diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 8dafa7e476..2db772516f 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -9,7 +9,7 @@ if(POLICY CMP0074) endif() # set policy to silence warnings about missing executable permissions in # pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW -if (POLICY CMP0109) +if(POLICY CMP0109) cmake_policy(SET CMP0109 OLD) endif() ######################################## @@ -77,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR}) include(CheckIncludeFileCXX) # set required compiler flags and compiler/CPU arch specific optimizations -if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") +if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512") @@ -91,6 +91,11 @@ set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions") +# export all symbols when building a .dll file on windows +if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS) + set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON) +endif() + ######################################################################## # User input options # ######################################################################## @@ -120,6 +125,12 @@ file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES}) add_library(lammps ${ALL_SOURCES}) + +# tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers +if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) + set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") +endif() + add_executable(lmp ${MAIN_SOURCES}) target_link_libraries(lmp PRIVATE lammps) set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) @@ -132,8 +143,8 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF - USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB + USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN) @@ -162,12 +173,13 @@ if(NOT CMAKE_CROSSCOMPILING) find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) else() + set(MPI_CXX_SKIP_MPICXX TRUE) option(BUILD_MPI "Build MPI version" OFF) endif() if(BUILD_MPI) # We use a non-standard procedure to cross-compile with MPI on Windows - if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) include(MPI4WIN) target_link_libraries(lammps PUBLIC MPI::MPI_CXX) else() @@ -201,7 +213,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES}) # posix_memalign is not available on Windows -if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") +if(CMAKE_SYSTEM_NAME STREQUAL "Windows") set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE) else() set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable") @@ -243,8 +255,9 @@ if(BUILD_OMP) message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") endif() - if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR + if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. @@ -307,7 +320,7 @@ find_program(GZIP_EXECUTABLE gzip) find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE) option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND}) if(WITH_GZIP) - if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)) target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP) else() message(FATAL_ERROR "gzip executable not found") @@ -318,7 +331,7 @@ find_program(FFMPEG_EXECUTABLE ffmpeg) find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE) option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND}) if(WITH_FFMPEG) - if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)) target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG) else() message(FATAL_ERROR "ffmpeg executable not found") @@ -335,10 +348,10 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED +foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) if(PKG_${PKG_WITH_INCL}) - include(Packages/${PKG_WITH_INCL}) + include(Packages/${PKG_WITH_INCL}) endif() endforeach() @@ -433,7 +446,7 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) - if(PKG_LIB STREQUAL mesont) + if(PKG_LIB STREQUAL "mesont") enable_language(Fortran) file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90) @@ -445,9 +458,9 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE}) target_link_libraries(lammps PRIVATE ${PKG_LIB}) - if(PKG_LIB STREQUAL awpmd) + if(PKG_LIB STREQUAL "awpmd") target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include) - elseif(PKG_LIB STREQUAL h5md) + elseif(PKG_LIB STREQUAL "h5md") target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS}) else() target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}) @@ -460,7 +473,7 @@ if(PKG_USER-AWPMD) endif() if(PKG_USER-ATC) - if(LAMMPS_SIZES STREQUAL BIGBIG) + if(LAMMPS_SIZES STREQUAL "BIGBIG") message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") endif() target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES}) @@ -504,7 +517,7 @@ endif() # and the MPI library - if use - has to be linked right before those # and after everything else that is compiled locally ###################################################################### -if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") +if(CMAKE_SYSTEM_NAME STREQUAL "Windows") target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi) endif() @@ -553,8 +566,8 @@ add_dependencies(lammps gitversion) # Actually add executable and lib to build ############################################ get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) -list (FIND LANGUAGES "Fortran" _index) -if(${_index} GREATER -1) +list(FIND LANGUAGES "Fortran" _index) +if(_index GREATER -1) target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) endif() set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h @@ -632,7 +645,7 @@ if(BUILD_SHARED_LIBS) else() find_package(Python COMPONENTS Interpreter) endif() - if (Python_EXECUTABLE) + if(Python_EXECUTABLE) add_custom_target( install-python ${CMAKE_COMMAND} -E remove_directory build COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h @@ -665,7 +678,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON) else() find_package(Python COMPONENTS Interpreter) endif() - if (Python_EXECUTABLE) + if(Python_EXECUTABLE) file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python) install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})") endif() @@ -710,15 +723,15 @@ if(OPTIONS) message(" Options: ${OPTIONS}") endif() get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) -list (FIND LANGUAGES "Fortran" _index) -if(${_index} GREATER -1) +list(FIND LANGUAGES "Fortran" _index) +if(_index GREATER -1) message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER} Type: ${CMAKE_Fortran_COMPILER_ID} Version: ${CMAKE_Fortran_COMPILER_VERSION} Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}") endif() -list (FIND LANGUAGES "C" _index) -if(${_index} GREATER -1) +list(FIND LANGUAGES "C" _index) +if(_index GREATER -1) message(STATUS "C compiler: ${CMAKE_C_COMPILER} Type: ${CMAKE_C_COMPILER_ID} Version: ${CMAKE_C_COMPILER_VERSION} @@ -783,7 +796,7 @@ if(PKG_KSPACE) endif() if(PKG_KOKKOS) if(Kokkos_ENABLE_CUDA) - if (${FFT} STREQUAL "KISS") + if(FFT STREQUAL "KISS") message(STATUS "Kokkos FFT: KISS") else() message(STATUS "Kokkos FFT: cuFFT") diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake new file mode 100644 index 0000000000..8a97b7dd81 --- /dev/null +++ b/cmake/Modules/FindN2P2.cmake @@ -0,0 +1,61 @@ +include(FindPackageHandleStandardArgs) + +# Check if N2P2_DIR is set manually. +if (DEFINED ENV{N2P2_DIR}) + set(N2P2_DIR "${N2P2_DIR}") +# If not, try if directory "lib/hdnnp/n2p2" exists. +else() + get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH) + if (EXISTS ${_fullpath}) + set(N2P2_DIR "${_fullpath}") + endif() +endif() + +# Set path to include directory. +find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include") +# Two libraries need to be linked: libnnp and libnnpif. +find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib") +find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib") +# Users could compile n2p2 with extra flags which are then also required for +# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2 +# writes a file with cmake commands, e.g. +# +# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS) +# +# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake. +find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib") + +find_package_handle_standard_args(N2P2 DEFAULT_MSG + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA) + +if(N2P2_FOUND) + if (NOT TARGET N2P2::N2P2) + # n2p2 core library "libnnp" + add_library(N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNP PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNP}) + # n2p2 interface library "libnnpif" + add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(N2P2::LIBNNPIF PROPERTIES + INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR} + IMPORTED_LOCATION ${N2P2_LIBNNPIF}) + # Put libnnp, libnnpif and include directory together. + add_library(N2P2::N2P2 INTERFACE IMPORTED) + set_property(TARGET N2P2::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP) + set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA}) + endif() +endif() + +mark_as_advanced( + N2P2_DIR + N2P2_INCLUDE_DIR + N2P2_LIBNNP + N2P2_LIBNNPIF + N2P2_CMAKE_EXTRA +) diff --git a/cmake/Modules/GTest.cmake b/cmake/Modules/GTest.cmake index 677ed5f4af..211b506d2f 100644 --- a/cmake/Modules/GTest.cmake +++ b/cmake/Modules/GTest.cmake @@ -1,6 +1,6 @@ message(STATUS "Downloading and building Google Test library") -if(CMAKE_BUILD_TYPE STREQUAL Debug) +if(CMAKE_BUILD_TYPE STREQUAL "Debug") set(GTEST_LIB_POSTFIX d) else() set(GTEST_LIB_POSTFIX) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 41dcfc5b2f..6cb23db12a 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -106,7 +106,7 @@ function(FetchPotentials pkgfolder potfolder) endfunction(FetchPotentials) # set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux -if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release)) +if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release)) file(STRINGS /etc/os-release distro REGEX "^NAME=") string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}") file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=") diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 3b07246e80..2b6977005d 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA") # ensure that no *cubin.h files exist from a compile in the lib/gpu folder file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h) - if (GPU_LIB_OLD_CUBIN_HEADERS) + if(GPU_LIB_OLD_CUBIN_HEADERS) message(FATAL_ERROR "########################################################################\n" "Found file(s) generated by the make-based build system in lib/gpu\n" "Please run\n" @@ -154,7 +154,7 @@ elseif(GPU_API STREQUAL "OPENCL") endif() option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default}) mark_as_advanced(USE_STATIC_OPENCL_LOADER) - if (USE_STATIC_OPENCL_LOADER) + if(USE_STATIC_OPENCL_LOADER) include(OpenCLLoader) else() find_package(OpenCL REQUIRED) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index e0e32730ec..4b4a7ae6f2 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -99,7 +99,7 @@ if(PKG_KSPACE) ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) if(Kokkos_ENABLE_CUDA) - if(NOT ${FFT} STREQUAL "KISS") + if(NOT (FFT STREQUAL "KISS")) target_compile_definitions(lammps PRIVATE -DFFT_CUFFT) target_link_libraries(lammps PRIVATE cufft) endif() diff --git a/cmake/Modules/Packages/MESSAGE.cmake b/cmake/Modules/Packages/MESSAGE.cmake index 6ff4e322aa..b5a61a1607 100644 --- a/cmake/Modules/Packages/MESSAGE.cmake +++ b/cmake/Modules/Packages/MESSAGE.cmake @@ -1,4 +1,4 @@ -if(LAMMPS_SIZES STREQUAL BIGBIG) +if(LAMMPS_SIZES STREQUAL "BIGBIG") message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG") endif() option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/USER-HDNNP.cmake new file mode 100644 index 0000000000..41d066a235 --- /dev/null +++ b/cmake/Modules/Packages/USER-HDNNP.cmake @@ -0,0 +1,124 @@ +find_package(N2P2 QUIET) +if(N2P2_FOUND) + set(DOWNLOAD_N2P2_DEFAULT OFF) +else() + set(DOWNLOAD_N2P2_DEFAULT ON) +endif() +option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT}) +if(DOWNLOAD_N2P2) + set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball") + set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball") + mark_as_advanced(N2P2_URL) + mark_as_advanced(N2P2_MD5) + + # adjust settings from detected compiler to compiler platform in n2p2 library + # set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7) + if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")) + set(N2P2_COMP llvm) + set(N2P2_CXX_STD "-std=c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + set(N2P2_COMP intel) + set(N2P2_CXX_STD "-std=c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + set(N2P2_COMP gnu) + set(N2P2_CXX_STD "-std=gnu++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") + set(N2P2_COMP gnu) + set(N2P2_CXX_STD "--c++11") + else() # default + set(N2P2_COMP "") + endif() + + # pass on archive creator command. prefer compiler specific version, if set. + # important when using cross compiler. + if(CMAKE_CXX_COMPILER_AR) + set(N2P2_AR ${CMAKE_CXX_COMPILER_AR}) + else() + set(N2P2_AR ${CMAKE_AR}) + endif() + + # adjust compilation of n2p2 library to whether MPI is requested in LAMMPS or not + # need special care for compiling for MPICH2 with Linux-to-Windows cross compiler. + if(NOT BUILD_MPI) + set(N2P2_PROJECT_OPTIONS "-DN2P2_NO_MPI") + else() + # get path to MPI include directory when cross-compiling to windows + if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES) + set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1") + set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER}) + endif() + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES) + set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1") + set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER}) + endif() + endif() + + # override compiler (optimization) flags in n2p2 library to flags used for LAMMPS + # specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler + # this convoluted way gets correct quoting/escaping when configuring the external project + string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) + set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}") + set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG=" + "PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}" + "PROJECT_AR=${N2P2_AR}") + # echo final flag for debugging + message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}") + + # download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling) + include(ExternalProject) + ExternalProject_Add(n2p2_build + URL ${N2P2_URL} + URL_MD5 ${N2P2_MD5} + UPDATE_COMMAND "" + CONFIGURE_COMMAND "" + PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp + BUILD_COMMAND make -f makefile libnnpif ${N2P2_BUILD_OPTIONS} + BUILD_ALWAYS YES + INSTALL_COMMAND "" + BUILD_IN_SOURCE 1 + LOG_BUILD ON + SOURCE_SUBDIR src/ + BUILD_BYPRODUCTS /lib/libnnp.a /lib/libnnpif.a + ) + + # create imported target LAMMPS::N2P2 from two libraries nnp and nnpif + ExternalProject_get_property(n2p2_build SOURCE_DIR) + # n2p2 core library "libnnp" + add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED) + set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include") + # n2p2 interface library "libnnpif" + add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED) + set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include") + # nnpif library has MPI calls if MPI is enabled, so we must link with MPI libs + if(BUILD_MPI) + set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES + INTERFACE_LINK_LIBRARIES MPI::MPI_CXX) + if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING) + add_dependencies(LAMMPS::N2P2::LIBNNPIF MPI::MPI_CXX) + endif() + endif() + + # final step to define imported target + add_library(LAMMPS::N2P2 INTERFACE IMPORTED) + set_property(TARGET LAMMPS::N2P2 PROPERTY + INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP) + target_link_libraries(lammps PRIVATE LAMMPS::N2P2) + + add_dependencies(LAMMPS::N2P2 n2p2_build) + # work around issues with older CMake versions + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + file(MAKE_DIRECTORY "${SOURCE_DIR}/lib") +else() + find_package(N2P2) + if(NOT N2P2_FOUND) + message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it") + endif() + target_link_libraries(lammps PRIVATE N2P2::N2P2) + include(${N2P2_CMAKE_EXTRAS}) +endif() diff --git a/cmake/Modules/Packages/USER-MDI.cmake b/cmake/Modules/Packages/USER-MDI.cmake index 88d7b5e498..a75160a6d6 100644 --- a/cmake/Modules/Packages/USER-MDI.cmake +++ b/cmake/Modules/Packages/USER-MDI.cmake @@ -17,7 +17,7 @@ if(DOWNLOAD_MDI) # only ON/OFF are allowed for "mpi" flag when building MDI library # so translate boolean value of BUILD_MPI # always disable MPI when cross-compiling to Windows. - if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) + if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)) set(MDI_USE_MPI ON) else() set(MDI_USE_MPI OFF) @@ -27,12 +27,12 @@ if(DOWNLOAD_MDI) set(MDI_USE_PYTHON_PLUGINS OFF) if(CMAKE_VERSION VERSION_LESS 3.12) find_package(PythonLibs QUIET) # Deprecated since version 3.12 - if (PYTHONLIBS_FOUND) + if(PYTHONLIBS_FOUND) set(MDI_USE_PYTHON_PLUGINS ON) endif() else() find_package(Python QUIET COMPONENTS Development) - if (Python_Development_FOUND) + if(Python_Development_FOUND) set(MDI_USE_PYTHON_PLUGINS ON) endif() endif() @@ -85,7 +85,7 @@ if(DOWNLOAD_MDI) endif() # need to add support for dlopen/dlsym, except when compiling for Windows. - if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows")) list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}") endif() if(MDI_DEP_LIBS) diff --git a/cmake/Modules/PreventInSourceBuilds.cmake b/cmake/Modules/PreventInSourceBuilds.cmake index 31f2376aa1..f9b8fc3368 100644 --- a/cmake/Modules/PreventInSourceBuilds.cmake +++ b/cmake/Modules/PreventInSourceBuilds.cmake @@ -9,7 +9,7 @@ function(prevent_in_source_builds) get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) # disallow in-source builds - if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}") + if(("${srcdir}" STREQUAL "${bindir}") OR ("${srcdir2}" STREQUAL "${bindir}") OR ("${srcdir3}" STREQUAL "${bindir}")) message(FATAL_ERROR "\ CMake must not to be run in the source directory. \ diff --git a/cmake/Modules/Testing.cmake b/cmake/Modules/Testing.cmake index d1fa97a7a8..2bb9c4757b 100644 --- a/cmake/Modules/Testing.cmake +++ b/cmake/Modules/Testing.cmake @@ -19,11 +19,11 @@ if(ENABLE_TESTING) # we need to build and link a LOT of tester executables, so it is worth checking if # a faster linker is available. requires GNU or Clang compiler, newer CMake. # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails) - if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) - AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") - OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))) - if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04)) - OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30))) + if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) + AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))) + if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04)) + OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30))) include(CheckCXXCompilerFlag) set(CMAKE_CUSTOM_LINKER_DEFAULT default) check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG) @@ -58,7 +58,7 @@ if(ENABLE_TESTING) endif() # Compiler specific features for testing -if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") +if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) mark_as_advanced(ENABLE_COVERAGE) if(ENABLE_COVERAGE) @@ -83,7 +83,7 @@ mark_as_advanced(ENABLE_IWYU) if(ENABLE_IWYU) # enforce these settings set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE) - if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))) + if(NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))) message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers") endif() # detect the "native" header folder so we can include them first @@ -91,7 +91,7 @@ if(ENABLE_IWYU) string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS}) find_program(IWYU_EXE NAMES include-what-you-use iwyu) find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) - if (IWYU_EXE AND IWYU_TOOL) + if(IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp diff --git a/cmake/Modules/Tools.cmake b/cmake/Modules/Tools.cmake index 078b4ebcf4..29b21dc390 100644 --- a/cmake/Modules/Tools.cmake +++ b/cmake/Modules/Tools.cmake @@ -45,7 +45,7 @@ if(BUILD_LAMMPS_SHELL) target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell) # workaround for broken readline pkg-config file on FreeBSD - if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD) + if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD") target_include_directories(lammps-shell PRIVATE /usr/local/include) endif() target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 7c0d1baeb7..df93599056 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION - USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK USER-YAFF) + USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP + USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 5647c61833..d84caebe28 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE - USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION - USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK USER-YAFF) + USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP + USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index e622211190..ab2b9f15a3 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -2,8 +2,8 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF - USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP + USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP USER-PACE USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 17d6e09df3..08a3a531a1 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -3,9 +3,9 @@ set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG PYTHON VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT - USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS - USER-SMD USER-VTK) + USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE + USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP + USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/doc/Makefile b/doc/Makefile index f63f91454c..d5671b8895 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -10,7 +10,6 @@ endif BUILDDIR = ${CURDIR} RSTDIR = $(BUILDDIR)/src VENV = $(BUILDDIR)/docenv -TXT2RST = $(VENV)/bin/txt2rst ANCHORCHECK = $(VENV)/bin/rst_anchor_check SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config MATHJAX = $(SPHINXCONFIG)/_static/mathjax @@ -59,7 +58,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc # we only want to use explicitly listed files. DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') -.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen +.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen # ------------------------------------------ @@ -205,6 +204,9 @@ package_check : $(VENV) deactivate ;\ ) +char_check : + @( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : ) + xmlgen : doxygen/xml/index.xml doxygen/Doxyfile: doxygen/Doxyfile.in @@ -230,7 +232,7 @@ $(VENV): $(MATHJAX): @git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@ -$(TXT2RST) $(ANCHORCHECK): $(VENV) +$(ANCHORCHECK): $(VENV) @( \ . $(VENV)/bin/activate; \ (cd utils/converters;\ diff --git a/doc/lammps.1 b/doc/lammps.1 index 11438ac5c3..9d712a42f0 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -34,7 +34,7 @@ semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. -See https://lammps.sandia.gov/ for more information and documentation. +See https://www.lammps.org/ for more information and documentation. .SH EXECUTABLE NAME The diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index 7789ae6e7b..a4a1076831 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -1129,6 +1129,9 @@ Bibliography **(Sutmann)** Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013) +**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems. + In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014. + **(Swinburne)** Swinburne and Marinica, Physical Review Letters, 120, 1 (2018) @@ -1285,9 +1288,6 @@ Bibliography **(Wennberg)** Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013). -**(Who)** - Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012). - **(Wicaksono1)** Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016). diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 25ef36b430..8be4b2309f 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -48,6 +48,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-AWPMD ` * :ref:`USER-COLVARS ` * :ref:`USER-H5MD ` + * :ref:`USER-HDNNP ` * :ref:`USER-INTEL ` * :ref:`USER-MDI ` * :ref:`USER-MESONT ` @@ -1470,6 +1471,60 @@ the HDF5 library. ---------- +.. _user-hdnnp: + +USER-HDNNP package +--------------------------------- + +To build with the USER-HDNNP package it is required to download and build the +external `n2p2 `__ library ``v2.1.4`` +(or higher). The LAMMPS build process offers an automatic download and +compilation of *n2p2* or allows you to choose the installation directory of +*n2p2* manually. Please see the boxes below for the CMake and traditional build +system for detailed information. + +In case of a manual installation of *n2p2* you only need to build the *n2p2* core +library ``libnnp`` and interface library ``libnnpif``. When using GCC it should +suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more +details please see ``lib/hdnnp/README`` and the `n2p2 build documentation +`__. + +.. tabs:: + + .. tab:: CMake build + + .. code-block:: bash + + -D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes + -D N2P2_DIR=path # n2p2 base directory (only needed if a custom location) + + If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and + built inside the CMake build directory. If the *n2p2* library is already + on your system (in a location CMake cannot find it), set the ``N2P2_DIR`` + to path where *n2p2* is located. If *n2p2* is located directly in + ``lib/hdnnp/n2p2`` it will be automatically found by CMake. + + .. tab:: Traditional make + + You can download and build the *n2p2* library manually if you prefer; + follow the instructions in ``lib/hdnnp/README``\ . You can also do it in + one step from the ``lammps/src`` dir, using a command like these, which + simply invoke the ``lib/hdnnp/Install.py`` script with the specified args: + + .. code-block:: bash + + $ make lib-hdnnp # print help message + $ make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-... + $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version + $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2 + + Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and + ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to + ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``, + respectively. When LAMMPS is built in ``src`` it will use these links. + +---------- + .. _user-intel: USER-INTEL package diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 91531f51ec..2b2993de50 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | -+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | -+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | -+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-HDNNP ` | :ref:`USER-INTEL ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +| :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | ++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ The mechanism for including packages is simple but different for CMake versus make. diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index b7baaa8581..258f2dab17 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -118,6 +118,7 @@ OPT. * :doc:`gw/zbl ` * :doc:`hbond/dreiding/lj (o) ` * :doc:`hbond/dreiding/morse (o) ` + * :doc:`hdnnp ` * :doc:`ilp/graphene/hbn ` * :doc:`kolmogorov/crespi/full ` * :doc:`kolmogorov/crespi/z ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 5463fff1aa..07a1794bd1 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -79,6 +79,7 @@ page gives those details. * :ref:`USER-EFF ` * :ref:`USER-FEP ` * :ref:`USER-H5MD ` + * :ref:`USER-HDNNP ` * :ref:`USER-INTEL ` * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` @@ -1639,6 +1640,39 @@ This package has :ref:`specific installation instructions ` on the :d ---------- +.. _PKG-USER-HDNNP: + +USER-HDNNP package +------------------ + +**Contents:** + +A :doc:`pair_style hdnnp ` command which allows to use +high-dimensional neural network potentials (HDNNPs), a form of machine learning +potentials. HDNNPs must be carefully trained prior to their application in a +molecular dynamics simulation. + +.. _n2p2: https://github.com/CompPhysVienna/n2p2 + +To use this package you must have the `n2p2 `_ library installed and +compiled on your system. + +**Author:** Andreas Singraber + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/USER-HDNNP: filenames -> commands +* src/USER-HDNNP/README +* lib/hdnnp/README +* :doc:`pair_style hdnnp ` +* examples/USER/hdnnp + +---------- + .. _PKG-USER-INTEL: USER-INTEL package diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index ad9ebc58d1..33226d1b1d 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -59,6 +59,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-HDNNP ` | High-dimensional neural network potentials | :doc:`pair_style hdnnp ` | USER/hdnnp | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 59f5b7f27c..8bbbae9155 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -278,7 +278,7 @@ pressure simulation with MSM will cause the code to run slower. ---------- The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library `_ which provides a variety of solver -methods which can be used with LAMMPS. The paper by :ref:`(Who) ` +methods which can be used with LAMMPS. The paper by :ref:`(Sutman) ` gives an overview of ScaFaCoS. ScaFaCoS was developed by a consortium of German research facilities @@ -550,7 +550,7 @@ Illinois at Urbana-Champaign, (2006). **(Cerda)** Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008) -.. _Who2012: +.. _Sutmann2014: -**(Who)** Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 -(2012). +**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems. + In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014. diff --git a/doc/src/pair_hdnnp.rst b/doc/src/pair_hdnnp.rst new file mode 100644 index 0000000000..77a87642c4 --- /dev/null +++ b/doc/src/pair_hdnnp.rst @@ -0,0 +1,230 @@ +.. index:: pair_style hdnnp + +pair_style hdnnp command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style hdnnp cutoff keyword value ... + +* cutoff = short-range cutoff of HDNNP (maximum symmetry function cutoff radius) +* zero or more keyword/value pairs may be appended +* keyword = *dir* or *showew* or *showewsum* or *maxew* or *resetew* or *cflength* or *cfenergy* +* value depends on the preceding keyword: + +.. parsed-literal:: + + *dir* value = directory + directory = Path to HDNNP configuration files + *showew* value = *yes* or *no* + *showewsum* value = summary + summary = Write EW summary every this many timesteps (*0* turns summary off) + *maxew* value = threshold + threshold = Maximum number of EWs allowed + *resetew* value = *yes* or *no* + *cflength* value = length + length = Length unit conversion factor + *cfenergy* value = energy + energy = Energy unit conversion factor + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style hdnnp 6.35 showew yes showewsum 100 maxew 1000 resetew yes cflength 1.8897261328 cfenergy 0.0367493254 + pair_coeff * * H O + + pair_style hdnnp 6.01 dir "./" showewsum 10000 + pair_coeff * * S Cu NULL Cu + +Description +""""""""""" + +This pair style adds an interaction based on the high-dimensional neural network +potential (HDNNP) method as presented in :ref:`(Behler and Parrinello 2007) +`. HDNNPs are machine learning potentials which require +careful training of neural networks prior to application in MD simulations. The +pair style uses an interface to the *n2p2* library :ref:`(Singraber, Behler and +Dellago 2019) ` which is available on Github +`here `__. Please see the *n2p2* +`documentation `__ for further details. +*n2p2* (and hence this pair style) is compatible with neural network potentials +trained with its own tools :ref:`(Singraber et al 2019) ` +and with `RuNNer `__. + +Only a single *pair_coeff* command with two asterisk wild-cards is used with this +pair style. Its additional arguments define the mapping of LAMMPS atom types to +n2p2 elements. + +.. code-block:: LAMMPS + + pair_coeff * * H O + +In the above example LAMMPS types 1 and 2 are mapped to the elements "H" and "O" +in n2p2, respectively. Multiple types may map to the same element, or some types +may not be mapped at all. For example, if the LAMMPS simulation has four atom +types, the command + +.. code-block:: LAMMPS + + pair_coeff * * H H O NULL + +maps atom types 1 and 2 to the element "H", type 3 to "O" and type 4 is not mapped +(indicated by NULL). Atoms mapped to NULL are ignored by the HDNNP calculation, +i.e. they do not contribute in any way to the evaluation of HDNNP energies and forces. +This may be useful in a setup with :doc:`hybrid pair styles `. + +---- + +The mandatory pair style argument *cutoff* must match the short-range cutoff radius +of the HDNNP. This corresponds to the maximum cutoff radius of all symmetry +functions (the atomic environment descriptors of HDNNPs) used. + +.. note:: + + The cutoff must be given in LAMMPS length units, even if the neural network + potential has been trained using a different unit system (see remarks about the + *cflength* and *cfenergy* keywords below for details). + +The numeric value may be slightly larger than the actual maximum symmetry +function cutoff radius (to account for rounding errors when converting units), +but must not be smaller. + +Use the *dir* keyword to specify the directory containing the HDNNP configuration +files. The directory must contain ``input.nn`` with neural network and symmetry +function setup, ``scaling.data`` with symmetry function scaling data and +``weights.???.data`` with weight parameters for each element. + +The keyword *showew* can be used to turn on/off the display of extrapolation +warnings (EWs) which are issued whenever a symmetry function value is out of +bounds defined by minimum/maximum values in ``scaling.data``. An extrapolation +warning may look like this: + +.. code-block:: LAMMPS + + ### NNP EXTRAPOLATION WARNING ### STRUCTURE: 0 ATOM: 119 ELEMENT: Cu SYMFUNC: 32 TYPE: 3 VALUE: 2.166E-02 MIN: 2.003E-05 MAX: 1.756E-02 + +stating that the value 2.166E-02 of symmetry function 32 of type 3 (Narrow Angular symmetry function), element Cu (see the log file for a symmetry function listing) was out +of bounds (maximum in ``scaling.data`` is 1.756E-02) for atom 119. Here, the +atom index refers to the LAMMPS tag (global index) and the structure index is +used to print out the MPI rank the atom belongs to. + +.. note:: + + The *showew* keyword should only be set to *yes* for debugging purposes. + Extrapolation warnings may add lots of overhead as they are communicated each + timestep. Also, if the simulation is run in a region where the HDNNP was not + correctly trained, lots of extrapolation warnings may clog log files and the + console. In a production run use *showewsum* instead. + +The keyword *showewsum* can be used to get an overview of extrapolation warnings +occurring during an MD simulation. The argument specifies the interval at which +extrapolation warning summaries are displayed and logged. An EW summary may look +like this: + +.. code-block:: LAMMPS + + ### NNP EW SUMMARY ### TS: 100 EW 11 EWPERSTEP 1.100E-01 + +Here, at timestep 100 the occurrence of 11 extrapolation warnings since the last +summary is reported, which corresponds to an EW rate of 0.11 per timestep. +Setting *showewsum* to 0 deactivates the EW summaries. + +A maximum number of allowed extrapolation warnings can be specified with the +*maxew* keyword. If the number of EWs exceeds the *maxew* argument the +simulation is stopped. Note however that this is merely an approximate threshold +since the check is only performed at the end of each timestep and each MPI +process counts individually to minimize communication overhead. + +The keyword *resetew* alters the behavior of the above mentioned *maxew* +threshold. If *resetew* is set to *yes* the threshold is applied on a +per-timestep basis and the internal EW counters are reset at the beginning of +each timestep. With *resetew* set to *no* the counters accumulate EWs along the +whole trajectory. + +If the training of a neural network potential has been performed with different +physical units for length and energy than those set in LAMMPS, it is still +possible to use the potential when the unit conversion factors are provided via +the *cflength* and *cfenergy* keywords. If for example, the HDNNP was +parameterized with Bohr and Hartree training data and symmetry function +parameters (i.e. distances and energies in "input.nn" are given in Bohr and +Hartree) but LAMMPS is set to use *metal* units (Angstrom and eV) the correct +conversion factors are: + +.. code-block:: LAMMPS + + cflength 1.8897261328 + + cfenergy 0.0367493254 + +Thus, arguments of *cflength* and *cfenergy* are the multiplicative factors +required to convert lengths and energies given in LAMMPS units to respective +quantities in native HDNNP units (1 Angstrom = 1.8897261328 Bohr, 1 eV = +0.0367493254 Hartree). + +---- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This style does not support mixing. The :doc:`pair_coeff ` command +should only be invoked with asterisk wild cards (see above). + +This style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This style does not write information to :doc:`binary restart files `. +Thus, you need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This style can only be used via the *pair* keyword of the :doc:`run_style respa +` command. It does not support the *inner*\ , *middle*\ , *outer* +keywords. + +Restrictions +"""""""""""" + +This pair style is part of the USER-HDNNP package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` doc +page for more info. + +Please report bugs and feature requests to the `n2p2 GitHub issue page +`__. + +Related commands +^^^^^^^^^^^^^^^^ + +:doc:`pair_coeff `, :doc:`pair_hybrid `, :doc:`units ` + +Default +^^^^^^^ + +The default options are *dir* = "hdnnp/", *showew* = yes, *showewsum* = 0, *maxew* += 0, *resetew* = no, *cflength* = 1.0, *cfenergy* = 1.0. + +---- + +.. _Behler_Parrinello_2007: + +**(Behler and Parrinello 2007)** `Behler, J.; Parrinello, M. Generalized +Neural-Network Representation of High-Dimensional Potential-Energy Surfaces. +Phys. Rev. Lett. 2007, 98 (14), 146401. +`__ + +.. _Singraber_Behler_Dellago_2019: + +**(Singraber, Behler and Dellago 2019)** `Singraber, A.; Behler, J.; Dellago, C. +Library-Based LAMMPS Implementation of High-Dimensional Neural Network +Potentials. J. Chem. Theory Comput. 2019, 15 (3), 1827-1840 +`__ + +.. _Singraber_et_al_2019: + +**(Singraber et al 2019)** `Singraber, A.; Morawietz, T.; Behler, J.; Dellago, +C. Parallel Multistream Training of High-Dimensional Neural Network Potentials. +J. Chem. Theory Comput. 2019, 15 (5), 3075-3092. +`__ diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index ce74b0d873..a5ae41d5d9 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -182,6 +182,7 @@ accelerated styles exist. * :doc:`gw/zbl ` - Gao-Weber potential with a repulsive ZBL core * :doc:`hbond/dreiding/lj ` - DREIDING hydrogen bonding LJ potential * :doc:`hbond/dreiding/morse ` - DREIDING hydrogen bonding Morse potential +* :doc:`hdnnp ` - High-dimensional neural network potential * :doc:`ilp/graphene/hbn ` - registry-dependent interlayer potential (ILP) * :doc:`kim ` - interface to potentials provided by KIM project * :doc:`kolmogorov/crespi/full ` - Kolmogorov-Crespi (KC) potential with no simplifications diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py old mode 100644 new mode 100755 index 64a1308601..5d4ee428e2 --- a/doc/utils/converters/lammpsdoc/rst_anchor_check.py +++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python3 +#!/usr/bin/env python3 # LAMMPS Documentation Utilities # # Scan for duplicate anchor labels in documentation files diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py index d85669bcc1..275c9b0c0b 100644 --- a/doc/utils/converters/setup.py +++ b/doc/utils/converters/setup.py @@ -1,7 +1,7 @@ from setuptools import setup setup(name='LAMMPS Documentation Utilities', - version='2.0.0', + version='2.0.1', description='Utilities to convert existing LAMMPS documentation text files into ReStructured Text', url='https://github.com/rbberger/lammps-doc-utils', author='Richard Berger', @@ -11,8 +11,6 @@ setup(name='LAMMPS Documentation Utilities', test_suite='nose.collector', tests_require=['nose'], entry_points = { - "console_scripts": ['txt2html = lammpsdoc.txt2html:main', - 'txt2rst = lammpsdoc.txt2rst:main', - 'rst_anchor_check = lammpsdoc.rst_anchor_check:main '] + "console_scripts": ['rst_anchor_check = lammpsdoc.rst_anchor_check:main '] }, ) diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index ff7e8a6f39..7a6fbaf7a0 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -360,7 +360,7 @@ with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The primary author of the code is Steve Plimpton, who can be emailed -at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has +at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has more information about the code and its uses. """ diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 6133729b8a..d92cf4694e 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -187,6 +187,7 @@ backends Baczewski Bagi Bagnold +Bajaj Bkappa Bal balancer @@ -1228,6 +1229,8 @@ hbn hbnewflag hbond hcp +hdnnp +HDNNP heatconduction Hebbeker Hebenstreit @@ -1570,6 +1573,7 @@ Koning Kooser Korn Koskinen +Koslowski Kosovan Koster Kosztin @@ -2953,6 +2957,7 @@ shrinkexceed Shugaev si SiC +Siegmund Siepmann Sievers sigmoid @@ -3618,6 +3623,7 @@ yx yy yz Zannoni +Zavattieri zbl ZBL Zc diff --git a/examples/USER/hdnnp/data.H2O-360mol b/examples/USER/hdnnp/data.H2O-360mol new file mode 100644 index 0000000000..3791f07585 --- /dev/null +++ b/examples/USER/hdnnp/data.H2O-360mol @@ -0,0 +1,1096 @@ +LAMMPS data file, 360 water molecules + +1080 atoms +2 atom types + +0.0 2.2695686722465727E+01 xlo xhi +0.0 2.3586033624598713E+01 ylo yhi +0.0 2.2237130028217017E+01 zlo zhi + +Masses + +1 1.00794 +2 15.9994 + +Atoms # atomic + +1 2 1.7548118361224624E+01 7.3699168122955889E+00 5.5591101411055377E-01 +2 1 1.7052018361224619E+01 7.5604368122955892E+00 1.3882600141105546E+00 +3 1 1.8473918361224619E+01 7.4162968122955890E+00 8.4111101411055411E-01 +4 2 9.1706683612246138E+00 1.2915816812295594E+01 2.5107200141105555E+00 +5 1 9.7830883612246140E+00 1.2151816812295593E+01 2.3347500141105550E+00 +6 1 9.1892283612246164E+00 1.3443216812295594E+01 1.6591000141105545E+00 +7 2 1.8399218361224623E+01 1.7424016812295601E+01 6.5473300141105586E+00 +8 1 1.8345918361224623E+01 1.8268716812295594E+01 7.0339200141105591E+00 +9 1 1.9026818361224624E+01 1.6834816812295600E+01 7.0045500141105599E+00 +10 2 5.7216883612246123E+00 1.6305516812295600E+01 1.0104620014110562E+01 +11 1 6.2668083612246122E+00 1.5517116812295598E+01 9.8182400141105628E+00 +12 1 6.2385083612246124E+00 1.6937316812295599E+01 1.0608050014110562E+01 +13 2 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2.0712450014110569E+01 +1042 2 7.0554283612246129E+00 1.6077516812295599E+01 1.7628950014110565E+01 +1043 1 6.9981783612246131E+00 1.6403416812295596E+01 1.6704450014110570E+01 +1044 1 7.7722083612246129E+00 1.5403516812295596E+01 1.7707550014110570E+01 +1045 2 9.1948983612246149E+00 1.0623516812295591E+01 9.8707000141105627E+00 +1046 1 8.5664583612246137E+00 1.0414716812295591E+01 9.1563400141105618E+00 +1047 1 8.9125783612246146E+00 1.1463416812295593E+01 1.0255350014110562E+01 +1048 2 3.4275083612246098E+00 1.4718216812295594E+01 1.7487000141105546E+00 +1049 1 2.7882983612246091E+00 1.5297516812295596E+01 1.3626300141105543E+00 +1050 1 3.7876783612246099E+00 1.5291116812295597E+01 2.4465400141105555E+00 +1051 2 1.3184418361224617E+01 1.6254416812295595E+01 1.6217400141105547E+00 +1052 1 1.2358318361224617E+01 1.5655016812295598E+01 1.4601300141105547E+00 +1053 1 1.3636118361224620E+01 1.6118716812295595E+01 7.4275201411055392E-01 +1054 2 2.1478318361224627E+01 9.3499668122955910E+00 1.3041450014110564E+01 +1055 1 2.0571518361224623E+01 9.4989368122955913E+00 1.3473650014110564E+01 +1056 1 2.1367718361224625E+01 9.0415068122955891E+00 1.2126950014110564E+01 +1057 2 1.3240818361224617E+01 2.1513516812295602E+01 7.6613400141105599E+00 +1058 1 1.3173218361224619E+01 2.0794016812295602E+01 8.3871300141105607E+00 +1059 1 1.2721018361224617E+01 2.1148516812295600E+01 6.8687800141105599E+00 +1060 2 1.0706218361224616E+01 9.0730668122955915E+00 1.2194050014110564E+01 +1061 1 1.0209918361224616E+01 9.5840168122955909E+00 1.1511850014110562E+01 +1062 1 1.0127718361224616E+01 8.2990868122955899E+00 1.2386250014110566E+01 +1063 2 9.8246936122460771E-01 9.5211468122955907E+00 1.0116250014110562E+01 +1064 1 1.2453883612246077E+00 1.0440616812295591E+01 1.0422250014110562E+01 +1065 1 1.6324283612246082E+00 8.8711068122955901E+00 1.0428050014110564E+01 +1066 2 2.1805418361224621E+01 1.8063116812295597E+01 1.9102050014110567E+01 +1067 1 2.1618318361224627E+01 1.8993216812295604E+01 1.8788850014110569E+01 +1068 1 8.4032061224607005E-02 1.8152616812295598E+01 1.9376750014110570E+01 +1069 2 4.9490783612246112E+00 4.5899568122955863E+00 4.0229100141105567E+00 +1070 1 4.9939883612246110E+00 5.4655868122955873E+00 4.4890400141105573E+00 +1071 1 4.2701383612246104E+00 4.0452668122955862E+00 4.5228100141105569E+00 +1072 2 1.8242218361224626E+01 2.9008968122955854E+00 1.5903950014110567E+01 +1073 1 1.8887118361224626E+01 2.5084568122955848E+00 1.5204150014110565E+01 +1074 1 1.8162418361224624E+01 2.1789868122955851E+00 1.6617050014110568E+01 +1075 2 3.9899383612246102E+00 1.9364416812295598E+01 1.3871050014110565E+01 +1076 1 4.3833283612246108E+00 2.0252516812295600E+01 1.3695350014110566E+01 +1077 1 3.1540783612246095E+00 1.9562116812295599E+01 1.4347050014110566E+01 +1078 2 7.0537683612246127E+00 1.4620616812295594E+01 6.4024900141105583E+00 +1079 1 7.6585583612246131E+00 1.3942216812295593E+01 6.0279100141105584E+00 +1080 1 6.2108683612246125E+00 1.4238816812295596E+01 6.6619400141105594E+00 diff --git a/examples/USER/hdnnp/hdnnp-data/input.nn b/examples/USER/hdnnp/hdnnp-data/input.nn new file mode 100644 index 0000000000..885ec0ec70 --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/input.nn @@ -0,0 +1,120 @@ +############################################################################### +# HDNNP for water H2O +############################################################################### +# Length unit : Bohr +# Energy unit : Ha +# Reference method: RPBE-D3 +############################################################################### + +############################################################################### +# DATA SET NORMALIZATION +############################################################################### +# This section was automatically added by nnp-norm. +mean_energy -2.5521343547039809E+01 +conv_energy 2.4265748255366972E+02 +conv_length 5.8038448995319847E+00 +############################################################################### + +############################################################################### +# GENERAL NNP SETTINGS +############################################################################### +# These keywords are (almost) always required. +number_of_elements 2 # Number of elements. +elements H O # Specification of elements. +#atom_energy H -0.45890771 # Free atom reference energy (H). +#atom_energy O -74.94518524 # Free atom reference energy (O). +cutoff_type 2 # Cutoff type. +scale_symmetry_functions # Scale all symmetry functions with min/max values. +#scale_symmetry_functions_sigma # Scale all symmetry functions with sigma. +scale_min_short 0.0 # Minimum value for scaling. +scale_max_short 1.0 # Maximum value for scaling. +center_symmetry_functions # Center all symmetry functions, i.e. subtract mean value. +global_hidden_layers_short 2 # Number of hidden layers. +global_nodes_short 25 25 # Number of nodes in each hidden layer. +global_activation_short t t l # Activation function for each hidden layer and output layer. +#normalize_nodes # Normalize input of nodes. + +############################################################################### +# SYMMETRY FUNCTIONS +############################################################################### + +# Radial symmetry function (type 2): +#symfunction_short 2 + +# Narrow Angular symmetry function (type 3): +#symfunction_short 3 + +# Wide Angular symmetry function (type 9): +#symfunction_short 9 + +# radial H H +symfunction_short H 2 H 0.001 0.0 12.00 +symfunction_short H 2 H 0.01 0.0 12.00 +symfunction_short H 2 H 0.03 0.0 12.00 +symfunction_short H 2 H 0.06 0.0 12.00 +symfunction_short H 2 H 0.15 1.9 12.00 +symfunction_short H 2 H 0.30 1.9 12.00 +symfunction_short H 2 H 0.60 1.9 12.00 +symfunction_short H 2 H 1.50 1.9 12.00 + +# radial H O / O H +symfunction_short H 2 O 0.001 0.0 12.00 +symfunction_short H 2 O 0.01 0.0 12.00 +symfunction_short H 2 O 0.03 0.0 12.00 +symfunction_short H 2 O 0.06 0.0 12.00 +symfunction_short H 2 O 0.15 0.9 12.00 +symfunction_short H 2 O 0.30 0.9 12.00 +symfunction_short H 2 O 0.60 0.9 12.00 +symfunction_short H 2 O 1.50 0.9 12.00 + +symfunction_short O 2 H 0.001 0.0 12.00 +symfunction_short O 2 H 0.01 0.0 12.00 +symfunction_short O 2 H 0.03 0.0 12.00 +symfunction_short O 2 H 0.06 0.0 12.00 +symfunction_short O 2 H 0.15 0.9 12.00 +symfunction_short O 2 H 0.30 0.9 12.00 +symfunction_short O 2 H 0.60 0.9 12.00 +symfunction_short O 2 H 1.50 0.9 12.00 + +# radial O O +symfunction_short O 2 O 0.001 0.0 12.00 +symfunction_short O 2 O 0.01 0.0 12.00 +symfunction_short O 2 O 0.03 0.0 12.00 +symfunction_short O 2 O 0.06 0.0 12.00 +symfunction_short O 2 O 0.15 4.0 12.00 +symfunction_short O 2 O 0.30 4.0 12.00 +symfunction_short O 2 O 0.60 4.0 12.00 +symfunction_short O 2 O 1.50 4.0 12.00 + +# angular +symfunction_short H 3 O H 0.2 1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.07 1.0 1.0 12.00000 +symfunction_short H 3 O H 0.07 1.0 1.0 12.00000 +symfunction_short O 3 H H 0.07 -1.0 1.0 12.00000 +symfunction_short H 3 O H 0.07 -1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.03 1.0 1.0 12.00000 +symfunction_short H 3 O H 0.03 1.0 1.0 12.00000 +symfunction_short O 3 H H 0.03 -1.0 1.0 12.00000 +symfunction_short H 3 O H 0.03 -1.0 1.0 12.00000 + +symfunction_short O 3 H H 0.01 1.0 4.0 12.00000 +symfunction_short H 3 O H 0.01 1.0 4.0 12.00000 +symfunction_short O 3 H H 0.01 -1.0 4.0 12.00000 +symfunction_short H 3 O H 0.01 -1.0 4.0 12.00000 + +symfunction_short O 3 O H 0.03 1.0 1.0 12.00000 +symfunction_short O 3 O H 0.03 -1.0 1.0 12.00000 +symfunction_short O 3 O H 0.001 1.0 4.0 12.00000 +symfunction_short O 3 O H 0.001 -1.0 4.0 12.00000 + +symfunction_short H 3 O O 0.03 1.0 1.0 12.00000 +symfunction_short H 3 O O 0.03 -1.0 1.0 12.00000 +symfunction_short H 3 O O 0.001 1.0 4.0 12.00000 +symfunction_short H 3 O O 0.001 -1.0 4.0 12.00000 + +symfunction_short O 3 O O 0.03 1.0 1.0 12.00000 +symfunction_short O 3 O O 0.03 -1.0 1.0 12.00000 +symfunction_short O 3 O O 0.001 1.0 4.0 12.00000 +symfunction_short O 3 O O 0.001 -1.0 4.0 12.00000 diff --git a/examples/USER/hdnnp/hdnnp-data/scaling.data b/examples/USER/hdnnp/hdnnp-data/scaling.data new file mode 100644 index 0000000000..2a9e0ad7a6 --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/scaling.data @@ -0,0 +1,72 @@ +################################################################################ +# Symmetry function scaling data. +################################################################################ +# Col Name Description +################################################################################ +# 1 e_index Element index. +# 2 sf_index Symmetry function index. +# 3 sf_min Symmetry function minimum. +# 4 sf_max Symmetry function maximum. +# 5 sf_mean Symmetry function mean. +# 6 sf_sigma Symmetry function sigma. +######################################################################################################################### +# 1 2 3 4 5 6 +# e_index sf_index sf_min sf_max sf_mean sf_sigma +######################################################################################################################### + 1 1 1.0882016636170764E+00 9.6166419119419064E+00 2.2691752247542194E+00 6.7883526611658462E-01 + 1 2 7.3274438904180561E-01 5.0028559321574191E+00 1.3272332317543580E+00 3.3936750181780473E-01 + 1 3 7.6010783783215696E-01 7.1427942966219815E+00 1.6470726712825305E+00 5.0771115927383836E-01 + 1 4 5.4842285884800812E-01 3.7661771168267726E+00 1.0163698211361718E+00 2.5362958053787776E-01 + 1 5 4.0080665126604625E-01 4.1469832401668629E+00 9.0925040981537897E-01 2.9758019277508319E-01 + 1 6 3.6209352253798227E-01 2.2678239402766054E+00 6.4931154122889623E-01 1.4835420345383032E-01 + 1 7 1.8919103878435897E-01 2.2292652677252804E+00 4.5693857051003817E-01 1.5976079618578123E-01 + 1 8 2.6704178695764313E-01 1.3208742362468955E+00 4.2395636902644862E-01 8.0492394978461931E-02 + 1 9 2.4513099752055156E-01 9.4751160662053002E-01 3.6244199023263673E-01 5.2993540556109331E-02 + 1 10 2.2248910067848982E-01 2.7596216013647377E+00 5.3891576898130766E-01 2.0137334230483950E-01 + 1 11 1.4743601726548086E-01 5.5599270746969276E-01 2.6773972195910817E-01 2.6188094566404998E-02 + 1 12 9.9110926426029380E-02 1.7265405335201480E+00 2.9553976311554875E-01 1.1619768775752932E-01 + 1 13 6.5093699123904267E-02 3.4521757733971170E-01 1.8521249136783141E-01 1.9741155185936318E-02 + 1 14 3.1653527247865069E-02 9.1293170125596168E-01 1.5025164684953513E-01 5.3480187368038674E-02 + 1 15 2.9202821602466694E-03 2.6453981776124141E-01 7.6525296616004684E-02 1.8780956137549487E-02 + 1 16 3.2145385719803329E-04 2.8696425565429240E-01 4.5792284631233672E-02 2.3263495133568998E-02 + 1 17 2.4693757528509622E-04 1.3848731138266304E-01 1.7693289653297604E-02 9.7460303038080908E-03 + 1 18 5.0992836797990751E-03 5.8319173651547385E-01 2.3851656540978389E-02 3.7790771891778152E-02 + 1 19 3.2282960174310170E-04 2.1613962298381925E-01 1.7072560754702336E-02 1.4026518665786077E-02 + 1 20 4.9647513277769700E-02 1.6851617426880194E+00 1.4541325969622534E-01 1.0954306125703028E-01 + 1 21 3.4073471604482227E-03 3.1637071808861689E-01 1.8422597685566724E-02 2.0125274191649719E-02 + 1 22 1.3121382132811807E-04 1.0258348935693713E-01 6.3684016949344113E-03 6.6071626858835051E-03 + 1 23 3.3813162813665906E-02 9.1618560879938926E-01 8.1266384503339575E-02 5.7918502576695730E-02 + 1 24 4.1708500446352870E-04 1.5785966980407021E-01 4.6646981268568697E-03 9.8630700614506465E-03 + 1 25 7.3528900917695290E-04 5.9225627251013026E-02 3.7042174075139758E-03 3.3118079036492621E-03 + 1 26 8.9828333062972592E-03 1.9426085555380754E-01 2.4093377110646338E-02 1.0980657457661532E-02 + 1 27 2.1228022180417653E-04 8.7777813240869640E-03 2.0550705761547970E-03 5.8802103858137246E-04 + 2 1 1.5142595331454245E+00 1.0005711988559998E+01 2.6544664635087183E+00 6.7806617585688911E-01 + 2 2 4.4366445360926199E-01 4.6195409357987076E+00 9.6587051599896101E-01 3.3688559575009042E-01 + 2 3 1.1907810568758714E+00 7.5323544094345003E+00 2.0327396422723472E+00 5.0607867531004169E-01 + 2 4 2.7576036468694687E-01 3.3862131032504492E+00 6.5929732667024776E-01 2.5004687333979903E-01 + 2 5 8.0580777590695674E-01 4.5356481255168557E+00 1.2986230824577940E+00 2.9449908325462404E-01 + 2 6 1.0517053799863604E-01 1.8909877539194515E+00 3.0673921331641835E-01 1.4198497108573313E-01 + 2 7 5.6949141690859706E-01 2.6154328621607852E+00 8.4791273805289546E-01 1.5714071578589769E-01 + 2 8 2.3251646720171416E-02 9.3641034200657891E-01 1.1140979781150941E-01 6.9796654369842781E-02 + 2 9 5.1354161698115419E-01 1.8545341781448565E+00 7.2488398046527269E-01 9.8011511620611044E-02 + 2 10 1.1057465545812291E-01 2.9121456897811342E+00 4.7474421797982730E-01 2.3441807910092233E-01 + 2 11 3.5269317308496489E-01 1.0714592032613128E+00 5.3547944391821678E-01 4.5179661104166338E-02 + 2 12 3.0424313539726355E-02 2.5277642768509305E+00 3.1652845366685045E-01 2.1026891409654727E-01 + 2 13 1.5980022688828247E-01 6.6348817066386512E-01 3.7042498273566293E-01 3.0753700953611234E-02 + 2 14 2.7781847150922931E-03 2.3030057819082539E+00 1.7737800292869690E-01 1.8600239464755819E-01 + 2 15 9.5641036809349829E-03 3.9085233064570807E-01 1.5305059323200970E-01 2.7862233984302390E-02 + 2 16 3.7500170432292374E-06 2.0367068825281995E+00 5.4144316535640342E-02 1.4305857218443538E-01 + 2 17 2.4726232100491033E-03 3.4335400617385042E-01 1.6684597803376652E-02 2.1902951351570905E-02 + 2 18 1.7405672406959600E-05 5.6319316766205302E-02 9.5478184601751693E-04 3.3588039002222358E-03 + 2 19 5.4785372164647961E-02 3.0182597583971442E+00 2.0392031625072374E-01 2.0088721011517138E-01 + 2 20 1.3795234987637416E-03 4.9878800454061323E-01 1.2788265359933434E-02 3.1829452602194934E-02 + 2 21 6.6852772684814245E-03 2.6739582842775905E-01 3.0851859894574358E-02 1.7089886758420030E-02 + 2 22 1.7021399438214336E-02 1.4167796508898451E+00 7.6274174813506748E-02 9.2852504206357669E-02 + 2 23 1.9759831791959857E-02 4.0756378297923890E-01 4.8843503112397949E-02 2.5474332458885439E-02 + 2 24 5.2768632746659245E-04 2.3324050667069166E-01 7.2057238727819412E-03 1.4495435261027742E-02 + 2 25 1.1144879740881719E-05 3.5285772934088612E-02 4.2545240948261025E-04 2.0471375111485984E-03 + 2 26 1.6013752685265073E-02 8.2245409953473059E-01 5.0845479076508403E-02 5.2802834522172923E-02 + 2 27 3.9898424495541764E-03 7.8557031440100300E-01 3.6926675414383096E-02 5.0474458307624794E-02 + 2 28 4.0523818189746699E-05 9.8448068666705968E-02 1.2119235889230262E-03 5.7945700128174639E-03 + 2 29 6.0374649986214514E-03 9.9251766407842473E-02 1.6156539248049700E-02 5.5245068674135743E-03 + 2 30 2.9595491075765732E-03 1.5478537567691833E-01 1.1641055270110553E-02 8.9415193910804703E-03 diff --git a/examples/USER/hdnnp/hdnnp-data/weights.001.data b/examples/USER/hdnnp/hdnnp-data/weights.001.data new file mode 100644 index 0000000000..deb5012acb --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/weights.001.data @@ -0,0 +1,1392 @@ +################################################################################ +# Neural network connection values (weights and biases). +################################################################################ +# Col Name Description +################################################################################ +# 1 connection Neural network connection value. +# 2 t Connection type (a = weight, b = bias). +# 3 index Index enumerating weights. +# 4 l_s Starting point layer (end point layer for biases). +# 5 n_s Starting point neuron in starting layer (end point neuron for biases). +# 6 l_e End point layer. +# 7 n_e End point neuron in end layer. +################################################################################ +# 1 2 3 4 5 6 7 +# connection t index l_s n_s l_e n_e +############################################################ + 1.2539155865352127E+00 a 1 0 1 1 1 + 2.2490365890661286E+00 a 2 0 1 1 2 + 4.9361851928374572E+00 a 3 0 1 1 3 + -2.3971991574908125E+00 a 4 0 1 1 4 + -1.8596992303156465E+00 a 5 0 1 1 5 + 3.8287764168815897E+00 a 6 0 1 1 6 + 7.4523181738636106E+00 a 7 0 1 1 7 + 6.0971861116881998E+00 a 8 0 1 1 8 + -8.7239359226117639E+00 a 9 0 1 1 9 + -1.8255232070184267E+01 a 10 0 1 1 10 + -7.8065643887610179E+00 a 11 0 1 1 11 + 1.4247237398130265E+01 a 12 0 1 1 12 + -3.2217879518334338E+00 a 13 0 1 1 13 + -5.7395252086520712E+00 a 14 0 1 1 14 + 2.0353040522911576E+00 a 15 0 1 1 15 + 7.7520578160630560E+00 a 16 0 1 1 16 + 2.9357257867412252E+00 a 17 0 1 1 17 + -2.9719860930100790E+00 a 18 0 1 1 18 + 8.9245382590288980E+00 a 19 0 1 1 19 + 6.6848134049442169E+00 a 20 0 1 1 20 + -2.2992719903495891E+00 a 21 0 1 1 21 + -1.4401533482181721E+01 a 22 0 1 1 22 + -2.0574070545285186E+00 a 23 0 1 1 23 + 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1287 1 24 2 12 + -6.7540631566041298E-01 a 1288 1 24 2 13 + -1.4565321192168545E+00 a 1289 1 24 2 14 + -1.3315414628143039E+00 a 1290 1 24 2 15 + 1.2552098425264056E+00 a 1291 1 24 2 16 + -1.1701558601459501E+00 a 1292 1 24 2 17 + 2.1967564647703792E+00 a 1293 1 24 2 18 + 3.6767594091430167E-01 a 1294 1 24 2 19 + 1.4791781996464841E+00 a 1295 1 24 2 20 + -2.4597335939693896E+00 a 1296 1 24 2 21 + 1.8222789722776007E+00 a 1297 1 24 2 22 + -2.4818384588216302E+00 a 1298 1 24 2 23 + -1.3359962912345340E+00 a 1299 1 24 2 24 + -1.6060924344568878E-02 a 1300 1 24 2 25 + -1.1558703878945702E+00 a 1301 1 25 2 1 + 5.5859771317693908E-02 a 1302 1 25 2 2 + -1.9275021348316721E+00 a 1303 1 25 2 3 + 4.2881321046205173E-01 a 1304 1 25 2 4 + 6.6308764508018558E-01 a 1305 1 25 2 5 + -2.5357661809360188E-01 a 1306 1 25 2 6 + 7.7965409617466697E-01 a 1307 1 25 2 7 + -1.9470416731652336E+00 a 1308 1 25 2 8 + 2.0923659915641873E-01 a 1309 1 25 2 9 + 8.9211452410465542E-01 a 1310 1 25 2 10 + 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11 3 1 + 1.2413851904356363E+00 a 1362 2 12 3 1 + -6.3168181712211169E-01 a 1363 2 13 3 1 + 7.6424175125347729E+00 a 1364 2 14 3 1 + -1.3477038299214714E+00 a 1365 2 15 3 1 + -1.6064659765754943E+00 a 1366 2 16 3 1 + -8.9624380518145874E-01 a 1367 2 17 3 1 + -1.0509865792522375E+00 a 1368 2 18 3 1 + 8.1847872933853638E-01 a 1369 2 19 3 1 + 1.2845504810303034E+00 a 1370 2 20 3 1 + -5.1879822944368881E-01 a 1371 2 21 3 1 + -7.2018714033119180E-01 a 1372 2 22 3 1 + 5.9870832883780798E+00 a 1373 2 23 3 1 + -6.0589155387470683E-01 a 1374 2 24 3 1 + 5.0177609140285355E+00 a 1375 2 25 3 1 + 9.7386086372975722E+00 b 1376 3 1 diff --git a/examples/USER/hdnnp/hdnnp-data/weights.008.data b/examples/USER/hdnnp/hdnnp-data/weights.008.data new file mode 100644 index 0000000000..fbdbaa1411 --- /dev/null +++ b/examples/USER/hdnnp/hdnnp-data/weights.008.data @@ -0,0 +1,1467 @@ +################################################################################ +# Neural network connection values (weights and biases). +################################################################################ +# Col Name Description +################################################################################ +# 1 connection Neural network connection value. +# 2 t Connection type (a = weight, b = bias). +# 3 index Index enumerating weights. +# 4 l_s Starting point layer (end point layer for biases). +# 5 n_s Starting point neuron in starting layer (end point neuron for biases). +# 6 l_e End point layer. +# 7 n_e End point neuron in end layer. +################################################################################ +# 1 2 3 4 5 6 7 +# connection t index l_s n_s l_e n_e +############################################################ + -4.2252995889643252E-01 a 1 0 1 1 1 + -6.0555645962054347E+00 a 2 0 1 1 2 + 1.4040722027928377E+01 a 3 0 1 1 3 + -2.7041370011942618E+00 a 4 0 1 1 4 + -3.8202743208058858E+00 a 5 0 1 1 5 + -3.3612643261393358E+00 a 6 0 1 1 6 + -2.0418101025905258E+00 a 7 0 1 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+############################################################################### +clear +# Configuration files +variable cfgFile string "data.H2O-360mol" +# Timesteps +variable numSteps equal 10 +variable dt equal 0.0005 +# HDNNP +variable hdnnpCutoff equal 6.36 +variable hdnnpDir string "hdnnp-data" + +############################################################################### +# GENERAL SETUP +############################################################################### +units metal +boundary p p p +atom_style atomic +read_data ${cfgFile} +timestep ${dt} +thermo 1 + +############################################################################### +# HDNNP +############################################################################### +pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254 +pair_coeff * * H O + +############################################################################### +# INTEGRATOR +############################################################################### +fix INT all nve + +############################################################################### +# OUTPUT +############################################################################### +dump 1 all atom 1 dump.hdnnp + +############################################################################### +# SIMULATION +############################################################################### +run ${numSteps} diff --git a/lib/README b/lib/README index 26c3fad9e0..2b7a38f5db 100644 --- a/lib/README +++ b/lib/README @@ -27,6 +27,8 @@ gpu general GPU routines, GPU package from Mike Brown (ORNL) h5md ch5md library for output of MD data in HDF5 format from Pierre de Buyl (KU Leuven) +hdnnp hooks to n2p2, neural network potential package, used by USER-HDNNP + from Andreas Singraber kim hooks to the KIM library, used by KIM package from Ryan Elliott and Ellad Tadmor (U Minn) kokkos Kokkos package for GPU and many-core acceleration diff --git a/lib/hdnnp/Install.py b/lib/hdnnp/Install.py new file mode 100644 index 0000000000..3b232f400b --- /dev/null +++ b/lib/hdnnp/Install.py @@ -0,0 +1,122 @@ +#!/usr/bin/env python + +""" +Install.py tool to download, unpack, build, and link to the n2p2 library +used to automate the steps described in the README file in this dir +""" + +from __future__ import print_function +import sys, os, platform, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import get_cpus, fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = "2.1.4" + +# help message + +HELP = """ +Syntax from src dir: make lib-hdnnp args="-b" + or: make lib-hdnnp args="-b -v 2.1.4" + or: make lib-hdnnp args="-p /usr/local/n2p2" + +Syntax from lib dir: python Install.py -b -v 2.1.4 + or: python Install.py -b + or: python Install.py -p /usr/local/n2p2 + +Example: + +make lib-hdnnp args="-b" # download/build in lib/hdnnp/n2p2 +make lib-hdnnp args="-p $HOME/n2p2" # use existing n2p2 installation in $HOME/n2p2 +""" + +# known checksums for different n2p2 versions. used to validate the download. +checksums = { \ + '2.1.4' : '9595b066636cd6b90b0fef93398297a5', \ + } + +# parse and process arguments + +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the n2p2 library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing n2p2 installation") +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), + help="set version of n2p2 to download and build (default: %s)" % version) + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) + +buildflag = args.build +pathflag = args.path is not None +n2p2path = args.path + +homepath = fullpath('.') +homedir = "%s/n2p2" % (homepath) + +if pathflag: + if not os.path.isdir(n2p2path): + sys.exit("n2p2 path %s does not exist" % n2p2path) + homedir = fullpath(n2p2path) + if not os.path.isfile(os.path.join(homedir, 'include', 'InterfaceLammps.h')): + sys.exit("No n2p2 installation found at %s" % n2p2path) + +# download and unpack n2p2 tarball + +if buildflag: + url = "https://github.com/CompPhysVienna/n2p2/archive/v%s.tar.gz" % (version) + filename = "n2p2-%s.tar.gz" %version + print("Downloading n2p2 ...") + geturl(url, filename) + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], filename): + sys.exit("Checksum for n2p2 library does not match") + + print("Unpacking n2p2 source tarball ...") + if os.path.exists("%s/n2p2-%s" % (homepath, version)): + shutil.rmtree("%s/n2p2-%s" % (homepath, version)) + if os.path.exists(homedir): + shutil.rmtree(homedir) + cmd = 'cd "%s"; tar -xzvf %s' % (homepath, filename) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + os.remove(os.path.join(homepath, filename)) + + # build n2p2 + print("Building n2p2 ...") + n_cpus = get_cpus() + cmd = 'unset MAKEFLAGS MAKELEVEL MAKEOVERRIDES MFLAGS && cd %s/n2p2-%s/src && make -j%d libnnpif' % (homepath, version, n_cpus) + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + + # set correct homedir for linking step + homedir = "%s/n2p2-%s" % (homepath, version) + +# create 2 links in lib/hdnnp to n2p2 installation dir + +print("Creating links to n2p2 include and lib files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") +if os.path.isfile("Makefile.lammps") or os.path.islink("Makefile.lammps"): + os.remove("Makefile.lammps") +os.symlink(os.path.join(homedir, 'include'), 'includelink') +os.symlink(os.path.join(homedir, 'lib'), 'liblink') +os.symlink(os.path.join(homedir, 'lib', 'Makefile.lammps-extra'), 'Makefile.lammps') diff --git a/lib/hdnnp/README b/lib/hdnnp/README new file mode 100644 index 0000000000..ed61f211ea --- /dev/null +++ b/lib/hdnnp/README @@ -0,0 +1,75 @@ +The USER-HDNNP package requires access to pre-compiled libraries of the n2p2 +package (https://github.com/CompPhysVienna/n2p2). More precisely, the n2p2 core +library ("libnnp"), the interface library ("libnnpif"), some headers and extra +build helper files are needed. These files will be created automatically during +the n2p2 build process. + +This file gives some basic instructions on how to compile n2p2 manually. How to +integrate it then in the LAMMPS build process or how to use the automatic +download and build option is described in detail on the USER-HDNNP build +instructions page of the LAMMPS documentation. + +IMPORTANT: The n2p2 version must be "v2.1.4" or higher. + +Basic build instructions for n2p2 +================================= + +The n2p2 software package comes with lots of useful tools for creating and +applying high-dimensional neural network potentials (HDNNPs). In order to use +n2p2 together with LAMMPS only some parts of the n2p2 code need to be compiled. +As an example, everything related to HDNNP training is not required and would +only add unwanted library dependencies. Hence, the build infrastructure of n2p2 +is designed to allow a separate build of the LAMMPS interface. + +After downloading n2p2, change to the "src" directory and simply execute + + make libnnpif + +which should create the following files needed by the USER-HDNNP package: + + * "n2p2/lib/libnnp.a" + * "n2p2/lib/libnnpif.a" + * "n2p2/lib/lammps-extra.cmake" + * "n2p2/lib/Makefile.lammps-extra" + * "n2p2/include/InterfaceLammps.h" and many other header files. + +If you prefer dynamically linked libraries use + + make MODE=shared libnnpif + +instead (by default MODE=static) which will create *.so versions of the +libraries. By default, n2p2 uses the GNU C++ compiler and the corresponding +settings can be found in "n2p2/src/makefile.gnu". Other makefile presets are +also available (e.g. "makefile.intel") and can be activated by supplying the +"COMP" argument: + + make COMP=intel libnnpif + +Please make sure that your compiler settings for n2p2 and LAMMPS are compatible +(avoid mixing different compilers). + +If you want to build a serial version of LAMMPS with USER-HDNNP package n2p2 must +also be built with MPI disabled. This can be achieved with a preprocessor flag +(-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in the +provided compiler-specific settings makefiles. For example, if you use the GNU +compiler simply remove the comment character '#' in front of the corresponding +line (around line 49) in "makefile.gnu". It should then look like this: + + PROJECT_OPTIONS+= -DN2P2_NO_MPI + +After compiling n2p2 with this flag turned on you can build a serial LAMMPS +version with "-D BUILD_MPI=off" (CMake) or "make serial" (traditional). + +For more information about the n2p2 build process please visit +https://compphysvienna.github.io/n2p2/topics/build.html or ask questions on the +Github issue page (https://github.com/CompPhysVienna/n2p2/issues). + +Testing a successful build of LAMMPS with USER-HDNNP +==================================================== + +An example is provided in the LAMMPS directory "examples/USER/hdnnp" which runs +10 timesteps with 360 water molecules. The neural network potential is defined +via files in the "hdnnp-data" subdirectory. Use the "in.hdnnp" LAMMPS script file +to run the simulation. You should see a large output of the n2p2 library when +the pair style "hdnnp" is initialized, followed by the LAMMPS per-timestep +output. diff --git a/src/.gitignore b/src/.gitignore index 9c2a4b041b..b63256d931 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -990,6 +990,8 @@ /pair_hbond_dreiding_lj.h /pair_hbond_dreiding_morse.cpp /pair_hbond_dreiding_morse.h +/pair_hdnnp.cpp +/pair_hdnnp.h /pair_ilp_graphene_hbn.cpp /pair_ilp_graphene_hbn.h /pair_kolmogorov_crespi_full.cpp diff --git a/src/Makefile b/src/Makefile index a0de708070..271e2fe026 100644 --- a/src/Makefile +++ b/src/Makefile @@ -53,7 +53,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \ user-cgsdk user-colvars user-diffraction user-dpd user-drude \ - user-eff user-fep user-h5md user-intel user-lb user-manifold \ + user-eff user-fep user-h5md user-hdnnp user-intel user-lb user-manifold \ user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \ user-mofff \user-molfile user-netcdf user-omp user-phonon \ user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \ @@ -61,7 +61,7 @@ PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-mdi \ + user-adios user-atc user-awpmd user-colvars user-h5md user-hdnnp user-lb user-mdi \ user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \ user-scafacos user-smd user-vtk @@ -71,7 +71,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont user-mdi PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ + user-adios user-h5md user-hdnnp user-molfile user-netcdf user-pace user-plumed \ user-qmmm user-quip user-scafacos user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) diff --git a/src/USER-HDNNP/Install.sh b/src/USER-HDNNP/Install.sh new file mode 100644 index 0000000000..74e5f1b91e --- /dev/null +++ b/src/USER-HDNNP/Install.sh @@ -0,0 +1,66 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*hdnnp[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/hdnnp/includelink |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/hdnnp/liblink |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(hdnnp_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(hdnnp_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(hdnnp_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/hdnnp\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*hdnnp[^ \t]* //g' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/USER-HDNNP/README b/src/USER-HDNNP/README new file mode 100644 index 0000000000..690db8a714 --- /dev/null +++ b/src/USER-HDNNP/README @@ -0,0 +1,26 @@ +This package implements the "pair_style hdnnp" command which can be used in a +LAMMPS input script. This pair style allows to use pre-trained high-dimensional +neural network potentials[1] via an interface to the n2p2 library +(https://github.com/CompPhysVienna/n2p2)[2]. + +Please see the main documentation for the "pair_style hdnnp" command for further +details on how the pair style is used. An example is provided in the +"examples/USER/hdnnp" directory of LAMMPS. + +The USER-HDNNP package requires the external library n2p2 which must be +downloaded and compiled before starting the build process of LAMMPS. A +guideline on how to build n2p2 is presented in "lib/hdnnp/README". This package +supports the LAMMPS build process via CMake and traditional makefiles, please +see the LAMMPS manual section on building with external libraries for more +details. + +This package was created by Andreas Singraber, please ask questions/report bugs +on the n2p2 Github issues page (https://github.com/CompPhysVienna/n2p2/issues). + +[1] Behler, J.; Parrinello, M. Generalized Neural-Network Representation of +High-Dimensional Potential-Energy Surfaces. Phys. Rev. Lett. 2007, 98 (14), +146401. https://doi.org/10.1103/PhysRevLett.98.146401 + +[2] Singraber, A.; Behler, J.; Dellago, C. Library-Based +LAMMPS Implementation of High-Dimensional Neural Network Potentials. J. Chem. +Theory Comput. 2019, 15 (3), 1827-1840. https://doi.org/10.1021/acs.jctc.8b00770 diff --git a/src/USER-HDNNP/pair_hdnnp.cpp b/src/USER-HDNNP/pair_hdnnp.cpp new file mode 100644 index 0000000000..af64f98f75 --- /dev/null +++ b/src/USER-HDNNP/pair_hdnnp.cpp @@ -0,0 +1,400 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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. + + This file initially came from n2p2 (https://github.com/CompPhysVienna/n2p2) + Copyright (2018) Andreas Singraber (University of Vienna) + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Andreas Singraber +------------------------------------------------------------------------- */ + +#include "pair_hdnnp.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" + +#include "InterfaceLammps.h" // n2p2 interface header + +using namespace LAMMPS_NS; + +static const char cite_user_hdnnp_package[] = + "USER-HDNNP package: 10.1021/acs.jctc.8b00770\n\n" + "@Article{Singraber19,\n" + " author = {Singraber, Andreas and Behler, J{\"o}rg and Dellago, Christoph},\n" + " title = {Library-{{Based LAMMPS Implementation}} of {{High}}-{{Dimensional Neural Network Potentials}}},\n" + " year = {2019},\n" + " month = mar,\n" + " volume = {15},\n" + " pages = {1827--1840},\n" + " doi = {10.1021/acs.jctc.8b00770},\n" + " journal = {J.~Chem.~Theory~Comput.},\n" + " number = {3}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairHDNNP::PairHDNNP(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_user_hdnnp_package); + + single_enable = 0; // 1 if single() routine exists + restartinfo = 0; // 1 if pair style writes restart info + one_coeff = 1; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + unit_convert_flag = 0; // TODO: Check possible values. value != 0 indicates support for unit conversion. + reinitflag = 0; // 1 if compatible with fix adapt and alike + + interface = new nnp::InterfaceLammps(); +} + +/* ---------------------------------------------------------------------- */ + +PairHDNNP::~PairHDNNP() +{ + delete interface; + memory->destroy(setflag); + memory->destroy(cutsq); +} + +/* ---------------------------------------------------------------------- */ + +void PairHDNNP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + // Set number of local atoms and add element. + interface->setLocalAtoms(atom->nlocal,atom->type); + // Transfer tags separately. Interface::setLocalTags is overloaded internally + // to work with both -DLAMMPS_SMALLBIG (tagint = int) and -DLAMMPS_BIGBIG + // (tagint = int64_t) + interface->setLocalTags(atom->tag); + + // Transfer local neighbor list to n2p2 interface. + transferNeighborList(); + + // Compute symmetry functions, atomic neural networks and add up energy. + interface->process(); + + // Do all stuff related to extrapolation warnings. + if(showew == true || showewsum > 0 || maxew >= 0) { + handleExtrapolationWarnings(); + } + + // Calculate forces of local and ghost atoms. + interface->getForces(atom->f); + + // Add energy contribution to total energy. + if (eflag_global) + ev_tally(0,0,atom->nlocal,1,interface->getEnergy(),0.0,0.0,0.0,0.0,0.0); + + // Add atomic energy if requested (CAUTION: no physical meaning!). + if (eflag_atom) + for (int i = 0; i < atom->nlocal; ++i) + eatom[i] = interface->getAtomicEnergy(i); + + // If virial needed calculate via F dot r. + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairHDNNP::settings(int narg, char **arg) +{ + int iarg = 0; + + if (narg < 1) error->all(FLERR,"Illegal pair_style command"); + + maxCutoffRadius = utils::numeric(FLERR,arg[0],false,lmp); + iarg++; + + // default settings + directory = utils::strdup("hdnnp/"); + showew = true; + showewsum = 0; + maxew = 0; + resetew = false; + cflength = 1.0; + cfenergy = 1.0; + numExtrapolationWarningsTotal = 0; + numExtrapolationWarningsSummary = 0; + + while(iarg < narg) { + // set HDNNP directory + if (strcmp(arg[iarg],"dir") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + delete[] directory; + directory = utils::strdup(arg[iarg+1]); + iarg += 2; + // show extrapolation warnings + } else if (strcmp(arg[iarg],"showew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + if (strcmp(arg[iarg+1],"yes") == 0) + showew = true; + else if (strcmp(arg[iarg+1],"no") == 0) + showew = false; + else + error->all(FLERR,"Illegal pair_style command"); + iarg += 2; + // show extrapolation warning summary + } else if (strcmp(arg[iarg],"showewsum") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + showewsum = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // maximum allowed extrapolation warnings + } else if (strcmp(arg[iarg],"maxew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + maxew = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // reset extrapolation warning counter + } else if (strcmp(arg[iarg],"resetew") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + if (strcmp(arg[iarg+1],"yes") == 0) + resetew = true; + else if (strcmp(arg[iarg+1],"no") == 0) + resetew = false; + else + error->all(FLERR,"Illegal pair_style command"); + iarg += 2; + // length unit conversion factor + } else if (strcmp(arg[iarg],"cflength") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + cflength = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + // energy unit conversion factor + } else if (strcmp(arg[iarg],"cfenergy") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal pair_style command"); + cfenergy = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else error->all(FLERR,"Illegal pair_style command"); + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairHDNNP::coeff(int narg, char **arg) +{ + int n = atom->ntypes; + + if (!allocated) allocate(); + + if (narg != 2 + n) + error->all(FLERR,"Incorrect args for pair coefficients"); + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + int *map = new int[n+1]; + for (int i = 0; i < n; i++) map[i] = 0; + + emap = ""; + for (int i = 2; i < narg; i++) { + if (strcmp(arg[i],"NULL") != 0) { + if (i != 2) emap += ","; + emap += std::to_string(i-1) + ":" + arg[i]; + map[i-1] = 1; + } + } + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] > 0 && map[j] > 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + + delete[] map; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairHDNNP::init_style() +{ + int irequest = neighbor->request((void *) this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // Return immediately if HDNNP setup is already completed. + if (interface->isInitialized()) return; + + // Activate screen and logfile output only for rank 0. + if (comm->me == 0) { + if (lmp->screen != nullptr) + interface->log.registerCFilePointer(&(lmp->screen)); + if (lmp->logfile != nullptr) + interface->log.registerCFilePointer(&(lmp->logfile)); + } + + // Initialize interface on all processors. + interface->initialize(directory, + emap.c_str(), + showew, + resetew, + showewsum, + maxew, + cflength, + cfenergy, + maxCutoffRadius, + atom->ntypes, + comm->me); + + // LAMMPS cutoff radius (given via pair_coeff) should not be smaller than + // maximum symmetry function cutoff radius. + if (maxCutoffRadius < interface->getMaxCutoffRadius()) + error->all(FLERR,"Inconsistent cutoff radius"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairHDNNP::init_one(int, int) +{ + return maxCutoffRadius; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairHDNNP::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); // TODO: Is this required? +} + +void PairHDNNP::transferNeighborList() +{ + // Transfer neighbor list to n2p2. + double rc2 = maxCutoffRadius * maxCutoffRadius; + for (int ii = 0; ii < list->inum; ++ii) { + int i = list->ilist[ii]; + for (int jj = 0; jj < list->numneigh[i]; ++jj) { + int j = list->firstneigh[i][jj]; + j &= NEIGHMASK; + double dx = atom->x[i][0] - atom->x[j][0]; + double dy = atom->x[i][1] - atom->x[j][1]; + double dz = atom->x[i][2] - atom->x[j][2]; + double d2 = dx * dx + dy * dy + dz * dz; + if (d2 <= rc2) { + interface->addNeighbor(i,j,atom->tag[j],atom->type[j],dx,dy,dz,d2); + } + } + } +} + +void PairHDNNP::handleExtrapolationWarnings() +{ + // Get number of extrapolation warnings for local atoms. + long numCurrentEW = (long)interface->getNumExtrapolationWarnings(); + + // Update (or set, resetew == true) total warnings counter. + if (resetew) numExtrapolationWarningsTotal = numCurrentEW; + else numExtrapolationWarningsTotal += numCurrentEW; + + // Update warnings summary counter. + if(showewsum > 0) { + numExtrapolationWarningsSummary += numCurrentEW; + } + + // If requested write extrapolation warnings. + // Requires communication of all symmetry functions statistics entries to + // rank 0. + if(showew > 0) { + // First collect an overview of extrapolation warnings per process. + long *numEWPerProc = nullptr; + if(comm->me == 0) numEWPerProc = new long[comm->nprocs]; + MPI_Gather(&numCurrentEW, 1, MPI_LONG, numEWPerProc, 1, MPI_LONG, 0, world); + + if(comm->me == 0) { + for(int i=1;inprocs;i++) { + if(numEWPerProc[i] > 0) { + long bs = 0; + MPI_Status ms; + // Get buffer size. + MPI_Recv(&bs, 1, MPI_LONG, i, 0, world, &ms); + char *buf = new char[bs]; + // Receive buffer. + MPI_Recv(buf, bs, MPI_BYTE, i, 0, world, &ms); + interface->extractEWBuffer(buf, bs); + delete[] buf; + } + } + interface->writeExtrapolationWarnings(); + } + else if(numCurrentEW > 0) { + // Get desired buffer length for all extrapolation warning entries. + long bs = interface->getEWBufferSize(); + // Allocate and fill buffer. + char *buf = new char[bs]; + interface->fillEWBuffer(buf, bs); + // Send buffer size and buffer. + MPI_Send(&bs, 1, MPI_LONG, 0, 0, world); + MPI_Send(buf, bs, MPI_BYTE, 0, 0, world); + delete[] buf; + } + + if(comm->me == 0) delete[] numEWPerProc; + } + + // If requested gather number of warnings to display summary. + if(showewsum > 0 && update->ntimestep % showewsum == 0) { + long globalEW = 0; + // Communicate the sum over all processors to proc 0. + MPI_Reduce(&numExtrapolationWarningsSummary, + &globalEW, 1, MPI_LONG, MPI_SUM, 0, world); + // Write to screen or logfile. + if(comm->me == 0) + utils::logmesg(lmp,"### NNP EW SUMMARY ### TS: {:10d} EW {:10d} EWPERSTEP {:10.3e}\n", + update->ntimestep, globalEW, double(globalEW) / showewsum); + // Reset summary counter. + numExtrapolationWarningsSummary = 0; + } + + // Stop if maximum number of extrapolation warnings is exceeded. + if (numExtrapolationWarningsTotal > maxew) { + error->one(FLERR,"Too many extrapolation warnings"); + } + + // Reset internal extrapolation warnings counters. + interface->clearExtrapolationWarnings(); +} diff --git a/src/USER-HDNNP/pair_hdnnp.h b/src/USER-HDNNP/pair_hdnnp.h new file mode 100644 index 0000000000..9ad2969b8c --- /dev/null +++ b/src/USER-HDNNP/pair_hdnnp.h @@ -0,0 +1,73 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + 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. + + This file initially came from n2p2 (https://github.com/CompPhysVienna/n2p2) + Copyright (2018) Andreas Singraber (University of Vienna) + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Andreas Singraber +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(hdnnp,PairHDNNP) + +#else + +#ifndef LMP_PAIR_HDNNP_H +#define LMP_PAIR_HDNNP_H + +#include "pair.h" + +namespace nnp { + class InterfaceLammps; +} + +namespace LAMMPS_NS { + +class PairHDNNP : public Pair { + + public: + + PairHDNNP(class LAMMPS *); + virtual ~PairHDNNP(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + + protected: + + virtual void allocate(); + void transferNeighborList(); + void handleExtrapolationWarnings(); + + bool showew; + bool resetew; + int showewsum; + int maxew; + long numExtrapolationWarningsTotal; + long numExtrapolationWarningsSummary; + double cflength; + double cfenergy; + double maxCutoffRadius; + char *directory; + std::string emap; + nnp::InterfaceLammps *interface; +}; + +} + +#endif +#endif diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 20f1b5a2fd..a9d3fa61e2 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -264,6 +264,8 @@ void PairQUIP::coeff(int narg, char **arg) quip_file = utils::strdup(arg[2]); quip_string = utils::strdup(arg[3]); + n_quip_file = strlen(quip_file); + n_quip_string = strlen(quip_string); for (int i = 4; i < narg; i++) { if (strcmp(arg[i],"NULL") == 0) diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index 9987fdb071..176e22a391 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -1,6 +1,6 @@ # build LAMMPS plugins, but not on Windows -if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" AND PKG_PLUGIN) +if((NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows")) AND PKG_PLUGIN) ExternalProject_Add(plugins SOURCE_DIR "${LAMMPS_DIR}/examples/plugins" BINARY_DIR ${CMAKE_BINARY_DIR}/build-plugins diff --git a/unittest/force-styles/CMakeLists.txt b/unittest/force-styles/CMakeLists.txt index 86b0f4fdaf..8e84e10c62 100644 --- a/unittest/force-styles/CMakeLists.txt +++ b/unittest/force-styles/CMakeLists.txt @@ -15,7 +15,7 @@ if(CMAKE_VERSION VERSION_LESS 3.12) else() find_package(Python COMPONENTS Interpreter) endif() -if (Python_EXECUTABLE) +if(Python_EXECUTABLE) add_custom_target(check-tests ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check_tests.py -s ${LAMMPS_SOURCE_DIR} -t ${CMAKE_CURRENT_SOURCE_DIR}/tests @@ -33,7 +33,7 @@ else() target_link_libraries(style_tests PUBLIC mpi_stubs) endif() # propagate sanitizer options to test tools -if (ENABLE_SANITIZER AND (NOT ENABLE_SANITIZER STREQUAL "none")) +if(ENABLE_SANITIZER AND (NOT (ENABLE_SANITIZER STREQUAL "none"))) if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) target_compile_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER}) target_link_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER}) @@ -56,7 +56,7 @@ endif() # tests for a molecular systems and related pair styles file(GLOB MOL_PAIR_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/mol-pair-*.yaml) # cannot test MSM with single precision data -if (FFT_SINGLE) +if(FFT_SINGLE) list(FILTER MOL_PAIR_TESTS EXCLUDE REGEX "msm") endif() foreach(TEST ${MOL_PAIR_TESTS}) @@ -106,7 +106,7 @@ endforeach() # kspace style tester, currently uses the pair style tool file(GLOB KSPACE_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/kspace-*.yaml) # cannot test MSM with single precision data -if (FFT_SINGLE) +if(FFT_SINGLE) list(FILTER KSPACE_TESTS EXCLUDE REGEX "msm") endif() foreach(TEST ${KSPACE_TESTS})