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Merge branch 'master' into pair_rann

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# Conflicts:
#	cmake/CMakeLists.txt
#	cmake/presets/all_off.cmake
#	cmake/presets/all_on.cmake
This commit is contained in:
Axel Kohlmeyer
2021-05-26 15:17:30 -04:00
parent 7cc00e3fed 49ced1ed18
commit 012003c68a
3381 changed files with 9222 additions and 3574 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
.gitattributes vendored
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@ -2,3 +2,4 @@
.gitignore export-ignore .gitignore export-ignore
.github export-ignore .github export-ignore
.lgtm.yml export-ignore .lgtm.yml export-ignore
SECURITY.md export-ignore

20
README
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@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL). under the terms of the GNU Public License (GPL) version 2.
The primary author of the code is Steve Plimpton, who can be emailed 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. more information about the code and its uses.
The LAMMPS distribution includes the following files and directories: The LAMMPS distribution includes the following files and directories:
@ -37,14 +37,14 @@ tools pre- and post-processing tools
Point your browser at any of these files to get started: Point your browser at any of these files to get started:
https://lammps.sandia.gov/doc/Manual.html LAMMPS manual https://docs.lammps.org/Manual.html LAMMPS manual
https://lammps.sandia.gov/doc/Intro.html hi-level introduction https://docs.lammps.org/Intro.html hi-level introduction
https://lammps.sandia.gov/doc/Build.html how to build LAMMPS https://docs.lammps.org/Build.html how to build LAMMPS
https://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS https://docs.lammps.org/Run_head.html how to run LAMMPS
https://lammps.sandia.gov/doc/Commands_all.html Table of available commands https://docs.lammps.org/Commands_all.html Table of available commands
https://lammps.sandia.gov/doc/Library.html LAMMPS library interfaces https://docs.lammps.org/Library.html LAMMPS library interfaces
https://lammps.sandia.gov/doc/Modify.html how to modify and extend LAMMPS https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
https://lammps.sandia.gov/doc/Developer.html LAMMPS developer info https://docs.lammps.org/Developer.html LAMMPS developer info
You can also create these doc pages locally: You can also create these doc pages locally:

2
bench/POTENTIALS/README
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@ -1,7 +1,7 @@
These are input scripts used to run benchmark tests for many of the These are input scripts used to run benchmark tests for many of the
interatomic potentials in LAMMPS. The results of running these interatomic potentials in LAMMPS. The results of running these
scripts on different machines are shown on the Potentials section of scripts on different machines are shown on the Potentials section of
the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench). the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
Examples are shown below of how to run these scripts. Log files for Examples are shown below of how to run these scripts. Log files for
running them on 1 and 4 processors of a Linux box are included in the running them on 1 and 4 processors of a Linux box are included in the

4
bench/README
View File

@ -2,7 +2,7 @@ LAMMPS benchmark problems
This directory contains 5 benchmark problems which are discussed in This directory contains 5 benchmark problems which are discussed in
the Benchmark section of the LAMMPS documentation, and on the the Benchmark section of the LAMMPS documentation, and on the
Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench). Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
This directory also has several sub-directories: This directory also has several sub-directories:
@ -11,7 +11,7 @@ KEPLER benchmark scripts for GPU cluster with Kepler GPUs
POTENTIALS benchmarks scripts for various potentials in LAMMPS POTENTIALS benchmarks scripts for various potentials in LAMMPS
The results for all of these benchmarks are displayed and discussed on The results for all of these benchmarks are displayed and discussed on
the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench. the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
The remainder of this file refers to the 5 problems in the top-level The remainder of this file refers to the 5 problems in the top-level
of this directory and how to run them on CPUs, either in serial or of this directory and how to run them on CPUs, either in serial or

61
cmake/CMakeLists.txt
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@ -9,7 +9,7 @@ if(POLICY CMP0074)
endif() endif()
# set policy to silence warnings about missing executable permissions in # 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 # 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) cmake_policy(SET CMP0109 OLD)
endif() endif()
######################################## ########################################
@ -77,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckIncludeFileCXX) include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations # set required compiler flags and compiler/CPU arch specific optimizations
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512") set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@ -91,6 +91,11 @@ set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions") 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 # # User input options #
######################################################################## ########################################################################
@ -120,6 +125,12 @@ file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES}) list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
add_library(lammps ${ALL_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}) add_executable(lmp ${MAIN_SOURCES})
target_link_libraries(lmp PRIVATE lammps) target_link_libraries(lmp PRIVATE lammps)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) 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 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-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-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-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-RANN 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) 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) find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else() else()
set(MPI_CXX_SKIP_MPICXX TRUE)
option(BUILD_MPI "Build MPI version" OFF) option(BUILD_MPI "Build MPI version" OFF)
endif() endif()
if(BUILD_MPI) if(BUILD_MPI)
# We use a non-standard procedure to cross-compile with MPI on Windows # 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) include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX) target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else() else()
@ -201,7 +213,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES}) target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
# posix_memalign is not available on Windows # posix_memalign is not available on Windows
if(${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) set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
else() 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") 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") message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif() 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 "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 "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))) ((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. # 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) find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND}) option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
if(WITH_GZIP) 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) target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
else() else()
message(FATAL_ERROR "gzip executable not found") 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) find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND}) option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
if(WITH_FFMPEG) if(WITH_FFMPEG)
if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)) if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG) target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
else() else()
message(FATAL_ERROR "ffmpeg executable not found") message(FATAL_ERROR "ffmpeg executable not found")
@ -335,7 +348,7 @@ else()
set(CUDA_REQUEST_PIC) set(CUDA_REQUEST_PIC)
endif() endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
if(PKG_${PKG_WITH_INCL}) if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL})
@ -433,7 +446,7 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
if(PKG_${SIMPLE_LIB}) if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB) string(TOLOWER "${PKG_LIB}" PKG_LIB)
if(PKG_LIB STREQUAL mesont) if(PKG_LIB STREQUAL "mesont")
enable_language(Fortran) enable_language(Fortran)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90) ${LAMMPS_LIB_SOURCE_DIR}/${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}) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE}) set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB}) 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) 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}) target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
else() else()
target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}) target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
@ -460,7 +473,7 @@ if(PKG_USER-AWPMD)
endif() endif()
if(PKG_USER-ATC) 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") message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif() endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES}) target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
@ -504,7 +517,7 @@ endif()
# and the MPI library - if use - has to be linked right before those # and the MPI library - if use - has to be linked right before those
# and after everything else that is compiled locally # and after everything else that is compiled locally
###################################################################### ######################################################################
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi) target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
endif() endif()
@ -553,8 +566,8 @@ add_dependencies(lammps gitversion)
# Actually add executable and lib to build # Actually add executable and lib to build
############################################ ############################################
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index) list(FIND LANGUAGES "Fortran" _index)
if(${_index} GREATER -1) if(_index GREATER -1)
target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif() 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 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() else()
find_package(Python COMPONENTS Interpreter) find_package(Python COMPONENTS Interpreter)
endif() endif()
if (Python_EXECUTABLE) if(Python_EXECUTABLE)
add_custom_target( add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
@ -665,7 +678,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
else() else()
find_package(Python COMPONENTS Interpreter) find_package(Python COMPONENTS Interpreter)
endif() endif()
if (Python_EXECUTABLE) if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python) 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})") 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() endif()
@ -710,15 +723,15 @@ if(OPTIONS)
message(" Options: ${OPTIONS}") message(" Options: ${OPTIONS}")
endif() endif()
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index) list(FIND LANGUAGES "Fortran" _index)
if(${_index} GREATER -1) if(_index GREATER -1)
message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER} message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
Type: ${CMAKE_Fortran_COMPILER_ID} Type: ${CMAKE_Fortran_COMPILER_ID}
Version: ${CMAKE_Fortran_COMPILER_VERSION} Version: ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}") Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif() endif()
list (FIND LANGUAGES "C" _index) list(FIND LANGUAGES "C" _index)
if(${_index} GREATER -1) if(_index GREATER -1)
message(STATUS "C compiler: ${CMAKE_C_COMPILER} message(STATUS "C compiler: ${CMAKE_C_COMPILER}
Type: ${CMAKE_C_COMPILER_ID} Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION} Version: ${CMAKE_C_COMPILER_VERSION}
@ -783,7 +796,7 @@ if(PKG_KSPACE)
endif() endif()
if(PKG_KOKKOS) if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA) if(Kokkos_ENABLE_CUDA)
if (${FFT} STREQUAL "KISS") if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS") message(STATUS "Kokkos FFT: KISS")
else() else()
message(STATUS "Kokkos FFT: cuFFT") message(STATUS "Kokkos FFT: cuFFT")

10
cmake/Modules/CodingStandard.cmake
View File

@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py . ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR} WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors") COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target( add_custom_target(
check-permissions check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py . ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f . ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR} WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors") COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target( add_custom_target(
fix-permissions fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f . ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

61
cmake/Modules/FindN2P2.cmake Normal file
View File

@ -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") 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) set(GTEST_LIB_POSTFIX d)
else() else()
set(GTEST_LIB_POSTFIX) set(GTEST_LIB_POSTFIX)

2
cmake/Modules/LAMMPSUtils.cmake
View File

@ -106,7 +106,7 @@ function(FetchPotentials pkgfolder potfolder)
endfunction(FetchPotentials) endfunction(FetchPotentials)
# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux # 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=") file(STRINGS /etc/os-release distro REGEX "^NAME=")
string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}") string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=") 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 # 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) 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" message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n" "Found file(s) generated by the make-based build system in lib/gpu\n"
"Please run\n" "Please run\n"
@ -154,7 +154,7 @@ elseif(GPU_API STREQUAL "OPENCL")
endif() endif()
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default}) option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
mark_as_advanced(USE_STATIC_OPENCL_LOADER) mark_as_advanced(USE_STATIC_OPENCL_LOADER)
if (USE_STATIC_OPENCL_LOADER) if(USE_STATIC_OPENCL_LOADER)
include(OpenCLLoader) include(OpenCLLoader)
else() else()
find_package(OpenCL REQUIRED) 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}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(Kokkos_ENABLE_CUDA) if(Kokkos_ENABLE_CUDA)
if(NOT ${FFT} STREQUAL "KISS") if(NOT (FFT STREQUAL "KISS"))
target_compile_definitions(lammps PRIVATE -DFFT_CUFFT) target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
target_link_libraries(lammps PRIVATE cufft) target_link_libraries(lammps PRIVATE cufft)
endif() 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") message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif() endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)

124
cmake/Modules/Packages/USER-HDNNP.cmake Normal file
View File

@ -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 # only ON/OFF are allowed for "mpi" flag when building MDI library
# so translate boolean value of BUILD_MPI # so translate boolean value of BUILD_MPI
# always disable MPI when cross-compiling to Windows. # 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) set(MDI_USE_MPI ON)
else() else()
set(MDI_USE_MPI OFF) set(MDI_USE_MPI OFF)
@ -27,12 +27,12 @@ if(DOWNLOAD_MDI)
set(MDI_USE_PYTHON_PLUGINS OFF) set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12) if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonLibs QUIET) # Deprecated since version 3.12 find_package(PythonLibs QUIET) # Deprecated since version 3.12
if (PYTHONLIBS_FOUND) if(PYTHONLIBS_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON) set(MDI_USE_PYTHON_PLUGINS ON)
endif() endif()
else() else()
find_package(Python QUIET COMPONENTS Development) find_package(Python QUIET COMPONENTS Development)
if (Python_Development_FOUND) if(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON) set(MDI_USE_PYTHON_PLUGINS ON)
endif() endif()
endif() endif()
@ -85,7 +85,7 @@ if(DOWNLOAD_MDI)
endif() endif()
# need to add support for dlopen/dlsym, except when compiling for Windows. # 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}") list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")
endif() endif()
if(MDI_DEP_LIBS) if(MDI_DEP_LIBS)

2
cmake/Modules/PreventInSourceBuilds.cmake
View File

@ -9,7 +9,7 @@ function(prevent_in_source_builds)
get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
# disallow in-source builds # 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 "\ message(FATAL_ERROR "\
CMake must not to be run in the source directory. \ 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 # 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. # 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) # 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) if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))) OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04)) 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))) OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
include(CheckCXXCompilerFlag) include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default) set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG) check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@ -58,7 +58,7 @@ if(ENABLE_TESTING)
endif() endif()
# Compiler specific features for testing # 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) option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE) mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE) if(ENABLE_COVERAGE)
@ -83,7 +83,7 @@ mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU) if(ENABLE_IWYU)
# enforce these settings # enforce these settings
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE) 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") message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
endif() endif()
# detect the "native" header folder so we can include them first # 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}) 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_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) 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( add_custom_target(
iwyu 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 ${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) target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
# workaround for broken readline pkg-config file on FreeBSD # 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) target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif() endif()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE) target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)

2
cmake/pkgconfig/liblammps.pc.in
View File

@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@ Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov URL: https://www.lammps.org
Version: @PROJECT_VERSION@ Version: @PROJECT_VERSION@
Requires: Requires:
Libs: -L${libdir} -llammps@LAMMPS_MACHINE@ Libs: -L${libdir} -llammps@LAMMPS_MACHINE@

6
cmake/presets/all_off.cmake
View File

@ -7,9 +7,9 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK 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-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-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-TALLY USER-UEF USER-VTK USER-YAFF)

6
cmake/presets/all_on.cmake
View File

@ -9,9 +9,9 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK 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-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-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-TALLY USER-UEF USER-VTK USER-YAFF)

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 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD 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-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
USER-PACE USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC USER-PACE USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF 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 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE
USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
USER-SMD USER-VTK) USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB}) foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE) set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

16
doc/Makefile
View File

@ -10,7 +10,6 @@ endif
BUILDDIR = ${CURDIR} BUILDDIR = ${CURDIR}
RSTDIR = $(BUILDDIR)/src RSTDIR = $(BUILDDIR)/src
VENV = $(BUILDDIR)/docenv VENV = $(BUILDDIR)/docenv
TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/rst_anchor_check ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax 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. # 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_]\+ \+= *\(YES\|NO\|\)//') 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
# ------------------------------------------ # ------------------------------------------
@ -68,7 +67,6 @@ help:
@echo "Please use \`make <target>' where <target> is one of" @echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML pages in html dir" @echo " html create HTML pages in html dir"
@echo " pdf create Manual.pdf in this dir" @echo " pdf create Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers" @echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)" @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)" @echo " (requires ebook-convert tool from calibre)"
@ -185,13 +183,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@rm -rf latex/PDF/.[sg]* @rm -rf latex/PDF/.[sg]*
@echo "Build finished. Manual.pdf is in this directory." @echo "Build finished. Manual.pdf is in this directory."
fetch:
@rm -rf html_www Manual_www.pdf
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
anchor_check : $(ANCHORCHECK) anchor_check : $(ANCHORCHECK)
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
@ -213,6 +204,9 @@ package_check : $(VENV)
deactivate ;\ deactivate ;\
) )
char_check :
@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
xmlgen : doxygen/xml/index.xml xmlgen : doxygen/xml/index.xml
doxygen/Doxyfile: doxygen/Doxyfile.in doxygen/Doxyfile: doxygen/Doxyfile.in
@ -238,7 +232,7 @@ $(VENV):
$(MATHJAX): $(MATHJAX):
@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@ @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; \ . $(VENV)/bin/activate; \
(cd utils/converters;\ (cd utils/converters;\

13
doc/README
View File

@ -25,16 +25,11 @@ github-development-workflow.md notes on the LAMMPS development workflow
include-file-conventions.md notes on LAMMPS' include file conventions include-file-conventions.md notes on LAMMPS' include file conventions
documentation_conventions.md notes on writing documentation for LAMMPS documentation_conventions.md notes on writing documentation for LAMMPS
If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html If you downloaded a LAMMPS tarball from www.lammps.org, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to download them or build them. from GitHub then you either need to build them.
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web You can build the HTML and PDF files yourself, by typing "make html"
site. Just type "make fetch". This should create a html_www directory
and Manual_www.pdf file. These will always represent the latest published
patch/development version of LAMMPS.
(b) You can build the HTML and PDF files yourself, by typing "make html"
or by "make pdf", respectively. This requires various tools and files. or by "make pdf", respectively. This requires various tools and files.
Some of them have to be installed (more on that below). For the rest the Some of them have to be installed (more on that below). For the rest the
build process will attempt to download and install into a python virtual build process will attempt to download and install into a python virtual
@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software
---------------- ----------------
More details this can be found in the manual itself. The online More details this can be found in the manual itself. The online
version is at: https://lammps.sandia.gov/doc/Manual_build.html version is at: https://docs.lammps.org/Build_manual.html

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 model atoms or, more generically, as a parallel particle simulator at the
atomic, meso, or continuum scale. 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 .SH EXECUTABLE NAME
The The

6
doc/src/Bibliography.rst
View File

@ -1129,6 +1129,9 @@ Bibliography
**(Sutmann)** **(Sutmann)**
Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013) 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)**
Swinburne and Marinica, Physical Review Letters, 120, 1 (2018) Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)
@ -1285,9 +1288,6 @@ Bibliography
**(Wennberg)** **(Wennberg)**
Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013). 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)** **(Wicaksono1)**
Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016). Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).

30
doc/src/Build_development.rst
View File

@ -28,7 +28,7 @@ variable VERBOSE set to 1:
---------- ----------
.. _clang-tidy .. _clang-tidy:
Enable static code analysis with clang-tidy Enable static code analysis with clang-tidy
------------------------------------------- -------------------------------------------
@ -469,12 +469,24 @@ The following options are available.
.. code-block:: bash .. code-block:: bash
make check-whitespace # generate coverage report in HTML format make check-whitespace # search for files with whitespace issues
make fix-whitespace # generate coverage report in XML format make fix-whitespace # correct whitespace issues in files
make check-permissions # delete folder with HTML format coverage report make check-homepage # search for files with old LAMMPS homepage URLs
make fix-permissions # delete all collected coverage data and HTML output make fix-homepage # correct LAMMPS homepage URLs in files
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
For the code in the ``unittest`` tree we are using the `clang-format` For the code in the ``unittest`` and ``src`` trees we are transitioning
tool (Clang version 8.0 or later is required). If available, the source to use the `clang-format` tool to assist with having a consistent source
code files in the ``unittest`` tree can be updated to conform to the code style. The `clang-format` command bundled with Clang version 8.0
formatting settings using ``make format-tests``. or later is required. The configuration is in files ``.clang-format``
in the respective folders. Since the modifications from `clang-format`
can be significant and - especially for "legacy style code" - also is
not always improving readability, a large number of files currently have
a ``// clang-format off`` at the top, which will disable the processing.
Over time, files will be refactored and updated to that `clang-format`
may be applied to them (at least in part).
If `clang-format` is available, the source code files in the ``unittest``
tree can be updated to conform to the formatting settings using
``make format-tests`` and the files in ``src`` with ``make format-src``.

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-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>` * :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>` * :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-HDNNP <user-hdnnp>`
* :ref:`USER-INTEL <user-intel>` * :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>` * :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <user-mesont>` * :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:
USER-INTEL package USER-INTEL package

31
doc/src/Build_manual.rst
View File

@ -28,29 +28,18 @@ If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
the html folder and the PDF files should be included. the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one and PDF files are not included. You can build the HTML or PDF files yourself,
of two ways: by typing ``make html`` or ``make pdf`` in the ``doc`` folder. This requires
various tools and files. Some of them have to be installed (see below). For
a. You can "fetch" the current HTML and PDF files from the LAMMPS web the rest the build process will attempt to download and install them into
site. Just type ``make fetch``. This should download a ``html_www`` a python virtual environment and local folders.
directory and a ``Manual_www.pdf`` file. Note that if new LAMMPS features
have been added more recently than the date of your LAMMPS version, the
fetched documentation will include those changes (but your source code
will not, unless you update your local repository).
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf`` in the ``doc`` folder. This requires various tools
and files. Some of them have to be installed (see below). For the
rest the build process will attempt to download and install them into
a python virtual environment and local folders.
A current version of the manual (latest patch release, aka unstable A current version of the manual (latest patch release, aka unstable
branch) is is available online at: branch) is is available online at:
`https://lammps.sandia.gov/doc/Manual.html `https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual A version of the manual corresponding to the ongoing development (aka master branch)
corresponding to the ongoing development (aka master branch) is is available online at: `https://docs.lammps.org/latest/
available online at: `https://docs.lammps.org/ <https://docs.lammps.org/latest/>`_
<https://docs.lammps.org/>`_
Build using GNU make Build using GNU make
-------------------- --------------------
@ -257,4 +246,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org

18
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 These links take you to the extra instructions for those select
packages: packages:
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` | | :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:`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-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-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-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-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | | :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 The mechanism for including packages is simple but different for CMake
versus make. versus make.

1
doc/src/Commands_pair.rst
View File

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

6
doc/src/Errors_bugs.rst
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@ -5,8 +5,8 @@ If you are confident that you have found a bug in LAMMPS, please follow
the steps outlined below: the steps outlined below:
* Check the `New features and bug fixes * Check the `New features and bug fixes
<https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site <https://www.lammps.org/bug.html>`_ section of the `LAMMPS WWW site
<https://lammps.sandia.gov>`_ or the <https://www.lammps.org>`_ or the
`GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to `GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to
see if the bug has already been addressed in a patch release. see if the bug has already been addressed in a patch release.
* Check that your issue can be reproduced with the latest development * Check that your issue can be reproduced with the latest development
@ -17,7 +17,7 @@ the steps outlined below:
if your issue has already been reported and if it is still open. if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_ * Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
to see if there is already a fix for your bug pending. to see if there is already a fix for your bug pending.
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_ * Check the `mailing list archives <https://www.lammps.org/mail.html>`_
to see if the issue has been discussed before. to see if the issue has been discussed before.
If none of these steps yields any useful information, please file a new If none of these steps yields any useful information, please file a new

2
doc/src/Errors_common.rst
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@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a
timestep, specifying erroneous force field coefficients, or putting 2 timestep, specifying erroneous force field coefficients, or putting 2
atoms on top of each other! If you run into errors that LAMMPS atoms on top of each other! If you run into errors that LAMMPS
does not catch that you think it should flag, please send an email to does not catch that you think it should flag, please send an email to
the `developers <https://lammps.sandia.gov/authors.html>`_. the `developers <https://www.lammps.org/authors.html>`_.
If you get an error message about an invalid command in your input If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by script, you can determine what command is causing the problem by

2
doc/src/Errors_messages.rst
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@ -3871,7 +3871,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Fix orient/fcc found self twice* *Fix orient/fcc found self twice*
The neighbor lists used by fix orient/fcc are messed up. If this The neighbor lists used by fix orient/fcc are messed up. If this
error occurs, it is likely a bug, so send an email to the error occurs, it is likely a bug, so send an email to the
`developers <https://lammps.sandia.gov/authors.html>`_. `developers <https://www.lammps.org/authors.html>`_.
*Fix peri neigh does not exist* *Fix peri neigh does not exist*
Somehow a fix that the pair style defines has been deleted. Somehow a fix that the pair style defines has been deleted.

6
doc/src/Examples.rst
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@ -18,7 +18,7 @@ files and image files.
If you uncomment the :doc:`dump <dump>` command in the input script, a If you uncomment the :doc:`dump <dump>` command in the input script, a
text dump file will be produced, which can be animated by various text dump file will be produced, which can be animated by various
`visualization programs <https://lammps.sandia.gov/viz.html>`_. `visualization programs <https://www.lammps.org/viz.html>`_.
If you uncomment the :doc:`dump image <dump>` command in the input If you uncomment the :doc:`dump image <dump>` command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG script, and assuming you have built LAMMPS with a JPG library, JPG
@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the
:doc:`dump image <dump_image>` doc page. :doc:`dump image <dump_image>` doc page.
Animations of many of the examples can be viewed on the Movies section Animations of many of the examples can be viewed on the Movies section
of the `LAMMPS web site <https://lammps.sandia.gov/movies.html>`_. of the `LAMMPS web site <https://www.lammps.org/movies.html>`_.
There are two kinds of sub-directories in the examples folder. Lower There are two kinds of sub-directories in the examples folder. Lower
case named directories contain one or a few simple, quick-to-run case named directories contain one or a few simple, quick-to-run
@ -166,7 +166,7 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a *log.lammps*\ . You can visualize the dump file of snapshots with a
variety of third-party tools highlighted on the variety of third-party tools highlighted on the
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS `Visualization <https://www.lammps.org/viz.html>`_ page of the LAMMPS
web site. web site.
If you uncomment the :doc:`dump image <dump_image>` line(s) in the input If you uncomment the :doc:`dump image <dump_image>` line(s) in the input

2
doc/src/Howto.rst
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@ -3,7 +3,7 @@ Howto discussions
These doc pages describe how to perform various tasks with LAMMPS, These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The both for users and developers. The
`glossary <https://lammps.sandia.gov/glossary.html>`_ website page also lists MD `glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
terminology with links to corresponding LAMMPS manual pages. The terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples directory of the LAMMPS example input scripts included in the examples directory of the LAMMPS
distribution and highlighted on the :doc:`Examples <Examples>` doc page distribution and highlighted on the :doc:`Examples <Examples>` doc page

2
doc/src/Howto_wsl.rst
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@ -201,7 +201,7 @@ build configuration and any binaries generated during compilation.
There are countless ways to compile LAMMPS. It is beyond the scope of this There are countless ways to compile LAMMPS. It is beyond the scope of this
tutorial. If you want to find out more about what can be enabled, please tutorial. If you want to find out more about what can be enabled, please
consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_. consult the extensive `documentation <https://docs.lammps.org/Build_cmake.html>`_.
To compile a minimal version of LAMMPS, we're going to use a preset. To compile a minimal version of LAMMPS, we're going to use a preset.
Presets are a way to specify a collection of CMake options using a file. Presets are a way to specify a collection of CMake options using a file.

2
doc/src/Install_git.rst
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@ -78,7 +78,7 @@ this is as follows.
$ git checkout tagID $ git checkout tagID
Stable versions and what tagID to use for a particular stable version Stable versions and what tagID to use for a particular stable version
are discussed on `this page <https://lammps.sandia.gov/bug.html#version>`_. are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
Note that this command will print some warnings, because in order to get Note that this command will print some warnings, because in order to get
back to the latest revision and to be able to update with ``git pull`` back to the latest revision and to be able to update with ``git pull``
again, you will need to do ``git checkout unstable`` (or again, you will need to do ``git checkout unstable`` (or

2
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@ -10,7 +10,7 @@ If you prefer to download a tarball, as described on the
:doc:`tarball download <Install_tarball>` page, you can stay current by :doc:`tarball download <Install_tarball>` page, you can stay current by
downloading "patch files" when new patch releases are made. A link to downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the a patch file is posted on the
`bug fixes and new feature page <https://lammps.sandia.gov/bug.html>`_ `bug fixes and new feature page <https://www.lammps.org/bug.html>`_
of the LAMMPS website, along of the LAMMPS website, along
with a list of changed files and details about what is in the new patch with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local release. This page explains how to apply the patch file to your local

8
doc/src/Install_tarball.rst
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@ -4,10 +4,10 @@ Download source and documentation as a tarball
You can download a current LAMMPS tarball from the `download page <download_>`_ You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_. of the `LAMMPS website <lws_>`_.
.. _download: https://lammps.sandia.gov/download.html .. _download: https://www.lammps.org/download.html
.. _bug: https://lammps.sandia.gov/bug.html .. _bug: https://www.lammps.org/bug.html
.. _older: https://lammps.sandia.gov/tars .. _older: https://www.lammps.org/tars
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
You have two choices of tarballs, either the most recent stable You have two choices of tarballs, either the most recent stable
release or the most current patch release. Stable releases occur a release or the most current patch release. Stable releases occur a

6
doc/src/Intro_authors.rst
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@ -11,14 +11,14 @@ University:
* Richard Berger, richard.berger at temple.edu * Richard Berger, richard.berger at temple.edu
.. _sjp: http://www.cs.sandia.gov/~sjplimp .. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia, Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design. and Ray Shan, now at Materials Design.
---------- ----------
The `Authors page <https://lammps.sandia.gov/authors.html>`_ of the The `Authors page <https://www.lammps.org/authors.html>`_ of the
`LAMMPS website <lws_>`_ has a comprehensive list of all the individuals `LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
who have contributed code for a new feature or command or tool to who have contributed code for a new feature or command or tool to
LAMMPS. LAMMPS.
@ -46,7 +46,7 @@ general-purpose as it is without their expertise and efforts.
---------- ----------
As discussed on the `History page <https://lammps.sandia.gov/history.html>`_ of the website, LAMMPS As discussed on the `History page <https://www.lammps.org/history.html>`_ of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original partners. Folks involved in the design and testing of the original
version of LAMMPS were the following: version of LAMMPS were the following:

4
doc/src/Intro_citing.rst
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@ -38,8 +38,8 @@ In addition there are DOIs for individual stable releases. Currently there are:
Home page Home page
^^^^^^^^^ ^^^^^^^^^
The LAMMPS website at `https://lammps.sandia.gov/ The LAMMPS website at `https://www.lammps.org/
<https://lammps.sandia.gov>`_ is the canonical location for information <https://www.lammps.org>`_ is the canonical location for information
about LAMMPS and its features. about LAMMPS and its features.
Citing contributions Citing contributions

4
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@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
linear bead-spring polymer chains. The moltemplate program is a true linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` doc page for details on tools packaged with the :doc:`Tools <Tools>` doc page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website LAMMPS. The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
describes a variety of third party tools for this task. Furthermore, describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule topology information, as well as provide the option to insert molecule
@ -67,7 +67,7 @@ Here are suggestions on how to perform these tasks:
them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
movies from them. For high-quality, interactive visualization there are movies from them. For high-quality, interactive visualization there are
many excellent and free tools available. See the many excellent and free tools available. See the
`Visualization Tools <https://lammps.sandia.gov/viz.html>`_ page of the `Visualization Tools <https://www.lammps.org/viz.html>`_ page of the
LAMMPS website for LAMMPS website for
visualization packages that can process LAMMPS output data. visualization packages that can process LAMMPS output data.
* **Plotting:** See the next bullet about Pizza.py as well as the * **Plotting:** See the next bullet about Pizza.py as well as the

4
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@ -16,10 +16,10 @@ shared-memory boxes and distributed-memory clusters and
supercomputers. supercomputers.
.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface .. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
LAMMPS is written in C++. Earlier versions were written in F77 and LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the `History page <https://lammps.sandia.gov/history.html>`_ of F90. See the `History page <https://www.lammps.org/history.html>`_ of
the website for details. All versions can be downloaded from the the website for details. All versions can be downloaded from the
`LAMMPS website <lws_>`_. `LAMMPS website <lws_>`_.

40
doc/src/Intro_website.rst
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@ -5,31 +5,31 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some other useful resources LAMMPS, beyond what is in this manual. Some other useful resources
available online are listed below. available online are listed below.
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
* `Brief intro and recently added significant features <lws_>`_ * `Brief intro and recently added significant features <lws_>`_
* `List of features <https://lammps.sandia.gov/doc/Intro_features.html>`_ * `List of features <https://docs.lammps.org/Intro_features.html>`_
* `List of non-features <https://lammps.sandia.gov/doc/Intro_nonfeatures.html>`_ * `List of non-features <https://docs.lammps.org/Intro_nonfeatures.html>`_
* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_ * `Recent bug fixes and new features <https://www.lammps.org/bug.html>`_
* `Download info <https://lammps.sandia.gov/download.html>`_ * `Download info <https://www.lammps.org/download.html>`_
* `GitHub site <https://github.com/lammps/lammps>`_ * `GitHub site <https://github.com/lammps/lammps>`_
* `SourceForge site <https://sourceforge.net/projects/lammps>`_ * `SourceForge site <https://sourceforge.net/projects/lammps>`_
* `LAMMPS open-source license <https://lammps.sandia.gov/doc/Intro_opensource.html>`_ * `LAMMPS open-source license <https://docs.lammps.org/Intro_opensource.html>`_
* `Glossary of terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_ * `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_ * `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_ * `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
* `Mail list <https://lammps.sandia.gov/mail.html>`_ * `Mail list <https://www.lammps.org/mail.html>`_
* `Workshops <https://lammps.sandia.gov/workshops.html>`_ * `Workshops <https://www.lammps.org/workshops.html>`_
* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_ * `Tutorials <https://www.lammps.org/tutorials.html>`_
* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_ * `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_ * `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
* `Viz tools usable with LAMMPS <https://lammps.sandia.gov/viz.html>`_ * `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
* `Benchmark performance <https://lammps.sandia.gov/bench.html>`_ * `Benchmark performance <https://www.lammps.org/bench.html>`_
* `Publications that have cited LAMMPS <https://lammps.sandia.gov/papers.html>`_ * `Publications that have cited LAMMPS <https://www.lammps.org/papers.html>`_
* `Authors of LAMMPS <https://lammps.sandia.gov/authors.html>`_ * `Authors of LAMMPS <https://www.lammps.org/authors.html>`_
* `History of LAMMPS development <https://lammps.sandia.gov/history.html>`_ * `History of LAMMPS development <https://www.lammps.org/history.html>`_
* `Funding for LAMMPS <https://lammps.sandia.gov/funding.html>`_ * `Funding for LAMMPS <https://www.lammps.org/funding.html>`_

14
doc/src/Manual.rst
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@ -15,7 +15,7 @@ the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the The `LAMMPS website <lws_>`_ has a variety of information about the
code. It includes links to an on-line version of this manual, a code. It includes links to an on-line version of this manual, a
`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can `mailing list <https://www.lammps.org/mail.html>`_ where users can
post questions, and a `GitHub site <https://github.com/lammps/lammps>`_ post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
where all LAMMPS development is coordinated. where all LAMMPS development is coordinated.
@ -30,11 +30,13 @@ please :ref:`see this note <webbrowser>`.
----------- -----------
The manual is organized in two parts: The manual is organized in three parts:
1) the :ref:`User Guide <user_documentation>` for how to install 1) the :ref:`User Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>` and use LAMMPS, 2) the :ref:`Programmer Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS. programming languages and how to modify and extend LAMMPS, and 3) the
:ref:`Command Reference <command_reference>` which includes detailed
descriptions of all commands included in the LAMMPS code.
.. only:: html .. only:: html
@ -42,7 +44,7 @@ programming languages and how to modify and extend LAMMPS.
:doc:`this page <Commands_all>` since it gives quick access :doc:`this page <Commands_all>` since it gives quick access
the documentation for all LAMMPS commands. the documentation for all LAMMPS commands.
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
---------- ----------
@ -129,4 +131,4 @@ Indices and tables
where parts of the pages are not rendered as expected (e.g. the layout is where parts of the pages are not rendered as expected (e.g. the layout is
broken or mathematical expressions not typeset). In that case we broken or mathematical expressions not typeset). In that case we
recommend to install/use a different/newer web browser or use recommend to install/use a different/newer web browser or use
the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_. the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.

2
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@ -5,7 +5,7 @@ The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a 2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it in the next *patch* release, which are feature, we release it in the next *patch* release, which are
typically made every couple of weeks. Info on patch releases are on typically made every couple of weeks. Info on patch releases are on
`this website page <https://lammps.sandia.gov/bug.html>`_. Every few `this website page <https://www.lammps.org/bug.html>`_. Every few
months, the latest patch release is subjected to more thorough testing months, the latest patch release is subjected to more thorough testing
and labeled as a *stable* version. and labeled as a *stable* version.

14
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@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS
=============================================== ===============================================
We encourage users to submit new features or modifications for LAMMPS to We encourage users to submit new features or modifications for LAMMPS to
`the core developers <https://lammps.sandia.gov/authors.html>`_ so they `the core developers <https://www.lammps.org/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage and can be added to the LAMMPS distribution. The preferred way to manage and
coordinate this is via the LAMMPS project on `GitHub coordinate this is via the LAMMPS project on `GitHub
<https://github.com/lammps/lammps>`_. Please see the :doc:`GitHub <https://github.com/lammps/lammps>`_. Please see the :doc:`GitHub
@ -31,7 +31,7 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
you are working on. Only discussions related to LAMMPS development are you are working on. Only discussions related to LAMMPS development are
tolerated, so this is **NOT** for people that look for help with compiling, tolerated, so this is **NOT** for people that look for help with compiling,
installing, or using LAMMPS. Please contact the `lammps-users mailing installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead. list <https://www.lammps.org/mail.html>`_ for those purposes instead.
How quickly your contribution will be integrated depends largely on how How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how many and what much effort it will cause to integrate and test it, how many and what
@ -67,7 +67,7 @@ distribution removed (e.g. interface to FFTW). See the
With user packages and files, all we are really providing (aside from With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source the fame and fortune that accompanies having your name in the source
code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_ code and on the `Authors page <https://www.lammps.org/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make easily try out your new feature. This may help you find bugs or make
@ -81,13 +81,13 @@ unusual event).
If you prefer to actively develop and support your add-on If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the your package and web site from that page. Simply email the
`developers <https://lammps.sandia.gov/authors.html>`_ with info about `developers <https://www.lammps.org/authors.html>`_ with info about
your package and we will post it there. your package and we will post it there.
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
The previous sections of this doc page describe how to add new "style" The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of files of various kinds to LAMMPS. Packages are simply collections of
@ -96,7 +96,7 @@ LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you should `communicate with the changes in core LAMMPS files, you should `communicate with the
developers <https://lammps.sandia.gov/authors.html>`_, since we may or developers <https://www.lammps.org/authors.html>`_, since we may or
may not want to include those changes for some reason. An example of a may not want to include those changes for some reason. An example of a
trivial change is making a parent-class method "virtual" when you derive trivial change is making a parent-class method "virtual" when you derive
a new child class from it. a new child class from it.

96
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@ -79,6 +79,7 @@ page gives those details.
* :ref:`USER-EFF <PKG-USER-EFF>` * :ref:`USER-EFF <PKG-USER-EFF>`
* :ref:`USER-FEP <PKG-USER-FEP>` * :ref:`USER-FEP <PKG-USER-FEP>`
* :ref:`USER-H5MD <PKG-USER-H5MD>` * :ref:`USER-H5MD <PKG-USER-H5MD>`
* :ref:`USER-HDNNP <PKG-USER-HDNNP>`
* :ref:`USER-INTEL <PKG-USER-INTEL>` * :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`USER-LB <PKG-USER-LB>` * :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` * :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
@ -133,8 +134,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_ * `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE * examples/ASPHERE
* examples/ellipse * examples/ellipse
* https://lammps.sandia.gov/movies.html#line * https://www.lammps.org/movies.html#line
* https://lammps.sandia.gov/movies.html#tri * https://www.lammps.org/movies.html#tri
---------- ----------
@ -330,7 +331,7 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
* :doc:`package gpu <package>` * :doc:`package gpu <package>`
* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`) * :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
for styles followed by (g) for styles followed by (g)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site * `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
---------- ----------
@ -356,11 +357,11 @@ potentials.
* examples/granregion * examples/granregion
* examples/pour * examples/pour
* bench/in.chute * bench/in.chute
* https://lammps.sandia.gov/pictures.html#jamming * https://www.lammps.org/pictures.html#jamming
* https://lammps.sandia.gov/movies.html#hopper * https://www.lammps.org/movies.html#hopper
* https://lammps.sandia.gov/movies.html#dem * https://www.lammps.org/movies.html#dem
* https://lammps.sandia.gov/movies.html#brazil * https://www.lammps.org/movies.html#brazil
* https://lammps.sandia.gov/movies.html#granregion * https://www.lammps.org/movies.html#granregion
---------- ----------
@ -479,7 +480,7 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`, * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (k) :doc:`kspace <Commands_kspace>`) for styles followed by (k)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site * `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
---------- ----------
@ -603,7 +604,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix tfmc <fix_tfmc>` * :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>` * :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>` * :doc:`pair_style dsmc <pair_dsmc>`
* https://lammps.sandia.gov/movies.html#gcmc * https://www.lammps.org/movies.html#gcmc
---------- ----------
@ -660,8 +661,8 @@ listing, "ls src/MISC", to see the list of commands.
* :doc:`fix viscosity <fix_viscosity>` * :doc:`fix viscosity <fix_viscosity>`
* examples/KAPPA * examples/KAPPA
* examples/VISCOSITY * examples/VISCOSITY
* https://lammps.sandia.gov/pictures.html#ttm * https://www.lammps.org/pictures.html#ttm
* https://lammps.sandia.gov/movies.html#evaporation * https://www.lammps.org/movies.html#evaporation
---------- ----------
@ -816,7 +817,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* :doc:`OPT package <Speed_opt>` * :doc:`OPT package <Speed_opt>`
* :doc:`Section 2.6 -sf opt <Run_options>` * :doc:`Section 2.6 -sf opt <Run_options>`
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t) * Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site * `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
---------- ----------
@ -847,7 +848,7 @@ Foster (UTSA).
* :doc:`compute damage/atom <compute_damage_atom>` * :doc:`compute damage/atom <compute_damage_atom>`
* :doc:`compute plasticity/atom <compute_plasticity_atom>` * :doc:`compute plasticity/atom <compute_plasticity_atom>`
* examples/peri * examples/peri
* https://lammps.sandia.gov/movies.html#peri * https://www.lammps.org/movies.html#peri
---------- ----------
@ -1008,8 +1009,8 @@ Also several computes which calculate properties of rigid bodies.
* examples/ASPHERE * examples/ASPHERE
* examples/rigid * examples/rigid
* bench/in.rhodo * bench/in.rhodo
* https://lammps.sandia.gov/movies.html#box * https://www.lammps.org/movies.html#box
* https://lammps.sandia.gov/movies.html#star * https://www.lammps.org/movies.html#star
---------- ----------
@ -1110,9 +1111,9 @@ colloidal particles.
* :doc:`fix wall/srd <fix_wall_srd>` * :doc:`fix wall/srd <fix_wall_srd>`
* examples/srd * examples/srd
* examples/ASPHERE * examples/ASPHERE
* https://lammps.sandia.gov/movies.html#tri * https://www.lammps.org/movies.html#tri
* https://lammps.sandia.gov/movies.html#line * https://www.lammps.org/movies.html#line
* https://lammps.sandia.gov/movies.html#poly * https://www.lammps.org/movies.html#poly
---------- ----------
@ -1204,7 +1205,7 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
* src/USER-ATC/README * src/USER-ATC/README
* :doc:`fix atc <fix_atc>` * :doc:`fix atc <fix_atc>`
* examples/USER/atc * examples/USER/atc
* https://lammps.sandia.gov/pictures.html#atc * https://www.lammps.org/pictures.html#atc
---------- ----------
@ -1337,7 +1338,7 @@ acids.
* :doc:`pair_style lj/sdk/\* <pair_sdk>` * :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>` * :doc:`angle_style sdk <angle_sdk>`
* examples/USER/cgsdk * examples/USER/cgsdk
* https://lammps.sandia.gov/pictures.html#cg * https://www.lammps.org/pictures.html#cg
---------- ----------
@ -1574,7 +1575,7 @@ tools/eff; see its README file.
* examples/USER/eff * examples/USER/eff
* tools/eff/README * tools/eff/README
* tools/eff * tools/eff
* https://lammps.sandia.gov/movies.html#eff * https://www.lammps.org/movies.html#eff
---------- ----------
@ -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: .. _PKG-USER-INTEL:
USER-INTEL package USER-INTEL package
@ -1683,7 +1717,7 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`, * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i) :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
* src/USER-INTEL/TEST * src/USER-INTEL/TEST
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site * `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
---------- ----------
@ -1788,7 +1822,7 @@ Waltham, MA, USA)
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>` * :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>` * :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* examples/USER/manifold * examples/USER/manifold
* https://lammps.sandia.gov/movies.html#manifold * https://www.lammps.org/movies.html#manifold
---------- ----------
@ -1866,10 +1900,10 @@ algorithm.
* :doc:`pair_style tdpd <pair_mesodpd>` * :doc:`pair_style tdpd <pair_mesodpd>`
* :doc:`fix mvv/dpd <fix_mvv_dpd>` * :doc:`fix mvv/dpd <fix_mvv_dpd>`
* examples/USER/mesodpd * examples/USER/mesodpd
* https://lammps.sandia.gov/movies.html#mesodpd * https://www.lammps.org/movies.html#mesodpd
* examples/USER/meso * examples/USER/meso
* http://lammps.sandia.gov/movies.html#mesodpd * http://www.lammps.org/movies.html#mesodpd
---------- ----------
@ -2085,7 +2119,7 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`, * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (o) :doc:`kspace <Commands_kspace>`) for styles followed by (o)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site * `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
---------- ----------
@ -2268,8 +2302,8 @@ molecules, and chiral-sensitive reactions.
* src/USER-REACTION/README * src/USER-REACTION/README
* :doc:`fix bond/react <fix_bond_react>` * :doc:`fix bond/react <fix_bond_react>`
* examples/USER/reaction * examples/USER/reaction
* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_ * `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_ * `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org * reacter.org
---------- ----------
@ -2396,7 +2430,7 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do
* src/USER-SMD/README * src/USER-SMD/README
* doc/PDF/SMD_LAMMPS_userguide.pdf * doc/PDF/SMD_LAMMPS_userguide.pdf
* examples/USER/smd * examples/USER/smd
* https://lammps.sandia.gov/movies.html#smd * https://www.lammps.org/movies.html#smd
---------- ----------
@ -2453,7 +2487,7 @@ Dynamics, Ernst Mach Institute, Germany).
* src/USER-SPH/README * src/USER-SPH/README
* doc/PDF/SPH_LAMMPS_userguide.pdf * doc/PDF/SPH_LAMMPS_userguide.pdf
* examples/USER/sph * examples/USER/sph
* https://lammps.sandia.gov/movies.html#sph * https://www.lammps.org/movies.html#sph
---------- ----------

6
doc/src/Packages_standard.rst
View File

@ -39,13 +39,13 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style lj/.../dipole <pair_dipole>` | dipole | no | | :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style lj/.../dipole <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | int | | :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no | | :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext | | :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no | | :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no | | :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
@ -67,7 +67,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MSCG <PKG-MSCG>` | multi-scale coarse-graining wrapper | :doc:`fix mscg <fix_mscg>` | mscg | ext | | :ref:`MSCG <PKG-MSCG>` | multi-scale coarse-graining wrapper | :doc:`fix mscg <fix_mscg>` | mscg | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no | | :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no | | :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

6
doc/src/Packages_user.rst
View File

@ -59,7 +59,9 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext | | :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no | | :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 | | :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
@ -83,7 +85,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext | | :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no | | :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext | | :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

2
doc/src/Speed.rst
View File

@ -12,7 +12,7 @@ accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi co-processors. Intel Xeon Phi co-processors.
The `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
web site gives performance results for the various accelerator web site gives performance results for the various accelerator
packages discussed on the :doc:`Speed packages <Speed_packages>` doc packages discussed on the :doc:`Speed packages <Speed_packages>` doc
page, for several of the standard LAMMPS benchmark problems, as a page, for several of the standard LAMMPS benchmark problems, as a

8
doc/src/Speed_bench.rst
View File

@ -1,7 +1,7 @@
Benchmarks Benchmarks
========== ==========
Current LAMMPS performance is discussed on the `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_ Current LAMMPS performance is discussed on the `Benchmarks page <https://www.lammps.org/bench.html>`_ of the `LAMMPS website <lws_>`_
where timings and parallel efficiency are listed. The page has where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below: several sections, which are briefly described below:
@ -43,11 +43,11 @@ to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the The bench/POTENTIALS directory has input files which correspond to the
table of results on the table of results on the
`Potentials <https://lammps.sandia.gov/bench.html#potentials>`_ section of `Potentials <https://www.lammps.org/bench.html#potentials>`_ section of
the Benchmarks web page. So you can also run those test problems on the Benchmarks web page. So you can also run those test problems on
your machine. your machine.
The `billion-atom <https://lammps.sandia.gov/bench.html#billion>`_ section The `billion-atom <https://www.lammps.org/bench.html#billion>`_ section
of the Benchmarks web page has performance data for very large of the Benchmarks web page has performance data for very large
benchmark runs of simple Lennard-Jones (LJ) models, which use the benchmark runs of simple Lennard-Jones (LJ) models, which use the
bench/in.lj input script. bench/in.lj input script.
@ -73,4 +73,4 @@ estimate parallel performance for multi-node runs using the same logic
as for all-MPI mode, except that now you will typically need many more as for all-MPI mode, except that now you will typically need many more
atoms/node to achieve good scalability. atoms/node to achieve good scalability.
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org

2
doc/src/Speed_gpu.rst
View File

@ -152,7 +152,7 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is
usually resulting in inferior performance compared to using LAMMPS' native usually resulting in inferior performance compared to using LAMMPS' native
threading and vectorization support in the USER-OMP and USER-INTEL packages. threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the GPU package on various LAMMPS web site for performance of the GPU package on various
hardware, including the Titan HPC platform at ORNL. hardware, including the Titan HPC platform at ORNL.

2
doc/src/Speed_kokkos.rst
View File

@ -406,7 +406,7 @@ Generally speaking, the following rules of thumb apply:
package also can increase the vector length of vector instructions package also can increase the vector length of vector instructions
by switching to single or mixed precision mode. by switching to single or mixed precision mode.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the KOKKOS package on different LAMMPS web site for performance of the KOKKOS package on different
hardware. hardware.

2
doc/src/Speed_packages.rst
View File

@ -145,7 +145,7 @@ sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in the accelerator packages on various machines. See the README files in
those directories. those directories.
As mentioned above, the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS web site gives
performance results for the various accelerator packages for several performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms. size and number of compute nodes, on different hardware platforms.

6
doc/src/Tools.rst
View File

@ -6,15 +6,15 @@ molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A list steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links: of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_ * `Pre/Post processing <https://www.lammps.org/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_ * `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
* `Pizza.py toolkit <pizza_>`_ * `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
Sandia which provides tools for doing setup, analysis, plotting, and Sandia which provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. visualization for LAMMPS simulations.
.. _lws: https://lammps.sandia.gov .. _lws: https://www.lammps.org
.. _pizza: https://pizza.sandia.gov .. _pizza: https://pizza.sandia.gov
.. _python: https://www.python.org .. _python: https://www.python.org

2
doc/src/atom_modify.rst
View File

@ -80,7 +80,7 @@ LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The *map* keyword thus generate an error if one does not exist. The *map* keyword thus
allows you to force the creation of a map. The *yes* value will allows you to force the creation of a map. The *yes* value will
create either an *array* or *hash* style map, as explained in the next create either an *array* or *hash* style map, as explained in the next
paragraph. The *array* and *hash* values create an atom-style or paragraph. The *array* and *hash* values create an array-style or
hash-style map respectively. hash-style map respectively.
For an *array*\ -style map, each processor stores a lookup table of For an *array*\ -style map, each processor stores a lookup table of

2
doc/src/fix_wall_gran_region.rst
View File

@ -65,7 +65,7 @@ non-granular particles and simpler wall geometries, respectively.
Here are snapshots of example models using this command. Corresponding Here are snapshots of example models using this command. Corresponding
input scripts can be found in examples/granregion. Movies of these input scripts can be found in examples/granregion. Movies of these
simulations are `here on the Movies page <https://lammps.sandia.gov/movies.html#granregion>`_ simulations are `here on the Movies page <https://www.lammps.org/movies.html#granregion>`_
of the LAMMPS web site. of the LAMMPS web site.
.. |wallgran1| image:: img/gran_funnel.png .. |wallgran1| image:: img/gran_funnel.png

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 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. gives an overview of ScaFaCoS.
ScaFaCoS was developed by a consortium of German research facilities 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) **(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 **(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
(2012). In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.

230
doc/src/pair_hdnnp.rst Normal file
View File

@ -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:`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/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse 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:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project * :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 * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications

2
doc/utils/converters/lammpsdoc/rst_anchor_check.py Normal file → Executable file
View File

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

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

@ -1,7 +1,7 @@
from setuptools import setup from setuptools import setup
setup(name='LAMMPS Documentation Utilities', 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', description='Utilities to convert existing LAMMPS documentation text files into ReStructured Text',
url='https://github.com/rbberger/lammps-doc-utils', url='https://github.com/rbberger/lammps-doc-utils',
author='Richard Berger', author='Richard Berger',
@ -11,8 +11,6 @@ setup(name='LAMMPS Documentation Utilities',
test_suite='nose.collector', test_suite='nose.collector',
tests_require=['nose'], tests_require=['nose'],
entry_points = { entry_points = {
"console_scripts": ['txt2html = lammpsdoc.txt2html:main', "console_scripts": ['rst_anchor_check = lammpsdoc.rst_anchor_check:main ']
'txt2rst = lammpsdoc.txt2rst:main',
'rst_anchor_check = lammpsdoc.rst_anchor_check:main ']
}, },
) )

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

@ -348,7 +348,7 @@ with funding from the DOE. It is an open-source code, distributed
freely under the terms of the GNU Public License (GPL). freely under the terms of the GNU Public License (GPL).
The primary author of the code is Steve Plimpton, who can be emailed 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. more information about the code and its uses.
""" """

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

@ -187,6 +187,7 @@ backends
Baczewski Baczewski
Bagi Bagi
Bagnold Bagnold
Bajaj
Bkappa Bkappa
Bal Bal
balancer balancer
@ -1228,6 +1229,8 @@ hbn
hbnewflag hbnewflag
hbond hbond
hcp hcp
hdnnp
HDNNP
heatconduction heatconduction
Hebbeker Hebbeker
Hebenstreit Hebenstreit
@ -1570,6 +1573,7 @@ Koning
Kooser Kooser
Korn Korn
Koskinen Koskinen
Koslowski
Kosovan Kosovan
Koster Koster
Kosztin Kosztin
@ -2953,6 +2957,7 @@ shrinkexceed
Shugaev Shugaev
si si
SiC SiC
Siegmund
Siepmann Siepmann
Sievers Sievers
sigmoid sigmoid
@ -3618,6 +3623,7 @@ yx
yy yy
yz yz
Zannoni Zannoni
Zavattieri
zbl zbl
ZBL ZBL
Zc Zc

4
examples/ASPHERE/README
View File

@ -10,7 +10,7 @@ systems. Some of the directories include a Python script, which can
be used with the Pizza.py tool to create the data file, e.g. for be used with the Pizza.py tool to create the data file, e.g. for
collections of rigid bodies. collections of rigid bodies.
The web site for Pizza.py is http://pizza.sandia.gov The web site for Pizza.py is https://pizza.sandia.gov
For example, If you have Pizza.py installed you can type "pizza.py -f For example, If you have Pizza.py installed you can type "pizza.py -f
box.py", which creates the data.box data file in the box dir. box.py", which creates the data.box data file in the box dir.
@ -18,7 +18,7 @@ box.py", which creates the data.box data file in the box dir.
If you uncomment the dump or dump image lines in the input scripts the If you uncomment the dump or dump image lines in the input scripts the
runs will produce dump files or JPG images which you can view or runs will produce dump files or JPG images which you can view or
animate. See the Movies page of the LAMMPS web site animate. See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of these (https://www.lammps.org/movies.html), for animations of these
scripts. Most were done using the dump image command. A few were scripts. Most were done using the dump image command. A few were
done using the gl tool in Pizza.py; the Pizza.py scripts that do the done using the gl tool in Pizza.py; the Pizza.py scripts that do the
animation are given in the directory, e.g. as line.viz.py. animation are given in the directory, e.g. as line.viz.py.

2
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------- /* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/ https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------- /* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/ https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------- /* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/ https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_mc/mc.cpp
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
examples/COUPLE/lammps_mc/mc.h
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
examples/COUPLE/lammps_mc/random_park.cpp
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_mc/random_park.h
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_nwchem/nwchem_wrap.py
View File

@ -2,7 +2,7 @@
# ---------------------------------------------------------------------- # ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories # https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov # Steve Plimpton, sjplimp@sandia.gov
# ---------------------------------------------------------------------- # ----------------------------------------------------------------------

2
examples/COUPLE/lammps_vasp/vasp_wrap.py
View File

@ -2,7 +2,7 @@
# ---------------------------------------------------------------------- # ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories # https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov # Steve Plimpton, sjplimp@sandia.gov
# ---------------------------------------------------------------------- # ----------------------------------------------------------------------

2
examples/COUPLE/multiple/multiple.cpp
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/ https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/simple/simple.cpp
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/ https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/README
View File

@ -37,7 +37,7 @@ produce dump snapshots of the running simulation in any of 3 formats.
If you uncomment the dump command in the input script, a text dump If you uncomment the dump command in the input script, a text dump
file will be produced, which can be animated by various visualization file will be produced, which can be animated by various visualization
programs (see http://lammps.sandia.gov/viz.html) such as Ovito, VMD, programs (see https://www.lammps.org/viz.html) such as Ovito, VMD,
or AtomEye. or AtomEye.
If you uncomment the dump image command in the input script, and If you uncomment the dump image command in the input script, and

2
examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
View File

@ -2,7 +2,7 @@
""" """
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/USER/cgdna/util/generate.py
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@ -2,7 +2,7 @@
""" """
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/USER/diffraction/Output/log.cite
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@ -1,5 +1,5 @@
This LAMMPS simulation made specific use of work described in the This LAMMPS simulation made specific use of work described in the
following references. See http://lammps.sandia.gov/cite.html following references. See https://www.lammps.org/cite.html
for details. for details.
compute_xrd command: compute_xrd command:

1096
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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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@ -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
examples/VISCOSITY/README
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@ -28,7 +28,7 @@ minute or so and produce the accompanying log files and profile files
(for velocity or momentum flux). (for velocity or momentum flux).
See the Movies page of the LAMMPS web site See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of the NEMD (https://www.lammps.org/movies.html), for animations of the NEMD
scripts, created using the dump image command. scripts, created using the dump image command.
The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut = The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut =

6
examples/kim/in.kim-pm-property
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@ -11,18 +11,18 @@
# argon. The material properties computed in LAMMPS are represented as a # argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See # standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and # `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details). # `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn` # Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command. # using the `kim property dump` command.
# #
# Requirement: # Requirement:
# #
# This example requires LAMMPS built with the Python 3.6 or later package # This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for # installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system. # more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the # After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the # kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for # `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details. # further details.
# #
# This example requires that the KIM Portable Model (PM) # This example requires that the KIM Portable Model (PM)

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@ -6,7 +6,7 @@
# the KIM package, is the KIM API library that must be downloaded from the # the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query' # OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the # command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further # `https://docs.lammps.org/Build_extras.html#kim` doc page for further
# details # details
# #
# This example requires that the KIM Models # This example requires that the KIM Models

6
examples/kim/log.10Feb21.in.kim-pm-property.clang.1
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@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021)
# argon. The material properties computed in LAMMPS are represented as a # argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See # standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and # `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details). # `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn` # Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command. # using the `kim property dump` command.
# #
# Requirement: # Requirement:
# #
# This example requires LAMMPS built with the Python 3.6 or later package # This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for # installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system. # more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the # After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the # kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for # `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details. # further details.
# #
# This example requires that the KIM Portable Model (PM) # This example requires that the KIM Portable Model (PM)

6
examples/kim/log.10Feb21.in.kim-pm-property.clang.4
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@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021)
# argon. The material properties computed in LAMMPS are represented as a # argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See # standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and # `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details). # `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn` # Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command. # using the `kim property dump` command.
# #
# Requirement: # Requirement:
# #
# This example requires LAMMPS built with the Python 3.6 or later package # This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for # installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system. # more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the # After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the # kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for # `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details. # further details.
# #
# This example requires that the KIM Portable Model (PM) # This example requires that the KIM Portable Model (PM)

2
examples/kim/log.10Feb21.in.kim-query.clang.1
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@ -7,7 +7,7 @@ LAMMPS (10 Feb 2021)
# the KIM package, is the KIM API library that must be downloaded from the # the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query' # OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the # command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further # `https://docs.lammps.org/Build_extras.html#kim` doc page for further
# details # details
# #
# This example requires that the KIM Models # This example requires that the KIM Models

2
examples/plugins/angle_zero2.cpp
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@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/angle_zero2.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/bond_zero2.cpp
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@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/bond_zero2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

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