FFT_FFTW3) || defined(FFT_NVPL) *(data_ptr++) *= norm; *(data_ptr++) *= norm; #elif defined(FFT_MKL) diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index f4ddeebc4d..34b9c3d4fc 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -31,6 +31,10 @@ typedef MKL_Complex8 FFT_DATA; typedef fftwf_complex FFT_DATA; #define FFTW_API(function) fftwf_##function +#elif defined(FFT_NVPL) +#include "nvpl_fftw.h" +typedef fftwf_complex FFT_DATA; +#define FFTW_API(function) fftwf_##function #else /* use a stripped down version of kiss fft as default fft */ @@ -64,6 +68,11 @@ typedef MKL_Complex16 FFT_DATA; typedef fftw_complex FFT_DATA; #define FFTW_API(function) fftw_##function +#elif defined(FFT_NVPL) +#include "nvpl_fftw.h" +typedef fftw_complex FFT_DATA; +#define FFTW_API(function) fftw_##function + #else /* use a stripped down version of kiss fft as default fft */ @@ -108,7 +117,7 @@ struct fft_plan_3d { DFTI_DESCRIPTOR *handle_fast; DFTI_DESCRIPTOR *handle_mid; DFTI_DESCRIPTOR *handle_slow; -#elif defined(FFT_FFTW3) +#elif defined(FFT_FFTW3) || defined(FFT_NVPL) FFTW_API(plan) plan_fast_forward; FFTW_API(plan) plan_fast_backward; FFTW_API(plan) plan_mid_forward; diff --git a/src/MAKE/MACHINES/Makefile.aurora b/src/MAKE/MACHINES/Makefile.aurora new file mode 100644 index 0000000000..7c656e6379 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aurora @@ -0,0 +1,121 @@ +# aurora = Intel Sapphire Rapids CPU, mpicxx compiler (compatible w/ GPU package) + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = mpicxx +OPTFLAGS = -DSHAKEATOMIC -DCOMMPARA -xSAPPHIRERAPIDS -O2 -ffp-model=fast -qoverride-limits -qopt-zmm-usage=high +CCFLAGS = -qopenmp -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) +CCFLAGS += -I$(MKLROOT)/include +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -qopenmp $(OPTFLAGS) +LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 3.5 of the manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 3.4 of the manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 3.5.2 of manual +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_MKL -DFFT_SINGLE +FFT_PATH = +FFT_LIB = + +# JPEG and/or PNG library +# see discussion in Section 3.5.4 of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@ + $(SIZE) $@ + +# Library targets + +$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS) + @rm -f ../$(ARLIB) + $(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ) + @rm -f $(ARLIB) + @ln -s ../$(ARLIB) $(ARLIB) + +$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + @rm -f $(SHLIB) + @ln -s ../$(SHLIB) $(SHLIB) + +# Compilation rules + +%.o:%.cpp + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + icx -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aurora_kokkos b/src/MAKE/MACHINES/Makefile.aurora_kokkos index a263d4cb8c..f164188dc0 100644 --- a/src/MAKE/MACHINES/Makefile.aurora_kokkos +++ b/src/MAKE/MACHINES/Makefile.aurora_kokkos @@ -7,12 +7,14 @@ SHELL = /bin/sh # specify flags and libraries needed for your compiler CC = mpicxx -CCFLAGS = -g -O3 -DNDEBUG +CCFLAGS = -g -O3 -DNDEBUG -w +CCFLAGS += -fsycl-device-code-split=per_kernel SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx LINKFLAGS = -g -O3 +LINKFLAGS += -flink-huge-device-code -fsycl-max-parallel-link-jobs=64 LIB = SIZE = size @@ -52,9 +54,9 @@ MPI_LIB = # PATH = path for FFT library # LIB = name of FFT library -FFT_INC = -FFT_PATH = -FFT_LIB = +FFT_INC = -DFFT_KOKKOS_MKL_GPU -DFFT_SINGLE -I${MKL_ROOT}/include +FFT_PATH = -L${MKL_ROOT}/lib -L${TBB_ROOT}/lib/intel64/gcc4.8 +FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -ltbb # JPEG and/or PNG library # see discussion in Section 3.5.4 of manual @@ -116,6 +118,6 @@ depend : fastdep.exe $(SRC) @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 fastdep.exe: ../DEPEND/fastdep.c - cc -O -o $@ $< + icx -O -o $@ $< sinclude .depend diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index cd035781c8..ddf14f6804 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -218,7 +218,7 @@ void FixChargeRegulation::init() { int flagall = flag; MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); - if (flagall && comm->me == 0) + if (flagall) error->all(FLERR, "fix charge/regulation cannot exchange " "individual atoms (ions) belonging to a molecule"); } diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index e0f1cd243b..8fb778207b 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -564,7 +564,7 @@ void FixGCMC::init() if (molecule[i]) flag = 1; int flagall; MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); - if (flagall && comm->me == 0) + if (flagall) error->all(FLERR, "Fix gcmc cannot exchange individual atoms belonging to a molecule"); } @@ -579,7 +579,7 @@ void FixGCMC::init() if (molecule[i] == 0) flag = 1; int flagall; MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); - if (flagall && comm->me == 0) + if (flagall) error->all(FLERR, "All mol IDs should be set for fix gcmc group atoms"); } diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 2c76050430..c72beb5051 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -356,7 +356,7 @@ void FixWidom::init() if (molecule[i] == 0) flag = 1; int flagall; MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); - if (flagall && comm->me == 0) + if (flagall) error->all(FLERR, "All mol IDs should be set for fix widom group atoms"); } diff --git a/src/ML-IAP/mliap_descriptor.cpp b/src/ML-IAP/mliap_descriptor.cpp index 34f81c3902..b8acd6329e 100644 --- a/src/ML-IAP/mliap_descriptor.cpp +++ b/src/ML-IAP/mliap_descriptor.cpp @@ -28,6 +28,7 @@ MLIAPDescriptor::MLIAPDescriptor(LAMMPS *lmp) : cutghost(nullptr), radelem(nullptr), wjelem(nullptr) { cutmax = 0.0; + allocated_elements = 0; } /* ---------------------------------------------------------------------- */ diff --git a/src/ML-IAP/mliap_descriptor_ace.cpp b/src/ML-IAP/mliap_descriptor_ace.cpp index fd059b822b..b13699193c 100644 --- a/src/ML-IAP/mliap_descriptor_ace.cpp +++ b/src/ML-IAP/mliap_descriptor_ace.cpp @@ -57,7 +57,6 @@ MLIAPDescriptorACE::MLIAPDescriptorACE(LAMMPS *_lmp, char *yacefilename) : { acemlimpl = new ACE_ML_impl; - allocated_elements = 0; //read in file with CG coefficients or c_tilde coefficients ctilde_file = yacefilename; delete acemlimpl->basis_set; diff --git a/src/ML-QUIP/pair_quip.cpp b/src/ML-QUIP/pair_quip.cpp index a2de4bf38a..35ba4ff8e4 100644 --- a/src/ML-QUIP/pair_quip.cpp +++ b/src/ML-QUIP/pair_quip.cpp @@ -286,7 +286,7 @@ void PairQUIP::coeff(int narg, char **arg) // and returns the necessary size of quip_potential. This behavior // is invoked by setting n_potential_quip to 0. n_quip_potential = 0; - quip_potential = new int[0]; + quip_potential = new int[1]; quip_lammps_potential_initialise(quip_potential, &n_quip_potential, &cutoff, quip_file, &n_quip_file, quip_string, &n_quip_string); delete[] quip_potential; diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 274f8bc2a3..4536cc8e05 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -396,14 +396,14 @@ void PairHbondDreidingLJ::init_style() // and computing forces on A,H which may be on different procs if (atom->molecular == Atom::ATOMIC) - error->all(FLERR,"Pair style hbond/dreiding requires molecular system"); + error->all(FLERR,"Pair style hbond/dreiding/lj requires molecular system"); if (atom->tag_enable == 0) - error->all(FLERR,"Pair style hbond/dreiding requires atom IDs"); + error->all(FLERR,"Pair style hbond/dreiding/lj requires atom IDs"); if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Pair style hbond/dreiding requires an atom map, " + error->all(FLERR,"Pair style hbond/dreiding/lj requires an atom map, " "see atom_modify"); if (force->newton_pair == 0) - error->all(FLERR,"Pair style hbond/dreiding requires newton pair on"); + error->all(FLERR,"Pair style hbond/dreiding/lj requires newton pair on"); // set donor[M]/acceptor[M] if any atom of type M is a donor/acceptor @@ -419,7 +419,7 @@ void PairHbondDreidingLJ::init_style() acceptor[j] = 1; } - if (!anyflag) error->all(FLERR,"No pair hbond/dreiding coefficients set"); + if (!anyflag) error->all(FLERR,"No pair hbond/dreiding/lj coefficients set"); // set additional param values // offset is for LJ only, angle term is not included diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index c8bc0a627d..d976b66460 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -323,14 +323,14 @@ void PairHbondDreidingMorse::init_style() // and computing forces on A,H which may be on different procs if (atom->molecular == Atom::ATOMIC) - error->all(FLERR,"Pair style hbond/dreiding requires molecular system"); + error->all(FLERR,"Pair style hbond/dreiding/morse requires molecular system"); if (atom->tag_enable == 0) - error->all(FLERR,"Pair style hbond/dreiding requires atom IDs"); + error->all(FLERR,"Pair style hbond/dreiding/morse requires atom IDs"); if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Pair style hbond/dreiding requires an atom map, " + error->all(FLERR,"Pair style hbond/dreiding/morse requires an atom map, " "see atom_modify"); if (force->newton_pair == 0) - error->all(FLERR,"Pair style hbond/dreiding requires newton pair on"); + error->all(FLERR,"Pair style hbond/dreiding/morse requires newton pair on"); // set donor[M]/acceptor[M] if any atom of type M is a donor/acceptor @@ -346,7 +346,7 @@ void PairHbondDreidingMorse::init_style() acceptor[j] = 1; } - if (!anyflag) error->all(FLERR,"No pair hbond/dreiding coefficients set"); + if (!anyflag) error->all(FLERR,"No pair hbond/dreiding/morse coefficients set"); // set additional param values // offset is for Morse only, angle term is not included diff --git a/src/angle_write.cpp b/src/angle_write.cpp index 48420ae7be..1be5f1acac 100644 --- a/src/angle_write.cpp +++ b/src/angle_write.cpp @@ -148,8 +148,10 @@ void AngleWrite::command(int narg, char **arg) FILE *coeffs; char line[MAXLINE] = {'\0'}; coeffs = fopen(coeffs_file.c_str(), "r"); + if (!coeffs) + error->one(FLERR, "Unable to open temporary file {}: {}", coeffs_file, utils::getsyserror()); for (int i = 0; i < atom->nangletypes; ++i) { - fgets(line, MAXLINE, coeffs); + utils::sfgets(FLERR, line, MAXLINE, coeffs, coeffs_file.c_str(), error); writer->input->one(fmt::format("angle_coeff {}", line)); } fclose(coeffs); diff --git a/src/atom.cpp b/src/atom.cpp index 729541e8cd..128a532fc8 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1911,7 +1911,11 @@ void Atom::allocate_type_arrays() if (avec->mass_type == AtomVec::PER_TYPE) { mass = new double[ntypes+1]; mass_setflag = new int[ntypes+1]; - for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0; + // start loop from 0 to avoid uninitialized access when operating on the whole array + for (int itype = 0; itype <= ntypes; itype++) { + mass_setflag[itype] = 0; + mass[itype] = 0.0; + } } } @@ -2739,20 +2743,21 @@ Classes rarely need to check on ghost communication and so `find_custom` is typically preferred to this function. See :doc:`pair amoeba ` for an example where checking ghost communication is necessary. \endverbatim - * \param name Name of the property (w/o a "i_" or "d_" or "i2_" or "d2_" prefix) - * \param &flag Returns data type of property: 0 for int, 1 for double - * \param &cols Returns number of values: 0 for a single value, 1 or more for a vector of values - * \param &ghost Returns whether property is communicated to ghost atoms: 0 for no, 1 for yes + * \param name Name of the property (w/o a "i_" or "d_" or "i2_" or "d2_" prefix) + * \param &flag Returns data type of property: 0 for int, 1 for double + * \param &cols Returns number of values: 0 for a single value, 1 or more for a vector of values + * \param &ghost Returns whether property is communicated to ghost atoms: 0 for no, 1 for yes * \return index of property in the respective list of properties */ int Atom::find_custom_ghost(const char *name, int &flag, int &cols, int &ghost) { int i = find_custom(name, flag, cols); + ghost = 0; if (i == -1) return i; if ((flag == 0) && (cols == 0)) ghost = ivghost[i]; else if ((flag == 1) && (cols == 0)) ghost = dvghost[i]; - else if ((flag == 0) && (cols == 1)) ghost = iaghost[i]; - else if ((flag == 1) && (cols == 1)) ghost = daghost[i]; + else if ((flag == 0) && (cols > 0)) ghost = iaghost[i]; + else if ((flag == 1) && (cols > 0)) ghost = daghost[i]; return i; } @@ -2999,11 +3004,13 @@ length of the data area, and a short description. - N double values defined by fix property/atom array name *See also* - :cpp:func:`lammps_extract_atom` + :cpp:func:`lammps_extract_atom`, + :cpp:func:`lammps_extract_atom_datatype`, + :cpp:func:`lammps_extract_atom_size` \endverbatim * - * \sa extract_datatype + * \sa extract_datatype, extract_size * * \param name string with the keyword of the desired property. Typically the name of the pointer variable returned @@ -3142,7 +3149,7 @@ void *Atom::extract(const char *name) \endverbatim * - * \sa extract + * \sa extract extract_size * * \param name string with the keyword of the desired property. * \return data type constant for desired property or -1 */ @@ -3177,10 +3184,14 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"temperature") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"heatflow") == 0) return LAMMPS_DOUBLE; + // PERI package (and in part MACHDYN) + if (strcmp(name,"vfrac") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"s0") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"x0") == 0) return LAMMPS_DOUBLE_2D; + // AWPMD package (and in part EFF and ELECTRODE) + if (strcmp(name,"espin") == 0) return LAMMPS_INT; if (strcmp(name,"spin") == 0) return LAMMPS_INT; // backwards compatibility if (strcmp(name,"eradius") == 0) return LAMMPS_DOUBLE; @@ -3248,14 +3259,255 @@ int Atom::extract_datatype(const char *name) if (!array) index = find_custom(&name[2],flag,cols); else index = find_custom(&name[3],flag,cols); + // consistency checks if (index < 0) return -1; if (which != flag) return -1; if ((!array && cols) || (array && !cols)) return -1; - if (which == 0) return LAMMPS_INT; - else return LAMMPS_DOUBLE; + if (!which && !array) return LAMMPS_INT; + if (which && !array) return LAMMPS_DOUBLE; + if (!which && array) return LAMMPS_INT_2D; + if (which && array) return LAMMPS_DOUBLE_2D; } + return -1; +} +/** Provide vector or array size info of internal data of the Atom class + * +\verbatim embed:rst + +.. versionadded:: TBD + +\endverbatim + * + * \sa extract extract_datatype + * + * \param name string with the keyword of the desired property. + * \param type either LMP_SIZE_ROWS or LMP_SIZE_COLS for per-atom array or ignored + * \return size of the vector or size of the array for the requested dimension or -1 */ + +int Atom::extract_size(const char *name, int type) +{ + // -------------------------------------------------------------------- + // 6th customization section: customize by adding new variable name + + const auto datatype = extract_datatype(name); + const auto nall = nlocal + nghost; + const auto ghost_vel = comm->ghost_velocity; + + if ((datatype == LAMMPS_DOUBLE_2D) || (datatype == LAMMPS_INT_2D)) { + if (type == LMP_SIZE_ROWS) { + if (strcmp(name,"x") == 0) return nall; + if (strcmp(name,"v") == 0) { + if (ghost_vel) return nall; + else return nlocal; + } + if (strcmp(name,"f") == 0) return nall; + if (strcmp(name,"mu") == 0) return nall; + if (strcmp(name,"omega") == 0) { + if (ghost_vel) return nall; + else return nlocal; + } + if (strcmp(name,"angmom") == 0) { + if (ghost_vel) return nall; + else return nlocal; + } + if (strcmp(name,"torque") == 0) return nlocal; + if (strcmp(name,"quat") == 0) { + if (ghost_vel) return nall; + else return nlocal; + } + + // PERI package + + if (strcmp(name,"x0") == 0) return nall; + + // SPIN package + + if (strcmp(name,"sp") == 0) return nall; + if (strcmp(name,"fm") == 0) return nlocal; + if (strcmp(name,"fm_long") == 0) return nlocal; + + // AWPMD package + + if (strcmp(name,"cs") == 0) { + if (ghost_vel) return nall; + else return nlocal; + } + if (strcmp(name,"csforce") == 0) return nlocal; + if (strcmp(name,"vforce") == 0) return nlocal; + + // SPH package + + if (strcmp(name,"vest") == 0) return nall; + + // MACHDYN package + + if (strcmp(name, "smd_data_9") == 0) return LAMMPS_DOUBLE_2D; + if (strcmp(name, "smd_stress") == 0) return LAMMPS_DOUBLE_2D; + + } else if (type == LMP_SIZE_COLS) { + + if (strcmp(name,"x") == 0) return 3; + if (strcmp(name,"v") == 0) return 3; + if (strcmp(name,"f") == 0) return 3; + if (strcmp(name,"mu") == 0) return 4; + if (strcmp(name,"omega") == 0) return 3; + if (strcmp(name,"angmom") == 0) return 3; + if (strcmp(name,"torque") == 0) return 3; + if (strcmp(name,"quat") == 0) return 4; + + // PERI package + + if (strcmp(name,"x0") == 0) return 3; + + // SPIN package + + if (strcmp(name,"sp") == 0) return 4; + if (strcmp(name,"fm") == 0) return 3; + if (strcmp(name,"fm_long") == 0) return 3; + + // AWPMD package + + if (strcmp(name,"cs") == 0) return 2; + if (strcmp(name,"csforce") == 0) return 2; + if (strcmp(name,"vforce") == 0) return 3; + + // SPH package + + if (strcmp(name,"vest") == 0) return 3; + + // MACHDYN package + + if (strcmp(name, "smd_data_9") == 0) return 9; + if (strcmp(name, "smd_stress") == 0) return 6; + } + + // custom arrays + + if (utils::strmatch(name,"^[id]2_")) { + int which = 0; + if (name[0] == 'd') which = 1; + + int index,flag,cols,ghost; + index = find_custom_ghost(&name[3],flag,cols,ghost); + + // consistency checks + if (index < 0) return -1; + if (which != flag) return -1; + if (!cols) return -1; + + if (type == LMP_SIZE_ROWS) { + if (ghost) return nall; + else return nlocal; + } else if (type == LMP_SIZE_COLS) { + return cols; + } + } + } else { + + if (strcmp(name,"mass") == 0) return ntypes + 1; + + if (strcmp(name,"id") == 0) return nall; + if (strcmp(name,"type") == 0) return nall; + if (strcmp(name,"mask") == 0) return nall; + if (strcmp(name,"image") == 0) return nlocal; + if (strcmp(name,"molecule") == 0) return nall; + if (strcmp(name,"q") == 0) return nall; + if (strcmp(name,"radius") == 0) return nall; + if (strcmp(name,"rmass") == 0) return nall; + + // ASPHERE package + + if (strcmp(name,"ellipsoid") == 0) return nlocal; + + // BODY package + + if (strcmp(name,"line") == 0) return nlocal; + if (strcmp(name,"tri") == 0) return nlocal; + if (strcmp(name,"body") == 0) return nlocal; + + // PERI package (and in part MACHDYN) + + if (strcmp(name,"vfrac") == 0) return nall; + if (strcmp(name,"s0") == 0) return nall; + + // AWPMD package (and in part EFF and ELECTRODE) + + if (strcmp(name,"espin") == 0) return nall; + if (strcmp(name,"spin") == 0) return nall; // backwards compatibility + if (strcmp(name,"eradius") == 0) return nall; + if (strcmp(name,"ervel") == 0) return nlocal; + if (strcmp(name,"erforce") == 0) return nlocal; + if (strcmp(name,"ervelforce") == 0) return nlocal; + if (strcmp(name,"etag") == 0) return nall; + + // CG-DNA package + + if (strcmp(name,"id5p") == 0) return nall; + + // RHEO package + + if (strcmp(name,"temperature") == 0) return nlocal; + if (strcmp(name,"heatflow") == 0) return nlocal; + if (strcmp(name,"rheo_status") == 0) return nall; + if (strcmp(name,"conductivity") == 0) return nlocal; + if (strcmp(name,"pressure") == 0) return nlocal; + if (strcmp(name,"viscosity") == 0) return nlocal; + + // SPH package + + if (strcmp(name,"rho") == 0) return nall; + if (strcmp(name,"drho") == 0) return nlocal; + if (strcmp(name,"esph") == 0) return nall; + if (strcmp(name,"desph") == 0) return nlocal; + if (strcmp(name,"cv") == 0) return nall; + + // MACHDYN package + + if (strcmp(name, "contact_radius") == 0) return nall; + if (strcmp(name, "eff_plastic_strain") == 0) return nlocal; + if (strcmp(name, "eff_plastic_strain_rate") == 0) return nlocal; + if (strcmp(name, "damage") == 0) return nlocal; + + // DPD-REACT package + + if (strcmp(name,"dpdTheta") == 0) return nall; + + // DPD-MESO package + + if (strcmp(name,"edpd_temp") == 0) return nall; + + // DIELECTRIC package + + if (strcmp(name,"area") == 0) return nall; + if (strcmp(name,"ed") == 0) return nall; + if (strcmp(name,"em") == 0) return nall; + if (strcmp(name,"epsilon") == 0) return nall; + if (strcmp(name,"curvature") == 0) return nall; + if (strcmp(name,"q_unscaled") == 0) return nall; + + // end of customization section + // -------------------------------------------------------------------- + + // custom vectors + + if (utils::strmatch(name,"^[id]_")) { + int which = 0; + if (name[0] == 'd') which = 1; + + int index,flag,cols,ghost; + index = find_custom_ghost(&name[2],flag,cols,ghost); + + // consistency checks + if (index < 0) return -1; + if (which != flag) return -1; + if (cols) return -1; + + if (ghost) return nall; + else return nlocal; + } + } return -1; } diff --git a/src/atom.h b/src/atom.h index bd5b352cd0..c98f06cbe8 100644 --- a/src/atom.h +++ b/src/atom.h @@ -378,6 +378,7 @@ class Atom : protected Pointers { void *extract(const char *); int extract_datatype(const char *); + int extract_size(const char *, int); inline int *get_map_array() { return map_array; }; inline int get_map_size() { return map_tag_max + 1; }; diff --git a/src/dihedral_write.cpp b/src/dihedral_write.cpp index dd1ca1de6a..1d0f908e2c 100644 --- a/src/dihedral_write.cpp +++ b/src/dihedral_write.cpp @@ -149,8 +149,10 @@ void DihedralWrite::command(int narg, char **arg) FILE *coeffs; char line[MAXLINE] = {'\0'}; coeffs = fopen(coeffs_file.c_str(), "r"); + if (!coeffs) + error->one(FLERR, "Unable to open temporary file {}: {}", utils::getsyserror()); for (int i = 0; i < atom->ndihedraltypes; ++i) { - fgets(line, MAXLINE, coeffs); + utils::sfgets(FLERR, line, MAXLINE, coeffs, coeffs_file.c_str(), error); writer->input->one(fmt::format("dihedral_coeff {}", line)); } fclose(coeffs); diff --git a/src/error.h b/src/error.h index 89d168652a..805bd4cd0d 100644 --- a/src/error.h +++ b/src/error.h @@ -29,14 +29,14 @@ class Error : protected Pointers { [[noreturn]] void all(const std::string &, int, const std::string &); template - void all(const std::string &file, int line, const std::string &format, Args &&...args) + [[noreturn]] void all(const std::string &file, int line, const std::string &format, Args &&...args) { _all(file, line, format, fmt::make_format_args(args...)); } [[noreturn]] void one(const std::string &, int, const std::string &); template - void one(const std::string &file, int line, const std::string &format, Args &&...args) + [[noreturn]] void one(const std::string &file, int line, const std::string &format, Args &&...args) { _one(file, line, format, fmt::make_format_args(args...)); } diff --git a/src/info.cpp b/src/info.cpp index 98ed06f498..2bacea69cf 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -1316,6 +1316,10 @@ std::string Info::get_fft_info() #else fft_info += "FFT library = MKL\n"; #endif +#elif defined(FFT_MKL_GPU) + fft_info += "FFT library = MKL GPU\n"; +#elif defined(FFT_NVPL) + fft_info += "FFT library = NVPL\n"; #elif defined(FFT_FFTW3) #if defined(FFT_FFTW_THREADS) fft_info += "FFT library = FFTW3 with threads\n"; @@ -1338,12 +1342,16 @@ std::string Info::get_fft_info() #else fft_info += "KOKKOS FFT library = FFTW3\n"; #endif +#elif defined(FFT_KOKKOS_NVPL) + fft_info += "KOKKOS FFT library = NVPL\n"; #elif defined(FFT_KOKKOS_MKL) #if defined(FFT_KOKKOS_MKL_THREADS) fft_info += "KOKKOS FFT library = MKL with threads\n"; #else fft_info += "KOKKOS FFT library = MKL\n"; #endif +#elif defined(FFT_KOKKOS_MKL_GPU) + fft_info += "KOKKOS FFT library = MKL GPU\n"; #else fft_info += "KOKKOS FFT library = KISS\n"; #endif diff --git a/src/library.cpp b/src/library.cpp index 950702c420..29cec30488 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -2087,10 +2087,13 @@ int lammps_map_atom(void *handle, const void *id) .. versionadded:: 18Sep2020 -This function returns an integer that encodes the data type of the per-atom -property with the specified name. See :cpp:enum:`_LMP_DATATYPE_CONST` for valid -values. Callers of :cpp:func:`lammps_extract_atom` can use this information -to then decide how to cast the ``void *`` pointer and access the data. +This function returns an integer that encodes the data type of the +per-atom property with the specified name. See +:cpp:enum:`_LMP_DATATYPE_CONST` for valid values. Callers of +:cpp:func:`lammps_extract_atom` can use this information to decide how +to cast the ``void *`` pointer and access the data. In addition, +:cpp:func:`lammps_extract_atom_size` can be used to get information +about the vector or array dimensions. \endverbatim * @@ -2108,18 +2111,53 @@ int lammps_extract_atom_datatype(void *handle, const char *name) /* ---------------------------------------------------------------------- */ +/** Get dimension info of a LAMMPS per-atom property + * +\verbatim embed:rst + +.. versionadded:: TBD + +This function returns an integer with the size of the per-atom +property with the specified name. This allows to accurately determine +the size of the per-atom data vectors or arrays. For per-atom arrays, +the *type* argument is required to return either the number of rows or the +number of columns. It is ignored for per-atom vectors. + +Callers of :cpp:func:`lammps_extract_atom` can use this information in +combination with the result from :cpp:func:`lammps_extract_atom_datatype` +to decide how to cast the ``void *`` pointer and access the data. + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance + * \param name string with the name of the extracted property + * \param type either LMP_SIZE_ROWS or LMP_SIZE_COLS if *name* refers + to a per-atom array otherwise ignored + * \return integer with the size of the vector or array dimension or -1 + * */ + +int lammps_extract_atom_size(void *handle, const char *name, int type) +{ + auto lmp = (LAMMPS *) handle; + return lmp->atom->extract_size(name, type); +} + +/* ---------------------------------------------------------------------- */ + /** Get pointer to a LAMMPS per-atom property. * \verbatim embed:rst -This function returns a pointer to the location of per-atom properties -(and per-atom-type properties in the case of the 'mass' keyword). -Per-atom data is distributed across sub-domains and thus MPI ranks. The -returned pointer is cast to ``void *`` and needs to be cast to a pointer -of data type that the entity represents. +This function returns a pointer to the location of per-atom properties (and +per-atom-type properties in the case of the 'mass' keyword). Per-atom data is +distributed across sub-domains and thus MPI ranks. The returned pointer is cast +to ``void *`` and needs to be cast to a pointer of data type that the entity +represents. You can use the functions :cpp:func:`lammps_extract_atom_datatype` +and :cpp:func:`lammps_extract_atom_size` to determine data type, dimensions and +sizes of the storage pointed to by the returned pointer. -A table with supported keywords is included in the documentation -of the :cpp:func:`Atom::extract() ` function. +A table with supported keywords is included in the documentation of the +:cpp:func:`Atom::extract() ` function. .. warning:: @@ -7027,5 +7065,5 @@ int lammps_python_api_version() { } // Local Variables: -// fill-column: 72 +// fill-column: 80 // End: diff --git a/src/library.h b/src/library.h index ff16aaa088..dbfd32a542 100644 --- a/src/library.h +++ b/src/library.h @@ -172,6 +172,7 @@ int lammps_map_atom(void *handle, const void *id); * ---------------------------------------------------------------------- */ int lammps_extract_atom_datatype(void *handle, const char *name); +int lammps_extract_atom_size(void *handle, const char *name, int type); void *lammps_extract_atom(void *handle, const char *name); /* ---------------------------------------------------------------------- diff --git a/src/lmpfftsettings.h b/src/lmpfftsettings.h index 1b9c89274c..3bcab4a61b 100644 --- a/src/lmpfftsettings.h +++ b/src/lmpfftsettings.h @@ -39,6 +39,8 @@ #define LMP_FFT_LIB "FFTW3" #elif defined(FFT_MKL) #define LMP_FFT_LIB "MKL FFT" +#elif defined(FFT_MKL_GPU) +#define LMP_FFT_LIB "MKL GPU FFT" #elif defined(FFT_CUFFT) #define LMP_FFT_LIB "cuFFT" #elif defined(FFT_HIPFFT) diff --git a/src/version.h b/src/version.h index 7ef4ade45e..9c382b3768 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1,2 @@ #define LAMMPS_VERSION "29 Aug 2024" +#define LAMMPS_UPDATE "Development" diff --git a/tools/lammps-gui/CMakeLists.txt b/tools/lammps-gui/CMakeLists.txt index 1dfd8f451d..fc111f5c64 100644 --- a/tools/lammps-gui/CMakeLists.txt +++ b/tools/lammps-gui/CMakeLists.txt @@ -1,6 +1,6 @@ cmake_minimum_required(VERSION 3.16) -project(lammps-gui VERSION 1.6.10 LANGUAGES CXX) +project(lammps-gui VERSION 1.6.11 LANGUAGES CXX) set(CMAKE_AUTOUIC ON) set(CMAKE_AUTOMOC ON) @@ -86,9 +86,7 @@ else() add_compile_options(/wd4244) add_compile_options(/wd4267) add_compile_options(/wd4250) - if(LAMMPS_EXCEPTIONS) - add_compile_options(/EHsc) - endif() + add_compile_options(/EHsc) endif() add_compile_definitions(_CRT_SECURE_NO_WARNINGS) endif() diff --git a/tools/lammps-gui/lammps-gui.appdata.xml b/tools/lammps-gui/lammps-gui.appdata.xml index 66a15223a2..4c8843957e 100644 --- a/tools/lammps-gui/lammps-gui.appdata.xml +++ b/tools/lammps-gui/lammps-gui.appdata.xml @@ -54,6 +54,10 @@ + + + + Resolve plugin mode issues. diff --git a/tools/msi2lmp/src/GetParameters.c b/tools/msi2lmp/src/GetParameters.c index 921e37491f..b7796de939 100644 --- a/tools/msi2lmp/src/GetParameters.c +++ b/tools/msi2lmp/src/GetParameters.c @@ -44,7 +44,7 @@ void GetParameters() for (i=0; i < no_atom_types; i++) { backwards = -1; - strncpy(potential_types[0],atomtypes[i].potential,5); + memcpy(potential_types[0],atomtypes[i].potential,5); k = find_match(1,potential_types,ff_atomtypes,&backwards); if (k < 0) { printf(" Unable to find mass for %s\n",atomtypes[i].potential); @@ -63,7 +63,7 @@ void GetParameters() for (i=0; i < no_atom_types; i++) { backwards = 0; for (j=0; j < 2; j++) atomtypes[i].params[j] = 0.0; - strncpy(potential_types[0],atomtypes[i].potential,5); + memcpy(potential_types[0],atomtypes[i].potential,5); k = find_match(1,potential_types,ff_vdw,&backwards); if (k < 0) { get_equivs(1,potential_types,equiv_types); @@ -101,7 +101,7 @@ void GetParameters() printf("\n Atom Types, Masses and VDW Parameters\n"); for (i=0; i < no_atom_types; i++) { printf(" %3s %8.4f %8.4f %8.4f\n", - atomtypes[i].potential,atomtypes[i].mass, atomtypes[i].params[0],atomtypes[i].params[1]); + atomtypes[i].potential,atomtypes[i].mass,atomtypes[i].params[0],atomtypes[i].params[1]); } } @@ -115,8 +115,7 @@ void GetParameters() backwards = 0; for (j=0; j < 4; j++) bondtypes[i].params[j] = 0.0; for (j=0; j < 2; j++) - strncpy(potential_types[j], - atomtypes[bondtypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[bondtypes[i].types[j]].potential,5); k = find_match(2,potential_types,ff_bond,&backwards); if (k < 0) { get_equivs(2,potential_types,equiv_types); @@ -172,7 +171,7 @@ void GetParameters() backwards = 0; for (j=0; j < 4; j++) angletypes[i].params[j] = 0.0; for (j=0; j < 3; j++) - strncpy(potential_types[j],atomtypes[angletypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[angletypes[i].types[j]].potential,5); k = find_match(3,potential_types,ff_ang,&backwards); if (k < 0) { get_equivs(3,potential_types,equiv_types); @@ -295,8 +294,7 @@ void GetParameters() for (j=0; j < 6; j++) dihedraltypes[i].params[j] = 0.0; for (j=0; j < 4; j++) - strncpy(potential_types[j], - atomtypes[dihedraltypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[dihedraltypes[i].types[j]].potential,5); backwards = 0; k = find_match(4,potential_types,ff_tor,&backwards); @@ -614,8 +612,7 @@ void GetParameters() for (i=0; i < no_oop_types; i++) { for (j=0; j < 3; j++) ooptypes[i].params[j] = 0.0; for (j=0; j < 4; j++) - strncpy(potential_types[j], - atomtypes[ooptypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[ooptypes[i].types[j]].potential,5); k = find_improper_body_data(potential_types,ff_oop,&rearrange); if (k < 0) { @@ -658,8 +655,7 @@ void GetParameters() for (j=0; j < 3; j++) ooptypes[i].params[j] = 0.0; for (j=0; j < 4; j++) - strncpy(potential_types[j], - atomtypes[ooptypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[ooptypes[i].types[j]].potential,5); k = find_trigonal_body_data(potential_types,ff_oop); if (k < 0) { get_equivs(5,potential_types,equiv_types); @@ -715,8 +711,7 @@ void GetParameters() for (j=0; j < 6; j++) ooptypes[i].angleangle_params[j] = 0.0; for (j=0; j < 4; j++) - strncpy(potential_types[j], - atomtypes[ooptypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[ooptypes[i].types[j]].potential,5); tabc = get_t0(ooptypes[i].types[0], @@ -763,8 +758,7 @@ void GetParameters() for (i=0; i < no_angleangle_types; i++) { for (j=0; j < 6; j++) angleangletypes[i].params[j] = 0.0; for (j=0; j < 4; j++) - strncpy(potential_types[j], - atomtypes[angleangletypes[i].types[j]].potential,5); + memcpy(potential_types[j],atomtypes[angleangletypes[i].types[j]].potential,5); tabc = get_t0(angleangletypes[i].types[0], angleangletypes[i].types[1], @@ -841,44 +835,44 @@ int find_improper_body_data(char types1[][5],struct FrcFieldItem item, /* a b d c */ *rearrange_ptr = 1; - strncpy(mirror_types[0],types1[0],5); - strncpy(mirror_types[1],types1[1],5); - strncpy(mirror_types[2],types1[3],5); - strncpy(mirror_types[3],types1[2],5); + memcpy(mirror_types[0],types1[0],5); + memcpy(mirror_types[1],types1[1],5); + memcpy(mirror_types[2],types1[3],5); + memcpy(mirror_types[3],types1[2],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* d b a c */ *rearrange_ptr = 2; - strncpy(mirror_types[0],types1[3],5); - strncpy(mirror_types[2],types1[0],5); - strncpy(mirror_types[3],types1[2],5); + memcpy(mirror_types[0],types1[3],5); + memcpy(mirror_types[2],types1[0],5); + memcpy(mirror_types[3],types1[2],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* d b c a */ *rearrange_ptr = 3; - strncpy(mirror_types[2],types1[2],5); - strncpy(mirror_types[3],types1[0],5); + memcpy(mirror_types[2],types1[2],5); + memcpy(mirror_types[3],types1[0],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* c b a d */ *rearrange_ptr = 4; - strncpy(mirror_types[0],types1[2],5); - strncpy(mirror_types[2],types1[0],5); - strncpy(mirror_types[3],types1[3],5); + memcpy(mirror_types[0],types1[2],5); + memcpy(mirror_types[2],types1[0],5); + memcpy(mirror_types[3],types1[3],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* c b d a */ *rearrange_ptr = 5; - strncpy(mirror_types[2],types1[3],5); - strncpy(mirror_types[3],types1[0],5); + memcpy(mirror_types[2],types1[3],5); + memcpy(mirror_types[3],types1[0],5); k = find_match(4,mirror_types,item,&backwards); return k; } @@ -973,39 +967,39 @@ int find_trigonal_body_data(char types1[][5],struct FrcFieldItem item) /* a b d c */ - strncpy(mirror_types[0],types1[0],5); - strncpy(mirror_types[1],types1[1],5); - strncpy(mirror_types[2],types1[3],5); - strncpy(mirror_types[3],types1[2],5); + memcpy(mirror_types[0],types1[0],5); + memcpy(mirror_types[1],types1[1],5); + memcpy(mirror_types[2],types1[3],5); + memcpy(mirror_types[3],types1[2],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* d b a c */ - strncpy(mirror_types[0],types1[3],5); - strncpy(mirror_types[2],types1[0],5); - strncpy(mirror_types[3],types1[2],5); + memcpy(mirror_types[0],types1[3],5); + memcpy(mirror_types[2],types1[0],5); + memcpy(mirror_types[3],types1[2],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* d b c a */ - strncpy(mirror_types[2],types1[2],5); - strncpy(mirror_types[3],types1[0],5); + memcpy(mirror_types[2],types1[2],5); + memcpy(mirror_types[3],types1[0],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* c b a d */ - strncpy(mirror_types[0],types1[2],5); - strncpy(mirror_types[2],types1[0],5); - strncpy(mirror_types[3],types1[3],5); + memcpy(mirror_types[0],types1[2],5); + memcpy(mirror_types[2],types1[0],5); + memcpy(mirror_types[3],types1[3],5); k = find_match(4,mirror_types,item,&backwards); if (k >= 0) return k; /* c b d a */ - strncpy(mirror_types[2],types1[3],5); - strncpy(mirror_types[3],types1[0],5); + memcpy(mirror_types[2],types1[3],5); + memcpy(mirror_types[3],types1[0],5); k = find_match(4,mirror_types,item,&backwards); return k; } @@ -1015,41 +1009,41 @@ int find_angleangle_data(char types1[][5],struct FrcFieldItem item,int kloc[3]) int k,backwards = -1; char mirror_types[4][5]; - strncpy(mirror_types[1],types1[1],5); + memcpy(mirror_types[1],types1[1],5); /* go for first parameter a b c d or d b c a */ k = find_match(4,types1,item,&backwards); if (k < 0) { - strncpy(mirror_types[0],types1[3],5); - strncpy(mirror_types[2],types1[2],5); - strncpy(mirror_types[3],types1[0],5); + memcpy(mirror_types[0],types1[3],5); + memcpy(mirror_types[2],types1[2],5); + memcpy(mirror_types[3],types1[0],5); k = find_match(4,mirror_types,item,&backwards); } kloc[0] = k; /* go for second parameter d b a c or c b a d */ - strncpy(mirror_types[0],types1[3],5); - strncpy(mirror_types[2],types1[0],5); - strncpy(mirror_types[3],types1[2],5); + memcpy(mirror_types[0],types1[3],5); + memcpy(mirror_types[2],types1[0],5); + memcpy(mirror_types[3],types1[2],5); k = find_match(4,mirror_types,item,&backwards); if (k < 0) { - strncpy(mirror_types[0],types1[2],5); - strncpy(mirror_types[3],types1[3],5); + memcpy(mirror_types[0],types1[2],5); + memcpy(mirror_types[3],types1[3],5); k = find_match(4,mirror_types,item,&backwards); } kloc[1] = k; /* go for third parameter a b d c or c b d a */ - strncpy(mirror_types[0],types1[0],5); - strncpy(mirror_types[2],types1[3],5); - strncpy(mirror_types[3],types1[2],5); + memcpy(mirror_types[0],types1[0],5); + memcpy(mirror_types[2],types1[3],5); + memcpy(mirror_types[3],types1[2],5); k = find_match(4,mirror_types,item,&backwards); if (k < 0) { - strncpy(mirror_types[0],types1[2],5); - strncpy(mirror_types[3],types1[0],5); + memcpy(mirror_types[0],types1[2],5); + memcpy(mirror_types[3],types1[0],5); k = find_match(4,mirror_types,item,&backwards); } kloc[2] = k; @@ -1250,25 +1244,25 @@ void get_equivs(int ic,char potential_types[][5],char equiv_types[][5]) switch (ic) { case 1: k = find_equiv_type(potential_types[0]); - if (k > -1) strncpy(equiv_types[0],equivalence.data[k].ff_types[1],5); + if (k > -1) memcpy(equiv_types[0],equivalence.data[k].ff_types[1],5); break; case 2: for (i=0; i < 2; i++) { k = find_equiv_type(potential_types[i]); - if (k > -1) strncpy(equiv_types[i],equivalence.data[k].ff_types[2],5); + if (k > -1) memcpy(equiv_types[i],equivalence.data[k].ff_types[2],5); } break; case 3: for (i=0; i < 3; i++) { k = find_equiv_type(potential_types[i]); - if (k > -1) strncpy(equiv_types[i],equivalence.data[k].ff_types[3],5); + if (k > -1) memcpy(equiv_types[i],equivalence.data[k].ff_types[3],5); } break; case 4: for (i=0; i < 4; i++) { k = find_equiv_type(potential_types[i]); - if (k > -1) strncpy(equiv_types[i],equivalence.data[k].ff_types[4],5); + if (k > -1) memcpy(equiv_types[i],equivalence.data[k].ff_types[4],5); } break; @@ -1276,7 +1270,7 @@ void get_equivs(int ic,char potential_types[][5],char equiv_types[][5]) for (i=0; i < 4; i++) { k = find_equiv_type(potential_types[i]); if (k > -1) - strncpy(equiv_types[i],equivalence.data[k].ff_types[5],5); + memcpy(equiv_types[i],equivalence.data[k].ff_types[5],5); } break; default: diff --git a/tools/msi2lmp/src/MakeLists.c b/tools/msi2lmp/src/MakeLists.c index 18b261a561..4f9a9f1548 100644 --- a/tools/msi2lmp/src/MakeLists.c +++ b/tools/msi2lmp/src/MakeLists.c @@ -476,7 +476,7 @@ void build_atomtypes_list() { int j,k,n,match,atom_type=0; - strncpy(atomtypes[0].potential,atoms[0].potential,5); + memcpy(atomtypes[0].potential,atoms[0].potential,5); atoms[0].type = 0; atomtypes[0].no_connect = atoms[0].no_connect; @@ -497,7 +497,7 @@ void build_atomtypes_list() if (match == 0) { atom_type = n; atomtypes[n].no_connect = atoms[j].no_connect; - strncpy(atomtypes[n++].potential,atoms[j].potential,5); + memcpy(atomtypes[n++].potential,atoms[j].potential,5); } if (n >= MAX_ATOM_TYPES) { fprintf(stderr,"Too many atom types (> 100) - error\n"); diff --git a/tools/msi2lmp/src/ReadMdfFile.c b/tools/msi2lmp/src/ReadMdfFile.c index 96a6a01ab2..253121d001 100644 --- a/tools/msi2lmp/src/ReadMdfFile.c +++ b/tools/msi2lmp/src/ReadMdfFile.c @@ -144,7 +144,7 @@ void ReadMdfFile(void) molecule[n].residue[j].end = i; molecule[n].residue[++j].start = i; - strncpy(molecule[n].residue[j].name,atoms[i].residue_string,MAX_NAME); + memcpy(molecule[n].residue[j].name,atoms[i].residue_string,MAX_NAME); } } molecule[n].residue[j].end = molecule[n].end; @@ -167,10 +167,9 @@ void ReadMdfFile(void) for (n=0; n < no_molecules; n++) { for (j=0; j < molecule[n].no_residues; j++) { - for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end; - i++) { + for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end; i++) { for (l=0; l < atoms[i].no_connect; l++) { - strncpy(temp_string,atoms[i].connections[l],MAX_STRING); + memcpy(temp_string,atoms[i].connections[l],MAX_STRING); temp_residue = strtok(temp_string,":"); temp_atom_name = strtok(NULL,"%"); diff --git a/tools/msi2lmp/src/SearchAndFill.c b/tools/msi2lmp/src/SearchAndFill.c index 35de0c81fe..a26554aeaa 100644 --- a/tools/msi2lmp/src/SearchAndFill.c +++ b/tools/msi2lmp/src/SearchAndFill.c @@ -212,7 +212,7 @@ void SearchAndFill(struct FrcFieldItem *item) item->data[replace].ver = version; item->data[replace].ref = reference; for (i=0; i < item->number_of_members; i++) { - strncpy(item->data[replace].ff_types[i],atom_types[i],5); + memcpy(item->data[replace].ff_types[i],atom_types[i],5); } for (i=0; i < item->number_of_parameters; i++) { item->data[replace].ff_param[i] = parameters[i]; @@ -230,7 +230,7 @@ void SearchAndFill(struct FrcFieldItem *item) item->data[ctr].ver = version; item->data[ctr].ref = reference; for (i=0; i < item->number_of_members; i++) { - strncpy(item->data[ctr].ff_types[i],atom_types[i],5); + memcpy(item->data[ctr].ff_types[i],atom_types[i],5); } for (i=0; i < item->number_of_parameters; i++) { item->data[ctr].ff_param[i] = parameters[i]; diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index 68aaf566b2..8228fd0f7f 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -2,6 +2,10 @@ * * msi2lmp.exe * +* v3.9.11 AK - Replace call to strncpy() with memcpy() when copying atom type strings +* to avoid problems with fixed array sizes +* - update tests for newer LAMMPS versions +* * v3.9.10 AK - Substitute UTF-8 characters in .frc files with known ASCII equivalents * - add help message output * diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index 3e1de85cbe..ca745bdc6e 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -36,7 +36,7 @@ #include /* IWYU pragma: export */ -#define MSI2LMP_VERSION "v3.9.10 / 10 Mar 2023" +#define MSI2LMP_VERSION "v3.9.11 / 6 Sep 2024" #define PI_180 0.01745329251994329576 diff --git a/tools/msi2lmp/test/data-compare.pl b/tools/msi2lmp/test/data-compare.pl index 7411f2a017..38bbed051d 100755 --- a/tools/msi2lmp/test/data-compare.pl +++ b/tools/msi2lmp/test/data-compare.pl @@ -2,11 +2,12 @@ # Tool to validate and compare two LAMMPS data files # with "inexact" floating point comparisons # July 2013 by Axel Kohlmeyer +# last update September 2024 by Axel Kohlmeyer use strict; use warnings; -my $version = 'v0.3'; +my $version = 'v0.4'; # delta for floating point comparisons. my $small = 1.0e-4; @@ -596,6 +597,26 @@ sub read_data { last; } + # apply sort + if ($data->{nbonds} > 1) { + my ($did_swap, $num) = (1, $data->{nbonds}); + while ($did_swap) { + $did_swap = 0; + for ($i=0; $i < $num-1; ++$i) { + $j = $i+1; + if (($data->{bond1}[$i] > $data->{bond1}[$j]) + or (($data->{bond1}[$i] == $data->{bond1}[$j]) + and ($data->{bond2}[$i] > $data->{bond2}[$j]))) { + $did_swap = 1; + my @tmp = ($data->{bondt}[$i], $data->{bond1}[$i], $data->{bond2}[$i]); + ($data->{bondt}[$i], $data->{bond1}[$i], $data->{bond2}[$i]) = + ($data->{bondt}[$j], $data->{bond1}[$j], $data->{bond2}[$j]); + ($data->{bondt}[$j], $data->{bond1}[$j], $data->{bond2}[$j]) = @tmp; + } + } + --$num; + } + } } elsif ($1 eq "Angles") { $data->{anglet} = []; $data->{angle1} = []; @@ -638,6 +659,33 @@ sub read_data { last; } + # apply sort + if ($data->{nangles} > 1) { + my ($did_swap, $num) = (1, $data->{nangles}); + while ($did_swap) { + $did_swap = 0; + for ($i=0; $i < $num-1; ++$i) { + $j = $i+1; + if (($data->{angle1}[$i] > $data->{angle1}[$j]) + or (($data->{angle1}[$i] == $data->{angle1}[$j]) + and ($data->{angle2}[$i] > $data->{angle2}[$j])) + or (($data->{angle1}[$i] == $data->{angle1}[$j]) + and ($data->{angle2}[$i] == $data->{angle2}[$j]) + and ($data->{angle3}[$i] > $data->{angle3}[$j]))) { + $did_swap = 1; + my @tmp = ($data->{anglet}[$i], $data->{angle1}[$i], + $data->{angle2}[$i], $data->{angle3}[$i]); + ($data->{anglet}[$i], $data->{angle1}[$i], + $data->{angle2}[$i], $data->{angle3}[$i]) = + ($data->{anglet}[$j], $data->{angle1}[$j], + $data->{angle2}[$j], $data->{angle3}[$j]); + ($data->{anglet}[$j], $data->{angle1}[$j], + $data->{angle2}[$j], $data->{angle3}[$j]) = @tmp; + } + } + --$num; + } + } } elsif ($1 eq "Dihedrals") { $data->{dihedralt} = []; $data->{dihedral1} = []; @@ -684,6 +732,38 @@ sub read_data { last; } + # apply sort + if ($data->{ndihedrals} > 1) { + my ($did_swap, $num) = (1, $data->{ndihedrals}); + while ($did_swap) { + $did_swap = 0; + for ($i=0; $i < $num-1; ++$i) { + $j = $i+1; + if (($data->{dihedral1}[$i] > $data->{dihedral1}[$j]) + or (($data->{dihedral1}[$i] == $data->{dihedral1}[$j]) + and ($data->{dihedral2}[$i] > $data->{dihedral2}[$j])) + or (($data->{dihedral1}[$i] == $data->{dihedral1}[$j]) + and ($data->{dihedral2}[$i] == $data->{dihedral2}[$j]) + and ($data->{dihedral3}[$i] > $data->{dihedral3}[$j])) + or (($data->{dihedral1}[$i] == $data->{dihedral1}[$j]) + and ($data->{dihedral2}[$i] == $data->{dihedral2}[$j]) + and ($data->{dihedral3}[$i] == $data->{dihedral3}[$j]) + and ($data->{dihedral4}[$i] > $data->{dihedral4}[$j]))) { + $did_swap = 1; + my @tmp = ($data->{dihedralt}[$i], $data->{dihedral1}[$i], + $data->{dihedral2}[$i], $data->{dihedral3}[$i], + $data->{dihedral4}[$i]); + ($data->{dihedralt}[$i], $data->{dihedral1}[$i], $data->{dihedral2}[$i], + $data->{dihedral3}[$i], $data->{dihedral4}[$i]) = + ($data->{dihedralt}[$j], $data->{dihedral1}[$j], + $data->{dihedral2}[$j], $data->{dihedral3}[$j], $data->{dihedral4}[$j]); + ($data->{dihedralt}[$j], $data->{dihedral1}[$j], $data->{dihedral2}[$j], + $data->{dihedral3}[$j], $data->{dihedral4}[$j]) = @tmp; + } + } + --$num; + } + } } elsif ($1 eq "Impropers") { $data->{impropert} = []; $data->{improper1} = []; @@ -730,6 +810,39 @@ sub read_data { last; } + # apply sort + if ($data->{nimpropers} > 1) { + my ($did_swap, $num) = (1, $data->{nimpropers}); + while ($did_swap) { + $did_swap = 0; + for ($i=0; $i < $num-1; ++$i) { + $j = $i+1; + if (($data->{improper1}[$i] > $data->{improper1}[$j]) + or (($data->{improper1}[$i] == $data->{improper1}[$j]) + and ($data->{improper2}[$i] > $data->{improper2}[$j])) + or (($data->{improper1}[$i] == $data->{improper1}[$j]) + and ($data->{improper2}[$i] == $data->{improper2}[$j]) + and ($data->{improper3}[$i] > $data->{improper3}[$j])) + or (($data->{improper1}[$i] == $data->{improper1}[$j]) + and ($data->{improper2}[$i] == $data->{improper2}[$j]) + and ($data->{improper3}[$i] == $data->{improper3}[$j]) + and ($data->{improper4}[$i] > $data->{improper4}[$j]))) { + $did_swap = 1; + my @tmp = ($data->{impropert}[$i], $data->{improper1}[$i], + $data->{improper2}[$i], $data->{improper3}[$i], + $data->{improper4}[$i]); + ($data->{impropert}[$i], $data->{improper1}[$i], $data->{improper2}[$i], + $data->{improper3}[$i], $data->{improper4}[$i]) = + ($data->{impropert}[$j], $data->{improper1}[$j], + $data->{improper2}[$j], $data->{improper3}[$j], $data->{improper4}[$j]); + ($data->{impropert}[$j], $data->{improper1}[$j], $data->{improper2}[$j], + $data->{improper3}[$j], $data->{improper4}[$j]) = @tmp; + } + } + --$num; + } + } + } else { die "Bad data: $_"; } diff --git a/tools/msi2lmp/test/in.PyAC_bulk-clayff b/tools/msi2lmp/test/in.PyAC_bulk-clayff index 1c6663a679..923891b920 100644 --- a/tools/msi2lmp/test/in.PyAC_bulk-clayff +++ b/tools/msi2lmp/test/in.PyAC_bulk-clayff @@ -5,9 +5,9 @@ atom_style full pair_style lj/cut/coul/long 15.0 pair_modify mix geometric bond_style harmonic -kspace_style pppm 1.0e-5 read_data PyAC_bulk-clayff.data +kspace_style pppm 1.0e-5 thermo_style multi minimize 0.0 0.0 100 1000 diff --git a/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data b/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data index 6b6602d69d..0a304ea296 100644 --- a/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data +++ b/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data @@ -1,4 +1,4 @@ -LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for PyAC_bulk-clayff +LAMMPS data file. msi2lmp v3.9.10 / 10 Mar 2023 / CGCMM for PyAC_bulk-clayff 1280 atoms 128 bonds @@ -11,7 +11,7 @@ LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for PyAC_bulk-clayff -10.320000000 10.320000000 xlo xhi -17.931646038 17.931646038 ylo yhi - -9.196614681 9.196614681 zlo zhi + -9.189871922 9.189871922 zlo zhi 0.225338675 -3.393877748 -0.363656523 xy xz yz Masses @@ -676,27 +676,27 @@ Atoms # full 638 1 3 -1.050000 -0.590722660 -5.885450799 -3.293650032 1 1 0 # ob 639 1 3 -1.050000 0.277898824 -8.390728187 -3.055632561 1 1 0 # ob 640 1 5 0.425000 -4.694842406 -6.184112754 -1.194847627 1 1 0 # ho - 641 1 1 1.575000 0.889889112 1.315464043 9.189872068 0 0 0 # ao - 642 1 2 2.100000 5.101961261 9.067732250 -6.523590700 0 0 1 # st - 643 1 2 2.100000 5.138292081 3.048848378 -6.517157818 0 0 1 # st - 644 1 3 -1.050000 4.852463935 0.176965538 -8.141927041 0 0 1 # ob - 645 1 3 -1.050000 5.291802919 2.921349398 -8.139170101 0 0 1 # ob - 646 1 4 -0.950000 2.692063605 1.889886595 -8.209932150 0 0 1 # oh - 647 1 3 -1.050000 1.366795516 3.605171499 -5.905112111 0 0 1 # ob - 648 1 3 -1.050000 4.839493963 1.584366125 -5.909707262 0 0 1 # ob - 649 1 3 -1.050000 3.970872479 4.089643514 -6.147724732 0 0 1 # ob - 650 1 5 0.425000 3.783613862 1.883028080 -8.008509666 0 0 1 # ho - 651 1 1 1.575000 3.498056417 5.798375353 9.189872068 0 0 0 # ao - 652 1 2 2.100000 2.493793956 4.584820940 -6.523590700 0 0 1 # st - 653 1 2 2.100000 2.586459538 7.531759689 -6.517157818 0 0 1 # st - 654 1 3 -1.050000 2.300631392 4.659876849 -8.141927041 0 0 1 # ob - 655 1 3 -1.050000 2.739970376 7.404260709 -8.139170101 0 0 1 # ob - 656 1 4 -0.950000 5.300230909 6.372797905 -8.209932150 0 0 1 # oh - 657 1 3 -1.050000 3.974962821 8.088082810 -5.905112111 0 0 1 # ob - 658 1 3 -1.050000 2.287661420 6.067277436 -5.909707262 0 0 1 # ob - 659 1 3 -1.050000 1.419039936 8.572554825 -6.147724732 0 0 1 # ob - 660 1 5 0.425000 6.391781167 6.365939391 -8.008509666 0 0 1 # ho - 661 1 1 1.575000 0.932567998 7.286701985 9.189872068 0 0 0 # ao + 641 1 1 1.575000 4.283766860 1.679120566 -9.189871776 0 0 1 # ao + 642 1 2 2.100000 5.101961261 9.067732250 -6.510105182 0 0 1 # st + 643 1 2 2.100000 5.138292081 3.048848378 -6.503672300 0 0 1 # st + 644 1 3 -1.050000 4.852463935 0.176965538 -8.128441523 0 0 1 # ob + 645 1 3 -1.050000 5.291802919 2.921349398 -8.125684583 0 0 1 # ob + 646 1 4 -0.950000 2.692063605 1.889886595 -8.196446632 0 0 1 # oh + 647 1 3 -1.050000 1.366795516 3.605171499 -5.891626593 0 0 1 # ob + 648 1 3 -1.050000 4.839493963 1.584366125 -5.896221744 0 0 1 # ob + 649 1 3 -1.050000 3.970872479 4.089643514 -6.134239214 0 0 1 # ob + 650 1 5 0.425000 3.783613862 1.883028080 -7.995024148 0 0 1 # ho + 651 1 1 1.575000 6.891934165 6.162031876 -9.189871776 0 0 1 # ao + 652 1 2 2.100000 2.493793956 4.584820940 -6.510105182 0 0 1 # st + 653 1 2 2.100000 2.586459538 7.531759689 -6.503672300 0 0 1 # st + 654 1 3 -1.050000 2.300631392 4.659876849 -8.128441523 0 0 1 # ob + 655 1 3 -1.050000 2.739970376 7.404260709 -8.125684583 0 0 1 # ob + 656 1 4 -0.950000 5.300230909 6.372797905 -8.196446632 0 0 1 # oh + 657 1 3 -1.050000 3.974962821 8.088082810 -5.891626593 0 0 1 # ob + 658 1 3 -1.050000 2.287661420 6.067277436 -5.896221744 0 0 1 # ob + 659 1 3 -1.050000 1.419039936 8.572554825 -6.134239214 0 0 1 # ob + 660 1 5 0.425000 6.391781167 6.365939391 -7.995024148 0 0 1 # ho + 661 1 1 1.575000 4.326445746 7.650358508 -9.189871776 0 0 1 # ao 662 1 2 2.100000 0.114373597 -0.101909699 6.510105475 0 0 0 # st 663 1 2 2.100000 0.078042778 5.916974173 6.503672592 0 0 0 # st 664 1 3 -1.050000 0.363870923 8.788857013 8.128441816 0 0 0 # ob @@ -706,7 +706,7 @@ Atoms # full 668 1 3 -1.050000 0.376840895 7.381456426 5.896222036 0 0 0 # ob 669 1 3 -1.050000 1.245462379 4.876179037 6.134239507 0 0 0 # ob 670 1 5 0.425000 1.432720996 7.082794471 7.995024441 0 0 0 # ho - 671 1 1 1.575000 -1.675599307 2.803790675 9.189872068 0 0 0 # ao + 671 1 1 1.575000 1.718278441 3.167447198 -9.189871776 0 0 1 # ao 672 1 2 2.100000 2.722540902 4.381001611 6.510105475 0 0 0 # st 673 1 2 2.100000 2.629875320 1.434062862 6.503672592 0 0 0 # st 674 1 3 -1.050000 2.915703466 4.305945702 8.128441816 0 0 0 # ob @@ -716,27 +716,27 @@ Atoms # full 678 1 3 -1.050000 2.928673438 2.898545115 5.896222036 0 0 0 # ob 679 1 3 -1.050000 3.797294922 0.393267726 6.134239507 0 0 0 # ob 680 1 5 0.425000 -1.175446309 2.599883160 7.995024441 0 0 0 # ho - 681 1 1 1.575000 6.049888960 1.315464043 9.189872068 0 0 0 # ao - 682 1 2 2.100000 -10.378038892 9.067732250 -6.523590700 1 0 1 # st - 683 1 2 2.100000 -10.341708072 3.048848378 -6.517157818 1 0 1 # st - 684 1 3 -1.050000 10.012463782 0.176965538 -8.141927041 0 0 1 # ob - 685 1 3 -1.050000 -10.188197233 2.921349398 -8.139170101 1 0 1 # ob - 686 1 4 -0.950000 7.852063452 1.889886595 -8.209932150 0 0 1 # oh - 687 1 3 -1.050000 6.526795364 3.605171499 -5.905112111 0 0 1 # ob - 688 1 3 -1.050000 -10.640506189 1.584366125 -5.909707262 1 0 1 # ob - 689 1 3 -1.050000 9.130872326 4.089643514 -6.147724732 0 0 1 # ob - 690 1 5 0.425000 8.943613710 1.883028080 -8.008509666 0 0 1 # ho - 691 1 1 1.575000 -11.981943736 5.798375353 9.189872068 1 0 0 # ao - 692 1 2 2.100000 7.653793804 4.584820940 -6.523590700 0 0 1 # st - 693 1 2 2.100000 7.746459385 7.531759689 -6.517157818 0 0 1 # st - 694 1 3 -1.050000 7.460631240 4.659876849 -8.141927041 0 0 1 # ob - 695 1 3 -1.050000 7.899970224 7.404260709 -8.139170101 0 0 1 # ob - 696 1 4 -0.950000 -10.179769243 6.372797905 -8.209932150 1 0 1 # oh - 697 1 3 -1.050000 9.134962668 8.088082810 -5.905112111 0 0 1 # ob - 698 1 3 -1.050000 7.447661268 6.067277436 -5.909707262 0 0 1 # ob - 699 1 3 -1.050000 6.579039784 8.572554825 -6.147724732 0 0 1 # ob - 700 1 5 0.425000 -9.088218986 6.365939391 -8.008509666 1 0 1 # ho - 701 1 1 1.575000 6.092567845 7.286701985 9.189872068 0 0 0 # ao + 681 1 1 1.575000 9.443766708 1.679120566 -9.189871776 0 0 1 # ao + 682 1 2 2.100000 -10.378038892 9.067732250 -6.510105182 1 0 1 # st + 683 1 2 2.100000 -10.341708072 3.048848378 -6.503672300 1 0 1 # st + 684 1 3 -1.050000 10.012463782 0.176965538 -8.128441523 0 0 1 # ob + 685 1 3 -1.050000 -10.188197233 2.921349398 -8.125684583 1 0 1 # ob + 686 1 4 -0.950000 7.852063452 1.889886595 -8.196446632 0 0 1 # oh + 687 1 3 -1.050000 6.526795364 3.605171499 -5.891626593 0 0 1 # ob + 688 1 3 -1.050000 -10.640506189 1.584366125 -5.896221744 1 0 1 # ob + 689 1 3 -1.050000 9.130872326 4.089643514 -6.134239214 0 0 1 # ob + 690 1 5 0.425000 8.943613710 1.883028080 -7.995024148 0 0 1 # ho + 691 1 1 1.575000 -8.588065988 6.162031876 -9.189871776 1 0 1 # ao + 692 1 2 2.100000 7.653793804 4.584820940 -6.510105182 0 0 1 # st + 693 1 2 2.100000 7.746459385 7.531759689 -6.503672300 0 0 1 # st + 694 1 3 -1.050000 7.460631240 4.659876849 -8.128441523 0 0 1 # ob + 695 1 3 -1.050000 7.899970224 7.404260709 -8.125684583 0 0 1 # ob + 696 1 4 -0.950000 -10.179769243 6.372797905 -8.196446632 1 0 1 # oh + 697 1 3 -1.050000 9.134962668 8.088082810 -5.891626593 0 0 1 # ob + 698 1 3 -1.050000 7.447661268 6.067277436 -5.896221744 0 0 1 # ob + 699 1 3 -1.050000 6.579039784 8.572554825 -6.134239214 0 0 1 # ob + 700 1 5 0.425000 -9.088218986 6.365939391 -7.995024148 1 0 1 # ho + 701 1 1 1.575000 9.486445593 7.650358508 -9.189871776 0 0 1 # ao 702 1 2 2.100000 5.274373445 -0.101909699 6.510105475 0 0 0 # st 703 1 2 2.100000 5.238042625 5.916974173 6.503672592 0 0 0 # st 704 1 3 -1.050000 5.523870771 8.788857013 8.128441816 0 0 0 # ob @@ -746,7 +746,7 @@ Atoms # full 708 1 3 -1.050000 5.536840742 7.381456426 5.896222036 0 0 0 # ob 709 1 3 -1.050000 6.405462227 4.876179037 6.134239507 0 0 0 # ob 710 1 5 0.425000 6.592720843 7.082794471 7.995024441 0 0 0 # ho - 711 1 1 1.575000 3.484400541 2.803790675 9.189872068 0 0 0 # ao + 711 1 1 1.575000 6.878278289 3.167447198 -9.189871776 0 0 1 # ao 712 1 2 2.100000 -12.757459251 4.381001611 6.510105475 1 0 0 # st 713 1 2 2.100000 -12.850124832 1.434062862 6.503672592 1 0 0 # st 714 1 3 -1.050000 -12.564296687 4.305945702 8.128441816 1 0 0 # ob @@ -756,27 +756,27 @@ Atoms # full 718 1 3 -1.050000 -12.551326715 2.898545115 5.896222036 1 0 0 # ob 719 1 3 -1.050000 -11.682705231 0.393267726 6.134239507 1 0 0 # ob 720 1 5 0.425000 3.984553539 2.599883160 7.995024441 0 0 0 # ho - 721 1 1 1.575000 -9.430111193 1.315464043 9.189872068 1 0 0 # ao - 722 1 2 2.100000 -5.218039044 9.067732250 -6.523590700 1 0 1 # st - 723 1 2 2.100000 -5.181708225 3.048848378 -6.517157818 1 0 1 # st - 724 1 3 -1.050000 -5.467536370 0.176965538 -8.141927041 1 0 1 # ob - 725 1 3 -1.050000 -5.028197386 2.921349398 -8.139170101 1 0 1 # ob - 726 1 4 -0.950000 -7.627936701 1.889886595 -8.209932150 1 0 1 # oh - 727 1 3 -1.050000 -8.953204789 3.605171499 -5.905112111 1 0 1 # ob - 728 1 3 -1.050000 -5.480506342 1.584366125 -5.909707262 1 0 1 # ob - 729 1 3 -1.050000 -6.349127826 4.089643514 -6.147724732 1 0 1 # ob - 730 1 5 0.425000 -6.536386443 1.883028080 -8.008509666 1 0 1 # ho - 731 1 1 1.575000 -6.821943888 5.798375353 9.189872068 1 0 0 # ao - 732 1 2 2.100000 -7.826206349 4.584820940 -6.523590700 1 0 1 # st - 733 1 2 2.100000 -7.733540767 7.531759689 -6.517157818 1 0 1 # st - 734 1 3 -1.050000 -8.019368913 4.659876849 -8.141927041 1 0 1 # ob - 735 1 3 -1.050000 -7.580029929 7.404260709 -8.139170101 1 0 1 # ob - 736 1 4 -0.950000 -5.019769396 6.372797905 -8.209932150 1 0 1 # oh - 737 1 3 -1.050000 -6.345037484 8.088082810 -5.905112111 1 0 1 # ob - 738 1 3 -1.050000 -8.032338885 6.067277436 -5.909707262 1 0 1 # ob - 739 1 3 -1.050000 -8.900960369 8.572554825 -6.147724732 1 0 1 # ob - 740 1 5 0.425000 -3.928219138 6.365939391 -8.008509666 1 0 1 # ho - 741 1 1 1.575000 -9.387432307 7.286701985 9.189872068 1 0 0 # ao + 721 1 1 1.575000 -6.036233445 1.679120566 -9.189871776 1 0 1 # ao + 722 1 2 2.100000 -5.218039044 9.067732250 -6.510105182 1 0 1 # st + 723 1 2 2.100000 -5.181708225 3.048848378 -6.503672300 1 0 1 # st + 724 1 3 -1.050000 -5.467536370 0.176965538 -8.128441523 1 0 1 # ob + 725 1 3 -1.050000 -5.028197386 2.921349398 -8.125684583 1 0 1 # ob + 726 1 4 -0.950000 -7.627936701 1.889886595 -8.196446632 1 0 1 # oh + 727 1 3 -1.050000 -8.953204789 3.605171499 -5.891626593 1 0 1 # ob + 728 1 3 -1.050000 -5.480506342 1.584366125 -5.896221744 1 0 1 # ob + 729 1 3 -1.050000 -6.349127826 4.089643514 -6.134239214 1 0 1 # ob + 730 1 5 0.425000 -6.536386443 1.883028080 -7.995024148 1 0 1 # ho + 731 1 1 1.575000 -3.428066140 6.162031876 -9.189871776 1 0 1 # ao + 732 1 2 2.100000 -7.826206349 4.584820940 -6.510105182 1 0 1 # st + 733 1 2 2.100000 -7.733540767 7.531759689 -6.503672300 1 0 1 # st + 734 1 3 -1.050000 -8.019368913 4.659876849 -8.128441523 1 0 1 # ob + 735 1 3 -1.050000 -7.580029929 7.404260709 -8.125684583 1 0 1 # ob + 736 1 4 -0.950000 -5.019769396 6.372797905 -8.196446632 1 0 1 # oh + 737 1 3 -1.050000 -6.345037484 8.088082810 -5.891626593 1 0 1 # ob + 738 1 3 -1.050000 -8.032338885 6.067277436 -5.896221744 1 0 1 # ob + 739 1 3 -1.050000 -8.900960369 8.572554825 -6.134239214 1 0 1 # ob + 740 1 5 0.425000 -3.928219138 6.365939391 -7.995024148 1 0 1 # ho + 741 1 1 1.575000 -5.993554559 7.650358508 -9.189871776 1 0 1 # ao 742 1 2 2.100000 -10.205626708 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-2.593026305 -8.196446632 1 1 1 # oh + 1177 1 3 -1.050000 9.078628279 -0.877741400 -5.891626593 0 1 1 # ob + 1178 1 3 -1.050000 7.391326878 -2.898546774 -5.896221744 0 1 1 # ob + 1179 1 3 -1.050000 6.522705394 -0.393269386 -6.134239214 0 1 1 # ob + 1180 1 5 0.425000 -9.144553375 -2.599884819 -7.995024148 1 1 1 # ho + 1181 1 1 1.575000 9.430111204 -1.315465702 -9.189871776 0 1 1 # ao 1182 1 2 2.100000 5.218039055 -9.067733910 6.510105475 0 1 0 # st 1183 1 2 2.100000 5.181708235 -3.048850038 6.503672592 0 1 0 # st 1184 1 3 -1.050000 5.467536381 -0.176967197 8.128441816 0 1 0 # ob @@ -1226,7 +1226,7 @@ Atoms # full 1188 1 3 -1.050000 5.480506353 -1.584367785 5.896222036 0 1 0 # ob 1189 1 3 -1.050000 6.349127837 -4.089645173 6.134239507 0 1 0 # ob 1190 1 5 0.425000 6.536386454 -1.883029740 7.995024441 0 1 0 # ho - 1191 1 1 1.575000 3.428066151 -6.162033536 9.189872068 0 1 0 # ao + 1191 1 1 1.575000 6.821943899 -5.798377013 -9.189871776 0 1 1 # ao 1192 1 2 2.100000 -12.813793640 -4.584822599 6.510105475 1 1 0 # st 1193 1 2 2.100000 -12.906459222 -7.531761349 6.503672592 1 1 0 # st 1194 1 3 -1.050000 -12.620631076 -4.659878508 8.128441816 1 1 0 # ob @@ -1236,27 +1236,27 @@ Atoms # full 1198 1 3 -1.050000 -12.607661104 -6.067279095 5.896222036 1 1 0 # ob 1199 1 3 -1.050000 -11.739039620 -8.572556484 6.134239507 1 1 0 # ob 1200 1 5 0.425000 3.928219149 -6.365941050 7.995024441 0 1 0 # ho - 1201 1 1 1.575000 -9.486445582 -7.650360168 9.189872068 1 1 0 # ao - 1202 1 2 2.100000 -5.274373434 0.101908040 -6.523590700 1 1 1 # st - 1203 1 2 2.100000 -5.238042614 -5.916975832 -6.517157818 1 1 1 # st - 1204 1 3 -1.050000 -5.523870760 -8.788858673 -8.141927041 1 1 1 # ob - 1205 1 3 -1.050000 -5.084531776 -6.044474812 -8.139170101 1 1 1 # ob - 1206 1 4 -0.950000 -7.684271090 -7.075937616 -8.209932150 1 1 1 # oh - 1207 1 3 -1.050000 -9.009539178 -5.360652711 -5.905112111 1 1 1 # ob - 1208 1 3 -1.050000 -5.536840731 -7.381458085 -5.909707262 1 1 1 # ob - 1209 1 3 -1.050000 -6.405462216 -4.876180697 -6.147724732 1 1 1 # ob - 1210 1 5 0.425000 -6.592720833 -7.082796130 -8.008509666 1 1 1 # ho - 1211 1 1 1.575000 -6.878278278 -3.167448857 9.189872068 1 1 0 # ao - 1212 1 2 2.100000 -7.882540739 -4.381003271 -6.523590700 1 1 1 # st - 1213 1 2 2.100000 -7.789875157 -1.434064521 -6.517157818 1 1 1 # st - 1214 1 3 -1.050000 -8.075703302 -4.305947362 -8.141927041 1 1 1 # ob - 1215 1 3 -1.050000 -7.636364318 -1.561563502 -8.139170101 1 1 1 # ob - 1216 1 4 -0.950000 -5.076103786 -2.593026305 -8.209932150 1 1 1 # oh - 1217 1 3 -1.050000 -6.401371874 -0.877741400 -5.905112111 1 1 1 # ob - 1218 1 3 -1.050000 -8.088673274 -2.898546774 -5.909707262 1 1 1 # ob - 1219 1 3 -1.050000 -8.957294759 -0.393269386 -6.147724732 1 1 1 # ob - 1220 1 5 0.425000 -3.984553528 -2.599884819 -8.008509666 1 1 1 # ho - 1221 1 1 1.575000 -9.443766697 -1.679122225 9.189872068 1 1 0 # ao + 1201 1 1 1.575000 -6.092567834 -7.286703645 -9.189871776 1 1 1 # ao + 1202 1 2 2.100000 -5.274373434 0.101908040 -6.510105182 1 1 1 # st + 1203 1 2 2.100000 -5.238042614 -5.916975832 -6.503672300 1 1 1 # st + 1204 1 3 -1.050000 -5.523870760 -8.788858673 -8.128441523 1 1 1 # ob + 1205 1 3 -1.050000 -5.084531776 -6.044474812 -8.125684583 1 1 1 # ob + 1206 1 4 -0.950000 -7.684271090 -7.075937616 -8.196446632 1 1 1 # oh + 1207 1 3 -1.050000 -9.009539178 -5.360652711 -5.891626593 1 1 1 # ob + 1208 1 3 -1.050000 -5.536840731 -7.381458085 -5.896221744 1 1 1 # ob + 1209 1 3 -1.050000 -6.405462216 -4.876180697 -6.134239214 1 1 1 # ob + 1210 1 5 0.425000 -6.592720833 -7.082796130 -7.995024148 1 1 1 # ho + 1211 1 1 1.575000 -3.484400530 -2.803792334 -9.189871776 1 1 1 # ao + 1212 1 2 2.100000 -7.882540739 -4.381003271 -6.510105182 1 1 1 # st + 1213 1 2 2.100000 -7.789875157 -1.434064521 -6.503672300 1 1 1 # st + 1214 1 3 -1.050000 -8.075703302 -4.305947362 -8.128441523 1 1 1 # ob + 1215 1 3 -1.050000 -7.636364318 -1.561563502 -8.125684583 1 1 1 # ob + 1216 1 4 -0.950000 -5.076103786 -2.593026305 -8.196446632 1 1 1 # oh + 1217 1 3 -1.050000 -6.401371874 -0.877741400 -5.891626593 1 1 1 # ob + 1218 1 3 -1.050000 -8.088673274 -2.898546774 -5.896221744 1 1 1 # ob + 1219 1 3 -1.050000 -8.957294759 -0.393269386 -6.134239214 1 1 1 # ob + 1220 1 5 0.425000 -3.984553528 -2.599884819 -7.995024148 1 1 1 # ho + 1221 1 1 1.575000 -6.049888949 -1.315465702 -9.189871776 1 1 1 # ao 1222 1 2 2.100000 -10.261961097 -9.067733910 6.510105475 1 1 0 # st 1223 1 2 2.100000 -10.298291917 -3.048850038 6.503672592 1 1 0 # st 1224 1 3 -1.050000 -10.012463772 -0.176967197 8.128441816 1 1 0 # ob @@ -1266,7 +1266,7 @@ Atoms # full 1228 1 3 -1.050000 -9.999493800 -1.584367785 5.896222036 1 1 0 # ob 1229 1 3 -1.050000 -9.130872315 -4.089645173 6.134239507 1 1 0 # ob 1230 1 5 0.425000 -8.943613699 -1.883029740 7.995024441 1 1 0 # ho - 1231 1 1 1.575000 -12.051934002 -6.162033536 9.189872068 1 1 0 # ao + 1231 1 1 1.575000 -8.658056254 -5.798377013 -9.189871776 1 1 1 # ao 1232 1 2 2.100000 -7.653793793 -4.584822599 6.510105475 1 1 0 # st 1233 1 2 2.100000 -7.746459374 -7.531761349 6.503672592 1 1 0 # st 1234 1 3 -1.050000 -7.460631229 -4.659878508 8.128441816 1 1 0 # ob @@ -1276,27 +1276,27 @@ Atoms # full 1238 1 3 -1.050000 -7.447661257 -6.067279095 5.896222036 1 1 0 # ob 1239 1 3 -1.050000 -6.579039773 -8.572556484 6.134239507 1 1 0 # ob 1240 1 5 0.425000 -11.551781003 -6.365941050 7.995024441 1 1 0 # ho - 1241 1 1 1.575000 -4.326445735 -7.650360168 9.189872068 1 1 0 # ao - 1242 1 2 2.100000 -0.114373587 0.101908040 -6.523590700 1 1 1 # st - 1243 1 2 2.100000 -0.078042767 -5.916975832 -6.517157818 1 1 1 # st - 1244 1 3 -1.050000 -0.363870912 -8.788858673 -8.141927041 1 1 1 # ob - 1245 1 3 -1.050000 0.075468072 -6.044474812 -8.139170101 1 1 1 # ob - 1246 1 4 -0.950000 -2.524271243 -7.075937616 -8.209932150 1 1 1 # oh - 1247 1 3 -1.050000 -3.849539331 -5.360652711 -5.905112111 1 1 1 # ob - 1248 1 3 -1.050000 -0.376840884 -7.381458085 -5.909707262 1 1 1 # ob - 1249 1 3 -1.050000 -1.245462368 -4.876180697 -6.147724732 1 1 1 # ob - 1250 1 5 0.425000 -1.432720985 -7.082796130 -8.008509666 1 1 1 # ho - 1251 1 1 1.575000 -1.718278430 -3.167448857 9.189872068 1 1 0 # ao - 1252 1 2 2.100000 -2.722540891 -4.381003271 -6.523590700 1 1 1 # st - 1253 1 2 2.100000 -2.629875310 -1.434064521 -6.517157818 1 1 1 # st - 1254 1 3 -1.050000 -2.915703455 -4.305947362 -8.141927041 1 1 1 # ob - 1255 1 3 -1.050000 -2.476364471 -1.561563502 -8.139170101 1 1 1 # ob - 1256 1 4 -0.950000 0.083896062 -2.593026305 -8.209932150 1 1 1 # oh - 1257 1 3 -1.050000 -1.241372026 -0.877741400 -5.905112111 1 1 1 # ob - 1258 1 3 -1.050000 -2.928673427 -2.898546774 -5.909707262 1 1 1 # ob - 1259 1 3 -1.050000 -3.797294911 -0.393269386 -6.147724732 1 1 1 # ob - 1260 1 5 0.425000 1.175446320 -2.599884819 -8.008509666 1 1 1 # ho - 1261 1 1 1.575000 -4.283766850 -1.679122225 9.189872068 1 1 0 # ao + 1241 1 1 1.575000 -0.932567987 -7.286703645 -9.189871776 1 1 1 # ao + 1242 1 2 2.100000 -0.114373587 0.101908040 -6.510105182 1 1 1 # st + 1243 1 2 2.100000 -0.078042767 -5.916975832 -6.503672300 1 1 1 # st + 1244 1 3 -1.050000 -0.363870912 -8.788858673 -8.128441523 1 1 1 # ob + 1245 1 3 -1.050000 0.075468072 -6.044474812 -8.125684583 1 1 1 # ob + 1246 1 4 -0.950000 -2.524271243 -7.075937616 -8.196446632 1 1 1 # oh + 1247 1 3 -1.050000 -3.849539331 -5.360652711 -5.891626593 1 1 1 # ob + 1248 1 3 -1.050000 -0.376840884 -7.381458085 -5.896221744 1 1 1 # ob + 1249 1 3 -1.050000 -1.245462368 -4.876180697 -6.134239214 1 1 1 # ob + 1250 1 5 0.425000 -1.432720985 -7.082796130 -7.995024148 1 1 1 # ho + 1251 1 1 1.575000 1.675599318 -2.803792334 -9.189871776 1 1 1 # ao + 1252 1 2 2.100000 -2.722540891 -4.381003271 -6.510105182 1 1 1 # st + 1253 1 2 2.100000 -2.629875310 -1.434064521 -6.503672300 1 1 1 # st + 1254 1 3 -1.050000 -2.915703455 -4.305947362 -8.128441523 1 1 1 # ob + 1255 1 3 -1.050000 -2.476364471 -1.561563502 -8.125684583 1 1 1 # ob + 1256 1 4 -0.950000 0.083896062 -2.593026305 -8.196446632 1 1 1 # oh + 1257 1 3 -1.050000 -1.241372026 -0.877741400 -5.891626593 1 1 1 # ob + 1258 1 3 -1.050000 -2.928673427 -2.898546774 -5.896221744 1 1 1 # ob + 1259 1 3 -1.050000 -3.797294911 -0.393269386 -6.134239214 1 1 1 # ob + 1260 1 5 0.425000 1.175446320 -2.599884819 -7.995024148 1 1 1 # ho + 1261 1 1 1.575000 -0.889889102 -1.315465702 -9.189871776 1 1 1 # ao 1262 1 2 2.100000 -5.101961250 -9.067733910 6.510105475 1 1 0 # st 1263 1 2 2.100000 -5.138292070 -3.048850038 6.503672592 1 1 0 # st 1264 1 3 -1.050000 -4.852463924 -0.176967197 8.128441816 1 1 0 # ob @@ -1306,7 +1306,7 @@ Atoms # full 1268 1 3 -1.050000 -4.839493952 -1.584367785 5.896222036 1 1 0 # ob 1269 1 3 -1.050000 -3.970872468 -4.089645173 6.134239507 1 1 0 # ob 1270 1 5 0.425000 -3.783613851 -1.883029740 7.995024441 1 1 0 # ho - 1271 1 1 1.575000 -6.891934154 -6.162033536 9.189872068 1 1 0 # ao + 1271 1 1 1.575000 -3.498056406 -5.798377013 -9.189871776 1 1 1 # ao 1272 1 2 2.100000 -2.493793945 -4.584822599 6.510105475 1 1 0 # st 1273 1 2 2.100000 -2.586459527 -7.531761349 6.503672592 1 1 0 # st 1274 1 3 -1.050000 -2.300631381 -4.659878508 8.128441816 1 1 0 # ob diff --git a/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2 b/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2 index 4ee3c34e08..c37bbbfb6e 100644 --- a/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2 +++ b/tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2 @@ -1,18 +1,18 @@ -LAMMPS data file via write_data, version 5 Oct 2016, timestep = 97 +LAMMPS data file via write_data, version 29 Aug 2024, timestep = 94, units = real 1280 atoms 5 atom types 128 bonds 1 bond types --1.0320000000000000e+01 1.0320000000000000e+01 xlo xhi --1.7931646038000000e+01 1.7931646038000000e+01 ylo yhi --9.1966146809999998e+00 9.1966146809999998e+00 zlo zhi -2.2533867499999999e-01 -3.3938777480000000e+00 -3.6365652300000001e-01 xy xz yz +-10.32 10.32 xlo xhi +-17.931646038 17.931646038 ylo yhi +-9.189871922 9.189871922 zlo zhi +0.225338675 -3.393877748 -0.363656523 xy xz yz Masses -1 26.9815 +1 26.98154 2 28.0855 3 15.9994 4 15.9994 @@ -32,2697 +32,2697 @@ Bond Coeffs # harmonic Atoms # full -1 1 1 1.5750000000000000e+00 2.5999859887541152e+00 1.4895295600930361e+00 -3.2684095454396100e-03 0 0 0 -2 1 2 2.1000000000000001e+00 3.3890158510276365e+00 8.8633001207774171e+00 2.7539653683351801e+00 0 0 0 -3 1 2 2.1000000000000001e+00 3.4122910819528869e+00 2.8524994338649421e+00 2.7618119426027334e+00 0 0 0 -4 1 3 -1.0500000000000000e+00 3.1917106615190871e+00 -3.1338269933883112e-02 1.1357135267887219e+00 0 0 0 -5 1 3 -1.0500000000000000e+00 3.5469715140592335e+00 2.7595296221569008e+00 1.1370155152705124e+00 0 0 0 -6 1 4 -9.4999999999999996e-01 9.0629865585113478e-01 1.5632893985929819e+00 1.0069802353213007e+00 0 0 0 -7 1 3 -1.0500000000000000e+00 -4.4288757751145802e-01 3.5553420116799757e+00 3.2357631024135358e+00 0 0 0 -8 1 3 -1.0500000000000000e+00 3.3001891233613350e+00 1.3781620274833877e+00 3.2374587487515178e+00 0 0 0 -9 1 3 -1.0500000000000000e+00 2.1467877066985572e+00 3.7041759320173213e+00 3.0459627186065976e+00 0 0 0 -10 1 5 4.2499999999999999e-01 3.9940955153589464e-01 6.8440286676932871e-01 1.1507107600825695e+00 0 0 0 -11 1 1 1.5750000000000000e+00 5.2081610166521486e+00 5.9724603411204953e+00 -3.2678269427819373e-03 0 0 0 -12 1 2 2.1000000000000001e+00 7.8082390717283801e-01 4.3803873151640857e+00 2.7539573196414509e+00 0 0 0 -13 1 2 2.1000000000000001e+00 8.6049184758384811e-01 7.3353954630155727e+00 2.7618077229661608e+00 0 0 0 -14 1 3 -1.0500000000000000e+00 6.3985291874622341e-01 4.4515561398457919e+00 1.1357491950576897e+00 0 0 0 -15 1 3 -1.0500000000000000e+00 9.9516171983727020e-01 7.2424161873666044e+00 1.1369982112775414e+00 0 0 0 -16 1 4 -9.4999999999999996e-01 3.5145105035101025e+00 6.0462386370433165e+00 1.0069819170376704e+00 0 0 0 -17 1 3 -1.0500000000000000e+00 2.1653116942489294e+00 8.0382453753562579e+00 3.2357864576820852e+00 0 0 0 -18 1 3 -1.0500000000000000e+00 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760 +104 1 786 790 +105 1 796 800 +106 1 6 10 +107 1 16 20 +108 1 46 50 +109 1 136 140 +110 1 666 670 +111 1 676 680 +112 1 716 720 +113 1 216 220 +114 1 246 250 +115 1 256 260 +116 1 286 290 +117 1 866 870 +118 1 906 910 +119 1 916 920 +120 1 946 950 +121 1 956 960 +122 1 166 170 +123 1 176 180 +124 1 206 210 +125 1 296 300 +126 1 826 830 +127 1 836 840 +128 1 876 880 diff --git a/tools/msi2lmp/test/reference/ethane-oplsaa.data2 b/tools/msi2lmp/test/reference/ethane-oplsaa.data2 index 7932115e6e..cf058a4ca9 100644 --- a/tools/msi2lmp/test/reference/ethane-oplsaa.data2 +++ b/tools/msi2lmp/test/reference/ethane-oplsaa.data2 @@ -1,4 +1,4 @@ -LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 60 +LAMMPS data file via write_data, version 29 Aug 2024, timestep = 64, units = real 8 atoms 2 atom types @@ -9,13 +9,13 @@ LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 60 9 dihedrals 1 dihedral types --5.0000000000000000e+00 5.0000000000000000e+00 xlo xhi --5.0000000000000000e+00 5.0000000000000000e+00 ylo yhi --5.0000000000000000e+00 5.0000000000000000e+00 zlo zhi +-5 5 xlo xhi +-5 5 ylo yhi +-5 5 zlo zhi Masses -1 12.0112 +1 12.01115 2 1.00797 Pair Coeffs # lj/cut/coul/cut @@ -39,25 +39,25 @@ Dihedral Coeffs # opls Atoms # full -1 1 1 -1.7999999999999999e-01 4.4520961794662339e+00 -4.8331316055118139e+00 4.9921953697666774e+00 0 1 -1 -2 1 1 -1.7999999999999999e-01 -4.0208267456132498e+00 -4.9408970766661060e+00 -4.9962668603193716e+00 1 1 0 -3 1 2 5.9999999999999998e-02 4.1241637410618237e+00 -3.9187715229527775e+00 4.4953501727331462e+00 0 1 -1 -4 1 2 5.9999999999999998e-02 3.9927847754165149e+00 4.3246628372301563e+00 4.4708516600772406e+00 0 0 -1 -5 1 2 5.9999999999999998e-02 4.0591846610420355e+00 -4.8176278098672096e+00 -3.9904372631272924e+00 0 1 0 -6 1 2 5.9999999999999998e-02 -3.5762405194770461e+00 -4.0716394256255244e+00 -4.5137080084717223e+00 1 1 0 -7 1 2 5.9999999999999998e-02 -3.6936651570105905e+00 4.1740778258698201e+00 -4.4511582014826949e+00 1 0 0 -8 1 2 5.9999999999999998e-02 -3.6211369348857190e+00 4.9967667775234554e+00 3.9920131308240276e+00 1 0 -1 +1 1 1 -0.18 4.450690671089314 -4.83133647736812 4.992428212375868 0 1 -1 +2 1 1 -0.18 -4.022291647324266 -4.942324611094984 -4.995836359730008 1 1 0 +3 1 2 0.06 4.1294147504666165 -3.9160894986014068 4.495489435092607 0 1 -1 +4 1 2 0.06 3.9961668185396193 4.3269540139496785 4.470098784261843 0 0 -1 +5 1 2 0.06 4.059021520856406 -4.816007407764785 -3.990885907539094 0 1 0 +6 1 2 0.06 -3.5752328984263166 -4.071671221696795 -4.5159098704661425 1 1 0 +7 1 2 0.06 -3.6980390300174055 4.172581688097945 -4.448408184535642 1 0 0 +8 1 2 0.06 -3.6233701851839633 4.991333514478468 3.9918638905405723 1 0 -1 Velocities -1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 Bonds diff --git a/tools/msi2lmp/test/runtests.sh b/tools/msi2lmp/test/runtests.sh index b81c8637cd..2cfbcb9f72 100755 --- a/tools/msi2lmp/test/runtests.sh +++ b/tools/msi2lmp/test/runtests.sh @@ -2,8 +2,8 @@ MSI2LMP_LIBRARY=../frc_files VALGRIND='valgrind -v --track-origins=yes --show-reachable=yes --leak-check=full' -MSI2LMP=../src/msi2lmp.exe -LAMMPS=../../../src/lmp_serial +MSI2LMP=../../../build-test/msi2lmp +LAMMPS=../../../build-test/lmp CHECKDATA=./data-compare.pl if [ ! -x $MSI2LMP ] diff --git a/tools/swig/lammps.i b/tools/swig/lammps.i index 9bef047da4..11f5a270a1 100644 --- a/tools/swig/lammps.i +++ b/tools/swig/lammps.i @@ -130,6 +130,7 @@ extern void *lammps_extract_pair(void *handle, const char *name); extern int lammps_map_atom(void *handle, const void *id); extern int lammps_extract_atom_datatype(void *handle, const char *name); +extern int lammps_extract_atom_size(void *handle, const char *name, int type); extern void *lammps_extract_atom(void *handle, const char *name); extern void *lammps_extract_compute(void *handle, const char *id, int, int); @@ -319,6 +320,7 @@ extern void *lammps_extract_pair(void *handle, const char *name); extern int lammps_map_atom(void *handle, const void *id); extern int lammps_extract_atom_datatype(void *handle, const char *name); +extern int lammps_extract_atom_size(void *handle, const char *name, int type); extern void *lammps_extract_atom(void *handle, const char *name); extern void *lammps_extract_compute(void *handle, const char *id, int, int); diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index 3d0eeef5ea..737015ccdc 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -49,6 +49,7 @@ protected: if (verbose) std::cout << output; EXPECT_THAT(output, StartsWith("LAMMPS (")); } + void TearDown() override { ::testing::internal::CaptureStdout(); @@ -470,9 +471,9 @@ TEST_F(LibraryProperties, global) EXPECT_EQ(lammps_extract_global_datatype(lmp, "xlattice"), LAMMPS_DOUBLE); EXPECT_EQ(lammps_extract_global_datatype(lmp, "ylattice"), LAMMPS_DOUBLE); EXPECT_EQ(lammps_extract_global_datatype(lmp, "zlattice"), LAMMPS_DOUBLE); - auto *xlattice = (double *)lammps_extract_global(lmp, "xlattice"); - auto *ylattice = (double *)lammps_extract_global(lmp, "ylattice"); - auto *zlattice = (double *)lammps_extract_global(lmp, "zlattice"); + auto *xlattice = (double *)lammps_extract_global(lmp, "xlattice"); + auto *ylattice = (double *)lammps_extract_global(lmp, "ylattice"); + auto *zlattice = (double *)lammps_extract_global(lmp, "zlattice"); EXPECT_NE(xlattice, nullptr); EXPECT_NE(ylattice, nullptr); EXPECT_NE(zlattice, nullptr); @@ -484,9 +485,9 @@ TEST_F(LibraryProperties, global) lammps_command(lmp, "units real"); lammps_command(lmp, "lattice fcc 2.0"); if (!verbose) ::testing::internal::GetCapturedStdout(); - xlattice = (double *)lammps_extract_global(lmp, "xlattice"); - ylattice = (double *)lammps_extract_global(lmp, "ylattice"); - zlattice = (double *)lammps_extract_global(lmp, "zlattice"); + xlattice = (double *)lammps_extract_global(lmp, "xlattice"); + ylattice = (double *)lammps_extract_global(lmp, "ylattice"); + zlattice = (double *)lammps_extract_global(lmp, "zlattice"); EXPECT_NE(xlattice, nullptr); EXPECT_NE(ylattice, nullptr); EXPECT_NE(zlattice, nullptr); @@ -694,11 +695,10 @@ TEST_F(LibraryProperties, has_error) class AtomProperties : public ::testing::Test { protected: void *lmp; + int ntypes, nlocal, nall; - AtomProperties() = default; - ; + AtomProperties() = default; ~AtomProperties() override = default; - ; void SetUp() override { @@ -713,11 +713,30 @@ protected: if (verbose) std::cout << output; EXPECT_THAT(output, StartsWith("LAMMPS (")); ::testing::internal::CaptureStdout(); + lammps_command(lmp, "fix props all property/atom i_one i2_two 2 d_three d2_four 2"); + lammps_command(lmp, "fix rmass all property/atom mol q rmass ghost yes"); lammps_command(lmp, "region box block 0 2 0 2 0 2"); lammps_command(lmp, "create_box 1 box"); lammps_command(lmp, "mass 1 3.0"); lammps_command(lmp, "create_atoms 1 single 1.0 1.0 1.5"); lammps_command(lmp, "create_atoms 1 single 0.2 0.1 0.1"); + lammps_command(lmp, "set group all mass 2.0"); + lammps_command(lmp, "set atom 1 charge -1"); + lammps_command(lmp, "set atom 2 charge 1"); + lammps_command(lmp, "set atom 1 mol 2"); + lammps_command(lmp, "set atom 2 mol 1"); + lammps_command(lmp, "set atom 1 i_one -3"); + lammps_command(lmp, "set atom 2 i_one 3"); + lammps_command(lmp, "set atom 1 d_three -1.3"); + lammps_command(lmp, "set atom 2 d_three 3.5"); + lammps_command(lmp, "set atom 1 i_two[1] -3"); + lammps_command(lmp, "set atom 2 i_two[2] 3"); + lammps_command(lmp, "set atom * d_four[1] -1.3"); + lammps_command(lmp, "set atom * d_four[2] 3.5"); + ntypes = lammps_extract_setting(lmp, "ntypes"); + nlocal = lammps_extract_setting(lmp, "nlocal"); + nall = lammps_extract_setting(lmp, "nall"); + output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; } @@ -740,14 +759,42 @@ TEST_F(AtomProperties, invalid) TEST_F(AtomProperties, mass) { EXPECT_EQ(lammps_extract_atom_datatype(lmp, "mass"), LAMMPS_DOUBLE); + EXPECT_EQ(lammps_extract_atom_size(lmp, "mass", 0), ntypes + 1); auto *mass = (double *)lammps_extract_atom(lmp, "mass"); ASSERT_NE(mass, nullptr); ASSERT_DOUBLE_EQ(mass[1], 3.0); + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "rmass"), LAMMPS_DOUBLE); + EXPECT_EQ(lammps_extract_atom_size(lmp, "rmass", 0), nall); + mass = (double *)lammps_extract_atom(lmp, "rmass"); + ASSERT_NE(mass, nullptr); + ASSERT_DOUBLE_EQ(mass[0], 2.0); + ASSERT_DOUBLE_EQ(mass[1], 2.0); +} + +TEST_F(AtomProperties, charge) +{ + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "q"), LAMMPS_DOUBLE); + EXPECT_EQ(lammps_extract_atom_size(lmp, "rmass", 0), nall); + auto *charge = (double *)lammps_extract_atom(lmp, "q"); + ASSERT_NE(charge, nullptr); + ASSERT_DOUBLE_EQ(charge[0], -1.0); + ASSERT_DOUBLE_EQ(charge[1], 1.0); +} + +TEST_F(AtomProperties, molecule) +{ + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "molecule"), LAMMPS_TAGINT); + EXPECT_EQ(lammps_extract_atom_size(lmp, "molecule", 0), nall); + auto *molecule = (tagint *)lammps_extract_atom(lmp, "molecule"); + ASSERT_NE(molecule, nullptr); + ASSERT_EQ(molecule[0], 2); + ASSERT_EQ(molecule[1], 1); } TEST_F(AtomProperties, id) { EXPECT_EQ(lammps_extract_atom_datatype(lmp, "id"), LAMMPS_TAGINT); + EXPECT_EQ(lammps_extract_atom_size(lmp, "id", 0), nall); auto *id = (tagint *)lammps_extract_atom(lmp, "id"); ASSERT_NE(id, nullptr); ASSERT_EQ(id[0], 1); @@ -757,6 +804,7 @@ TEST_F(AtomProperties, id) TEST_F(AtomProperties, type) { EXPECT_EQ(lammps_extract_atom_datatype(lmp, "type"), LAMMPS_INT); + EXPECT_EQ(lammps_extract_atom_size(lmp, "type", 0), nall); int *type = (int *)lammps_extract_atom(lmp, "type"); ASSERT_NE(type, nullptr); ASSERT_EQ(type[0], 1); @@ -766,6 +814,8 @@ TEST_F(AtomProperties, type) TEST_F(AtomProperties, position) { EXPECT_EQ(lammps_extract_atom_datatype(lmp, "x"), LAMMPS_DOUBLE_2D); + EXPECT_EQ(lammps_extract_atom_size(lmp, "x", LMP_SIZE_ROWS), nall); + EXPECT_EQ(lammps_extract_atom_size(lmp, "x", LMP_SIZE_COLS), 3); auto **x = (double **)lammps_extract_atom(lmp, "x"); ASSERT_NE(x, nullptr); EXPECT_DOUBLE_EQ(x[0][0], 1.0); @@ -776,6 +826,41 @@ TEST_F(AtomProperties, position) EXPECT_DOUBLE_EQ(x[1][2], 0.1); } +TEST_F(AtomProperties, custom) +{ + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "i_one"), LAMMPS_INT); + EXPECT_EQ(lammps_extract_atom_size(lmp, "i_one", 0), nlocal); + auto *one = (int *)lammps_extract_atom(lmp, "i_one"); + ASSERT_NE(one, nullptr); + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "i2_two"), LAMMPS_INT_2D); + EXPECT_EQ(lammps_extract_atom_size(lmp, "i2_two", LMP_SIZE_ROWS), nlocal); + EXPECT_EQ(lammps_extract_atom_size(lmp, "i2_two", LMP_SIZE_COLS), 2); + auto **two = (int **)lammps_extract_atom(lmp, "i2_two"); + ASSERT_NE(two, nullptr); + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "d_three"), LAMMPS_DOUBLE); + EXPECT_EQ(lammps_extract_atom_size(lmp, "d_three", 0), nlocal); + auto *three = (double *)lammps_extract_atom(lmp, "d_three"); + ASSERT_NE(three, nullptr); + EXPECT_EQ(lammps_extract_atom_datatype(lmp, "d2_four"), LAMMPS_DOUBLE_2D); + EXPECT_EQ(lammps_extract_atom_size(lmp, "d2_four", LMP_SIZE_ROWS), nlocal); + EXPECT_EQ(lammps_extract_atom_size(lmp, "d2_four", LMP_SIZE_COLS), 2); + auto **four = (double **)lammps_extract_atom(lmp, "d2_four"); + ASSERT_NE(four, nullptr); + + EXPECT_EQ(one[0], -3); + EXPECT_EQ(one[1], 3); + EXPECT_EQ(two[0][0], -3); + EXPECT_EQ(two[0][1], 0); + EXPECT_EQ(two[1][0], 0); + EXPECT_EQ(two[1][1], 3); + EXPECT_DOUBLE_EQ(three[0], -1.3); + EXPECT_DOUBLE_EQ(three[1], 3.5); + EXPECT_DOUBLE_EQ(four[0][0], -1.3); + EXPECT_DOUBLE_EQ(four[0][1], 3.5); + EXPECT_DOUBLE_EQ(four[1][0], -1.3); + EXPECT_DOUBLE_EQ(four[1][1], 3.5); +} + TEST(SystemSettings, kokkos) { if (!lammps_config_has_package("KOKKOS")) GTEST_SKIP(); diff --git a/unittest/force-styles/check_tests.py b/unittest/force-styles/check_tests.py index 4dba8f9b9e..7305168ecb 100755 --- a/unittest/force-styles/check_tests.py +++ b/unittest/force-styles/check_tests.py @@ -88,10 +88,9 @@ for header in headers: style = m[1] if upper.match(style): continue - if style in ['reax/c', 'reax/c/omp', 'reax/c/kk', - 'reax/c/kk/device', 'reax/c/kk/host', - 'reax/c/species', 'reax/c/bonds', - 'reax/c/species/kk', 'reax/c/bonds/kk', 'meam/c']: + if style in ['lj/sdk', 'lj/sdk/coul/long', 'lj/sdk/coul/msm', 'sdk', 'lj/sdk/gpu', + 'lj/sdk/coul/long/gpu', 'lj/sdk/omp', 'lj/sdk/coul/long/omp', 'sdk/omp', + 'lj/sdk/coul/msm/omp', 'lj/sdk/kk', 'lj/sdk/coul/long/kk', 'sdk/kk']: continue # detect, process, and flag suffix styles: @@ -176,11 +175,12 @@ def check_tests(name,styles,yaml,search,skip=()): counter = 0 counter += check_tests('pair',pair,'*-pair-*.yaml', - '.*pair_style:\\s*((\\S+).*)?',skip=('meam','lj/sf')) + '.*pair_style:\\s*((\\S+).*)?', + skip=('lj/sf','lj/sdk', 'lj/sdk/coul/long', 'lj/sdk/coul/msm')) counter += check_tests('bond',bond,'bond-*.yaml', '.*bond_style:\\s*((\\S+).*)?') counter += check_tests('angle',angle,'angle-*.yaml', - '.*angle_style:\\s*((\\S+).*)?') + '.*angle_style:\\s*((\\S+).*)?', skip=('sdk')) counter += check_tests('dihedral',dihedral,'dihedral-*.yaml', '.*dihedral_style:\\s*((\\S+).*)?') counter += check_tests('improper',improper,'improper-*.yaml', diff --git a/unittest/fortran/keepstuff.f90 b/unittest/fortran/keepstuff.f90 index 63184e1006..c964c8a9c6 100644 --- a/unittest/fortran/keepstuff.f90 +++ b/unittest/fortran/keepstuff.f90 @@ -4,9 +4,9 @@ MODULE keepstuff TYPE(LAMMPS), SAVE :: lmp INTEGER, SAVE :: mycomm CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: demo_input = & - [ CHARACTER(LEN=40) :: & - 'region box block 0 $x 0 2 0 2', & - 'create_box 1 box', & + [ CHARACTER(LEN=40) :: & + 'region box block 0 $x 0 2 0 2', & + 'create_box 1 box', & 'create_atoms 1 single 1.0 1.0 ${zpos}' ] CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: big_input = & [ CHARACTER(LEN=40) :: & @@ -14,15 +14,26 @@ MODULE keepstuff 'create_box 1 box', & 'create_atoms 1 single 1.0 1.0 ${zpos}' ] CHARACTER(LEN=40), DIMENSION(2), PARAMETER :: cont_input = & - [ CHARACTER(LEN=40) :: & - 'create_atoms 1 single &', & + [ CHARACTER(LEN=40) :: & + 'create_atoms 1 single &', & ' 0.2 0.1 0.1' ] + CHARACTER(LEN=60), DIMENSION(18), PARAMETER :: prop_input = & + [ CHARACTER(LEN=60) :: 'fix 1 all nve', 'mass 1 3.0', & + 'fix 2 all property/atom mol q rmass ghost yes', & + 'fix 3 all property/atom i_one i2_two 2 d_three d2_four 2', & + 'set group all mass 2.0', 'set atom 1 charge -1', & + 'set atom 2 charge 1', 'set atom 1 mol 2', 'set atom 2 mol 1', & + 'set atom 1 i_one -3', 'set atom 2 i_one 3', & + 'set atom 1 d_three -1.3', 'set atom 2 d_three 3.5', & + 'set atom 1 i_two[1] -3', 'set atom 2 i_two[2] 3', & + 'set atom * d_four[1] -1.3', 'set atom * d_four[2] 3.5', & + 'run 0 post no' ] CHARACTER(LEN=40), DIMENSION(1), PARAMETER :: more_input = & [ CHARACTER(LEN=40) :: 'create_atoms 1 single 0.5 0.5 0.5' ] CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: pair_input = & - [ CHARACTER(LEN=40) :: & - 'pair_style lj/cut 2.5', & - 'pair_coeff 1 1 1.0 1.0', & + [ CHARACTER(LEN=40) :: & + 'pair_style lj/cut 2.5', & + 'pair_coeff 1 1 1.0 1.0', & 'mass 1 2.0' ] INTERFACE @@ -63,4 +74,3 @@ CONTAINS END FUNCTION f2c_string END MODULE keepstuff - diff --git a/unittest/fortran/test_fortran_extract_atom.f90 b/unittest/fortran/test_fortran_extract_atom.f90 index 262e5de47d..0c5a52ef25 100644 --- a/unittest/fortran/test_fortran_extract_atom.f90 +++ b/unittest/fortran/test_fortran_extract_atom.f90 @@ -24,12 +24,13 @@ END SUBROUTINE f_lammps_close SUBROUTINE f_lammps_setup_extract_atom() BIND(C) USE LIBLAMMPS - USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input + USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input, prop_input IMPLICIT NONE CALL lmp%commands_list(big_input) CALL lmp%commands_list(cont_input) CALL lmp%commands_list(pair_input) + CALL lmp%commands_list(prop_input) END SUBROUTINE f_lammps_setup_extract_atom FUNCTION f_lammps_extract_atom_mass() BIND(C) @@ -44,6 +45,19 @@ FUNCTION f_lammps_extract_atom_mass() BIND(C) f_lammps_extract_atom_mass = mass(1) END FUNCTION f_lammps_extract_atom_mass +FUNCTION f_lammps_extract_atom_mass_size() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_extract_atom_mass_size, ntypes + REAL(c_double), DIMENSION(:), POINTER :: mass => NULL() + + ntypes = lmp%extract_setting('ntypes') + mass = lmp%extract_atom('mass') + f_lammps_extract_atom_mass_size = SIZE(mass) +END FUNCTION f_lammps_extract_atom_mass_size + FUNCTION f_lammps_extract_atom_tag_int(i) BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int USE LIBLAMMPS @@ -83,6 +97,18 @@ FUNCTION f_lammps_extract_atom_type(i) BIND(C) f_lammps_extract_atom_type = atype(i) END FUNCTION f_lammps_extract_atom_type +FUNCTION f_lammps_extract_atom_type_size() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_extract_atom_type_size + INTEGER(c_int), DIMENSION(:), POINTER :: atype => NULL() + + atype = lmp%extract_atom('type') + f_lammps_extract_atom_type_size = size(atype) +END FUNCTION f_lammps_extract_atom_type_size + FUNCTION f_lammps_extract_atom_mask(i) BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE LIBLAMMPS @@ -109,6 +135,19 @@ SUBROUTINE f_lammps_extract_atom_x(i, x) BIND(C) x = xptr(:,i) END SUBROUTINE f_lammps_extract_atom_x +FUNCTION f_lammps_extract_atom_x_size(i) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: i + INTEGER(c_int) :: f_lammps_extract_atom_x_size + REAL(c_double), DIMENSION(:,:), POINTER :: xptr => NULL() + + xptr = lmp%extract_atom('x') + f_lammps_extract_atom_x_size = SIZE(xptr, i) +END FUNCTION f_lammps_extract_atom_x_size + SUBROUTINE f_lammps_extract_atom_v(i, v) BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int USE LIBLAMMPS @@ -121,3 +160,16 @@ SUBROUTINE f_lammps_extract_atom_v(i, v) BIND(C) vptr = lmp%extract_atom('v') v = vptr(:,i) END SUBROUTINE f_lammps_extract_atom_v + +FUNCTION f_lammps_extract_atom_v_size(i) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: i + INTEGER(c_int) :: f_lammps_extract_atom_v_size + REAL(c_double), DIMENSION(:,:), POINTER :: xptr => NULL() + + xptr = lmp%extract_atom('v') + f_lammps_extract_atom_v_size = SIZE(xptr, i) +END FUNCTION f_lammps_extract_atom_v_size diff --git a/unittest/fortran/wrap_extract_atom.cpp b/unittest/fortran/wrap_extract_atom.cpp index 2552d6a10f..9430959b2b 100644 --- a/unittest/fortran/wrap_extract_atom.cpp +++ b/unittest/fortran/wrap_extract_atom.cpp @@ -1,6 +1,7 @@ // unit tests for extracting Atom class data from a LAMMPS instance through the // Fortran wrapper +#include "atom.h" #include "lammps.h" #include "library.h" #include @@ -16,12 +17,16 @@ void *f_lammps_with_args(); void f_lammps_close(); void f_lammps_setup_extract_atom(); double f_lammps_extract_atom_mass(); +int f_lammps_extract_atom_mass_size(); int f_lammps_extract_atom_tag_int(int); int64_t f_lammps_extract_atom_tag_int64(int64_t); int f_lammps_extract_atom_type(int); +int f_lammps_extract_atom_type_size(); int f_lammps_extract_atom_mask(int); void f_lammps_extract_atom_x(int, double *); +int f_lammps_extract_atom_x_size(int); void f_lammps_extract_atom_v(int, double *); +int f_lammps_extract_atom_v_size(int); } class LAMMPS_extract_atom : public ::testing::Test { @@ -50,7 +55,9 @@ protected: TEST_F(LAMMPS_extract_atom, mass) { f_lammps_setup_extract_atom(); - EXPECT_DOUBLE_EQ(f_lammps_extract_atom_mass(), 2.0); + int ntypes = lmp->atom->ntypes; + EXPECT_DOUBLE_EQ(f_lammps_extract_atom_mass(), 3.0); + EXPECT_EQ(f_lammps_extract_atom_mass_size(), ntypes + 1); }; TEST_F(LAMMPS_extract_atom, tag) @@ -68,8 +75,10 @@ TEST_F(LAMMPS_extract_atom, tag) TEST_F(LAMMPS_extract_atom, type) { f_lammps_setup_extract_atom(); + int nall = lmp->atom->nlocal + lmp->atom->nghost; EXPECT_EQ(f_lammps_extract_atom_type(1), 1); EXPECT_EQ(f_lammps_extract_atom_type(2), 1); + EXPECT_EQ(f_lammps_extract_atom_type_size(), nall); }; TEST_F(LAMMPS_extract_atom, mask) @@ -86,6 +95,7 @@ TEST_F(LAMMPS_extract_atom, mask) TEST_F(LAMMPS_extract_atom, x) { f_lammps_setup_extract_atom(); + int nall = lmp->atom->nlocal + lmp->atom->nghost; double x1[3]; double x2[3]; f_lammps_extract_atom_x(1, x1); @@ -96,11 +106,15 @@ TEST_F(LAMMPS_extract_atom, x) EXPECT_DOUBLE_EQ(x2[0], 0.2); EXPECT_DOUBLE_EQ(x2[1], 0.1); EXPECT_DOUBLE_EQ(x2[2], 0.1); + // in Fortran row and column are swapped + EXPECT_EQ(f_lammps_extract_atom_x_size(1), 3); + EXPECT_EQ(f_lammps_extract_atom_x_size(2), nall); } TEST_F(LAMMPS_extract_atom, v) { f_lammps_setup_extract_atom(); + int nall = lmp->atom->nlocal + lmp->atom->nghost; double v1[3]; double v2[3]; f_lammps_extract_atom_v(1, v1); @@ -117,4 +131,13 @@ TEST_F(LAMMPS_extract_atom, v) EXPECT_DOUBLE_EQ(v1[0], 1.0); EXPECT_DOUBLE_EQ(v1[1], 2.0); EXPECT_DOUBLE_EQ(v1[2], 3.0); + // in Fortran row and column are swapped! + EXPECT_EQ(f_lammps_extract_atom_v_size(1), 3); + EXPECT_EQ(f_lammps_extract_atom_v_size(2), lmp->atom->nlocal); + lammps_command(lmp, "comm_modify vel yes"); + lammps_command(lmp, "run 0 post no"); + EXPECT_EQ(f_lammps_extract_atom_v_size(1), 3); + EXPECT_EQ(f_lammps_extract_atom_v_size(2), nall); } + +// TODO: write tests for custom properties diff --git a/unittest/python/python-numpy.py b/unittest/python/python-numpy.py index 839e5d03af..4930527a61 100644 --- a/unittest/python/python-numpy.py +++ b/unittest/python/python-numpy.py @@ -155,67 +155,104 @@ class PythonNumpy(unittest.TestCase): self.assertEqual(values[1,0], 1.5) self.assertEqual(values[1,3], 1.5) - def testExtractAtomDeprecated(self): - self.lmp.command("units lj") - self.lmp.command("atom_style atomic") - self.lmp.command("atom_modify map array") - self.lmp.command("region box block 0 2 0 2 0 2") - self.lmp.command("create_box 1 box") - - x = [ - 1.0, 1.0, 1.0, - 1.0, 1.0, 1.5 - ] - - types = [1, 1] - - self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) - nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) - self.assertEqual(nlocal, 2) - - ident = self.lmp.numpy.extract_atom_iarray("id", nlocal, dim=1) - self.assertEqual(len(ident), 2) - - ntypes = self.lmp.extract_global("ntypes", LAMMPS_INT) - self.assertEqual(ntypes, 1) - - x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3) - v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) - self.assertEqual(len(x), 2) - self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) - self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) - self.assertEqual(len(v), 2) - def testExtractAtom(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("region box block 0 2 0 2 0 2") - self.lmp.command("create_box 1 box") + self.lmp.command("create_box 2 box") - x = [ - 1.0, 1.0, 1.0, - 1.0, 1.0, 1.5 - ] + x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5, 1.5, 1.0, 1.0 ] + types = [1, 2, 1] + ids = [1, 2, 3] + self.assertEqual(self.lmp.create_atoms(3, id=ids, type=types, x=x), 3) + self.lmp.command("mass * 2.0") + self.lmp.command("pair_style zero 1.1") + self.lmp.command("pair_coeff * *") + self.lmp.command("fix props all property/atom i_one i2_two 2 d_three d2_four 2"); + self.lmp.command("fix rmass all property/atom mol q rmass ghost yes"); + self.lmp.command("fix 1 all nve") + self.lmp.command("run 0 post no") + ntypes = self.lmp.extract_setting("ntypes"); + nlocal = self.lmp.extract_setting("nlocal"); + nall = self.lmp.extract_setting("nall"); + self.assertEqual(nlocal, 3) + self.assertEqual(ntypes, 2) + self.assertEqual(nall, 63) - types = [1, 1] + self.lmp.command("set atom 1 charge -1"); + self.lmp.command("set atom 2 charge 1"); + self.lmp.command("set atom 3 charge 0"); + self.lmp.command("set atom * mol 2"); + self.lmp.command("set atom 2 mol 1"); + self.lmp.command("set atom 1 i_one -3"); + self.lmp.command("set atom 2 i_one 3"); + self.lmp.command("set atom 2 d_three -1.3"); + self.lmp.command("set atom 3 d_three 3.5"); + self.lmp.command("set atom 1 i_two[1] -3"); + self.lmp.command("set atom 2 i_two[2] 3"); + self.lmp.command("set atom * d_four[1] -1.3"); + self.lmp.command("set atom * d_four[2] 3.5"); + self.lmp.command("run 0 post no") - self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) - nlocal = self.lmp.extract_global("nlocal") - self.assertEqual(nlocal, 2) + mass = self.lmp.numpy.extract_atom("mass") + self.assertEqual(len(mass), ntypes + 1) + self.assertTrue((mass == (0.0, 2.0, 2.0)).all()) + + rmass = self.lmp.numpy.extract_atom("rmass") + self.assertEqual(len(rmass), nall) + self.assertTrue((rmass[0:3] == (0.0, 0.0, 0.0)).all()) + + charge = self.lmp.numpy.extract_atom("q") + self.assertEqual(len(charge), nall) + self.assertTrue((charge[0:3] == (-1.0, 1.0, 0.0)).all()) + + molecule = self.lmp.numpy.extract_atom("molecule") + self.assertEqual(len(molecule), nall) + self.assertTrue((molecule[0:3] == (2, 1, 2)).all()) ident = self.lmp.numpy.extract_atom("id") - self.assertEqual(len(ident), 2) + self.assertEqual(len(ident), nall) + self.assertTrue((ident[0:3] == (1, 2, 3)).all()) - ntypes = self.lmp.extract_global("ntypes") - self.assertEqual(ntypes, 1) + atype = self.lmp.numpy.extract_atom("type") + self.assertEqual(len(atype), nall) + self.assertTrue((atype[0:3] == (1, 2, 1)).all()) x = self.lmp.numpy.extract_atom("x") v = self.lmp.numpy.extract_atom("v") - self.assertEqual(len(x), 2) + self.assertEqual(len(x), nall) + self.assertEqual(len(x[0]), 3) self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) - self.assertEqual(len(v), 2) + self.assertTrue((x[2] == (1.5, 1.0, 1.0)).all()) + self.assertEqual(len(v), nlocal) + self.assertEqual(len(v[0]), 3) + + self.lmp.command("comm_modify vel yes"); + self.lmp.command("run 0 post no") + + v = self.lmp.numpy.extract_atom("v") + self.assertEqual(len(v), nall) + + one = self.lmp.numpy.extract_atom("i_one") + two = self.lmp.numpy.extract_atom("i2_two") + three = self.lmp.numpy.extract_atom("d_three") + four = self.lmp.numpy.extract_atom("d2_four") + self.assertEqual(len(one), nlocal) + self.assertTrue((one == (-3, 3, 0)).all()) + self.assertEqual(len(two), nlocal) + self.assertEqual(len(two[0]), 2) + self.assertTrue((two[0] == (-3, 0)).all()) + self.assertTrue((two[1] == (0, 3)).all()) + self.assertTrue((two[2] == (0, 0)).all()) + self.assertEqual(len(three), nlocal) + self.assertTrue((three == (0.0, -1.3, 3.5)).all()) + self.assertEqual(len(four), nlocal) + self.assertEqual(len(four[0]), 2) + self.assertTrue((four[0] == (-1.3, 3.5)).all()) + self.assertTrue((four[1] == (-1.3, 3.5)).all()) + self.assertTrue((four[2] == (-1.3, 3.5)).all()) @unittest.skipIf(not has_full,"Gather bonds test") def testGatherBond_newton_on(self):