Resolved merging conflicts in three files
This commit is contained in:
Karl Hammond
4
README
4
README
@ -16,8 +16,8 @@ National Laboratories, a US Department of Energy facility, with
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funding from the DOE. It is an open-source code, distributed freely
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under the terms of the GNU Public License (GPL) version 2.
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The primary author of the code is Steve Plimpton, who can be emailed
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at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has
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The code is maintained by the LAMMPS development team who can be emailed
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at developers@lammps.org. The LAMMPS WWW Site at www.lammps.org has
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more information about the code and its uses.
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The LAMMPS distribution includes the following files and directories:
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@ -727,18 +727,17 @@ list(FIND LANGUAGES "Fortran" _index)
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if(_index GREATER -1)
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target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
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endif()
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set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
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input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
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pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
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if(LAMMPS_EXCEPTIONS)
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list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
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endif()
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set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
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error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
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library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
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platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
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set(LAMMPS_FMT_HEADERS core.h format.h)
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set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
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set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
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set_target_properties(lammps PROPERTIES PREFIX "lib")
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target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
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file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
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file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
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foreach(_HEADER ${LAMMPS_CXX_HEADERS})
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add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
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add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
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@ -747,6 +746,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
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install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
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endif()
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endforeach()
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foreach(_HEADER ${LAMMPS_FMT_HEADERS})
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add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
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add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
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add_dependencies(lammps fmt_${_HEADER})
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if(BUILD_SHARED_LIBS)
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install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
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endif()
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endforeach()
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target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
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add_library(LAMMPS::lammps ALIAS lammps)
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get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
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@ -969,9 +976,6 @@ if(PKG_GPU)
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endif()
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message(STATUS "GPU precision: ${GPU_PREC}")
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endif()
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if(PKG_KOKKOS)
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message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
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endif()
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if(PKG_KSPACE)
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message(STATUS "<<< FFT settings >>>
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-- Primary FFT lib: ${FFT}")
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@ -1,5 +1,10 @@
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# Find clang-format
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find_program(ClangFormat_EXECUTABLE NAMES clang-format
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clang-format-15.0
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clang-format-14.0
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clang-format-13.0
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clang-format-12.0
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clang-format-11.0
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clang-format-10.0
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clang-format-9.0
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clang-format-8.0
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@ -14,19 +19,27 @@ if(ClangFormat_EXECUTABLE)
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OUTPUT_VARIABLE clang_format_version
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ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
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if(clang_format_version MATCHES "^clang-format version .*")
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# Arch Linux
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if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
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# Arch Linux output:
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# clang-format version 10.0.0
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# Ubuntu 18.04 LTS Output
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#
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# Ubuntu 18.04 LTS output:
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# clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
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string(REGEX REPLACE "clang-format version ([0-9.]+).*"
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"\\1"
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#
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# Ubuntu 20.04 LTS output:
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# clang-format version 10.0.0-4ubuntu1
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#
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# Ubuntu 22.04 LTS output:
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# Ubuntu clang-format version 14.0.0-1ubuntu1
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#
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# Fedora 36 output:
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# clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
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string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
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"\\2"
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ClangFormat_VERSION
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"${clang_format_version}")
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elseif(clang_format_version MATCHES ".*LLVM version .*")
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# CentOS 7 Output
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# CentOS 7 output:
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# LLVM (http://llvm.org/):
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# LLVM version 3.4.2
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# Optimized build.
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@ -22,7 +22,7 @@ endif()
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if(Python_EXECUTABLE)
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get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
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find_program(Cythonize_EXECUTABLE
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NAMES cythonize3 cythonize cythonize.bat
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NAMES cythonize-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR} cythonize3 cythonize cythonize.bat
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HINTS ${_python_path})
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endif()
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@ -2,7 +2,13 @@
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set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
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if(PKG_PYTHON)
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find_package(Cythonize QUIET)
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if(Cythonize_FOUND)
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if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
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find_package(Python COMPONENTS NumPy QUIET)
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else()
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# assume we have NumPy
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set(Python_NumPy_FOUND ON)
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endif()
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if(Cythonize_FOUND AND Python_NumPy_FOUND)
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set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
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endif()
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endif()
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@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
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if(MLIAP_ENABLE_PYTHON)
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find_package(Cythonize REQUIRED)
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if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
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find_package(Python COMPONENTS NumPy REQUIRED)
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endif()
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if(NOT PKG_PYTHON)
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message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
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endif()
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@ -47,15 +47,15 @@ if(DOWNLOAD_PLUMED)
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endif()
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message(STATUS "PLUMED download requested - we will build our own")
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if(PLUMED_MODE STREQUAL "STATIC")
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set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
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set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
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elseif(PLUMED_MODE STREQUAL "SHARED")
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set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
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set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
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elseif(PLUMED_MODE STREQUAL "RUNTIME")
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set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
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set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
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endif()
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set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
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set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
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set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
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set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
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mark_as_advanced(PLUMED_URL)
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mark_as_advanced(PLUMED_MD5)
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@ -78,12 +78,12 @@ if(DOWNLOAD_PLUMED)
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add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
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add_dependencies(LAMMPS::PLUMED plumed_build)
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if(PLUMED_MODE STREQUAL "STATIC")
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set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
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set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
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elseif(PLUMED_MODE STREQUAL "SHARED")
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set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
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set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
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elseif(PLUMED_MODE STREQUAL "RUNTIME")
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set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
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set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
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set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
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set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
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endif()
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set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
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file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
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@ -96,7 +96,7 @@ else()
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elseif(PLUMED_MODE STREQUAL "SHARED")
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include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
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elseif(PLUMED_MODE STREQUAL "RUNTIME")
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set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
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set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
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include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
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endif()
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set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
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@ -1,4 +1,9 @@
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find_package(VTK REQUIRED NO_MODULE)
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include(${VTK_USE_FILE})
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target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
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target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
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if (VTK_MAJOR_VERSION VERSION_LESS 9.0)
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include(${VTK_USE_FILE})
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target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
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else()
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target_link_libraries(lammps PRIVATE VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
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vtk_module_autoinit(TARGETS lammps MODULES VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
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endif()
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16
doc/Makefile
16
doc/Makefile
@ -38,16 +38,14 @@ endif
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# override settings for PIP commands
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# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
|
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|
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#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
|
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|
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# temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
|
||||
SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
|
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SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
|
||||
|
||||
# grab list of sources from doxygen config file.
|
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# we only want to use explicitly listed files.
|
||||
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
|
||||
|
||||
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
|
||||
.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check xmlgen fasthtml
|
||||
|
||||
# ------------------------------------------
|
||||
|
||||
@ -89,6 +87,8 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
||||
@$(MAKE) $(MFLAGS) -C graphviz all
|
||||
@(\
|
||||
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||
sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
|
||||
touch $(RSTDIR)/Fortran.rst ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
|
||||
ln -sf Manual.html html/index.html;\
|
||||
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||
@ -114,7 +114,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
||||
@mkdir -p fasthtml
|
||||
@(\
|
||||
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||
sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
|
||||
touch $(RSTDIR)/Fortran.rst ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
|
||||
deactivate ;\
|
||||
)
|
||||
@rm -rf fasthtml/_sources
|
||||
@ -144,6 +146,8 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
|
||||
@cp src/JPG/*.* epub/JPG
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
|
||||
touch $(RSTDIR)/Fortran.rst ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
|
||||
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||
deactivate ;\
|
||||
@ -163,6 +167,8 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
|
||||
@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
|
||||
@(\
|
||||
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||
sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
touch $(RSTDIR)/Fortran.rst ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||
echo "############################################" ;\
|
||||
|
||||
@ -147,6 +147,16 @@ compile and will download and compile a specific recent version of the
|
||||
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
|
||||
for implementing the tests.
|
||||
|
||||
.. admonition:: Software version requirements for testing
|
||||
:class: note
|
||||
|
||||
The compiler and library version requirements for the testing
|
||||
framework are more strict than for the main part of LAMMPS. For
|
||||
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
|
||||
(version 4.8.x) are not sufficient. The CMake configuration will try
|
||||
to detect compatible versions and either skip incompatible tests or
|
||||
stop with an error.
|
||||
|
||||
After compilation is complete, the unit testing is started in the build
|
||||
folder using the ``ctest`` command, which is part of the CMake software.
|
||||
The output of this command will be looking something like this::
|
||||
|
||||
@ -7,7 +7,7 @@ source files provided as a supplement to a publication) that are written
|
||||
for an older version of LAMMPS and thus need to be updated to be
|
||||
compatible with the current version of LAMMPS. Due to the active
|
||||
development of LAMMPS it is likely to always be incomplete. Please
|
||||
contact developer@lammps.org in case you run across an issue that is not
|
||||
contact developers@lammps.org in case you run across an issue that is not
|
||||
(yet) listed here. Please also review the latest information about the
|
||||
LAMMPS :doc:`programming style conventions <Modify_style>`, especially
|
||||
if you are considering to submit the updated version for inclusion into
|
||||
|
||||
@ -1,11 +1,12 @@
|
||||
The :f:mod:`LIBLAMMPS` Fortran Module
|
||||
*************************************
|
||||
|
||||
The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from Fortran.
|
||||
It is based on the LAMMPS C library interface and
|
||||
requires a Fortran 2003-compatible compiler to be compiled. It is
|
||||
designed to be self-contained and not require any support functions
|
||||
written in C, C++, or Fortran other than those in the C library interface.
|
||||
The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from
|
||||
Fortran. It is based on the LAMMPS C library interface and requires a
|
||||
fully Fortran 2003-compatible compiler to be compiled. It is designed
|
||||
to be self-contained and not require any support functions written in C,
|
||||
C++, or Fortran other than those in the C library interface and the module
|
||||
itself.
|
||||
|
||||
While C libraries have a defined binary interface (ABI) and can thus be
|
||||
used from multiple compiler versions from different vendors as long
|
||||
@ -21,11 +22,11 @@ for a simple program using the Fortran interface would be:
|
||||
mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
|
||||
|
||||
Please note that the MPI compiler wrapper is only required when the
|
||||
calling the library from an MPI-parallelized program. Otherwise, using the
|
||||
fortran compiler (gfortran, ifort, flang, etc.) will suffice. It may be
|
||||
necessary to link to additional libraries, depending on how LAMMPS was
|
||||
configured and whether the LAMMPS library :doc:`was compiled as a static
|
||||
or dynamic library <Build_link>`.
|
||||
calling the library from an MPI-parallelized program. Otherwise, using
|
||||
the plain Fortran compiler (gfortran, ifort, flang, etc.) will suffice.
|
||||
It may be necessary to link to additional libraries, depending on how
|
||||
LAMMPS was configured and whether the LAMMPS library :doc:`was compiled
|
||||
as a static or dynamic library <Build_link>`.
|
||||
|
||||
If the LAMMPS library itself has been compiled with MPI support, the
|
||||
resulting executable will still be able to run LAMMPS in parallel with
|
||||
|
||||
@ -1736,8 +1736,6 @@ must be installed.
|
||||
|
||||
.. versionadded:: 30Jun2020
|
||||
|
||||
.. versionadded:: 30Jun2020
|
||||
|
||||
**Supporting info:**
|
||||
|
||||
* src/ML-IAP: filenames -> commands
|
||||
|
||||
@ -16,46 +16,47 @@ simulation. An example set of statistics is shown here:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
|
||||
Loop time of 0.942801 on 4 procs for 300 steps with 2004 atoms
|
||||
|
||||
Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
|
||||
97.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 54.985 ns/day, 0.436 hours/ns, 318.201 timesteps/s, 637.674 katom-step/s
|
||||
195.2% CPU use with 2 MPI tasks x 2 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section \| min time \| avg time \| max time \|%varavg\| %total
|
||||
---------------------------------------------------------------
|
||||
Pair \| 1.9808 \| 2.0134 \| 2.0318 \| 1.4 \| 71.60
|
||||
Bond \| 0.0021894 \| 0.0060319 \| 0.010058 \| 4.7 \| 0.21
|
||||
Kspace \| 0.3207 \| 0.3366 \| 0.36616 \| 3.1 \| 11.97
|
||||
Neigh \| 0.28411 \| 0.28464 \| 0.28516 \| 0.1 \| 10.12
|
||||
Comm \| 0.075732 \| 0.077018 \| 0.07883 \| 0.4 \| 2.74
|
||||
Output \| 0.00030518 \| 0.00042665 \| 0.00078821 \| 1.0 \| 0.02
|
||||
Modify \| 0.086606 \| 0.086631 \| 0.086668 \| 0.0 \| 3.08
|
||||
Other \| \| 0.007178 \| \| \| 0.26
|
||||
Pair \| 0.61419 \| 0.62872 \| 0.64325 \| 1.8 \| 66.69
|
||||
Bond \| 0.0028608 \| 0.0028899 \| 0.002919 \| 0.1 \| 0.31
|
||||
Kspace \| 0.12652 \| 0.14048 \| 0.15444 \| 3.7 \| 14.90
|
||||
Neigh \| 0.10242 \| 0.10242 \| 0.10242 \| 0.0 \| 10.86
|
||||
Comm \| 0.026753 \| 0.027593 \| 0.028434 \| 0.5 \| 2.93
|
||||
Output \| 0.00018341 \| 0.00030942 \| 0.00043542 \| 0.0 \| 0.03
|
||||
Modify \| 0.039117 \| 0.039348 \| 0.039579 \| 0.1 \| 4.17
|
||||
Other \| \| 0.001041 \| \| \| 0.11
|
||||
|
||||
Nlocal: 501 ave 508 max 490 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 6586.25 ave 6628 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 177007 ave 180562 max 170212 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nlocal: 1002 ave 1006 max 998 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8670.5 ave 8691 max 8650 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354010 ave 357257 max 350763 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708028
|
||||
Ave neighs/atom = 353.307
|
||||
Ave special neighs/atom = 2.34032
|
||||
Total # of neighbors = 708020
|
||||
Ave neighs/atom = 353.30339
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
----------
|
||||
|
||||
The first section provides a global loop timing summary. The *loop
|
||||
time* is the total wall-clock time for the simulation to run. The
|
||||
*Performance* line is provided for convenience to help predict how
|
||||
long it will take to run a desired physical simulation. The *CPU use*
|
||||
line provides the CPU utilization per MPI task; it should be close to
|
||||
100% times the number of OpenMP threads (or 1 of not using OpenMP).
|
||||
Lower numbers correspond to delays due to file I/O or insufficient
|
||||
thread utilization.
|
||||
The first section provides a global loop timing summary. The *loop time*
|
||||
is the total wall-clock time for the simulation to run. The
|
||||
*Performance* line is provided for convenience to help predict how long
|
||||
it will take to run a desired physical simulation and to have numbers
|
||||
useful for performance comparison between different simulation settings
|
||||
or system sizes. The *CPU use* line provides the CPU utilization per
|
||||
MPI task; it should be close to 100% times the number of OpenMP threads
|
||||
(or 1 of not using OpenMP). Lower numbers correspond to delays due to
|
||||
file I/O or insufficient thread utilization.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -23,15 +23,16 @@ Description
|
||||
"""""""""""
|
||||
|
||||
This command deletes all atoms, restores all settings to their default
|
||||
values, and frees all memory allocated by LAMMPS. Once a clear
|
||||
command has been executed, it is almost as if LAMMPS were starting
|
||||
over, with only the exceptions noted below. This command enables
|
||||
multiple jobs to be run sequentially from one input script.
|
||||
values, and frees all memory allocated by LAMMPS. Once a clear command
|
||||
has been executed, it is almost as if LAMMPS were starting over, with
|
||||
only the exceptions noted below. This command enables multiple jobs to
|
||||
be run sequentially from one input script.
|
||||
|
||||
These settings are not affected by a clear command: the working
|
||||
directory (:doc:`shell <shell>` command), log file status
|
||||
(:doc:`log <log>` command), echo status (:doc:`echo <echo>` command), and
|
||||
input script variables (:doc:`variable <variable>` command).
|
||||
directory (:doc:`shell <shell>` command), log file status (:doc:`log
|
||||
<log>` command), echo status (:doc:`echo <echo>` command), and input
|
||||
script variables except for *atomfile* style variables (:doc:`variable
|
||||
<variable>` command).
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -202,7 +202,7 @@ or multiple smaller files).
|
||||
to a dump file may be slightly outside the simulation box.
|
||||
Re-neighbor timesteps will not typically coincide with the
|
||||
timesteps dump snapshots are written. See the :doc:`dump_modify
|
||||
pbc <dump_modify>` command if you with to force coordinates to be
|
||||
pbc <dump_modify>` command if you wish to force coordinates to be
|
||||
strictly inside the simulation box.
|
||||
|
||||
.. note::
|
||||
|
||||
@ -404,6 +404,12 @@ atoms are present. The velocity of each created atom is initialized in
|
||||
a random direction with a magnitude calculated from the instantaneous
|
||||
temperature of the reaction site.
|
||||
|
||||
.. note::
|
||||
|
||||
The 'Coords' section must be included in the post-reaction template
|
||||
when creating atoms because these coordinates are used to determine
|
||||
where new atoms are inserted.
|
||||
|
||||
The handedness of atoms that are chiral centers can be enforced by
|
||||
listing their IDs in the ChiralIDs section. A chiral atom must be
|
||||
bonded to four atoms with mutually different atom types. This feature
|
||||
|
||||
@ -16,12 +16,12 @@ Syntax
|
||||
|
||||
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval*
|
||||
*delay* value = N
|
||||
N = delay building until this many steps since last build
|
||||
N = delay building neighbor lists until this many steps since last build
|
||||
*every* value = M
|
||||
M = build neighbor list every this many steps
|
||||
M = consider building neighbor lists every this many steps
|
||||
*check* value = *yes* or *no*
|
||||
*yes* = only build if some atom has moved half the skin distance or more
|
||||
*no* = always build on 1st step that *every* and *delay* are satisfied
|
||||
*yes* = only build if at least one atom has moved half the skin distance or more
|
||||
*no* = always build on 1st step where *every* and *delay* are conditions are satisfied
|
||||
*once* value = *yes* or *no*
|
||||
*yes* = only build neighbor list once at start of run and never rebuild
|
||||
*no* = rebuild neighbor list according to other settings
|
||||
@ -71,30 +71,53 @@ Description
|
||||
"""""""""""
|
||||
|
||||
This command sets parameters that affect the building and use of
|
||||
pairwise neighbor lists. Depending on what pair interactions and
|
||||
other commands are defined, a simulation may require one or more
|
||||
neighbor lists.
|
||||
pairwise neighbor lists. Depending on what pair interactions and other
|
||||
commands are defined, a simulation may require one or more neighbor
|
||||
lists.
|
||||
|
||||
The *every*, *delay*, *check*, and *once* options affect how often
|
||||
lists are built as a simulation runs. The *delay* setting means never
|
||||
build new lists until at least N steps after the previous build. The
|
||||
*every* setting means build lists every M steps (after the delay has
|
||||
The *every*, *delay*, *check*, and *once* options affect how often lists
|
||||
are built as a simulation runs. The *delay* setting means never build
|
||||
new lists until at least N steps after the previous build. The *every*
|
||||
setting means attempt to build lists every M steps (after the delay has
|
||||
passed). If the *check* setting is *no*, the lists are built on the
|
||||
first step that satisfies the *delay* and *every* settings. If the
|
||||
*check* setting is *yes*, then the *every* and *delay* settings
|
||||
determine when a build may possibly be performed, but an actual build
|
||||
only occurs if some atom has moved more than half the skin distance
|
||||
(specified in the :doc:`neighbor <neighbor>` command) since the last
|
||||
build.
|
||||
only occurs if at least one atom has moved more than half the neighbor
|
||||
skin distance (specified in the :doc:`neighbor <neighbor>` command)
|
||||
since the last neighbor list build.
|
||||
|
||||
If the *once* setting is yes, then the neighbor list is only built
|
||||
once at the beginning of each run, and never rebuilt, except on steps
|
||||
when a restart file is written, or steps when a fix forces a rebuild
|
||||
to occur (e.g. fixes that create or delete atoms, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`).
|
||||
This setting should only be made if you are certain atoms will not
|
||||
move far enough that the neighbor list should be rebuilt, e.g. running
|
||||
a simulation of a cold crystal. Note that it is not that expensive to
|
||||
check if neighbor lists should be rebuilt.
|
||||
.. admonition:: Impact of neighbor list settings
|
||||
:class: note
|
||||
|
||||
The choice of neighbor list settings can have a significant impact on
|
||||
the (parallel) performance of LAMMPS and the correctness of the
|
||||
simulation results. Since building the neighbor lists is time
|
||||
consuming, doing it less frequently can speed up a calculation. If
|
||||
the lists are rebuilt too infrequently, however, interacting pairs
|
||||
may be missing and thus the resulting pairwise interactions
|
||||
incorrect. The optimal settings depend on many factors like the
|
||||
properties of the simulated system (density, geometry, topology,
|
||||
temperature, pressure), the force field parameters and settings, the
|
||||
size of the timestep, neighbor list skin distance and more. The
|
||||
default settings are chosen to be very conservative to guarantee
|
||||
correctness of the simulation. They depend on the *check* flag
|
||||
heuristics to reduce the number of neighbor list rebuilds at a minor
|
||||
expense for executing the check. Determining the correctness of a
|
||||
specific choice of neighbor list settings is complicated by the fact
|
||||
that a neighbor list rebuild changes the order in which pairwise
|
||||
interactions are computed and thus
|
||||
- due to the limitations of floating-point math - the trajectory.
|
||||
|
||||
If the *once* setting is yes, then the neighbor list is only built once
|
||||
at the beginning of each run, and never rebuilt, except on steps when a
|
||||
restart file is written, or steps when a fix forces a rebuild to occur
|
||||
(e.g. fixes that create or delete atoms, such as :doc:`fix deposit
|
||||
<fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`). This setting
|
||||
should only be made if you are certain atoms will not move far enough
|
||||
that the neighbor list should be rebuilt, e.g. running a simulation of a
|
||||
cold crystal. Note that it is not that expensive to check if neighbor
|
||||
lists should be rebuilt.
|
||||
|
||||
When the rRESPA integrator is used (see the :doc:`run_style <run_style>`
|
||||
command), the *every* and *delay* parameters refer to the longest
|
||||
@ -234,11 +257,11 @@ depend on their atom type.
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
If the "delay" setting is non-zero, then it must be a multiple of the
|
||||
"every" setting.
|
||||
If the *delay* setting is non-zero, then it must be a multiple of the
|
||||
*every* setting.
|
||||
|
||||
The molecule/intra and molecule/inter exclude options can only be used
|
||||
with atom styles that define molecule IDs.
|
||||
The *molecule/intra* and *molecule/inter* exclusion options can only
|
||||
be used with atom styles that define molecule IDs.
|
||||
|
||||
The value of the *page* setting must be at least 10x larger than the
|
||||
*one* setting. This insures neighbor pages are not mostly empty
|
||||
@ -252,6 +275,6 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are delay = 10, every = 1, check = yes, once = no,
|
||||
The option defaults are delay = 0, every = 1, check = yes, once = no,
|
||||
cluster = no, include = all (same as no include option defined),
|
||||
exclude = none, page = 100000, one = 2000, and binsize = 0.0.
|
||||
|
||||
@ -58,22 +58,26 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lj/cut/dipole/cut 10.0
|
||||
pair_style lj/cut/dipole/cut 2.5 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0
|
||||
pair_coeff 2 3 0.8 1.0 2.5 4.0
|
||||
|
||||
pair_style lj/sf/dipole/sf 9.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0
|
||||
pair_coeff 2 3 0.8 1.0 2.5 4.0
|
||||
|
||||
pair_style lj/cut/dipole/long 10.0
|
||||
pair_style lj/cut/dipole/long 2.5 3.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0
|
||||
pair_coeff 2 3 0.8 1.0 3.0
|
||||
|
||||
pair_style lj/long/dipole/long long long 3.5 10.0
|
||||
pair_style lj/long/dipole/long long long 3.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 2 3 1.0 1.0 2.5 4.0
|
||||
pair_coeff 2 3 0.8 1.0
|
||||
|
||||
pair_style lj/long/dipole/long cut long 2.5 3.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 2 3 0.8 1.0 3.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -254,23 +258,28 @@ long-range LJ interactions, the :doc:`kspace_style ewald/disp
|
||||
|
||||
----------
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands, or by mixing as described below:
|
||||
The following coefficients must be defined for each pair of atoms types
|
||||
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
|
||||
or in the data file or restart files read by the :doc:`read_data
|
||||
<read_data>` or :doc:`read_restart <read_restart>` commands, or by
|
||||
mixing as described below:
|
||||
|
||||
* :math:`\epsilon` (energy units)
|
||||
* :math:`\sigma` (distance units)
|
||||
* cutoff1 (distance units)
|
||||
* cutoff2 (distance units)
|
||||
|
||||
The latter 2 coefficients are optional. If not specified, the global
|
||||
LJ and Coulombic cutoffs specified in the pair_style command are used.
|
||||
If only one cutoff is specified, it is used as the cutoff for both LJ
|
||||
and Coulombic interactions for this type pair. If both coefficients
|
||||
are specified, they are used as the LJ and Coulombic cutoffs for this
|
||||
type pair.
|
||||
The latter 2 coefficients are optional. If not specified, the global LJ
|
||||
and Coulombic cutoffs specified in the pair_style command are used. If
|
||||
only one cutoff is specified, it is used as the cutoff for both LJ and
|
||||
Coulombic interactions for this type pair. If both coefficients are
|
||||
specified, they are used as the LJ and Coulombic cutoffs for this type
|
||||
pair. When using a long-rang Coulomb solver, only a global Coulomb
|
||||
cutoff may be used and only the LJ cutoff may be changed with the
|
||||
:doc:`pair_coeff <pair_coeff>` command. When using the
|
||||
*lj/long/dipole/long* pair style with *long* *long* setting, only a
|
||||
single global cutoff may be provided and no cutoff for the
|
||||
:doc:`pair_coeff <pair_coeff>` command.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -57,7 +57,7 @@ The format of the list file is as follows:
|
||||
ID2 = atom ID of second atom
|
||||
style = style of interaction
|
||||
coeffs = list of coeffs
|
||||
cutoff = cutoff for interaction (optional, except for style *quartic*)
|
||||
cutoff = cutoff for interaction (optional)
|
||||
|
||||
The cutoff parameter is optional for all but the *quartic* interactions.
|
||||
If it is not specified, the global cutoff is used.
|
||||
@ -71,7 +71,7 @@ Here is an example file:
|
||||
15 259 lj126 1.0 1.0 50.0
|
||||
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
|
||||
18 470 harmonic 50.0 1.2 5.0
|
||||
19 332 quartic 5.0 -1.2 1.2 5.0
|
||||
19 332 quartic 10.0 5.0 -1.2 1.2
|
||||
|
||||
The style *lj126* computes pairwise interactions with the formula
|
||||
|
||||
@ -100,7 +100,7 @@ The style *harmonic* computes pairwise interactions with the formula
|
||||
|
||||
.. math::
|
||||
|
||||
E = K (r - r_0)^2
|
||||
E = K (r - r_0)^2 \qquad r < r_c
|
||||
|
||||
and the coefficients:
|
||||
|
||||
@ -113,16 +113,14 @@ The style *quartic* computes pairwise interactions with the formula
|
||||
|
||||
.. math::
|
||||
|
||||
E = K (r - r_c)^2 (r - r_c -b_1) (r - r_c - b_2) \qquad r < r_c
|
||||
E = K (r - r_0)^2 (r - r_0 -b_1) (r - r_0 - b_2) \qquad r < r_c
|
||||
|
||||
and the coefficients:
|
||||
|
||||
* :math:`K` (energy units)
|
||||
* :math:`r_0` (distance units)
|
||||
* :math:`b_1` (distance units)
|
||||
* :math:`b_2` (distance units)
|
||||
* :math:`r_c` (distance units)
|
||||
|
||||
Note that the per list entry cutoff :math:`r_c` is **required** for *quartic* interactions.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -112,7 +112,6 @@ requests to compute `gamma`, as shown in example below:
|
||||
compute max_pace_gamma all reduce max f_pace_gamma
|
||||
variable dump_skip equal "c_max_pace_gamma < 5"
|
||||
|
||||
|
||||
dump pace_dump all custom 20 extrapolative_structures.dump id x y z f_pace_gamma
|
||||
dump_modify pace_dump skip v_dump_skip
|
||||
|
||||
|
||||
@ -71,8 +71,14 @@ Also see the explanation of the :doc:`-restart command-line switch
|
||||
|
||||
This command can be used multiple times to add new atoms and their
|
||||
properties to an existing system by using the *add*, *offset*, and
|
||||
*shift* keywords. See more details below, which includes the use case
|
||||
for the *extra* keywords.
|
||||
*shift* keywords. However, it is important to understand that several
|
||||
system parameters, like the number of types of different kinds and per
|
||||
atom settings are **locked in** after the first *read_data* command,
|
||||
which means that no type ID (including its offset) may have a larger
|
||||
value when processing additional data files than what is set by the
|
||||
first data file and the corresponding *read_data* command options. See
|
||||
more details on this situation below, which includes the use case for
|
||||
the *extra* keywords.
|
||||
|
||||
The *group* keyword adds all the atoms in the data file to the
|
||||
specified group-ID. The group will be created if it does not already
|
||||
|
||||
@ -101,7 +101,7 @@ Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
|
||||
for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
|
||||
|
||||
Typically the best way to do this is to let the first partition choose
|
||||
its onn optimal layout, then require the second partition's layout to
|
||||
its own optimal layout, then require the second partition's layout to
|
||||
match the integer multiple constraint. See the
|
||||
:doc:`processors <processors>` command with its *part* keyword for a way
|
||||
to control this, e.g.
|
||||
|
||||
@ -213,6 +213,9 @@ from the list of active variables, and is thus available to be
|
||||
re-defined in a subsequent variable command. The *delete* style does
|
||||
the same thing.
|
||||
|
||||
Variables are **not** deleted by the :doc:`clear <clear>` command with
|
||||
the exception of atomfile-style variables.
|
||||
|
||||
----------
|
||||
|
||||
The :doc:`Commands parse <Commands_parse>` page explains how
|
||||
@ -265,7 +268,7 @@ the first string is assigned to the variable. Each time a
|
||||
string is assigned. All processors assign the same string to the
|
||||
variable.
|
||||
|
||||
*Index* style variables with a single string value can also be set by
|
||||
Index-style variables with a single string value can also be set by
|
||||
using the :doc:`command-line switch -var <Run_options>`.
|
||||
|
||||
The *loop* style is identical to the *index* style except that the
|
||||
@ -285,7 +288,7 @@ be one string for each processor partition or "world". LAMMPS can be
|
||||
run with multiple partitions via the :doc:`-partition command-line
|
||||
switch <Run_options>`. This variable command assigns one string to
|
||||
each world. All processors in the world are assigned the same string.
|
||||
The next command cannot be used with *equal* style variables, since
|
||||
The next command cannot be used with equal-style variables, since
|
||||
there is only one value per world. This style of variable is useful
|
||||
when you wish to run different simulations on different partitions, or
|
||||
when performing a parallel tempering simulation (see the :doc:`temper
|
||||
@ -303,7 +306,7 @@ string. This continues until all the variable strings are consumed.
|
||||
Thus, this command can be used to run 50 simulations on 8 processor
|
||||
partitions. The simulations will be run one after the other on
|
||||
whatever partition becomes available, until they are all finished.
|
||||
*Universe* style variables are incremented using the files
|
||||
Universe-style variables are incremented using the files
|
||||
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
|
||||
see in your directory during such a LAMMPS run.
|
||||
|
||||
@ -341,7 +344,9 @@ variable can be used to adapt the behavior of LAMMPS input scripts via
|
||||
environment variable settings, or to retrieve information that has
|
||||
been previously stored with the :doc:`shell putenv <shell>` command.
|
||||
Note that because environment variable settings are stored by the
|
||||
operating systems, they persist beyond a :doc:`clear <clear>` command.
|
||||
operating systems, they persist even if the corresponding *getenv*
|
||||
style variable is deleted, and also are set for sub-shells executed
|
||||
by the :doc:`shell <shell>` command.
|
||||
|
||||
For the *file* style, a filename is provided which contains a list of
|
||||
strings to assign to the variable, one per line. The strings can be
|
||||
@ -373,7 +378,9 @@ This means the variable can then be evaluated as many times as desired
|
||||
and will return those values. There are two ways to cause the next
|
||||
set of per-atom values from the file to be read: use the
|
||||
:doc:`next <next>` command or the next() function in an atom-style
|
||||
variable, as discussed below.
|
||||
variable, as discussed below. Unlike most variable styles
|
||||
atomfile-style variables are **deleted** during a :doc:`clear <clear>`
|
||||
command.
|
||||
|
||||
The rules for formatting the file are as follows. Each time a set of
|
||||
per-atom values is read, a non-blank line is searched for in the file.
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
#
|
||||
# Python rewrite of txt2html
|
||||
# The original txt2html was written in C by Steve Plimpton
|
||||
# (http://www.cs.sandia.gov/cgi-bin/sjplimp/)
|
||||
# (https://sjplimp.github.io/)
|
||||
#
|
||||
# Copyright (C) 2015 Richard Berger
|
||||
#
|
||||
|
||||
@ -38,7 +38,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext'))
|
||||
# -- General configuration ------------------------------------------------
|
||||
|
||||
# If your documentation needs a minimal Sphinx version, state it here.
|
||||
#needs_sphinx = '1.0'
|
||||
needs_sphinx = '5.2.0'
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be
|
||||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
|
||||
@ -53,10 +53,6 @@ extensions = [
|
||||
'tab_or_note',
|
||||
'breathe',
|
||||
]
|
||||
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
|
||||
# yet we can no longer use Sphinx 15.x, since that breaks with
|
||||
# newer version of the multiprocessor module.
|
||||
# 'sphinxcontrib.images',
|
||||
|
||||
images_config = {
|
||||
'default_image_width' : '25%',
|
||||
@ -413,9 +409,9 @@ at Sandia National Laboratories, a US Department of Energy facility,
|
||||
with funding from the DOE. It is an open-source code, distributed
|
||||
freely under the terms of the GNU Public License (GPL).
|
||||
|
||||
The primary author of the code is Steve Plimpton, who can be emailed
|
||||
at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has
|
||||
more information about the code and its uses.
|
||||
The LAMMPS developers can be contacted at developers@lammps.org.
|
||||
The LAMMPS WWW Site at www.lammps.org has more information about
|
||||
the code and its uses.
|
||||
"""
|
||||
|
||||
epub_author = 'The LAMMPS Developers'
|
||||
|
||||
@ -2540,7 +2540,6 @@ oneAPI
|
||||
onelevel
|
||||
oneway
|
||||
onlysalt
|
||||
onn
|
||||
ons
|
||||
OO
|
||||
Oord
|
||||
@ -2738,6 +2737,7 @@ Polym
|
||||
polymorph
|
||||
polymorphism
|
||||
Ponder
|
||||
Ponte
|
||||
popen
|
||||
Popoola
|
||||
Popov
|
||||
@ -3692,6 +3692,7 @@ vdw
|
||||
vdW
|
||||
vdwl
|
||||
vec
|
||||
Vecchio
|
||||
vectorial
|
||||
vectorization
|
||||
Vectorization
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
! https://www.lammps.org/, Sandia National Laboratories
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
! https://www.lammps.org/, Sandia National Laboratories
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS Development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS Development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! -------------------------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! LAMMPS Development team, developers@lammps.org
|
||||
! LAMMPS Development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
@ -19,8 +19,12 @@
|
||||
! Karl D. Hammond <hammondkd@missouri.edu>
|
||||
! University of Missouri, 2012-2020
|
||||
!
|
||||
! Contributing authors:
|
||||
! - Axel Kohlmeyer <akohlmey@gmail.com>, Temple University, 2020-2022
|
||||
! - Karl D. Hammond <hammondkd@missouri.edu> University of Missouri, 2022
|
||||
!
|
||||
! The Fortran module tries to follow the API of the C library interface
|
||||
! closely, but like the Python wrapper it employs an object-oriented
|
||||
! closely, but like the Python wrapper, it employs an object-oriented
|
||||
! approach. To accommodate the object-oriented approach, all exported
|
||||
! subroutines and functions have to be implemented in Fortran and
|
||||
! call the interfaced C-style functions with adapted calling conventions
|
||||
|
||||
@ -184,7 +184,7 @@ class UCL_Device {
|
||||
_cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props,
|
||||
&errorv);
|
||||
} else {
|
||||
cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, 0};
|
||||
cl_queue_properties props[] = {0};
|
||||
_cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props,
|
||||
&errorv);
|
||||
}
|
||||
|
||||
@ -741,6 +741,7 @@ void DeviceT::estimate_gpu_overhead(const int kernel_calls,
|
||||
}
|
||||
gpu_overhead/=10.0;
|
||||
gpu_driver_overhead/=10.0;
|
||||
gpu->sync();
|
||||
|
||||
if (_data_in_estimate>0) {
|
||||
delete [] host_data_in;
|
||||
@ -793,6 +794,7 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer<numtyp,acctyp> &ans,
|
||||
#ifdef USE_OPENCL
|
||||
// Workaround for timing issue on Intel OpenCL
|
||||
if (times[0] > 80e6) times[0]=0.0;
|
||||
if (times[1] > 80e6) times[1]=0.0;
|
||||
if (times[3] > 80e6) times[3]=0.0;
|
||||
if (times[5] > 80e6) times[5]=0.0;
|
||||
#endif
|
||||
@ -806,9 +808,8 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer<numtyp,acctyp> &ans,
|
||||
fprintf(screen,"--------------------------------\n");
|
||||
|
||||
if (time_device() && (times[3] > 0.0)) {
|
||||
if (times[0] > 0.0)
|
||||
fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/_replica_size);
|
||||
fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/_replica_size);
|
||||
if (times[0] > 0.0) fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/_replica_size);
|
||||
if (times[1] > 0.0) fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/_replica_size);
|
||||
if (nbor.gpu_nbor() > 0.0)
|
||||
fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/_replica_size);
|
||||
else
|
||||
@ -862,32 +863,34 @@ void DeviceT::output_kspace_times(UCL_Timer &time_in,
|
||||
double max_mb=mpi_max_bytes/(1024.0*1024.0);
|
||||
#ifdef USE_OPENCL
|
||||
// Workaround for timing issue on Intel OpenCL
|
||||
if (times[0] > 80e6) times[0]=0.0;
|
||||
if (times[1] > 80e6) times[1]=0.0;
|
||||
if (times[3] > 80e6) times[3]=0.0;
|
||||
if (times[5] > 80e6) times[5]=0.0;
|
||||
#endif
|
||||
|
||||
|
||||
if (replica_me()==0)
|
||||
if (screen && times[6]>0.0) {
|
||||
if (screen && (times[6] > 0.0)) {
|
||||
fprintf(screen,"\n\n-------------------------------------");
|
||||
fprintf(screen,"--------------------------------\n");
|
||||
fprintf(screen," Device Time Info (average) for kspace: ");
|
||||
fprintf(screen,"\n-------------------------------------");
|
||||
fprintf(screen,"--------------------------------\n");
|
||||
|
||||
if (time_device() && times[3]>0) {
|
||||
fprintf(screen,"Data Out: %.4f s.\n",times[0]/_replica_size);
|
||||
fprintf(screen,"Data In: %.4f s.\n",times[1]/_replica_size);
|
||||
if (time_device() && (times[3] > 0.0)) {
|
||||
if (times[0] > 0.0) fprintf(screen,"Data Out: %.4f s.\n",times[0]/_replica_size);
|
||||
if (times[1] > 0.0) fprintf(screen,"Data In: %.4f s.\n",times[1]/_replica_size);
|
||||
fprintf(screen,"Kernel (map): %.4f s.\n",times[2]/_replica_size);
|
||||
fprintf(screen,"Kernel (rho): %.4f s.\n",times[3]/_replica_size);
|
||||
fprintf(screen,"Force interp: %.4f s.\n",times[4]/_replica_size);
|
||||
fprintf(screen,"Total rho: %.4f s.\n",
|
||||
(times[0]+times[2]+times[3])/_replica_size);
|
||||
fprintf(screen,"Total interp: %.4f s.\n",
|
||||
(times[1]+times[4])/_replica_size);
|
||||
fprintf(screen,"Force copy: %.4f s.\n",times[5]/_replica_size);
|
||||
if (times[0] > 0.0)
|
||||
fprintf(screen,"Total rho: %.4f s.\n", (times[0]+times[2]+times[3])/_replica_size);
|
||||
if (times[1] > 0.0)
|
||||
fprintf(screen,"Total interp: %.4f s.\n", (times[1]+times[4])/_replica_size);
|
||||
if (times[5] > 0.0) fprintf(screen,"Force copy: %.4f s.\n",times[5]/_replica_size);
|
||||
fprintf(screen,"Total: %.4f s.\n",
|
||||
(times[0]+times[1]+times[2]+times[3]+times[4]+times[5])/
|
||||
_replica_size);
|
||||
(times[0]+times[1]+times[2]+times[3]+times[4]+times[5])/_replica_size);
|
||||
}
|
||||
fprintf(screen,"CPU Poisson: %.4f s.\n",times[6]/_replica_size);
|
||||
fprintf(screen,"CPU Data Cast: %.4f s.\n",times[8]/_replica_size);
|
||||
|
||||
@ -257,7 +257,7 @@ __kernel void k_lj_tip4p_reneigh(
|
||||
}
|
||||
if (i<inum && itype == typeH) {
|
||||
if (hneigh[i*4+2] != -1) {
|
||||
int iI, iH;
|
||||
int iI;
|
||||
iI = atom_mapping(map,tag[i] - 1);
|
||||
iO = closest_image(i,iI,sametag, x_);
|
||||
numtyp4 iIx; fetch4(iIx,iO,pos_tex); //x_[iI];
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
! ------------ ----------------------------------------------------------
|
||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! https://www.lammps.org/ Sandia National Laboratories
|
||||
! Steve Plimpton, sjplimp@sandia.gov
|
||||
! LAMMPS development team: developers@lammps.org
|
||||
!
|
||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
|
||||
|
||||
# settings
|
||||
|
||||
version = "2.7.4"
|
||||
version = "2.8.1"
|
||||
mode = "static"
|
||||
|
||||
# help message
|
||||
@ -58,7 +58,9 @@ checksums = { \
|
||||
'2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \
|
||||
'2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \
|
||||
'2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \
|
||||
'2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \
|
||||
'2.8.0' : '489b23daba70da78cf0506cbc31689c6', \
|
||||
'2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
|
||||
}
|
||||
|
||||
# parse and process arguments
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# Pizza.py toolkit, https://lammps.github.io/pizza
|
||||
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories
|
||||
#
|
||||
# Copyright (2005) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# Pizza.py toolkit, https://lammps.github.io/pizza
|
||||
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories
|
||||
#
|
||||
# Copyright (2005) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# Pizza.py toolkit, https://lammps.github.io/pizza
|
||||
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories
|
||||
#
|
||||
# Copyright (2005) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
@ -265,6 +265,7 @@ class lammps(object):
|
||||
|
||||
self.lib.lammps_encode_image_flags.restype = self.c_imageint
|
||||
|
||||
self.lib.lammps_config_has_package.argtypes = [c_char_p]
|
||||
self.lib.lammps_config_package_name.argtypes = [c_int, c_char_p, c_int]
|
||||
self.lib.lammps_config_accelerator.argtypes = [c_char_p, c_char_p, c_char_p]
|
||||
|
||||
@ -1627,6 +1628,23 @@ class lammps(object):
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def has_package(self, name):
|
||||
""" Report if the named package has been enabled in the LAMMPS shared library.
|
||||
|
||||
This is a wrapper around the :cpp:func:`lammps_config_has_package`
|
||||
function of the library interface.
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
:param name: name of the package
|
||||
:type name: string
|
||||
|
||||
:return: state of package availability
|
||||
:rtype: bool
|
||||
"""
|
||||
return self.lib.lammps_config_has_package(name.encode()) != 0
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
@property
|
||||
def accelerator_config(self):
|
||||
""" Return table with available accelerator configuration settings.
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -10,15 +10,15 @@ import warnings
|
||||
py_ver = sysconfig.get_config_vars('VERSION')[0]
|
||||
OS_name = platform.system()
|
||||
|
||||
if OS_name == "Linux":
|
||||
SHLIB_SUFFIX = '.so'
|
||||
library = 'libpython' + py_ver + SHLIB_SUFFIX
|
||||
elif OS_name == "Darwin":
|
||||
if OS_name == "Darwin":
|
||||
SHLIB_SUFFIX = '.dylib'
|
||||
library = 'libpython' + py_ver + SHLIB_SUFFIX
|
||||
elif OS_name == "Windows":
|
||||
SHLIB_SUFFIX = '.dll'
|
||||
library = 'python' + py_ver + SHLIB_SUFFIX
|
||||
else:
|
||||
SHLIB_SUFFIX = '.so'
|
||||
library = 'libpython' + py_ver + SHLIB_SUFFIX
|
||||
|
||||
try:
|
||||
pylib = ctypes.CDLL(library)
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# LAMMPS Development team: developers@lammps.org
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -46,8 +46,8 @@ else:
|
||||
setup(
|
||||
name = "lammps",
|
||||
version = get_lammps_version(),
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
author = "The LAMMPS Developers",
|
||||
author_email = "developers@lammps.org",
|
||||
url = "https://www.lammps.org",
|
||||
project_urls = {
|
||||
"Bug Tracker": "https://github.com/lammps/lammps/issues",
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user