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Merge remote-tracking branch 'origin/master' into doc_versions

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This commit is contained in:
Richard Berger
2021-05-26 15:54:56 -04:00
parent 14f989b086 49ced1ed18
commit 409dd02eae
49 changed files with 5585 additions and 96 deletions
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63
cmake/CMakeLists.txt
View File

@ -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")

61
cmake/Modules/FindN2P2.cmake Normal file
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@ -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
)

2
cmake/Modules/GTest.cmake
View File

@ -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)

2
cmake/Modules/LAMMPSUtils.cmake
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@ -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=")

4
cmake/Modules/Packages/GPU.cmake
View File

@ -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)

2
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -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()

2
cmake/Modules/Packages/MESSAGE.cmake
View File

@ -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)

124
cmake/Modules/Packages/USER-HDNNP.cmake Normal file
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@ -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 ${N2P2_BUILD_OPTIONS}
BUILD_ALWAYS YES
INSTALL_COMMAND ""
BUILD_IN_SOURCE 1
LOG_BUILD ON
SOURCE_SUBDIR src/
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libnnp.a <SOURCE_DIR>/lib/libnnpif.a
)
# create imported target LAMMPS::N2P2 from two libraries nnp and nnpif
ExternalProject_get_property(n2p2_build SOURCE_DIR)
# n2p2 core library "libnnp"
add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES
IMPORTED_LOCATION "${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()

8
cmake/Modules/Packages/USER-MDI.cmake
View File

@ -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)

2
cmake/Modules/PreventInSourceBuilds.cmake
View File

@ -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. \

16
cmake/Modules/Testing.cmake
View File

@ -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

2
cmake/Modules/Tools.cmake
View File

@ -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)

10
cmake/presets/all_off.cmake
View File

@ -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)

10
cmake/presets/all_on.cmake
View File

@ -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)

4
cmake/presets/mingw-cross.cmake
View File

@ -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

6
cmake/presets/nolib.cmake
View File

@ -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)

8
doc/Makefile
View File

@ -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;\

2
doc/lammps.1
View File

@ -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

6
doc/src/Bibliography.rst
View File

@ -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).

55
doc/src/Build_extras.rst
View File

@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-HDNNP <user-hdnnp>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <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 <https://github.com/CompPhysVienna/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
<https://compphysvienna.github.io/n2p2/topics/build.html>`__.
.. 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

22
doc/src/Build_package.rst
View File

@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
These links take you to the extra instructions for those select
packages:
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-HDNNP <user-hdnnp>` | :ref:`USER-INTEL <user-intel>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-MOLFILE <user-molfile>` | :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
The mechanism for including packages is simple but different for CMake
versus make.

1
doc/src/Commands_pair.rst
View File

@ -118,6 +118,7 @@ OPT.
* :doc:`gw/zbl <pair_gw>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`

34
doc/src/Packages_details.rst
View File

@ -79,6 +79,7 @@ page gives those details.
* :ref:`USER-EFF <PKG-USER-EFF>`
* :ref:`USER-FEP <PKG-USER-FEP>`
* :ref:`USER-H5MD <PKG-USER-H5MD>`
* :ref:`USER-HDNNP <PKG-USER-HDNNP>`
* :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
@ -1639,6 +1640,39 @@ This package has :ref:`specific installation instructions <user-h5md>` on the :d
----------
.. _PKG-USER-HDNNP:
USER-HDNNP package
------------------
**Contents:**
A :doc:`pair_style hdnnp <pair_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 <n2p2_>`_ library installed and
compiled on your system.
**Author:** Andreas Singraber
**Install:**
This package has :ref:`specific installation instructions <user-hdnnp>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-HDNNP: filenames -> commands
* src/USER-HDNNP/README
* lib/hdnnp/README
* :doc:`pair_style hdnnp <pair_hdnnp>`
* examples/USER/hdnnp
----------
.. _PKG-USER-INTEL:
USER-INTEL package

2
doc/src/Packages_user.rst
View File

@ -59,6 +59,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-HDNNP <PKG-USER-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | USER/hdnnp | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |

8
doc/src/kspace_style.rst
View File

@ -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 <http://www.scafacos.de>`_ which provides a variety of solver
methods which can be used with LAMMPS. The paper by :ref:`(Who) <Who2012>`
methods which can be used with LAMMPS. The paper by :ref:`(Sutman) <Sutmann2014>`
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.

230
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@ -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)
<Behler_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) <Singraber_Behler_Dellago_2019>` which is available on Github
`here <https://github.com/CompPhysVienna/n2p2>`__. Please see the *n2p2*
`documentation <https://compphysvienna.github.io/n2p2/>`__ 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) <Singraber_et_al_2019>`
and with `RuNNer <https://www.uni-goettingen.de/de/560580.html>`__.
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 <pair_hybrid>`.
----
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 <pair_coeff>` command
should only be invoked with asterisk wild cards (see above).
This style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This style does not write information to :doc:`binary restart files <restart>`.
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
<run_style>` 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 <Build_package>` doc
page for more info.
Please report bugs and feature requests to the `n2p2 GitHub issue page
<https://github.com/CompPhysVienna/n2p2/issues>`__.
Related commands
^^^^^^^^^^^^^^^^
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_hybrid <pair_hybrid>`, :doc:`units <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.
<https://doi.org/10.1103/PhysRevLett.98.146401>`__
.. _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
<https://doi.org/10.1021/acs.jctc.8b00770>`__
.. _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.
<https://doi.org/10.1021/acs.jctc.8b01092>`__

1
doc/src/pair_style.rst
View File

@ -182,6 +182,7 @@ accelerated styles exist.
* :doc:`gw/zbl <pair_gw>` - Gao-Weber potential with a repulsive ZBL core
* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications

2
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View File

@ -1,4 +1,4 @@
#! /usr/bin/env python3
#!/usr/bin/env python3
# LAMMPS Documentation Utilities
#
# Scan for duplicate anchor labels in documentation files

6
doc/utils/converters/setup.py
View File

@ -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 ']
},
)

2
doc/utils/sphinx-config/conf.py.in
View File

@ -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.
"""

6
doc/utils/sphinx-config/false_positives.txt
View File

@ -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

1096
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File diff suppressed because it is too large Load Diff

120
examples/USER/hdnnp/hdnnp-data/input.nn Normal file
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@ -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 <element-central> 2 <element-neighbor> <eta> <rshift> <rcutoff>
# Narrow Angular symmetry function (type 3):
#symfunction_short <element-central> 3 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff>
# Wide Angular symmetry function (type 9):
#symfunction_short <element-central> 9 <element-neighbor1> <element-neighbor2> <eta> <lambda> <zeta> <rcutoff>
# 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

72
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@ -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

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47
examples/USER/hdnnp/in.hdnnp Normal file
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@ -0,0 +1,47 @@
###############################################################################
# MD simulation for HDNNP water
###############################################################################
###############################################################################
# VARIABLES
###############################################################################
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}

2
lib/README
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@ -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

122
lib/hdnnp/Install.py Normal file
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@ -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')

75
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@ -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.

2
src/.gitignore vendored
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@ -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

6
src/Makefile
View File

@ -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)

66
src/USER-HDNNP/Install.sh Normal file
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@ -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

26
src/USER-HDNNP/README Normal file
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@ -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

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src/USER-HDNNP/pair_hdnnp.cpp Normal file
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@ -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;i<comm->nprocs;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();
}

73
src/USER-HDNNP/pair_hdnnp.h Normal file
View File

@ -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

2
src/USER-QUIP/pair_quip.cpp
View File

@ -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)

2
unittest/commands/CMakeLists.txt
View File

@ -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

8
unittest/force-styles/CMakeLists.txt
View File

@ -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})