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Merge branch 'lammps:develop' into compute-pace-update

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This commit is contained in:
jmgoff
2023-08-24 16:47:28 -06:00
committed by GitHub
parent 0a5aa5b1d2 dc3c8da52b
commit d54fb3eb47
1655 changed files with 73086 additions and 94589 deletions
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2
.github/CONTRIBUTING.md vendored
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@ -1,6 +1,6 @@
# Contributing to LAMMPS via GitHub
Thank your for considering to contribute to the LAMMPS software project.
Thank you for considering to contribute to the LAMMPS software project.
The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.

3
.gitignore vendored
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@ -57,3 +57,6 @@ out/x86
out/x64
src/Makefile.package-e
src/Makefile.package.settings-e
/cmake/build/x64-Debug-Clang
/install/x64-GUI-MSVC
/install

106
cmake/CMakeLists.txt
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@ -1,8 +1,9 @@
# -*- CMake -*- master configuration file for building LAMMPS
########################################
# CMake build system
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.10)
cmake_minimum_required(VERSION 3.16)
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
@ -12,22 +13,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
########################################
# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
if(CMAKE_VERSION VERSION_LESS 3.12)
unset(CONFIGURE_DEPENDS)
else()
set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
endif()
########################################
project(lammps CXX)
@ -136,15 +126,15 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
endif()
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@ -155,6 +145,7 @@ if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
@ -192,6 +183,7 @@ option(BUILD_SHARED_LIBS "Build shared library" OFF)
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
@ -202,8 +194,8 @@ else()
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
add_library(lammps ${ALL_SOURCES})
@ -277,8 +269,6 @@ set(STANDARD_PACKAGES
MOFFF
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
ORIENT
PERI
@ -384,15 +374,9 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
if(LAMMPS_EXCEPTIONS)
target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
endif()
# "hard" dependencies between packages resulting
# in an error instead of skipping over files
pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(SCAFACOS MPI)
@ -403,6 +387,7 @@ pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -440,14 +425,14 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
file(GLOB LINALG_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
add_library(linalg STATIC ${LINALG_SOURCES})
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
@ -465,12 +450,7 @@ option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
if(WITH_JPEG)
find_package(JPEG REQUIRED)
target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
if(CMAKE_VERSION VERSION_LESS 3.12)
target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE JPEG::JPEG)
endif()
endif()
find_package(PNG QUIET)
@ -520,7 +500,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM MSCG COMPRESS ML-PACE LEPTON)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -582,8 +562,8 @@ endforeach()
foreach(PKG ${STANDARD_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -599,19 +579,12 @@ foreach(PKG ${STANDARD_PACKAGES})
RegisterPackages(${${PKG}_SOURCES_DIR})
endforeach()
# packages that need defines set
foreach(PKG MPIIO)
if(PKG_${PKG})
target_compile_definitions(lammps PRIVATE -DLMP_${PKG})
endif()
endforeach()
# dedicated check for entire contents of accelerator packages
foreach(PKG ${SUFFIX_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -625,7 +598,7 @@ endforeach()
foreach(PKG_LIB POEMS ATC AWPMD H5MD)
if(PKG_${PKG_LIB})
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
file(GLOB_RECURSE ${PKG_LIB}_SOURCES CONFIGURE_DEPENDS
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
@ -795,9 +768,11 @@ include(Tools)
include(Documentation)
###############################################################################
# Install potential and force field files in data directory
# Install bench, potential and force field files in data directory
###############################################################################
set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_DATADIR}/lammps)
install(DIRECTORY ${LAMMPS_DIR}/bench DESTINATION ${LAMMPS_INSTALL_DATADIR})
install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
if(BUILD_TOOLS)
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
@ -818,20 +793,11 @@ install(
# This is primarily for people that only want to use the Python wrapper.
###############################################################################
if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
else()
@ -890,13 +856,23 @@ else()
endif()
include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
OUTPUT_VARIABLE GIT_DESCRIBE
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
message(STATUS "<<< Build configuration >>>
LAMMPS Version: ${PROJECT_VERSION}
LAMMPS Version: ${PROJECT_VERSION} ${GIT_DESCRIBE}
Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
CMake Version: ${CMAKE_VERSION}
Build type: ${LAMMPS_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
if(CMAKE_CROSSCOMPILING)
message(STATUS "Cross compiling on ${CMAKE_HOST_SYSTEM}")
endif()
###############################################################################
# Print package summary
###############################################################################
@ -940,11 +916,9 @@ if(_index GREATER -1)
endif()
message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}")
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
get_target_property(OPTIONS lammps LINK_OPTIONS)
if(OPTIONS)
get_target_property(OPTIONS lammps LINK_OPTIONS)
if(OPTIONS)
message(STATUS "Linker options: ${OPTIONS}")
endif()
endif()
if(CMAKE_EXE_LINKER_FLAGS)
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
@ -1025,6 +999,14 @@ endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)
message(STATUS "Loading LAMMPS library as plugin at run time")
else()
message(STATUS "Linking LAMMPS library at compile time")
endif()
endif()
if(ENABLE_TESTING)
message(STATUS "<<< Building Unit Tests >>>")
if(ENABLE_COVERAGE)

53
cmake/CMakeSettings.json
View File

@ -63,6 +63,11 @@
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_LAMMPS_GUI",
"value": "False",
"type": "BOOL"
}
]
},
@ -303,6 +308,54 @@
"type": "STRING"
}
]
},
{
"name": "x64-GUI-MSVC",
"generator": "Ninja",
"configurationType": "Release",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -D QT_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5 -D Qt5_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5",
"buildCommandArgs": "",
"ctestCommandArgs": "-V",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "False",
"type": "BOOL"
},
{
"name": "BUILD_MPI",
"value": "False",
"type": "BOOL"
},
{
"name": "WITH_PNG",
"value": "False",
"type": "BOOL"
},
{
"name": "BUILD_LAMMPS_GUI",
"value": "True",
"type": "BOOL"
}
]
}
]
}

16
cmake/Modules/CodingStandard.cmake
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@ -1,19 +1,11 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python3_VERSION ${PYTHON_VERSION_STRING})
endif()
else()
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.5)
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 COMPONENTS Interpreter QUIET)
endif()
find_package(Python3 COMPONENTS Interpreter)
if(Python3_EXECUTABLE)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .

12
cmake/Modules/Documentation.cmake
View File

@ -5,10 +5,6 @@ option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
# Current Sphinx versions require at least Python 3.8
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.8 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
else()
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
@ -18,11 +14,9 @@ if(BUILD_DOC)
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
endif()
find_package(Doxygen 1.8.10 REQUIRED)
file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command(
OUTPUT docenv
@ -80,7 +74,7 @@ if(BUILD_DOC)
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
file(GLOB MATHJAX_VERSION_DIR CONFIGURE_DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
endif()

12
cmake/Modules/FindClangFormat.cmake
View File

@ -1,5 +1,7 @@
# Find clang-format
find_program(ClangFormat_EXECUTABLE NAMES clang-format
clang-format-17.0
clang-format-16.0
clang-format-15.0
clang-format-14.0
clang-format-13.0
@ -19,7 +21,7 @@ if(ClangFormat_EXECUTABLE)
OUTPUT_VARIABLE clang_format_version
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
# Arch Linux output:
# clang-format version 10.0.0
#
@ -32,9 +34,15 @@ if(ClangFormat_EXECUTABLE)
# Ubuntu 22.04 LTS output:
# Ubuntu clang-format version 14.0.0-1ubuntu1
#
# Debian 11 output:
# Debian clang-format version 11.0.1-2
#
# Debian 12 output:
# Debian clang-format version 14.0.6
#
# Fedora 36 output:
# clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
"\\2"
ClangFormat_VERSION
"${clang_format_version}")

10
cmake/Modules/FindCythonize.cmake
View File

@ -7,15 +7,7 @@
# adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
#=============================================================================
if(CMAKE_VERSION VERSION_LESS 3.12)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python 3.6 COMPONENTS Interpreter QUIET)
endif()
find_package(Python 3.6 COMPONENTS Interpreter QUIET)
# Use the Cython executable that lives next to the Python executable
# if it is a local installation.

5
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -28,10 +28,9 @@ if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
endif()
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
@ -65,7 +64,7 @@ endfunction(validate_option)
# helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable)
file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
file(GLOB _dirs CONFIGURE_DEPENDS ${path})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})

6
cmake/Modules/LAMMPSUtils.cmake
View File

@ -41,7 +41,7 @@ endfunction()
# helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable)
file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
file(GLOB _dirs CONFIGURE_DEPENDS ${path})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})
@ -80,8 +80,8 @@ endfunction()
function(check_for_autogen_files source_dir)
message(STATUS "Running check for auto-generated files from make-based build system")
file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
foreach(_SRC ${SRC_AUTOGEN_FILES})

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

@ -1,6 +1,6 @@
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB COLVARS_SOURCES CONFIGURE_DEPENDS ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)

18
cmake/Modules/Packages/GPU.cmake
View File

@ -39,7 +39,7 @@ if (PKG_AMOEBA)
${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
endif()
file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(GLOB GPU_LIB_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
@ -64,11 +64,13 @@ if(GPU_API STREQUAL "CUDA")
endif()
set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
endif()
option(CUDA_BUILD_MULTIARCH "Enable building CUDA kernels for all supported GPU architectures" ON)
mark_as_advanced(GPU_BUILD_MULTIARCH)
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if(GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
@ -78,21 +80,22 @@ if(GPU_API STREQUAL "CUDA")
"########################################################################")
endif()
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
file(GLOB GPU_LIB_CUDPP_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
if(CUDA_BUILD_MULTIARCH)
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
@ -145,6 +148,7 @@ if(GPU_API STREQUAL "CUDA")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
endif()
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
@ -201,7 +205,7 @@ elseif(GPU_API STREQUAL "OPENCL")
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@ -331,7 +335,7 @@ elseif(GPU_API STREQUAL "HIP")
endif()
endif()
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
set(GPU_LIB_CU_HIP "")

5
cmake/Modules/Packages/KIM.cmake
View File

@ -1,12 +1,7 @@
set(KIM-API_MIN_VERSION 2.1.3)
find_package(CURL)
if(CURL_FOUND)
if(CMAKE_VERSION VERSION_LESS 3.12)
target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
mark_as_advanced(LMP_DEBUG_CURL)

15
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -1,7 +1,8 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
if(CMAKE_CXX_STANDARD LESS 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
# As of version 4.0.0 Kokkos requires C++17
if(CMAKE_CXX_STANDARD LESS 17)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to
be set to at least C++17")
endif()
########################################################################
@ -49,8 +50,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "34d7860d548c06a4040236d959c9f99a" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -75,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.7.02 REQUIRED CONFIG)
find_package(Kokkos 4.1.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -155,7 +156,7 @@ if(PKG_ML-IAP)
# Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
file(GLOB MLIAP_KOKKOS_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

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

@ -4,7 +4,7 @@ if(LEPTON_SOURCE_DIR)
endif()
set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
file(GLOB LEPTON_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
@ -15,7 +15,7 @@ else()
endif()
if(LEPTON_ENABLE_JIT)
file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
file(GLOB ASMJIT_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
endif()
add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})

24
cmake/Modules/Packages/MDI.cmake
View File

@ -26,30 +26,10 @@ if(DOWNLOAD_MDI)
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
find_package(Python QUIET COMPONENTS Development)
if(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# python plugins are not supported and thus must be always off on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
unset(Python_Development_FOUND)
@ -102,13 +82,9 @@ if(DOWNLOAD_MDI)
# if compiling with python plugins we need
# to add python libraries as dependency.
if(MDI_USE_PYTHON_PLUGINS)
if(CMAKE_VERSION VERSION_LESS 3.12)
list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
else()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
endif()
# need to add support for dlopen/dlsym, except when compiling for Windows.
if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")

15
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -2,12 +2,7 @@
set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
if(PKG_PYTHON)
find_package(Cythonize QUIET)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
find_package(Python COMPONENTS NumPy QUIET)
else()
# assume we have NumPy
set(Python_NumPy_FOUND ON)
endif()
if(Cythonize_FOUND AND Python_NumPy_FOUND)
set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
endif()
@ -17,24 +12,16 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
find_package(Python COMPONENTS NumPy REQUIRED)
endif()
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()
if(CMAKE_VERSION VERSION_LESS 3.12)
if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
else()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
endif()
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)

28
cmake/Modules/Packages/MSCG.cmake
View File

@ -1,28 +0,0 @@
find_package(GSL REQUIRED)
find_package(MSCG QUIET)
if(MSGC_FOUND)
set(DOWNLOAD_MSCG_DEFAULT OFF)
else()
set(DOWNLOAD_MSCG_DEFAULT ON)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)
include(ExternalCMakeProject)
ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
# set include and link library
target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
target_link_libraries(lammps PRIVATE mscg)
else()
find_package(MSCG)
if(NOT MSCG_FOUND)
message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIR, or set DOWNLOAD_MSCG=ON to download it")
endif()
target_link_libraries(lammps PRIVATE MSCG::MSCG)
endif()
target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})

26
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,29 +1,11 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
else()
if(NOT Python_INTERPRETER)
if(NOT Python_INTERPRETER)
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

4
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -1,5 +1,5 @@
function(FindStyleHeaders path style_class file_pattern headers)
file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
get_property(hlist GLOBAL PROPERTY ${headers})
foreach(file_name ${files})
@ -187,7 +187,7 @@ endfunction(DetectBuildSystemConflict)
function(FindPackagesHeaders path style_class file_pattern headers)
file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
get_property(plist GLOBAL PROPERTY ${headers})
foreach(file_name ${files})

20
cmake/Modules/Testing.cmake
View File

@ -6,7 +6,7 @@ if(ENABLE_TESTING)
find_program(VALGRIND_BINARY NAMES valgrind)
# generate custom suppression file
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
file(GLOB VALGRIND_SUPPRESSION_FILES CONFIGURE_DEPENDS ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
file(READ ${SUPP} SUPPRESSIONS)
file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
@ -19,7 +19,7 @@ if(ENABLE_TESTING)
# we need to build and link a LOT of tester executables, so it is worth checking if
# a faster linker is available. requires GNU or Clang compiler, newer CMake.
# also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
@ -66,17 +66,9 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
@ -118,16 +110,8 @@ validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")

15
cmake/Modules/Tools.cmake
View File

@ -26,7 +26,7 @@ if(BUILD_TOOLS)
enable_language(C)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
file(GLOB MSI2LMP_SOURCES CONFIGURE_DEPENDS ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES})
if(STANDARD_MATH_LIB)
target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
@ -37,12 +37,13 @@ if(BUILD_TOOLS)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
find_package(PkgConfig QUIET)
if(BUILD_LAMMPS_SHELL)
if(NOT PkgConfig_FOUND)
message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
if(NOT LAMMPS_EXCEPTIONS)
message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
endif()
# include resource compiler to embed icons into the executable on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@ -67,4 +68,8 @@ if(BUILD_LAMMPS_SHELL)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()
if(BUILD_LAMMPS_GUI)
get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)
add_subdirectory(${LAMMPS_GUI_DIR} ${LAMMPS_GUI_BIN})
endif()

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34
cmake/packaging/MacOSXBundleInfo.plist.in Normal file
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@ -0,0 +1,34 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>CFBundleDevelopmentRegion</key>
<string>en-US</string>
<key>CFBundleExecutable</key>
<string>${MACOSX_BUNDLE_EXECUTABLE_NAME}</string>
<key>CFBundleDisplayName</key>
<string>The LAMMPS Molecular Dynamics Software</string>
<key>CFBundleIconFile</key>
<string>lammps</string>
<key>CFBundleIdentifier</key>
<string>org.lammps.gui</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundleLongVersionString</key>
<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
<key>CFBundleName</key>
<string>LAMMPS</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>
<string>${MACOSX_BUNDLE_SHORT_VERSION_STRING}</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleVersion</key>
<string>${MACOSX_BUNDLE_BUNDLE_VERSION}</string>
<key>CSResourcesFileMapped</key>
<true/>
<key>NSHumanReadableCopyright</key>
<string>${MACOSX_BUNDLE_COPYRIGHT}</string>
</dict>
</plist>

69
cmake/packaging/README.macos Normal file
View File

@ -0,0 +1,69 @@
LAMMPS and LAMMPS GUI universal binaries for macOS (arm64/x86_64)
=================================================================
This package provides universal binaries of LAMMPS and LAMMPS GUI that should
run on macOS systems running running macOS version 11 (Big Sur) or newer. Note
the binaries are compiled without MPI support and contain a compatible subset
of the available packages.
The following individual commands are included:
binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt
After copying the lammps-gui folder into your Applications folder, please follow
these steps:
1. Open the Terminal app
2. Type the following command and press ENTER:
open ~/.zprofile
This will open a text editor for modifying the .zprofile file in your home
directory.
3. Add the following lines to the end of the file, save it, and close the editor
LAMMPS_INSTALL_DIR=/Applications/LAMMPS.app/Contents
LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
PATH=${LAMMPS_INSTALL_DIR}/bin:$PATH
export LAMMPS_POTENTIALS LAMMPS_BENCH_DIR PATH
4. In your existing terminal, type the following command make the settings active
source ~/.zprofile
Note, you don't have to type this in new terminals, since they will apply
the changes from .zprofile automatically.
Note: the above assumes you use the default shell (zsh) that comes with
MacOS. If you customized MacOS to use a different shell, you'll need to modify
that shell's init file (.cshrc, .bashrc, etc.) instead with appropiate commands
to modify the same environment variables.
5. Try running LAMMPS (which might fail, see step 7)
lmp -in ${LAMMPS_BENCH_DIR}/in.lj
6. Try running the LAMMPS GUI
lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo
Depending on the size and resolution of your screen, the fonts may
be too small to read. This can be adjusted by setting the environment
variable QT_FONT_DPI. The default value would be 72, so to increase
the fonts by a third one can add to the .zprofile file the line
export QT_FONT_DPI=96
and reload as shown above.
7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt)
MacOS will likely block the initial run of the executables, since they
were downloaded from the internet and are missing a known signature from an
identified developer. Go to "Settings" and search for "Security settings". It
should display a message that an executable like "lmp" was blocked. Press
"Open anyway", which might prompt you for your admin credentials. Afterwards
"lmp" and the other executables should work as expected.

77
cmake/packaging/build_linux_tgz.sh Executable file
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@ -0,0 +1,77 @@
#!/bin/bash
APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
echo "Remove debug info"
for s in ${DESTDIR}/bin/* ${DESTDIR}/lib/liblammps*
do \
test -f $s && strip --strip-debug $s
done
echo "Remove libc, gcc, and X11 related shared libs"
rm -f ${DESTDIR}/lib/ld*.so ${DESTDIR}/lib/ld*.so.[0-9]
rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}.so.?
rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}-[0-9].[0-9]*.so
rm -f ${DESTDIR}/lib/libX* ${DESTDIR}/lib/libxcb*
rm -f ${DESTDIR}/lib/libgcc_s*
rm -f ${DESTDIR}/lib/libstdc++*
# get qt dir
QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
EOF
# platform plugin
mkdir -p ${DESTDIR}/qt5plugins/platforms
cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
# get platform plugin dependencies
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
for dep in ${QTDEPS}
do \
cp ${dep} ${DESTDIR}/lib
done
echo "Add additional plugins for Qt"
for dir in styles imageformats
do \
cp -r ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
done
# get imageplugin dependencies
for s in ${DESTDIR}/qt5plugins/imageformats/*.so
do \
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
for dep in ${QTDEPS}
do \
cp ${dep} ${DESTDIR}/lib
done
done
echo "Set up wrapper script"
MYDIR=$(dirname "$0")
cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
for s in ${DESTDIR}/bin/*
do \
EXE=$(basename $s)
test ${EXE} = linux_wrapper.sh && continue
test ${EXE} = qt.conf && continue
ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
done
pushd ..
tar -czvvf LAMMPS-Linux-amd64.tar.gz LAMMPS_GUI
popd
echo "Cleanup dir"
rm -r ${DESTDIR}
exit 0

111
cmake/packaging/build_macos_dmg.sh Executable file
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@ -0,0 +1,111 @@
#!/bin/bash
APP_NAME=lammps-gui
echo "Delete old files, if they exist"
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS-macOS-multiarch.dmg
echo "Create initial dmg file with macdeployqt"
macdeployqt lammps-gui.app -dmg
echo "Create writable dmg file"
hdiutil convert ${APP_NAME}.dmg -format UDRW -o ${APP_NAME}-rw.dmg
echo "Mount writeable DMG file in read-write mode. Keep track of device and volume names"
DEVICE=$(hdiutil attach -readwrite -noverify ${APP_NAME}-rw.dmg | grep '^/dev/' | sed 1q | awk '{print $1}')
VOLUME=$(df | grep ${DEVICE} | sed -e 's/^.*\(\/Volumes\/\)/\1/')
sleep 2
echo "Create link to Application folder and move README and background image files"
pushd "${VOLUME}"
ln -s /Applications .
mv ${APP_NAME}.app/Contents/Resources/README.txt .
mkdir .background
mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
mv ${APP_NAME}.app LAMMPS.app
cd LAMMPS.app/Contents
echo "Attach icons to LAMMPS console and GUI executables"
echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o bin/lmp
SetFile -a C bin/lmp
Rez -a icon.rsrc -o MacOS/lammps-gui
SetFile -a C MacOS/lammps-gui
rm icon.rsrc
popd
echo 'Tell the Finder to resize the window, set the background,'
echo 'change the icon size, place the icons in the right position, etc.'
echo '
tell application "Finder"
tell disk "'${APP_NAME}'"
-- wait for the image to finish mounting
set open_attempts to 0
repeat while open_attempts < 4
try
open
delay 1
set open_attempts to 5
close
on error errStr number errorNumber
set open_attempts to open_attempts + 1
delay 10
end try
end repeat
delay 5
-- open the image the first time and save a .DS_Store
-- just the background and icon setup
open
set current view of container window to icon view
set theViewOptions to the icon view options of container window
set background picture of theViewOptions to file ".background:background.png"
set arrangement of theViewOptions to not arranged
set icon size of theViewOptions to 64
delay 5
close
-- next set up the position of the app and Applications symlink
-- plus hide all window decorations
open
update without registering applications
tell container window
set sidebar width to 0
set statusbar visible to false
set toolbar visible to false
set the bounds to { 100, 40, 868, 640 }
set position of item "'LAMMPS'.app" to { 190, 216 }
set position of item "Applications" to { 576, 216 }
set position of item "README.txt" to { 190, 400 }
end tell
update without registering applications
delay 5
close
-- one last open and close to check the results
open
delay 5
close
end tell
delay 1
end tell
' | osascript
sync
echo "Unmount modified disk image and convert to compressed read-only image"
hdiutil detach "${DEVICE}"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS-macOS-multiarch.dmg"
echo "Attach icon to .dmg file"
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o LAMMPS-macOS-multiarch.dmg
SetFile -a C LAMMPS-macOS-multiarch.dmg
rm icon.rsrc
echo "Delete temporary disk images"
rm -f "${APP_NAME}-rw.dmg"
rm -f "${APP_NAME}.dmg"
exit 0

64
cmake/packaging/build_windows_cross_zip.sh Executable file
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@ -0,0 +1,64 @@
#!/bin/bash
APP_NAME=lammps-gui
DESTDIR=${PWD}/LAMMPS_GUI
SYSROOT="$1"
echo "Delete old files, if they exist"
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
# no static libs needed
rm -rvf ${DESTDIR}/lib
# but the LAMMPS lib
echo "Copying required DLL files"
for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
do \
doskip=0
for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
do \
test ${dll} = ${skip}.dll && doskip=1
done
test ${doskip} -eq 1 && continue
test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
done
echo "Copy required Qt plugins"
mkdir -p ${DESTDIR}/qt5plugins
for plugin in imageformats platforms styles
do \
cp -r ${SYSROOT}/lib/qt5/plugins/${plugin} ${DESTDIR}/qt5plugins/
done
echo "Check dependencies of DLL files"
for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
do \
doskip=0
for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
do \
test ${dll} = ${skip}.dll && doskip=1
done
test ${doskip} -eq 1 && continue
test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
done
for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
do \
doskip=0
for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
do \
test ${dll} = ${skip}.dll && doskip=1
done
test ${doskip} -eq 1 && continue
test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
done
cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
EOF
zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI

28
cmake/packaging/build_windows_vs.cmake Normal file
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@ -0,0 +1,28 @@
# CMake script to be run post installation to build zipped package
# clean up old zipfile and deployment tree
file(REMOVE LAMMPS-Win10-amd64.zip)
file(REMOVE_RECURSE LAMMPS_GUI)
file(RENAME ${INSTNAME} LAMMPS_GUI)
# move all executables and dlls to main folder and delete bin folder
file(GLOB BINFILES LIST_DIRECTORIES FALSE LAMMPS_GUI/bin/*.exe LAMMPS_GUI/bin/*.dll)
foreach(bin ${BINFILES})
get_filename_component(exe ${bin} NAME)
file(RENAME ${bin} LAMMPS_GUI/${exe})
endforeach()
file(REMOVE_RECURSE LAMMPS_GUI/bin)
# create qt.conf so Qt will find its plugins
file(WRITE LAMMPS_GUI/qt.conf "[Paths]\r\nPlugins = qt5plugins\r\n")
# initialize environment and then run windeployqt to populate folder with missing dependencies and Qt plugins
file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r\nset PATH=${QT5_BIN_DIR};%PATH%\r\nwindeployqt --plugindir LAMMPS_GUI/qt5plugins --release LAMMPS_GUI/lammps-gui.exe --no-quick-import --no-webkit2 --no-translations --no-system-d3d-compiler --no-angle --no-opengl-sw\r\n")
execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
file(REMOVE qtdeploy.bat)
# create zip archive
file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS-Win10-amd64.zip")
execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
file(REMOVE makearchive.ps1)
file(REMOVE_RECURSE LAMMPS_GUI)

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18
cmake/packaging/linux_wrapper.sh Executable file
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@ -0,0 +1,18 @@
#!/bin/sh
# wrapper for bundled executables
# reset locale to avoid problems with decimal numbers
export LC_ALL=C
BASEDIR=$(dirname "$0")
EXENAME=$(basename "$0")
# append to LD_LIBRARY_PATH to prefer local (newer) libs
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
# set some environment variables for LAMMPS etc.
LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
exec "${BASEDIR}/bin/${EXENAME}" "$@"

30
cmake/packaging/png2iconset.sh Executable file
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@ -0,0 +1,30 @@
#!/bin/sh
if [ $# != 2 ]
then
echo "usage: $0 <pngfile> <iconset name>"
exit 1
fi
png="$1"
ico="$2"
if [ ! -f ${png} ]
then
echo "PNG Image $1 not found"
fi
rm -rf ${ico}.iconset
mkdir ${ico}.iconset
sips -z 16 16 ${png} --out ${ico}.iconset/icon_16x16.png
sips -z 32 32 ${png} --out ${ico}.iconset/icon_16x16@2x.png
sips -z 32 32 ${png} --out ${ico}.iconset/icon_32x32.png
sips -z 64 64 ${png} --out ${ico}.iconset/icon_32x32@2x.png
sips -z 128 128 ${png} --out ${ico}.iconset/icon_128x128.png
sips -z 256 256 ${png} --out ${ico}.iconset/icon_128x128@2x.png
sips -z 256 256 ${png} --out ${ico}.iconset/icon_256x256.png
sips -z 512 512 ${png} --out ${ico}.iconset/icon_256x256@2x.png
sips -z 512 512 ${png} --out ${ico}.iconset/icon_512x512.png
sips -z 1024 1024 ${png} --out ${ico}.iconset/icon_512x512@2x.png
iconutil -c icns ${ico}.iconset
rm -rf ${ico}.iconset

2
cmake/presets/all_off.cmake
View File

@ -63,8 +63,6 @@ set(ALL_PACKAGES
MOFFF
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
OPENMP
OPT

2
cmake/presets/all_on.cmake
View File

@ -65,8 +65,6 @@ set(ALL_PACKAGES
MOFFF
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
OPENMP
OPT

1
cmake/presets/download.cmake
View File

@ -9,7 +9,6 @@ endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)

14
cmake/presets/macos-multiarch.cmake Normal file
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@ -0,0 +1,14 @@
# preset that will build portable multi-arch binaries on macOS without MPI
set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE STRING "" FORCE)
set(CMAKE_OSX_DEPLOYMENT_TARGET 11.0 CACHE STRING "" FORCE)
set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)
set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE)

1
cmake/presets/mingw-cross.cmake
View File

@ -83,7 +83,6 @@ endforeach()
# these two packages require a full MPI implementation
if(BUILD_MPI)
set(PKG_MPIIO ON CACHE BOOL "" FORCE)
set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
endif()

2
cmake/presets/most.cmake
View File

@ -24,8 +24,8 @@ set(ALL_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX

2
cmake/presets/nolib.cmake
View File

@ -19,8 +19,6 @@ set(PACKAGES_WITH_LIB
ML-PACE
ML-QUIP
MOLFILE
MPIIO
MSCG
NETCDF
PLUMED
PYTHON

2
cmake/presets/windows.cmake
View File

@ -32,6 +32,7 @@ set(WIN_PACKAGES
INTERLAYER
KSPACE
LEPTON
MACHDYN
MANIFOLD
MANYBODY
MC
@ -45,6 +46,7 @@ set(WIN_PACKAGES
MOLECULE
MOLFILE
OPENMP
OPT
ORIENT
PERI
PHONON

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "15 June 2023" "2023-06-15"
.TH LAMMPS "1" "2 August 2023" "2023-08-2"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 15 June 2023
\- Molecular Dynamics Simulator. Version 2 August 2023
.SH SYNOPSIS
.B lmp

17
doc/src/Build_basics.rst
View File

@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
directory, or ``make`` from the ``src/STUBS`` dir. If the build
fails, you may need to edit the ``STUBS/Makefile`` for your
platform. The stubs library does not provide MPI/IO functions
required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
required by some LAMMPS packages, e.g. ``LATBOLTZ``,
and thus is not compatible with those packages.
.. note::
@ -128,14 +128,13 @@ and adds vectorization support when compiled with compatible compilers,
in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
package can be compiled to include OpenMP threading.
In addition, there are a few commands in LAMMPS that have native
OpenMP support included as well. These are commands in the ``MPIIO``,
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.
Furthermore, some packages support OpenMP threading indirectly through
the libraries they interface to: e.g. ``KSPACE``, and ``COLVARS``.
See the :doc:`Packages details <Packages_details>` page for more info
on these packages, and the pages for their respective commands for
OpenMP threading info.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the ``ML-SNAP``,
``DIFFRACTION``, and ``DPD-REACT`` packages. Furthermore, some packages
support OpenMP threading indirectly through the libraries they interface
to: e.g. ``KSPACE``, and ``COLVARS``. See the :doc:`Packages details
<Packages_details>` page for more info on these packages, and the pages
for their respective commands for OpenMP threading info.
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
and turn on their native OpenMP support and turn on their native OpenMP

16
doc/src/Build_cmake.rst
View File

@ -16,8 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
.. note::
LAMMPS currently requires that CMake version 3.10 or later is available;
version 3.12 or later is preferred.
LAMMPS currently requires that CMake version 3.16 or later is available.
.. warning::
@ -34,19 +33,18 @@ Advantages of using CMake
^^^^^^^^^^^^^^^^^^^^^^^^^
CMake is an alternative to compiling LAMMPS in the traditional way
through :doc:`(manually customized) makefiles <Build_make>` and a recent
addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL)
and Richard Berger (Temple U). Using CMake has multiple advantages that
are specifically helpful for people with limited experience in compiling
software or for people that want to modify or extend LAMMPS.
through :doc:`(manually customized) makefiles <Build_make>`. Using
CMake has multiple advantages that are specifically helpful for
people with limited experience in compiling software or for people
that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly.
- CMake can generate files for different build tools and integrated
development environments (IDE).
- CMake supports customization of settings with a command line, text
mode, or graphical user interface. No knowledge of file formats or
complex command line syntax is required.
mode, or graphical user interface. No manual editing of files,
knowledge of file formats or complex command line syntax is required.
- All enabled components are compiled in a single build operation.
- Automated dependency tracking for all files and configuration options.
- Support for true out-of-source compilation. Multiple configurations

130
doc/src/Build_extras.rst
View File

@ -52,7 +52,6 @@ This is the list of packages that may require additional steps.
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`
@ -140,6 +139,8 @@ CMake build
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU architectures
# value = yes (default) or no
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
# value = yes (default) or no
@ -158,41 +159,49 @@ CMake build
A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
CMake can detect which version of the CUDA toolkit is used and thus will try
to include support for **all** major GPU architectures supported by this toolkit.
Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather
than having to wait for the JIT compiler of the CUDA driver to translate
it. This behavior can be turned off (e.g. to speed up compilation) by
setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
is required and a GPU architecture of Kepler or later, which must *also* be
supported by the CUDA toolkit in use **and** the CUDA driver in use.
When compiling for OpenCL, OpenCL version 1.2 or later is required and the
GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later,
which must *also* be supported by the CUDA toolkit in use **and** the
CUDA driver in use. When compiling for OpenCL, OpenCL version 1.2 or
later is required and the GPU must be supported by the GPU driver and
OpenCL runtime bundled with the driver.
When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
When building with CMake, you **must NOT** build the GPU library in
``lib/gpu`` using the traditional build procedure. CMake will detect
files generated by that process and will terminate with an error and a
suggestion for how to remove them.
If you are compiling for OpenCL, the default setting is to download, build, and
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling for OpenCL, the default setting is to download,
build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This way no local OpenCL development headers or library
needs to be present and only OpenCL compatible drivers need to be
installed to use OpenCL. If this is not desired, you can set
:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
The GPU library has some multi-thread support using OpenMP. If LAMMPS is built
with ``-D BUILD_OMP=on`` this will also be enabled.
The GPU library has some multi-thread support using OpenMP. If LAMMPS
is built with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
If you are compiling with HIP, note that before running CMake you will
have to set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
necessary for :code:`hipcc` and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
.. code:: bash
@ -629,6 +638,12 @@ They must be specified in uppercase.
* - VEGA90A
- GPU
- AMD GPU MI200 GFX90A
* - NAVI1030
- GPU
- AMD GPU V620/W6800
* - NAVI1100
- GPU
- AMD GPU RX7900XTX
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
@ -651,7 +666,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 3.7.1 of the Kokkos library.
This list was last updated for version 4.0.1 of the Kokkos library.
.. tabs::
@ -921,59 +936,6 @@ Python version 3.6 or later.
----------
.. _mscg:
MSCG package
-----------------------
To build with this package, you must download and build the MS-CG
library. Building the MS-CG library requires that the GSL
(GNU Scientific Library) headers and libraries are installed on your
machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for
more details.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location)
If ``DOWNLOAD_MSCG`` is set, the MSCG library will be downloaded
and built inside the CMake build directory. If the MSCG library
is already on your system (in a location CMake cannot find it),
``MSCG_LIBRARY`` is the filename (plus path) of the MSCG library
file, not the directory the library file is in.
``MSCG_INCLUDE_DIR`` is the directory the MSCG include file is in.
.. tab:: Traditional make
You can download and build the MS-CG library manually if you
prefer; follow the instructions in ``lib/mscg/README``\ . You can
also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invokes the
``lib/mscg/Install.py`` script with the specified args:
.. code-block:: bash
make lib-mscg # print help message
make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial"
make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi"
make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
will be created in ``lib/mscg`` to point to the MS-CG
``src/installation`` dir. When LAMMPS is built in src it will use
these links. You should not need to edit the
``lib/mscg/Makefile.lammps`` file.
----------
.. _opt:
OPT package

1
doc/src/Build_package.rst
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@ -55,7 +55,6 @@ packages:
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`

26
doc/src/Build_settings.rst
View File

@ -459,27 +459,13 @@ those systems:
.. _exceptions:
Exception handling when using LAMMPS as a library
------------------------------------------------------------------
-------------------------------------------------
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions thrown from within LAMMPS.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS <other LMP_INC settings>
LAMMPS errors do not kill the calling code, but throw an exception. In
the C-library interface, the call stack is unwound and control returns
to the caller, e.g. to Python or a code that is coupled to LAMMPS and
the error status can be queried. When using C++ directly, the calling
code has to be set up to *catch* exceptions thrown from within LAMMPS.
.. note::

1
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@ -91,6 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`composition/atom (k) <compute_composition_atom>`
* :doc:`mliap <compute_mliap>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`

4
doc/src/Commands_dump.rst
View File

@ -23,17 +23,14 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`grid <dump>`
@ -51,7 +48,6 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

1
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@ -116,7 +116,6 @@ OPT.
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
* :doc:`msst <fix_msst>`
* :doc:`mvv/dpd <fix_mvv_dpd>`
* :doc:`mvv/edpd <fix_mvv_dpd>`

29
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@ -85,6 +85,35 @@ The same functionality is available through
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
MPIIO package
-------------
.. deprecated:: TBD
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
had been applied to the corresponding non-MPIIO commands. As a
consequence the MPIIO commands had become unreliable and sometimes
crashing LAMMPS or corrupting data. Similar functionality is available
through the :ref:`ADIOS package <PKG-ADIOS>` and the :ref:`NETCDF
package <PKG-NETCDF>`. Also, the :doc:`dump_modify nfile or dump_modify
fileper <dump_modify>` keywords may be used for an efficient way of
writing out dump files when running on large numbers of processors.
Similarly, the "nfile" and "fileper" keywords exist for restarts:
see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
:doc:`write_restart <write_restart>`.
MSCG package
------------
.. deprecated:: TBD
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software
<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
University of Chicago, which can be used independent from LAMMPS.
REAX package
------------

4
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@ -92,8 +92,8 @@ Arguments for these methods can be values returned by the
*setup_grid()* method (described below), which define the extent of
the grid cells (owned+ghost) the processor owns. These 4 methods
allocate memory for 2d (first two) and 3d (second two) grid data. The
two methods that end in "_one" allocate an array which stores a single
value per grid cell. The two that end in "_multi" allocate an array
two methods that end in "_offset" allocate an array which stores a single
value per grid cell. The two that end in "_last" allocate an array
which stores *Nvalues* per grid cell.
.. code-block:: c++

6
doc/src/Errors_messages.rst
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@ -7148,9 +7148,6 @@ keyword to allow for additional bonds to be formed
*Read_dump xyz fields do not have consistent scaling/wrapping*
Self-explanatory.
*Reading from MPI-IO filename when MPIIO package is not installed*
Self-explanatory.
*Reax_defs.h setting for NATDEF is too small*
Edit the setting in the ReaxFF library and re-compile the
library and re-build LAMMPS.
@ -8489,9 +8486,6 @@ keyword to allow for additional bonds to be formed
The write_restart command cannot be used before a read_data,
read_restart, or create_box command.
*Writing to MPI-IO filename when MPIIO package is not installed*
Self-explanatory.
*Zero length rotation vector with displace_atoms*
Self-explanatory.

2
doc/src/Examples.rst
View File

@ -104,8 +104,6 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| min | energy minimization of 2d LJ melt |
+-------------+------------------------------------------------------------------+
| mscg | parameterize a multi-scale coarse-graining (MSCG) model |
+-------------+------------------------------------------------------------------+
| msst | MSST shock dynamics |
+-------------+------------------------------------------------------------------+
| multi | multi neighboring for systems with large interaction disparities |

20
doc/src/Fortran.rst
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@ -2278,19 +2278,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. versionadded:: 3Nov2022
In case of an error, LAMMPS will either abort or throw a C++ exception.
The latter has to be :ref:`enabled at compile time <exceptions>`.
This function checks if exceptions were enabled.
When using the library interface with C++ exceptions enabled, the library
interface functions will "catch" them, and the error status can then be
checked by calling :f:func:`has_error`. The most recent error message can be
retrieved via :f:func:`get_last_error_message`.
This can allow one to restart a calculation or delete and recreate
the LAMMPS instance when a C++ exception occurs. One application
of using exceptions this way is the :ref:`lammps_shell`. If C++
exceptions are disabled and an error happens during a call to
LAMMPS or the Fortran API, the application will terminate.
When using the library interface, the library interface functions
will "catch" exceptions, and then the error status can be checked by
calling :f:func:`has_error`. The most recent error message can be
retrieved via :f:func:`get_last_error_message`. This allows to
restart a calculation or delete and recreate the LAMMPS instance when
a C++ exception occurs. One application of using exceptions this way
is the :ref:`lammps_shell`.
:to: :cpp:func:`lammps_config_has_exceptions`
:r has_exceptions:

1
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@ -100,6 +100,7 @@ Tutorials howto
Howto_cmake
Howto_github
Howto_lammps_gui
Howto_pylammps
Howto_wsl

41
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@ -1,11 +1,11 @@
Using CMake with LAMMPS tutorial
================================
Using CMake with LAMMPS
=======================
The support for building LAMMPS with CMake is a recent addition to
LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard
Berger (Temple U). One of the key strengths of CMake is that it is not
tied to a specific platform or build system and thus generate the files
necessary to build and develop for different build systems and on
Berger (LANL). One of the key strengths of CMake is that it is not
tied to a specific platform or build system. Instead it generates the
files necessary to build and develop for different build systems and on
different platforms. Note, that this applies to the build system itself
not the LAMMPS code. In other words, without additional porting effort,
it is not possible - for example - to compile LAMMPS with Visual C++ on
@ -14,7 +14,7 @@ necessary to program LAMMPS as a project in integrated development
environments (IDE) like Eclipse, Visual Studio, QtCreator, Xcode,
CodeBlocks, Kate and others.
A second important feature of CMake is, that it can detect and validate
A second important feature of CMake is that it can detect and validate
available libraries, optimal settings, available support tools and so
on, so that by default LAMMPS will take advantage of available tools
without requiring to provide the details about how to enable/integrate
@ -32,8 +32,8 @@ program ``cmake`` (or ``cmake3``), a text mode interactive user
interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user
interface (GUI) program ``cmake-gui``. All of them are portable
software available on all supported platforms and can be used
interchangeably. The minimum supported CMake version is 3.10 (3.12 or
later is recommended).
interchangeably. As of LAMMPS version 2 August 2023, the minimum
required CMake version is 3.16.
All details about features and settings for CMake are in the `CMake
online documentation <https://cmake.org/documentation/>`_. We focus
@ -43,11 +43,20 @@ Prerequisites
-------------
This tutorial assumes that you are operating in a command-line environment
using a shell like Bash.
using a shell like Bash or Zsh.
- Linux: any Terminal window will work
- macOS: launch the Terminal application.
- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
- Linux: any Terminal window will work or text console
- macOS: launch the Terminal application
- Windows 10 or 11: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
- other Unix-like operating systems like FreeBSD
.. note::
It is also possible to use CMake on Windows 10 or 11 through either the Microsoft
Visual Studio IDE with the bundled CMake or from the Windows command prompt using
a separately installed CMake package, both using the native Microsoft Visual C++
compilers and (optionally) the Microsoft MPI SDK. This tutorial, however, only
covers unix-like command line interfaces.
We also assume that you have downloaded and unpacked a recent LAMMPS source code package
or used Git to create a clone of the LAMMPS sources on your compilation machine.
@ -338,8 +347,6 @@ Some common LAMMPS specific variables
- common compiler flags, for optimization or instrumentation (default:)
* - ``LAMMPS_MACHINE``
- when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
* - ``LAMMPS_EXCEPTIONS``
- when set to ``on`` errors will throw a C++ exception instead of aborting (default: ``off``)
* - ``FFT``
- select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
* - ``FFT_SINGLE``
@ -412,9 +419,9 @@ interface (``ccmake`` or ``cmake-gui``).
Using a preset to select a compiler package (``clang.cmake``,
``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
are an exception to the mechanism of updating the configuration incrementally,
as they will trigger a reset of cached internal CMake settings and thus
reset settings to their default values.
are an exception to the mechanism of updating the configuration
incrementally, as they will trigger a reset of cached internal CMake
settings and thus reset settings to their default values.
Compilation and build targets
-----------------------------

402
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@ -0,0 +1,402 @@
Using the LAMMPS GUI
====================
LAMMPS GUI is a simple graphical text editor that is linked to the
:ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run LAMMPS
directly using the contents of the editor's text buffer as input.
This is similar to what people traditionally would do to run LAMMPS:
using a regular text editor to edit the input and run the necessary
commands, possibly including the text editor, too, from a command line
terminal window. That is quite effective when running LAMMPS on
high-performance computing facilities and when you are very proficient
in using the command line. The main benefit of a GUI application is
that this integrates well with graphical desktop environments and many
basic tasks can be done directly from within the GUI without switching
to a text console or requiring external programs or scripts to extract
data from the generated output. This makes it easier for beginners to
get started running simple LAMMPS simulations and thus very suitable for
tutorials on LAMMPS. But also makes it easier to switch to a full
featured text editor and more sophisticated visualization and analysis
tools.
-----
The following text provides a detailed tour of the features and
functionality of the LAMMPS GUI. This document describes LAMMPS GUI
version 1.2.
Main window
-----------
When LAMMPS GUI starts, it will show the main window with either an
empty buffer, or have a file loaded. In the latter case it may look like
the following:
.. image:: JPG/lammps-gui-main.png
:align: center
:scale: 50%
There is the menu bar at the top, then the main editor buffer with the
input file contents in the center with line numbers on the left and the
input colored according to the LAMMPS input file syntax. At the bottom
is the status bar, which shows the status of LAMMPS execution on the
left ("Ready." when idle) and the current working directory on the
right. The size of the main window will be stored when exiting and
restored when starting again. The name of the current file in the
buffer is shown in the window title and the text `*modified*` is added
in case the buffer has modifications that are not yet saved to a file.
Opening Files
^^^^^^^^^^^^^
The LAMMPS GUI application will try to open the first command line
argument as input file, further arguments are ignored. When no
argument is given LAMMPS GUI will start with an empty buffer.
Files can also be opened via the ``File`` menu or by drag-and-drop
of a file from a file manager to the editor window. Only one
file can be open at a time, so opening a new file with a filled
buffer will close this buffer and in case the buffer has unsaved
modifications will ask to either cancel the load, discard the
changes or save them.
Running LAMMPS
^^^^^^^^^^^^^^
From within the LAMMPS GUI main window LAMMPS can be started either from
the ``Run`` menu, by the hotkey `Ctrl-Enter` (`Command-Enter` on macOS),
or by clicking on the green button in the status bar. LAMMPS runs in a
separate thread, so the GUI stays responsive and thus it is able to
interact with the calculation and access its data. It is important to
note, that LAMMPS is using the contents of the input buffer for the run,
**not** the file it was read from. If there are unsaved changes in the
buffer, they *will* be used.
.. image:: JPG/lammps-gui-running.png
:align: center
:scale: 75%
While LAMMPS is running, the contents of the status bar change: on the
left side there is a text indicating that LAMMPS is running, which will
contain the selected number of threads, if thread-parallel acceleration
was selected in the ``Preferences`` dialog. On the right side, a
progress bar is shown that displays the estimated progress on the
current :doc:`run command <run>`. Additionally, two windows will open:
the log window with the captured screen output and the chart window with
a line graph created from the thermodynamic output of the run.
The run can be stopped cleanly by using either the ``Stop LAMMPS`` entry
in the ``Run`` menu, the hotkey `Ctrl-/` (`Command-/` on macOS), or
clicking on the red button in the status bar. This will cause that the
running LAMMPS process will complete the current iteration and then
stop. This is equivalent to the command :doc:`timer timeout 0 <timer>`
and implemented by calling the :cpp:func:`lammps_force_timeout()`
function of the LAMMPS C-library interface.
Viewing Snapshot Images
^^^^^^^^^^^^^^^^^^^^^^^
By selecting the ``View Image`` entry in the ``Run`` menu, by hitting
the `Ctrl-I` (`Command-I` on macOS) hotkey or by clicking on the
"palette" button in the status bar, LAMMPS GUI will issue a
:doc:`write_dump image <dump_image>` command and read the resulting
snapshot image into an image viewer window. When possible, LAMMPS
GUI will try to detect which elements the atoms correspond to (via
their mass) and then colorize them accordingly. Otherwise just some
predefined sequence of colors are assigned to different atom types.
.. image:: JPG/lammps-gui-image.png
:align: center
:scale: 50%
The default image size, some default image quality settings, the view
style and some colors can be changed in the ``Preferences`` dialog
window. From the image viewer window further adjustments can be made:
actual image size, high-quality rendering, anti-aliasing, view style,
display of box or axes, zoom factor. The the image can be rotated
horizontally and vertically and it is possible to only display the atoms
within a predefined group (default is "all"). After each change, the
image is rendered again and the display updated. The small palette icon
on the top left will be colored while LAMMPS is running to render the
image and it will be grayed out again, when it is done. When there are
many items to show and high quality images with anti-aliasing are
requested, re-rendering can take several seconds. From the ``File``
menu, the shown image can be saved to a file permanently or copied into
the cut-n-paste buffer for pasting into another application.
Editor Functions
^^^^^^^^^^^^^^^^
The editor has most the usual functionality that similar programs have:
text selection via mouse or with cursor moves while holding the Shift
key, Cut, Copy, Paste, Undo, Redo. All of these editing functions are
available via hotkeys. When trying to exit the editor with a modified
buffer, a dialog will pop up asking whether to cancel the quit, or don't
save or save the buffer's contents to a file.
Context Specific Help
^^^^^^^^^^^^^^^^^^^^^
.. image:: JPG/lammps-gui-popup-help.png
:align: center
:scale: 50%
A unique feature of the LAMMPS GUI is the option to look up the
documentation for the command in the current line. This can be achieved
by either clicking the right mouse button or by using the `Ctrl-?`
hotkey. When clicking the mouse there are additional entries in the
context menu that will open the corresponding documentation page in the
online LAMMPS documentation. When using the hotkey, the first of those
entries will be chosen directly.
Menu
----
The menu bar the entries ``File``, ``Edit``, ``Run``, ``View``, and ``About``.
Instead of using the mouse to click on them, the individual menus can also
be activated by hitting the `Alt` key together with the corresponding underlined
letter, that is `Alt-f` will activate the ``File`` menu. For the corresponding
activated sub-menus, also the underlined letter, together with the `Alt` key can
be used to select instead of the mouse.
File
^^^^
The ``File`` menu offers the usual options:
- ``New`` will clear the current buffer and reset the file name to ``*unknown*``
- ``Open`` will open a dialog to select a new file
- ``Save`` will save the current file; if the file name is ``*unknown*``
a dialog will open to select a new file name
- ``Save As`` will open a dialog to select and new file name and save
the buffer to it
- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog
will appear to either cancel the quit, save or don't save the file.
In addition, up to 5 recent file names will be listed after the ``Open``
entry that allows to re-open recent files. This list is stored when
quitting and recovered when starting again.
Edit
^^^^
The ``Edit`` menu offers the usual editor functions like ``Undo``,
``Redo``, ``Cut``, ``Copy``, ``Paste``, but also offers to open the
``Preferences`` dialog and to delete all stored preferences so they
will be reset to their defaults.
Run
^^^
The ``Run`` menu allows to start and stop a LAMMPS process. Rather than
calling the LAMMPS executable as a separate executable, the LAMMPS GUI
is linked to the LAMMPS library and thus can run LAMMPS internally
through the :ref:`LAMMPS C-library interface <lammps_c_api>`.
Specifically, a LAMMPS instance will be created by calling
:cpp:func:`lammps_open_no_mpi` and then the buffer contents run by
calling :cpp:func:`lammps_commands_string`. Certain commands and
features are only available, after a LAMMPS instance is created. Its
presence is indicated by a small LAMMPS ``L`` logo in the status bar at
the bottom left of the main window.
The LAMMPS calculation will be run in a concurrent thread so that the
GUI will stay responsive and will be updated during the run. This can
be used to tell the running LAMMPS instance to stop at the next
timestep. The ``Stop LAMMPS`` entry will do this by calling
:cpp:func:`lammps_force_timeout`, which is equivalent to a :doc:`timer
timeout 0 <timer>` command.
The ``Set Variables`` entry will open a dialog box where :doc:`index style variables <variable>`
can be set. Those variables will be passed to the LAMMPS instance when
it is created and are thus set *before* a run is started.
.. image:: JPG/lammps-gui-variables.png
:align: center
:scale: 75%
The ``Set Variables`` dialog will be pre-populated with entries that are
set as index variables in the input and any variables that are used but
not defined as far as the built-in parser can detect them. New rows for
additional variables can be added through the ``Add Row`` button and
existing rows deleted by clicking on the ``X`` icons on the right.
The ``View Image`` entry will send a :doc:`dump image <dump_image>`
command to the LAMMPS instance, read the resulting file, and show it in
an ``Image Viewer`` window.
The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
with a :doc:`data file <write_data>` of the current state of the system.
This option is only available, if the LAMMPS GUI can find the OVITO
executable in the system path.
The ``View in VMD`` entry will instead launch VMD, also to load a
:doc:`data file <write_data>` of the current state of the system. This
option is only available, if the LAMMPS GUI can find the VMD executable
in the system path.
View
^^^^
The ``View`` menu offers to show or hide the three optional windows
with log output, graphs, or images. The default settings for those
can be changed in the ``Preferences dialog``.
About
^^^^^
The ``About`` menu finally offers a couple of dialog windows and an
option to launch the LAMMPS online documentation in a web browser. The
``About LAMMPS GUI`` entry displays a dialog with a summary of the
configuration settings of the LAMMPS library in use and the version
number of LAMMPS GUI itself. The ``Quick Help`` displays a dialog with
a minimal description of LAMMPS GUI. And ``LAMMPS Manual`` will open
the main page of this LAMMPS documentation at https://docs.lammps.org/.
Preferences
-----------
The ``Preferences`` dialog allows to customize some of the behavior
and looks of the LAMMPS GUI application. The settings are grouped
and each group is displayed within a tab.
.. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
:width: 25%
.. |guiprefs2| image:: JPG/lammps-gui-prefs-accel.png
:width: 25%
.. |guiprefs3| image:: JPG/lammps-gui-prefs-image.png
:width: 25%
|guiprefs1| |guiprefs2| |guiprefs3|
General Settings:
^^^^^^^^^^^^^^^^^
- *Echo input to log:* when checked, all input commands, including
variable expansions, will be echoed to the log window. This is
equivalent to using `-echo screen` at the command line. There is no
log *file* produced since it always uses `-log none`.
- *Include citation details:* when checked full citation info will be
included to the log window. This is equivalent to using `-cite
screen` on the command line.
- *Show log window by default:* when checked, the screen output of a
LAMMPS run will be collected in a log window during the run
- *Show chart window by default:* when checked, the thermodynamic
output of a LAMMPS run will be collected and displayed in a chart
window as line graphs.
- *Replace log window on new run:* when checked, an existing log
window will be replaced on a new LAMMPS run, otherwise each run will
create a new log window.
- *Replace chart window on new run:* when checked, an existing chart
window will be replaced on a new LAMMPS run, otherwise each run will
create a new chart window.
- *Replace image window on new render:* when checked, an existing
chart window will be replaced when a new snapshot image is requested,
otherwise each command will create a new image window.
- *Path to LAMMPS Shared Library File:* this options is only available
when LAMMPS GUI was compiled to load the LAMMPS library at run time
instead of being linked to it directly. With the ``Browse..`` button
or by changing the text, a different shared library file with a
different compilation of LAMMPS with different settings or from a
different version can be loaded. After this setting was changed,
LAMMPS GUI needs to be re-launched.
- *Select Default Font:* Opens a font selection dialog where the type
and size for the default font (used for everything but the editor and
log) of the application can be set.
- *Select Text Font:* Opens a font selection dialog where the type and
size for the text editor and log font of the application can be set.
Accelerators:
^^^^^^^^^^^^^
This tab enables to select which accelerator package is used and is
equivalent to using the `-suffix` and `-package` flags on the command
line. Only settings supported by the LAMMPS library and local hardware
are available. The `Number of threads` field allows to set the maximum
number of threads for the accelerator packages that use threads.
Snapshot Image:
^^^^^^^^^^^^^^^
This tab allows to set some defaults for the snapshot images displayed
in the ``Image Viewer`` window, like its dimensions and the zoom factor
applied. The *Antialias* switch requests to render images with twice
the number of pixels for width and height and then smoothly scales the
image back to the requested size. This produces higher quality images
with smoother edges at the expense of requiring more CPU time to render
the image. The *HQ Image mode* option turns on using a screen space
ambient occlusion mode (SSAO) when rendering images. This is also more
time consuming, but produces a more 'spatial' representation of the
system. The *VDW Style* checkbox selects whether atoms are represented
by space filling spheres when checked or by smaller spheres and stick.
Finally there are a couple of drop down lists to select the background
and box color.
Hotkeys
-------
Almost all functionality is accessible from the menu or via hotkeys.
The following hotkeys are available (On macOS use the Command key
instead of Ctrl/Control).
.. list-table::
:header-rows: 1
:widths: auto
* - Hotkey
- Function
- Hotkey
- Function
- Hotkey
- Function
- Hotkey
- Function
* - Ctrl+N
- New File
- Ctrl+Z
- Undo edit
- Ctrl+Enter
- Run LAMMPS
- Ctrl+Shift+A
- About LAMMPS GUI
* - Ctrl+O
- Open File
- Ctrl+Shift+Z
- Redo edit
- Ctrl+/
- Stop Active Run
- Ctrl+Shift+H
- Quick Help
* - CTRL+S
- Save File
- Ctrl+C
- Copy text
- Ctrl+Shift+V
- Set Variables
- Ctrl+Shift+G
- LAMMPS GUI Howto
* - Ctrl+Shift+S
- Save File As
- Ctrl+X
- Cut text
- Ctrl+I
- Create Snapshot Image
- Ctrl+Shift+M
- LAMMPS Manual
* - Ctrl+Q
- Quit
- Ctrl+V
- Paste text
- Ctrl+P
- Preferences
- Ctrl+?
- Context Help
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In
case of conflicts the list above takes precedence.

26
doc/src/Howto_pylammps.rst
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@ -53,10 +53,10 @@ System-wide Installation
Step 1: Building LAMMPS as a shared library
"""""""""""""""""""""""""""""""""""""""""""
To use LAMMPS inside of Python it has to be compiled as shared library. This
library is then loaded by the Python interface. In this example we enable the
MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
output support enabled.
To use LAMMPS inside of Python it has to be compiled as shared
library. This library is then loaded by the Python interface. In this
example we enable the MOLECULE package and compile LAMMPS with PNG, JPEG
and FFMPEG output support enabled.
Step 1a: For the CMake based build system, the steps are:
@ -66,7 +66,7 @@ Step 1a: For the CMake based build system, the steps are:
cd $LAMMPS_DIR/build-shared
# MPI, PNG, Jpeg, FFMPEG are auto-detected
cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
cmake ../cmake -DPKG_MOLECULE=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
make
Step 1b: For the legacy, make based build system, the steps are:
@ -79,7 +79,7 @@ Step 1b: For the legacy, make based build system, the steps are:
make yes-MOLECULE
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg"
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
Step 2: Installing the LAMMPS Python package
""""""""""""""""""""""""""""""""""""""""""""
@ -356,18 +356,16 @@ Together with matplotlib plotting data out of LAMMPS becomes simple:
Error handling with PyLammps
----------------------------
Compiling the shared library with C++ exception support provides a better error
handling experience. Without exceptions the LAMMPS code will terminate the
current Python process with an error message. C++ exceptions allow capturing
them on the C++ side and rethrowing them on the Python side. This way you
can handle LAMMPS errors through the Python exception handling mechanism.
Using C++ exceptions in LAMMPS for errors allows capturing them on the
C++ side and rethrowing them on the Python side. This way you can handle
LAMMPS errors through the Python exception handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be terminated. It is
advised to save your data and terminate the Python instance as quickly as
possible.
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible.
Using PyLammps in IPython notebooks and Jupyter
-----------------------------------------------

2
doc/src/Install_mac.rst
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@ -5,7 +5,7 @@ LAMMPS can be downloaded, built, and configured for macOS with `Homebrew
<homebrew_>`_. (Alternatively, see the installation instructions for
:doc:`downloading an executable via Conda <Install_conda>`.) The
following LAMMPS packages are unavailable at this time because of
additional requirements not yet met: GPU, KOKKOS, MSCG, MPIIO, POEMS,
additional requirements not yet met: GPU, KOKKOS, MSCG, POEMS,
VORONOI.
After installing Homebrew, you can install LAMMPS on your system with

9
doc/src/Install_windows.rst
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@ -18,11 +18,10 @@ needed to run in parallel with MPI.
The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE,
ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK. The serial
version also does not include the MPIIO and LATBOLTZ packages. The
PYTHON package is only available in the Python installers that bundle a
Python runtime. The GPU package is compiled for OpenCL with mixed
precision kernels.
ML-QUIP, MSCG, NETCDF, QMMM, SCAFACOS, and VTK. The serial version also
does not include the LATBOLTZ package. The PYTHON package is only
available in the Python installers that bundle a Python runtime. The
GPU package is compiled for OpenCL with mixed precision kernels.
The LAMMPS library is compiled as a shared library and the
:doc:`LAMMPS Python module <Python_module>` is installed, so that

10
doc/src/Intro_portability.rst
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@ -12,7 +12,7 @@ Programming language standards
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Most of the C++ code currently requires a compiler compatible with the
C++11 standard, the KOKKOS package currently requires C++14. Most of
C++11 standard, the KOKKOS package currently requires C++17. Most of
the Python code is written to be compatible with Python 3.5 or later or
Python 2.7. Some Python scripts *require* Python 3 and a few others
still need to be ported from Python 2 to Python 3.
@ -25,7 +25,7 @@ LAMMPS can be compiled from source code using a (traditional) build
system based on shell scripts, a few shell utilities (grep, sed, cat,
tr) and the GNU make program. This requires running within a Bourne
shell (``/bin/sh``). Alternatively, a build system with different back ends
can be created using CMake. CMake must be at least version 3.10.
can be created using CMake. CMake must be at least version 3.16.
Operating systems
^^^^^^^^^^^^^^^^^
@ -62,9 +62,9 @@ regularly tested.
Portability compliance
^^^^^^^^^^^^^^^^^^^^^^
Only a subset of the LAMMPS source code is fully compliant to all of the
above mentioned standards. This is rather typical for projects like
LAMMPS that largely depend on contributions from the user community.
Only a subset of the LAMMPS source code is *fully* compliant to *all*
of the above mentioned standards. This is rather typical for projects
like LAMMPS that largely depend on contributions from the user community.
Not all contributors are trained as programmers and not all of them have
access to multiple platforms for testing. As part of the continuous
integration process, however, all contributions are automatically tested

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42
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@ -28,20 +28,34 @@ Include files (varied)
packages and hard-to-find bugs have regularly manifested in the
past.
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not**
contain any ``using`` statements. Typically, that would only be the
header for the base class. Instead, any include statements should
be put in the corresponding implementation files and forward
declarations be used. For implementation files, the "include what
you use" principle should be employed. However, there is the
notable exception that when the ``pointers.h`` header is included
(or one of the base classes derived from it) certain headers will
always be included and thus do not need to be explicitly specified.
These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`,
`utils.h`, `vector`, `fmt/format.h`, `climits`, `cinttypes`. This
also means any such file can assume that `FILE`, `NULL`, and
`INT_MAX` are defined.
- Header files, especially those defining a "style", should only use the
absolute minimum number of include files and **must not** contain any
``using`` statements. Typically, that would only be the header for the
base class. Instead, any include statements should be put in the
corresponding implementation files and forward declarations be used.
For implementation files, the "include what you use" principle should
be employed. However, there is the notable exception that when the
``pointers.h`` header is included (or the header of one of the classes
derived from it), certain headers will *always* be included and thus
do not need to be explicitly specified. These are: `mpi.h`,
`cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`, `vector`,
`fmt/format.h`, `climits`, `cinttypes`. This also means any such file
can assume that `FILE`, `NULL`, and `INT_MAX` are defined.
- Class members variables should not be initialized in the header file,
but instead should be initialized either in the initializer list of
the constructor or explicitly assigned in the body of the constructor.
If the member variable is relevant to the functionality of a class
(for example when it stores a value from a command line argument), the
member variable declaration is followed by a brief comment explaining
its purpose and what its values can be. Class members that are
pointers should always be initialized to ``nullptr`` in the
initializer list of the constructor. This reduces clutter in the
header and avoids accessing uninitialized pointers, which leads to
hard to debug issues, class members are often implicitly initialized
to ``NULL`` on the first use (but *not* after a :doc:`clear command
<clear>`). Please see the files ``reset_atoms_mol.h`` and
``reset_atoms_mol.cpp`` as an example.
- System headers or headers from installed libraries are included with
angular brackets (example: ``#include <vector>``), while local

68
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@ -87,8 +87,6 @@ page gives those details.
* :ref:`MOFFF <PKG-MOFFF>`
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MOLFILE <PKG-MOLFILE>`
* :ref:`MPIIO <PKG-MPIIO>`
* :ref:`MSCG <PKG-MSCG>`
* :ref:`NETCDF <PKG-NETCDF>`
* :ref:`OPENMP <PKG-OPENMP>`
* :ref:`OPT <PKG-OPT>`
@ -1257,7 +1255,7 @@ Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`, :ref:`INTEL
<PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which have styles
optimized for CPUs, KNLs, and GPUs.
You must have a C++14 compatible compiler to use this package.
You must have a C++17 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
expose compiler bugs, especially when compiling for maximum
performance at high optimization levels. Please see the file
@ -2034,70 +2032,6 @@ This package has :ref:`specific installation instructions <molfile>` on the :doc
----------
.. _PKG-MPIIO:
MPIIO package
-------------
**Contents:**
Support for parallel output/input of dump and restart files via the
MPIIO library. It adds :doc:`dump styles <dump>` with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
**Install:**
The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
**Supporting info:**
* src/MPIIO: filenames -> commands
* :doc:`dump <dump>`
* :doc:`restart <restart>`
* :doc:`write_restart <write_restart>`
* :doc:`read_restart <read_restart>`
----------
.. _PKG-MSCG:
MSCG package
------------
**Contents:**
A :doc:`fix mscg <fix_mscg>` command which can parameterize a
Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library <mscg-home_>`_.
.. _mscg-home: https://github.com/uchicago-voth/MSCG-release
To use this package you must have the MS-CG library available on your
system.
**Authors:** The fix was written by Lauren Abbott (Sandia). The MS-CG
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
**Install:**
This package has :ref:`specific installation instructions <mscg>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/MSCG: filenames -> commands
* src/MSCG/README
* lib/mscg/README
* examples/mscg
----------
.. _PKG-NETCDF:
NETCDF package

10
doc/src/Packages_list.rst
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@ -333,16 +333,6 @@ whether an extra library is needed to build and use the package:
- :doc:`dump molfile <dump_molfile>`
- n/a
- ext
* - :ref:`MPIIO <PKG-MPIIO>`
- MPI parallel I/O dump and restart
- :doc:`dump <dump>`
- n/a
- no
* - :ref:`MSCG <PKG-MSCG>`
- multi-scale coarse-graining wrapper
- :doc:`fix mscg <fix_mscg>`
- mscg
- ext
* - :ref:`NETCDF <PKG-NETCDF>`
- dump output via NetCDF
- :doc:`dump netcdf <dump_netcdf>`

18
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@ -1,11 +1,11 @@
Handling LAMMPS errors
*******************************
**********************
Compiling the shared library with :ref:`C++ exception support <exceptions>` provides a better error
handling experience. Without exceptions the LAMMPS code will terminate the
current Python process with an error message. C++ exceptions allow capturing
them on the C++ side and rethrowing them on the Python side. This way
LAMMPS errors can be handled through the Python exception handling mechanism.
The shared library is compiled with :ref:`C++ exception support
<exceptions>` to provide a better error handling experience. C++
exceptions allow capturing errors on the C++ side and rethrowing them on
the Python side. This way LAMMPS errors can be handled through the
Python exception handling mechanism.
.. code-block:: python
@ -31,6 +31,6 @@ LAMMPS errors can be handled through the Python exception handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be terminated. It is
advised to save your data and terminate the Python instance as quickly as
possible.
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible when running in parallel with MPI.

23
doc/src/Speed_kokkos.rst
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@ -18,7 +18,7 @@ package was developed primarily by Christian Trott (Sandia) and Stan
Moore (Sandia) with contributions of various styles by others,
including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
(Sandia). For more information on developing using Kokkos abstractions
see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.
see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
Kokkos currently provides support for 4 modes of execution (per MPI
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
@ -26,23 +26,30 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
produce an executable compatible with a specific hardware.
.. admonition:: C++14 support
.. admonition:: C++17 support
:class: note
Kokkos requires using a compiler that supports the c++14 standard. For
some compilers, it may be necessary to add a flag to enable c++14 support.
For example, the GNU compiler uses the -std=c++14 flag. For a list of
compilers that have been tested with the Kokkos library, see the Kokkos
`README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
Kokkos requires using a compiler that supports the c++17 standard. For
some compilers, it may be necessary to add a flag to enable c++17 support.
For example, the GNU compiler uses the -std=c++17 flag. For a list of
compilers that have been tested with the Kokkos library, see the
`requirements document of the Kokkos Wiki
<https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
.. admonition:: NVIDIA CUDA support
:class: note
To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit
software version 9.0 or later must be installed on your system. See
software version 11.0 or later must be installed on your system. See
the discussion for the :doc:`GPU package <Speed_gpu>` for details of
how to check and do this.
.. admonition:: AMD ROCm (HIP) support
:class: note
To build with Kokkos support for AMD GPUs, the AMD ROCm toolkit
software version 5.2.0 or later must be installed on your system.
.. admonition:: CUDA and MPI library compatibility
:class: note

190
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@ -93,6 +93,7 @@ Miscellaneous tools
* :ref:`i-pi <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS GUI <lammps_gui>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity/apptainer <singularity_tool>`
@ -634,6 +635,195 @@ you first need to use the :doc:`clear` command.
----------
.. _lammps_gui:
LAMMPS GUI
----------
.. versionadded:: 2Aug2023
Overview
^^^^^^^^
LAMMPS GUI is a simple graphical text editor that is linked to the
:ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run LAMMPS
directly using the contents of the editor's text buffer as input.
This is similar to what people traditionally would do to run LAMMPS:
using a regular text editor to edit the input and run the necessary
commands, possibly including the text editor, too, from a command line
terminal window. This similarity is a design goal. While making it easy
for beginners to start with LAMMPS, it is also the intention to simplify
the transition to workflows like most experienced LAMMPS users do.
All features have been extensively exposed to hotkeys, so that there is
also appeal for experienced LAMMPS users, too, especially for
prototyping and testing simulations setups.
Features
^^^^^^^^
A detailed discussion and explanation of all features and functionality
are in the :doc:`Howto_lammps_gui` tutorial Howto page.
Here are a few highlights of LAMMPS GUI
- Text editor with syntax highlighting customized for LAMMPS
- Text editor will switch working directory to folder of file in buffer
- Text editor will remember up to 5 recent files
- Context specific LAMMPS command help via online documentation
- LAMMPS is running in a concurrent thread, so the GUI remains responsive
- Support for accelerator packages
- Progress bar indicates that LAMMPS is running
- LAMMPS can be started and stopped with a hotkey
- Screen output is captured in a Log Window
- Thermodynamic output is captured and displayed as line graph in a Chart Window
- Visualization of current state in Image Viewer (via :doc:`dump image <dump_image>`)
- Many adjustable settings and preferences that are persistent
- Dialog to set variables from the LAMMPS command line
Parallelization
^^^^^^^^^^^^^^^
Due to its nature as a graphical application, it is not possible to use
the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading and GPU
acceleration is available and enabled by default.
Prerequisites and portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS GUI is programmed in C++ based on the C++11 standard and using
the `Qt GUI framework <https://www.qt.io/product/framework>`_.
Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
recommended; Qt 6.x not (yet) supported. Building LAMMPS with CMake is
required. The LAMMPS GUI has been successfully compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
Pre-compiled executables
^^^^^^^^^^^^^^^^^^^^^^^^
Pre-compiled LAMMPS executables including the GUI are currently
available from https://download.lammps.org/static or
https://github.com/lammps/lammps/releases. You can unpack the archives
(or mount the macOS disk image) and run the GUI directly in place. The
folder may also be moved around and added to the ``PATH`` environment
variable so the executables will be found automatically. The LAMMPS GUI
executable is called ``lammps-gui`` and either takes no arguments or
attempts to load the first argument as LAMMPS input file.
Compilation
^^^^^^^^^^^
The source for the LAMMPS GUI is included with the LAMMPS source code
distribution in the folder ``tools/lammps-gui`` and thus it can be can
be built as part of a regular LAMMPS compilation. :doc:`Using CMake
<Howto_cmake>` is required. To enable its compilation, the CMake
variable ``-D BUILD_LAMMPS_GUI=on`` must be set when creating the CMake
configuration. All other settings (compiler, flags, compile type) for
LAMMPS GUI are then inherited from the regular LAMMPS build. If the Qt
library is packaged for Linux distributions, then its location is
typically auto-detected since the required CMake configuration files are
stored in a location where CMake can find them without additional help.
Otherwise, the location of the Qt library installation must be indicated
by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
a folder inside the Qt installation that contains the file
``Qt5Config.cmake``.
It should be possible to build the LAMMPS GUI as a standalone
compilation (e.g. when LAMMPS has been compiled with traditional make),
then the CMake configuration needs to be told where to find the LAMMPS
headers and the LAMMPS library, via ``-D
LAMMPS_SOURCE_DIR=/path/to/lammps/src``. CMake will try to guess a
build folder with the LAMMPS library from that path, but it can also be
set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader library that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
``liblammps.dll`` (depending on the operating system). This has the
advantage that the LAMMPS library can be updated LAMMPS without having
to recompile the GUI. The ABI of the LAMMPS C-library interface is very
stable and generally backward compatible. This feature is enabled by
setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
Platform notes
^^^^^^^^^^^^^^
macOS
"""""
When building on macOS, the build procedure will try to manufacture a
drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
To build multi-arch executables that will run on both, arm64 and x86_64
architectures natively, it is necessary to set the CMake variable ``-D
CMAKE_OSX_ARCHITECTURES=arm64;x86_64``. To achieve wide compatibility
with different macOS versions, you can also set ``-D
CMAKE_OSX_DEPLOYMENT_TARGET=11.0`` which will set compatibility to macOS
11 (Big Sur) and later, even if you are compiling on a more recent macOS
version.
Windows
"""""""
On Windows either native compilation from within Visual Studio 2022 with
Visual C++ is supported and tested, or compilation with the MinGW / GCC
cross-compiler environment on Fedora Linux.
**Visual Studio**
Using CMake and Ninja as build system are required. Qt needs to be
installed, tested was a binary package downloaded from
https://www.qt.io, which installs into the ``C:\\Qt`` folder by default.
There is a custom `x64-GUI-MSVC` build configuration provided in the
``CMakeSettings.json`` file that Visual Studio uses to store different
compilation settings for project. Choosing this configuration will
activate building the `lammps-gui.exe` executable in addition to LAMMPS
through importing package selection from the ``windows.cmake`` preset
file and enabling building the LAMMPS GUI and disabling building with MPI.
When requesting an installation from the `Build` menu in Visual Studio,
it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the
executables and required dependent .dll files. This zip file can be
uncompressed and ``lammps-gui.exe`` run directly from there. The
uncompressed folder can be added to the ``PATH`` environment and LAMMPS
and LAMMPS GUI can be launched from anywhere from the command line.
**MinGW64 Cross-compiler**
The standard CMake build procedure can be applied and the
``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
command will automatically include a suitable CMake toolset file (the
regular cmake command can be used after that). After building the
libraries and executables, you can build the target 'zip'
(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
to stage all installed files into a LAMMPS_GUI folder and then
run a script to copy all required dependencies, some other files,
and create a zip file from it.
Linux
"""""
Version 5.12 or later of the Qt library is required. Those are provided
by, e.g., Ubuntu 20.04LTS. Thus older Linux distributions are not
likely to be supported, while more recent ones will work, even for
pre-compiled executables (see above). After compiling with
``cmake --build <build folder>``, use ``cmake --build <build
folder> --target tgz`` or ``make tgz`` to build a
``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
support libraries.
----------
.. _arc:
lmp2arc tool

1
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@ -245,6 +245,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
* :doc:`composition/atom <compute_composition_atom>` - local composition for each atom
* :doc:`mliap <compute_mliap>` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials
* :doc:`momentum <compute_momentum>` - translational momentum
* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms

118
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@ -0,0 +1,118 @@
.. index:: compute composition/atom
.. index:: compute composition/atom/kk
compute composition/atom command
================================
Accelerator Variants: *composition/atom/kk*
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID composition/atom keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* composition/atom = style name of this compute command
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *cutoff*
*cutoff* value = distance cutoff
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all composition/atom
compute 1 all composition/atom cutoff 9.0
comm_modify cutoff 9.0
Description
"""""""""""
.. versionadded:: TBD
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,
composition is defined as the number of atoms of a given type
(including the central atom) divided by (:math:`M+1`). For a given central atom,
the sum of all compositions equals one.
.. note::
This compute uses the number of atom types, not chemical species, assigned in
:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
species (i.e., Cu and Ni) assigned to four different atom types in
:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
output four fractional values. In those cases, the user may desire an extra
calculation step to consolidate per-type fractions into per-species fractions.
This calculation can be conducted within LAMMPS using another compute such as
:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
post-processing step.
----------
The optional keyword *cutoff* defines the distance cutoff used when
searching for neighbors. The default value is the cutoff specified by
the pair style. If no pair style is defined, then a cutoff must be
defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is
defined), the *comm_modify cutoff* option must also be set to match
that of the *cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral.
This is the default setting for the :doc:`special_bonds
<special_bonds>` command, and means those pairwise interactions do
not appear in the neighbor list. Because this compute uses the
neighbor list, it also means those pairs will not be included in
the order parameter. This difficulty can be circumvented by
writing a dump file, and using the :doc:`rerun <rerun>` command to
compute the order parameter for snapshots in the dump file. The
rerun script can use a :doc:`special_bonds <special_bonds>` command
that includes all pairs in the neighbor list.
----------
Output info
"""""""""""
This compute calculates a per-atom array with :math:`1 + N` columns, where :math:`N`
is the number of atom types. The first column is a count of the number of atoms
used to calculate composition (including the central atom), and each subsequent
column indicates the fraction of that atom type within the cutoff sphere.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>`
doc page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`comm_modify <comm_modify>`
Default
"""""""
The option defaults are *cutoff* = pair style cutoff.

20
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@ -19,6 +19,7 @@ Syntax
attributes = id, ix, iy, iz, x, y, z, xs, ys, zs, xc, yc, zc, xsc, ysc, zsc
id = ID of grid cell, x fastest, y next, z slowest
proc = processor ID (0 to Nprocs-1) which owns the grid cell
ix,iy,iz = grid indices in each dimension (1 to N inclusive)
x,y,z = coords of lower left corner of grid cell
xs,ys,zs = scaled coords of lower left corner of grid cell (0.0 to 1.0)
@ -30,8 +31,8 @@ Examples
.. code-block:: LAMMPS
compute 1 all property/grid id ix iy iz
compute 1 all property/grid id xc yc zc
compute 1 all property/grid 10 10 20 id ix iy iz
compute 1 all property/grid 100 100 1 id xc yc zc
Description
"""""""""""
@ -53,13 +54,20 @@ to output per-grid values from other computes of fixes, the grid size
specified for this command must be consistent with the grid sizes
used by the other commands.
The *id* attribute stores the grid ID for each grid cell. For a
global grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs
range from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d
grid varying fastest, then Y, then Z slowest. For 2d grids (in 2d
The *id* attribute is the grid ID for each grid cell. For a global
grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs range
from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d grid
varying fastest, then Y, then Z slowest. For 2d grids (in 2d
simulations), the grid IDs range from 1 to Nx*Ny, with X varying
fastest and Y slowest.
.. versionadded:: TBD
The *proc* attribute is the ID of the processor which owns the grid
cell. Processor IDs range from 0 to Nprocs - 1, where Nprocs is the
number of processors the simulation is running on. Each grid cell is
owned by a single processor.
The *ix*, *iy*, *iz* attributes are the indices of a grid cell in
each dimension. They range from 1 to Nx inclusive in the X dimension,
and similar for Y and Z.

44
doc/src/dump.rst
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@ -14,10 +14,6 @@
.. index:: dump custom/gz
.. index:: dump local/gz
.. index:: dump xyz/gz
.. index:: dump atom/mpiio
.. index:: dump cfg/mpiio
.. index:: dump custom/mpiio
.. index:: dump xyz/mpiio
.. index:: dump atom/zstd
.. index:: dump cfg/zstd
.. index:: dump custom/zstd
@ -63,7 +59,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml*
* N = dump on timesteps which are multiples of N
* file = name of file to write dump info to
* attribute1,attribute2,... = list of attributes for a particular style
@ -74,13 +70,11 @@ Syntax
*atom/adios* attributes = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*atom/gz* attributes = none
*atom/zstd* attributes = none
*atom/mpiio* attributes = none
*cfg* attributes = same as *custom* attributes, see below
*cfg/gz* attributes = same as *custom* attributes, see below
*cfg/zstd* attributes = same as *custom* attributes, see below
*cfg/mpiio* attributes = same as *custom* attributes, see below
*cfg/uef* attributes = same as *custom* attributes, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* attributes = see below
*custom*, *custom/gz*, *custom/zstd* attributes = see below
*custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios <dump_adios>` page
*dcd* attributes = none
*h5md* attributes = discussed on :doc:`dump h5md <dump_h5md>` page
@ -97,10 +91,9 @@ Syntax
*xyz* attributes = none
*xyz/gz* attributes = none
*xyz/zstd* attributes = none
*xyz/mpiio* attributes = none
*yaml* attributes = same as *custom* attributes, see below
* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* attributes:
* *custom* or *custom/gz* or *custom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* attributes:
.. parsed-literal::
@ -179,11 +172,9 @@ Examples
.. code-block:: LAMMPS
dump myDump all atom 100 dump.lammpstrj
dump myDump all atom/mpiio 100 dump.atom.mpiio
dump myDump all atom/gz 100 dump.atom.gz
dump myDump all atom/zstd 100 dump.atom.zst
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4a all custom 100 dump.myvel.lammpsbin id type x y z vx vy vz
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
@ -622,27 +613,10 @@ when running on large numbers of processors.
Note that using the "\*" and "%" characters together can produce a
large number of small dump files!
For styles that end with *mpiio* an ".mpiio" must appear somewhere in
the specified filename. These styles write their dump file in
parallel via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Note these styles are identical in command
syntax to the corresponding styles without "mpiio". Likewise, the
dump files produced by these MPI-IO styles are identical in format to
the files produced by their non-MPI-IO style counterparts. This means
you can write a dump file using MPI-IO and use the :doc:`read_dump
<read_dump>` command or perform other post-processing, just as if the
dump file was not written using MPI-IO.
.. deprecated:: TBD
Because MPI-IO dump files are one large file which all processors
write to, you cannot use the "%" wildcard character described above in
the filename. However you can use the ".bin" or ".lammpsbin" suffix
described below. Again, this file will be written in parallel and
have the same binary format as if it were written without MPI-IO.
.. warning::
The MPIIO package within LAMMPS is currently unmaintained and has
become unreliable. Use with caution.
The MPIIO package and the the corresponding "/mpiio" dump styles, except
for the unrelated "netcdf/mpiio" style were removed from LAMMPS.
----------
@ -956,11 +930,6 @@ the COMPRESS package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` page for
more info.
The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles
are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
The *xtc*, *dcd*, and *yaml* styles are part of the EXTRA-DUMP package.
They are only enabled if LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
@ -971,6 +940,7 @@ Related commands
:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
:doc:`dump cfg/uef <dump_cfg_uef>`, :doc:`dump h5md <dump_h5md>`,
:doc:`dump image <dump_image>`, :doc:`dump molfile <dump_molfile>`,
:doc:`dump netcdf <dump_netcdf>`, :doc:`dump netcdf/mpiio <dump_netcdf>`,
:doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`,
:doc:`write_dump <write_dump>`

53
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@ -24,7 +24,7 @@ Syntax
* color = atom attribute that determines color of each atom
* diameter = atom attribute that determines size of each atom
* zero or more keyword/value pairs may be appended
* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao*
* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *fsaa* or *ssao*
.. parsed-literal::
@ -85,6 +85,8 @@ Syntax
diam = diameter of subdomain lines as fraction of shortest box length
*shiny* value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
*fsaa* arg = yes/no
yes/no = do or do not apply anti-aliasing
*ssao* value = shading seed dfactor = SSAO depth shading
shading = *yes* or *no* = turn depth shading on/off
seed = random # seed (positive integer)
@ -597,13 +599,47 @@ image will appear. The *sfactor* value must be a value 0.0 <=
*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
and *sfactor* = 0 is a rough non-shiny surface.
The *ssao* keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If *yes* is set, then atoms further
away from the viewer are darkened via a randomized process, which is
perceived as depth. The calculation of this effect can increase the
cost of computing the image by roughly 2x. The strength of the effect
can be scaled by the *dfactor* parameter. If *no* is set, no depth
shading is performed.
.. versionadded:: TBD
The *fsaa* keyword can be used with the dump image command to improve
the image quality by enabling full scene anti-aliasing. Internally the
image is rendered at twice the width and height and then scaled down by
computing the average of each 2x2 block of pixels to produce a single
pixel in the final image at the original size. This produces images with
smoother, less ragged edges. The application of this algorithm can
increase the cost of computing the image by about 3x or more.
The *ssao* keyword turns on/off a screen space ambient occlusion (SSAO)
model for depth shading. If *yes* is set, then atoms further away from
the viewer are darkened via a randomized process, which is perceived as
depth. The strength of the effect can be scaled by the *dfactor*
parameter. If *no* is set, no depth shading is performed. The
calculation of this effect can increase the cost of computing the image
substantially by 5x or more, especially with larger images. When used
in combination with the *fsaa* keyword the computational cost of depth
shading is particularly large.
----------
Image Quality Settings
""""""""""""""""""""""
The two keywords *fsaa* and *ssao* can be used to improve the image
quality at the expense of additional computational cost to render the
images. The images below show from left to right the same render with
default settings, with *fsaa* added, with *ssao* added, and with both
keywords added.
.. |imagequality1| image:: JPG/image.default.png
:width: 24%
.. |imagequality2| image:: JPG/image.fsaa.png
:width: 24%
.. |imagequality3| image:: JPG/image.ssao.png
:width: 24%
.. |imagequality4| image:: JPG/image.both.png
:width: 24%
|imagequality1| |imagequality2| |imagequality3| |imagequality4|
----------
@ -1051,6 +1087,7 @@ The defaults for the dump_modify keywords specific to dump image and dump movie
* boxcolor = yellow
* color = 140 color names are pre-defined as listed below
* framerate = 24
* fsaa = no
* gmap = min max cf 0.0 2 min blue max red
----------

46
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@ -124,17 +124,6 @@ Description
Modify the parameters of a previously defined dump command. Not all
parameters are relevant to all dump styles.
As explained on the :doc:`dump <dump>` doc page, the *atom/mpiio*,
*custom/mpiio*, and *xyz/mpiio* dump styles are identical in command
syntax and in the format of the dump files they create, to the
corresponding styles without "mpiio", except the single dump file they
produce is written in parallel via the MPI-IO library. Thus if a
dump_modify option below is valid for the *atom* style, it is also
valid for the *atom/mpiio* style, and similarly for the other styles
which allow for use of MPI-IO.
----------
Unless otherwise noted, the following keywords apply to all the
various dump styles, including the :doc:`dump image <dump_image>` and
:doc:`dump movie <dump_image>` styles.
@ -181,19 +170,20 @@ extra buffering.
.. versionadded:: 4May2022
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, *cfg*, and *local* and their compressed,
ADIOS, and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
for dump styles: *atom*, *custom*, *cfg*, and *local* and their
compressed, ADIOS variants. The setting for *ID string* replaces the
default text with the provided string. *ID* can be a positive integer
when it represents the column number counting from the left, a negative
integer when it represents the column number from the right (i.e. -1 is
the last column/keyword), or a custom dump keyword (or compute, fix,
property, or variable reference) and then it replaces the string for
that specific keyword. For *atom* dump styles only the keywords "id",
"type", "x", "y", "z", "ix", "iy", "iz" can be accessed via string
regardless of whether scaled or unwrapped coordinates were enabled or
disabled, and it always assumes 8 columns for indexing regardless of
whether image flags are enabled or not. For dump style *cfg* only
changes to the "auxiliary" keywords (6th or later keyword) will become
visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
@ -417,10 +407,10 @@ performed with dump style *xtc*\ .
----------
The *format* keyword can be used to change the default numeric format output
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
options can be used with the *atom* and *xyz* styles.
The *format* keyword can be used to change the default numeric format
output by the text-based dump styles: *atom*, *local*, *custom*, *cfg*,
and *xyz* styles. Only the *line* or *none* options can be used with the
*atom* and *xyz* styles.
All the specified format strings are C-style formats, such as used by
the C/C++ printf() command. The *line* keyword takes a single

1
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@ -268,7 +268,6 @@ accelerated styles exist.
* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
* :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
* :doc:`move <fix_move>` - move atoms in a prescribed fashion
* :doc:`mscg <fix_mscg>` - apply MSCG method for force-matching to generate coarse grain models
* :doc:`msst <fix_msst>` - multi-scale shock technique (MSST) integration
* :doc:`mvv/dpd <fix_mvv_dpd>` - DPD using the modified velocity-Verlet integration algorithm
* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm

141
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@ -1,141 +0,0 @@
.. index:: fix mscg
fix mscg command
================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID mscg N keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* mscg = style name of this fix command
* N = envoke this fix every this many timesteps
* zero or more keyword/value pairs may be appended
* keyword = *range* or *name* or *max*
.. parsed-literal::
*range* arg = *on* or *off*
*on* = range finding functionality is performed
*off* = force matching functionality is performed
*name* args = name1 ... nameN
name1,...,nameN = string names for each atom type (1-Ntype)
*max* args = maxb maxa maxd
maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all mscg 1
fix 1 all mscg 1 range name A B
fix 1 all mscg 1 max 4 8 20
Description
"""""""""""
This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
snapshots from a dump file to generate potentials for coarse-grained
simulations from all-atom simulations, using a force-matching technique
(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
It makes use of the MS-CG library, written and maintained by Greg Voth's
group at the University of Chicago, which is freely available on their
`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
See instructions on obtaining and installing the MS-CG library in the
src/MSCG/README file, which must be done before you build LAMMPS with
this fix command and use the command in a LAMMPS input script.
An example script using this fix is provided the examples/mscg
directory.
The general workflow for using LAMMPS in conjunction with the MS-CG
library to create a coarse-grained model and run coarse-grained
simulations is as follows:
1. Perform all-atom simulations on the system to be coarse grained.
2. Generate a trajectory mapped to the coarse-grained model.
3. Create input files for the MS-CG library.
4. Run the range finder functionality of the MS-CG library.
5. Run the force matching functionality of the MS-CG library.
6. Check the results of the force matching.
7. Run coarse-grained simulations using the new coarse-grained potentials.
This fix can perform the range finding and force matching steps 4 and 5
of the above workflow when used in conjunction with the :doc:`rerun
<rerun>` command. It does not perform steps 1-3 and 6-7.
Step 2 can be performed using a Python script (cgmap), which defines the
coarse-grained model and converts a standard LAMMPS dump file for an
all-atom simulation (step 1) into a LAMMPS dump file which has the
positions of and forces on the coarse-grained beads. To use cgmap the
following repositories need to be downloaded and installed.
#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
In step 3, an input file named "control.in" is needed by the MS-CG
library which sets parameters for the range finding and force matching
functionalities. See the examples/mscg/control.in file as an example.
And see the documentation provided with the MS-CG library for more
info on this file.
When this fix is used to perform steps 4 and 5, the MS-CG library also
produces additional output files. The range finder functionality
(step 4) outputs files defining pair and bonded interaction ranges. The
force matching functionality (step 5) outputs tabulated force files for
every interaction in the system. Other diagnostic files can also be
output depending on the parameters in the MS-CG library input script.
Again, see the documentation provided with the MS-CG library for more
info.
----------
The *range* keyword specifies which MS-CG library functionality should
be invoked. If *on*, the step 4 range finder functionality is invoked.
*off*, the step 5 force matching functionality is invoked.
If the *name* keyword is used, string names are defined to associate
with the integer atom types in LAMMPS. *Ntype* names must be provided,
one for each atom type (1-Ntype).
The *max* keyword specifies the maximum number of bonds, angles, and
dihedrals a bead can have in the coarse-grained model.
Restrictions
""""""""""""
This fix is part of the MSCG package. It is only enabled if LAMMPS was
built with that package. Building the MSCG package also requires
external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
pages for more info.
Currently, the MS-CG library is not set up to run in parallel with MPI,
so this fix can only be used in a serial LAMMPS build and run on a
single processor.
Related commands
""""""""""""""""
none
Default
"""""""
The default keyword settings are range off, max 4 12 36.
----------
.. _Izvekov:
**(Izvekov)** Izvekov, Voth, J Chem Phys 123, 134105 (2005).
.. _Noid:
**(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
Chem Phys 128, 134105 (2008).

79
doc/src/fix_vector.rst
View File

@ -8,7 +8,7 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID vector Nevery value1 value2 ...
fix ID group-ID vector Nevery value1 value2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* vector = style name of this fix command
@ -25,6 +25,13 @@ Syntax
v_name = value calculated by an equal-style variable with name
v_name[I] = Ith component of vector-style variable with name
* zero or more keyword/args pairs may be appended
* keyword = *nmax*
.. parsed-literal::
*nmax* length = set maximal length of vector to <length>
Examples
""""""""
@ -32,21 +39,26 @@ Examples
fix 1 all vector 100 c_myTemp
fix 1 all vector 5 c_myTemp v_integral
fix 1 all vector 50 c_myTemp nmax 200
Description
"""""""""""
Use one or more global values as inputs every few timesteps, and
simply store them. For a single specified value, the values are
Use one or more global values as inputs every few timesteps, and simply
store them as a sequence. For a single specified value, the values are
stored as a global vector of growing length. For multiple specified
values, they are stored as rows in a global array, whose number of
rows is growing. The resulting vector or array can be used by other
values, they are stored as rows in a global array, whose number of rows
is growing. The resulting vector or array can be used by other
:doc:`output commands <Howto_output>`.
The optional *nmax* keyword can be used to restrict the length of the
vector to the given *length* value. Once the restricted vector is
filled, the oldest entry will be discarded when a entry is added.
One way to to use this command is to accumulate a vector that is
time-integrated using the :doc:`variable trap() <variable>` function.
For example the velocity auto-correlation function (VACF) can be
time-integrated, to yield a diffusion coefficient, as follows:
numerically integrated using the :doc:`variable trap() <variable>`
function. For example, the velocity auto-correlation function (VACF)
can be integrated, to yield a diffusion coefficient, as follows:
.. code-block:: LAMMPS
@ -77,6 +89,15 @@ The *Nevery* argument specifies on what timesteps the input values
will be used in order to be stored. Only timesteps that are a
multiple of *Nevery*, including timestep 0, will contribute values.
.. note::
:class: warning
If *Nevery* is a small number and the simulation runs for many
steps, the accumulated vector or array can become very large and
thus consume a lot of memory. The implementation limit is about
2 billion entries. Using the *nmax* keyword mentioned above can
avoid that by limiting the size of the vector.
Note that if you perform multiple runs, using the "pre no" option of
the :doc:`run <run>` command to avoid initialization on subsequent runs,
then you need to use the *stop* keyword with the first :doc:`run <run>`
@ -94,11 +115,12 @@ calculated by the compute is used.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix vector. Or it can be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
can thus be accessed by fix vector. Or it can be a compute defined not
in your input script, but by :doc:`thermodynamic output <thermo_style>`
or other fixes such as :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale
<fix_temp_rescale>`. See the doc pages for these commands which give
the IDs of these computes. Users can also write code for their own
compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
@ -108,7 +130,8 @@ calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
Users can also write code for their own fix styles and :doc:`add them to
LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. An equal-style or
@ -126,8 +149,9 @@ quantities to be stored by fix vector.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix produces a global vector or global array which can be
accessed by various :doc:`output commands <Howto_output>`. The values
@ -144,15 +168,15 @@ the vector are "intensive" or "extensive". If the fix produces an
array, then all elements in the array must be the same, either
"intensive" or "extensive". If a compute or fix provides the value
stored, then the compute or fix determines whether the value is
intensive or extensive; see the page for that compute or fix for
further info. Values produced by a variable are treated as intensive.
intensive or extensive; see the page for that compute or fix for further
info. Values produced by a variable are treated as intensive.
This fix can allocate storage for stored values accumulated over
multiple runs, using the *start* and *stop* keywords of the
:doc:`run <run>` command. See the :doc:`run <run>` command for details of
how to do this. If using the :doc:`run pre no <run>` command option,
this is required to allow the fix to allocate sufficient storage for
stored values.
multiple runs, using the *start* and *stop* keywords of the :doc:`run
<run>` command. See the :doc:`run <run>` command for details of how to
do this. If using the :doc:`run pre no <run>` command option, this is
required to allow the fix to allocate sufficient storage for stored
values.
This fix is not invoked during :doc:`energy minimization <minimize>`.
@ -165,7 +189,10 @@ Related commands
:doc:`compute <compute>`, :doc:`variable <variable>`
Default
"""""""
Defaults
""""""""
none
The default value of *nmax* is deduced from the number of steps
in a run (or multiple runs when using the *start* and *stop*
keywords of the :doc:`run command <run>`) divided by the choice
of *Nevery* plus 1.

20
doc/src/read_restart.rst
View File

@ -19,7 +19,6 @@ Examples
read_restart save.10000
read_restart restart.*
read_restart restart.*.mpiio
Description
"""""""""""
@ -120,22 +119,6 @@ different the number of processors in the current LAMMPS simulation.
This can be a fast mode of input on parallel machines that support
parallel I/O.
A restart file can also be read in parallel as one large binary file
via the MPI-IO library, assuming it was also written with MPI-IO.
MPI-IO is part of the MPI standard for versions 2.0 and above. Using
MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g.
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
----------
Here is the list of information included in a restart file, which
@ -268,8 +251,7 @@ information about these bonds is written to the restart file.
Restrictions
""""""""""""
To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
none
Related commands
""""""""""""""""

39
doc/src/restart.rst
View File

@ -33,7 +33,6 @@ Examples
restart 0
restart 1000 poly.restart
restart 1000 poly.restart.mpiio
restart 1000 restart.*.equil
restart 10000 poly.%.1 poly.%.2 nfile 10
restart v_mystep poly.restart
@ -81,21 +80,6 @@ of output and subsequent input on parallel machines that support
parallel I/O. The optional *fileper* and *nfile* keywords discussed
below can alter the number of files written.
The restart file can also be written in parallel as one large binary
file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
Restart files are written on timesteps that are a multiple of N but
not on the first timestep of a run or minimization. You can use the
:doc:`write_restart <write_restart>` command to write a restart file
@ -104,15 +88,17 @@ timestep of a run unless it is a multiple of N. A restart file is
written on the last timestep of a minimization if N > 0 and the
minimization converges.
Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the next timestep at which a
restart file will be written out. On that timestep, the variable will
be evaluated again to determine the next timestep, etc. Thus the
variable should return timestep values. See the stagger() and
logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
this context. Other similar math functions could easily be added as
options for :doc:`equal-style variables <variable>`.
Instead of a numeric value, N can be specified as an :doc:`equal-style
variable <variable>`, which should be specified as v_name, where name is
the variable name. In this case, the variable is evaluated at the
beginning of a run to determine the next timestep at which a restart
file will be written out. On that timestep, the variable will be
evaluated again to determine the next timestep, etc. Thus the variable
should return timestep values. See the stagger() and logfreq() and
stride() math functions for :doc:`equal-style variables <variable>`, as
examples of useful functions to use in this context. Other similar math
functions could easily be added as options for :doc:`equal-style
variables <variable>`.
For example, the following commands will write restart files
every step from 1100 to 1200, and could be useful for debugging
@ -170,8 +156,7 @@ next 3 processors and write it to a restart file.
Restrictions
""""""""""""
To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
none
Related commands
""""""""""""""""

30
doc/src/write_restart.rst
View File

@ -27,7 +27,6 @@ Examples
.. code-block:: LAMMPS
write_restart restart.equil
write_restart restart.equil.mpiio
write_restart poly.%.* nfile 10
Description
@ -53,32 +52,6 @@ output and subsequent input on parallel machines that support parallel
I/O. The optional *fileper* and *nfile* keywords discussed below can
alter the number of files written.
The restart file can also be written in parallel as one large binary
file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
cmake . -DPKG_MPIIO=on # enables the MPIIO package in the build folder
cmake --build . # recompiles LAMMPS with the package code included
.. tab:: Traditional make
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
Restart files can be read by a :doc:`read_restart <read_restart>`
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
@ -128,9 +101,6 @@ before the restart file is written. This means that your system must
be ready to perform a simulation before using this command (force
fields setup, atom masses initialized, etc).
To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
Related commands
""""""""""""""""

2
doc/utils/requirements.txt
View File

@ -1,4 +1,4 @@
Sphinx >= 5.3.0, <7.1.0
Sphinx >= 5.3.0, <7.2.0
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read

8
doc/utils/sphinx-config/false_positives.txt
View File

@ -1195,6 +1195,7 @@ Freitas
Frenkel
Friedrichs
fs
fsaa
fsh
fstyle
fsw
@ -1528,6 +1529,7 @@ inhomogeneous
init
initialdelay
initialisms
initializer
initializations
InitiatorIDs
initio
@ -2228,6 +2230,7 @@ monolayer
monopole
monovalent
Montalenti
Monterey
Montero
Monti
Mora
@ -3488,6 +3491,7 @@ supercell
superset
supersphere
Supinski
Sur
Surblys
surfactant
surfactants
@ -3619,6 +3623,7 @@ Tk
Tkin
tloop
tlsph
tm
tmax
Tmax
tmd
@ -3635,6 +3640,7 @@ tokyo
tol
tomic
toolchain
toolset
topologies
Toporov
Torder
@ -3833,6 +3839,7 @@ vectorized
Vegt
vel
Velázquez
Ventura
venv
Verlag
verlet
@ -4090,6 +4097,7 @@ zmq
zN
zs
zsc
Zsh
zst
Zstandard
zstd

18
examples/ASPHERE/tri/in.tri.srd
View File

@ -2,7 +2,7 @@
units lj
atom_style tri
atom_modify first big
atom_modify first big map yes
read_data data.tri.srd
@ -52,12 +52,12 @@ pair_coeff 1 2 0.0 1.0 0.0
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
fix 2 small srd 20 big 1.0 0.25 49894 &
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
fix 2 small srd 20 big 1.0 1.0 49894 &
search 0.2 cubic warn 0.0001 shift yes 49829 &
overlap yes collision noslip
overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
@ -73,8 +73,8 @@ compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
compute 10 all property/atom corner1x corner1y corner1z &
@ -93,9 +93,9 @@ unfix 3
change_box all triclinic
fix 2 small srd 20 big 1.0 0.25 49894 &
fix 2 small srd 20 big 1.0 1.0 49894 &
search 0.2 cubic warn 0.0001 shift yes 49829 &
overlap yes collision noslip tstat yes
overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type &

812
examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8 Normal file
View File

@ -0,0 +1,812 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big map yes
read_data data.tri.srd
Reading data file ...
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
read_data CPU = 0.007 seconds
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms 2 region box
Created 91125 atoms
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
create_atoms CPU = 0.002 seconds
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
Setting atom values ...
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 19 19 19
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
create bodies CPU = 0.000 seconds
125 rigid bodies with 1500 atoms
1.8601881 = max distance from body owner to body atom
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 17 17 17
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
SRD per actual grid cell = -3.9971745
SRD viscosity = -34.162587
big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.970837 35.150443
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 16.874681, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/3d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
0 0 1.4401779 0 -0.15917996 0 0
100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18
200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34
300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40
400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52
500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63
600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61
700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39
800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52
900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55
1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63
1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69
1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64
1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56
1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71
1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77
1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66
1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62
1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59
1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55
2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54
2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59
2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59
2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61
2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59
2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65
2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70
2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59
2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61
2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67
3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76
3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80
3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93
3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86
3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82
3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71
3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65
3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68
3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76
3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79
4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75
4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79
4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91
4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74
4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72
4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74
4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78
4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83
4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85
4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94
5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105
5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99
5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97
5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99
5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97
5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89
5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93
5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82
5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93
5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92
6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91
6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97
6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95
6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101
6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105
6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99
6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104
6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101
6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102
6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102
7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109
7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110
7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122
7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114
7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119
7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124
7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113
7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118
7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125
7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136
8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132
8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143
8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142
8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143
8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135
8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123
8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116
8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132
8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132
8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138
9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156
9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167
9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157
9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156
9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170
9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165
9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169
9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149
9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151
9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167
10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177
Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49
Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27
Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76
Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01
Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34
Other | | 0.2104 | | | 0.13
Nlocal: 2033.88 ave 2601 max 1413 min
Histogram: 1 2 0 0 0 0 2 1 1 1
Nghost: 1647.25 ave 1714 max 1617 min
Histogram: 4 0 1 0 0 1 1 0 0 1
Neighs: 12482.8 ave 17009 max 8679 min
Histogram: 1 1 1 0 1 1 2 0 0 1
Total # of neighbors = 99862
Ave neighs/atom = 6.1374224
Neighbor list builds = 562
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 13 13 13
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
SRD per actual grid cell = -2.775698
SRD viscosity = -12.180602
big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.14994 40
ave/max big velocity = 1.6952661 5.2200074
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 13.499745, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton/tri
stencil: half/multi/3d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0
10100 7.0770142 1.0021471 4.4491455 6.606701 1 141
10200 6.7628072 1.002308 4.152988 8.5190386 1 125
10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109
10400 6.3237519 1.0024029 3.8636034 9.4058128 1 95
10500 6.6411054 1.0026261 4.2975997 7.6122304 1 82
10600 5.7470775 1.0004827 3.7959947 7.3091777 1 67
10700 5.9744919 1.0014977 3.6885649 7.5517197 1 59
10800 5.8028731 1.0029627 3.7553961 6.2787087 1 49
10900 5.3755286 1.0019318 3.5334739 7.1318348 1 41
11000 5.3915962 1.001463 3.483172 7.6362496 1 40
11100 5.8683672 1.0022459 3.6697589 6.9711866 1 33
11200 5.4351801 0.99956703 3.4548447 7.0745257 1 29
11300 4.9397513 1.0008287 3.1990325 6.0917337 1 27
11400 4.9159845 1.0017862 3.0005677 7.653817 1 26
11500 4.9243103 1.0013135 3.1799841 7.744414 1 23
11600 5.2036357 1.0017984 3.2963749 7.540477 1 22
11700 4.8991892 1.0020757 3.1773032 8.7218471 1 27
11800 4.9489399 1.003438 3.1679764 7.1605486 1 26
11900 4.82398 1.0019946 3.1939566 7.1397869 1 21
12000 4.3531411 1.000532 2.8321416 7.6672501 1 23
12100 4.8226081 1.0018898 3.0382137 6.8343432 1 25
12200 4.7456418 1.0032116 2.9186038 7.3067818 1 20
12300 4.4280468 1.0005857 2.734593 8.0365684 1 22
12400 4.7311239 1.0000982 2.8898839 7.9231831 1 22
12500 4.7261054 1.0016127 2.9090517 7.6085854 1 24
12600 4.7719025 1.0016702 2.9736761 7.6101796 1 26
12700 4.386248 1.001394 2.8508378 6.4765102 1 28
12800 4.3313538 1.0019737 2.6258221 6.3164681 1 19
12900 4.2219861 1.0007469 2.5345699 7.0901077 1 22
13000 4.1775643 1.0011891 2.5807017 7.3579938 1 25
13100 4.3060837 1.0008671 2.5974066 6.9301328 1 22
13200 4.3529062 0.99996469 2.7571632 6.7806287 1 21
13300 4.2178709 1.000673 2.7819091 7.6449064 1 18
13400 4.2714169 1.0021294 2.7280794 8.0986691 1 18
13500 4.3430969 1.0037732 2.6768429 8.1267941 1 18
13600 4.3664374 1.0016083 2.6470186 6.2797727 1 20
13700 4.4904769 1.0008993 2.7885718 7.7410193 1 22
13800 4.2966193 1.001532 2.73862 7.9651302 1 21
13900 4.4003185 1.0009984 2.7484129 8.7160439 1 24
14000 4.5948292 1.0011748 2.9051777 7.842121 1 22
14100 4.6901122 1.0001265 2.9404111 8.9953816 1 20
14200 4.8517518 0.99998743 2.9647625 6.6450509 1 22
14300 4.889628 1.0018051 3.0891097 7.2671824 1 20
14400 4.578862 1.0010629 2.8239776 6.1317183 1 23
14500 4.0865406 1.0013917 2.5119661 6.864665 1 19
14600 4.30688 1.0009041 2.6817814 6.9007433 1 18
14700 4.1295726 1.002342 2.6032093 7.1441648 1 15
14800 4.2176021 1.0015157 2.7332903 6.8394683 1 16
14900 4.2012664 0.99986345 2.6498409 7.4568241 1 15
15000 4.6124269 1.0014751 2.9584178 7.9341875 1 16
15100 4.947327 1.0010615 3.0784409 7.6241305 1 21
15200 5.253281 1.002095 3.3093754 8.1872718 1 25
15300 5.2642369 1.0017799 3.1511136 7.4668389 1 25
15400 5.1967916 1.0029407 3.247548 8.0840111 1 23
15500 5.7465412 1.001896 3.468834 9.5990471 1 15
15600 6.2245772 1.0021086 3.6127689 7.8242016 1 19
15700 5.5626191 0.99984979 3.3893723 7.8124588 1 20
15800 5.5945727 1.0010291 3.3442448 7.0116922 1 17
15900 5.4450219 1.0006248 3.3132381 8.4803413 1 15
16000 5.7800459 1.001449 3.5002534 8.7989456 1 19
16100 6.1168718 1.0008109 3.8081142 8.0119729 1 18
16200 5.4901649 1.0020643 3.3673653 7.3483134 1 17
16300 5.4051694 1.0015652 3.3560012 7.4641983 1 19
16400 5.4237612 1.0012686 3.3816406 7.3845086 1 14
16500 5.1935593 1.001754 3.3340381 7.8607712 1 16
16600 5.539343 1.0021073 3.4164309 8.1541097 1 12
16700 5.8922923 1.0013792 3.553426 7.5220576 1 14
16800 5.956937 1.0005959 3.7630589 8.7417987 1 13
16900 5.469721 1.0016219 3.5531223 8.6721994 1 13
17000 5.3110154 1.001142 3.4167244 7.4644182 1 15
17100 5.9226035 0.99918238 4.0244287 6.5172028 1 16
17200 5.4897042 0.99981565 3.4350691 5.6840394 1 20
17300 5.4302636 1.0021571 3.421473 6.4317025 1 21
17400 5.5559131 1.0013807 3.4951403 6.874191 1 24
17500 5.4068006 1.0010448 3.4506835 7.7069504 1 22
17600 4.9283792 1.0007628 3.1736308 7.3098058 1 20
17700 4.9319722 0.99935896 3.0956257 8.2120111 1 15
17800 4.6842391 1.00037 2.9602433 7.4116352 1 17
17900 4.7714682 1.0009332 2.9666778 7.5925131 1 17
18000 4.7233188 1.0035687 3.0991778 7.1636357 1 10
18100 4.6487958 1.0020255 3.10781 6.8468658 1 12
18200 4.6284129 1.0012617 3.089724 6.3082275 1 13
18300 4.7136404 0.99962415 3.1261978 7.3359556 1 15
18400 5.0367681 1.0011016 3.2413493 8.3910633 1 14
18500 4.9658104 1.0025407 3.2420827 7.4701216 1 17
18600 4.6100059 1.0014508 3.0216884 6.553483 1 17
18700 4.3246452 1.0016721 2.7810363 6.7450293 1 19
18800 4.9415788 1.0012406 3.1661907 7.5544034 1 18
18900 5.3930915 1.000138 3.2557456 7.350955 1 21
19000 5.1938599 1.0007364 3.2398733 6.5397956 1 22
19100 5.4433048 1.0019191 3.2699245 8.3625772 1 22
19200 6.1303261 1.0004005 3.7823203 8.0537369 1 22
19300 5.5762518 1.0008117 3.5689121 8.3714373 1 22
19400 5.1316743 0.9999834 3.099381 7.405287 1 23
19500 5.2064799 1.0012007 3.3059455 7.3499127 1 25
19600 5.1650099 1.0023314 3.3759492 7.3637616 1 21
19700 5.8316278 1.0023317 3.601564 7.153887 1 19
19800 5.6435147 1.0010657 3.4967581 6.8899334 1 21
19900 5.4071193 0.99961357 3.4977894 6.1068438 1 20
20000 5.5058495 1.000982 3.5185057 8.5657603 1 19
20100 5.6551271 1.0025852 3.5672369 7.8242273 1 20
20200 5.7196886 1.002283 3.6010925 7.1449072 1 22
20300 5.5593553 1.0009987 3.4363398 8.4141755 1 21
20400 5.5550247 1.001081 3.3950874 8.0222131 1 20
20500 5.4510415 0.99997273 3.5505093 7.5243655 1 18
20600 5.8014064 1.0007611 3.8084579 7.6583499 1 18
20700 5.7337315 1.0020309 3.7973684 8.7376766 1 17
20800 5.2512898 0.99901254 3.5027763 7.8902791 1 14
20900 5.3245034 1.0014504 3.3354615 6.7030716 1 17
21000 5.2071731 1.0020459 3.3881369 5.8616999 1 20
21100 5.3187535 1.0010762 3.2845672 8.1422146 1 21
21200 5.5298545 0.99942313 3.4393978 7.1183144 1 22
21300 5.8430744 1.0008652 3.719408 7.8522038 1 20
21400 5.8190457 1.0017046 3.5624252 7.8150165 1 20
21500 6.004585 1.0035276 3.9161914 7.7719377 1 21
21600 6.7202635 0.99970072 3.9642141 8.7934294 1 18
21700 6.8590346 1.0007883 4.4285217 8.9014638 1 20
21800 6.627638 1.0012117 4.1154082 8.3153026 1 22
21900 7.8281047 1.0008299 4.8842343 8.4016227 1 20
22000 7.200038 1.0014681 4.4141419 9.4091956 1 18
22100 7.7442011 1.0018051 4.7850371 8.9885489 1 15
22200 7.4770203 1.0033558 4.7512643 8.4898148 1 17
22300 8.1080801 1.0000019 5.2725185 9.2314625 1 14
22400 7.8068311 1.0020672 4.9055683 8.4064748 1 12
22500 7.4594636 1.0008427 4.6586396 8.5102986 1 11
22600 6.9380609 1.0024634 4.2435619 10.395118 1 16
22700 6.9338066 1.001056 4.3436179 7.9126284 1 18
22800 6.8049493 1.0020052 4.1443407 7.8228868 1 18
22900 6.2280158 1.0021474 3.7695343 7.3179647 1 20
23000 5.649403 1.0017128 3.5941976 7.2964709 1 19
23100 5.3203116 1.001912 3.3807399 6.6454551 1 15
23200 5.8172882 1.0005742 3.6625896 8.4256312 1 15
23300 5.9647182 1.0015466 3.9106019 8.3303303 1 14
23400 5.9784055 1.0034542 3.7229235 7.7934273 1 14
23500 5.377627 1.00192 3.5481778 6.8195124 1 17
23600 5.4807136 1.0014662 3.563123 7.6356376 1 18
23700 5.8896329 1.0013553 3.7990694 8.5513408 1 13
23800 6.3463707 0.9999403 3.9609397 8.5741923 1 11
23900 6.656669 1.0014998 4.1993183 9.0862996 1 13
24000 7.583723 1.0025057 4.7628652 7.5007245 1 20
24100 6.9868359 1.0014089 4.4369841 7.692833 1 25
24200 7.1966062 1.0013149 4.4384528 9.5264821 1 18
24300 6.7765706 1.0007065 4.3500477 9.4974154 1 16
24400 7.0853466 1.0013246 4.409163 9.2215823 1 17
24500 6.9603823 1.0004247 4.4866051 7.7870058 1 20
24600 6.9208291 0.99953329 4.2298144 6.5732392 1 21
24700 6.5005518 1.0026848 4.0003505 7.8094715 1 22
24800 5.8421948 1.0012055 3.6686768 7.6078157 1 26
24900 5.8410604 1.0023428 3.746177 6.8971309 1 22
25000 5.8728511 1.0001747 3.7170134 7.4456816 1 19
25100 6.0217168 1.000624 3.7756108 6.6542452 1 20
25200 6.1939015 1.0017861 3.8943084 9.395821 1 25
25300 6.161998 1.0010373 3.9255122 6.2228884 1 28
25400 5.5850406 1.0018505 3.5129832 7.2551309 1 24
25500 6.0286276 1.0009028 3.8580887 6.8065265 1 24
25600 5.6262228 1.0005097 3.4574446 7.5061246 1 21
25700 6.1348187 1.0009828 3.8073512 7.4818375 1 17
25800 6.09781 1.0026426 3.9585383 9.0915939 1 21
25900 6.2673667 1.0002269 3.8182813 9.2134822 1 21
26000 6.6001776 1.0020444 4.041386 8.0403555 1 18
26100 6.3063025 1.0016633 3.8649839 8.8149734 1 19
26200 6.0046983 1.002332 3.5380766 8.6145656 1 17
26300 5.9627788 1.0005401 3.56864 6.7821213 1 15
26400 5.0547314 0.9998295 3.2106781 9.2935351 1 15
26500 5.256781 1.0013131 3.2946631 8.8590275 1 15
26600 5.6250355 1.0023929 3.5243033 8.8985058 1 17
26700 6.0197165 1.0018323 3.7973947 7.3093402 1 17
26800 5.4556541 1.0015309 3.4295107 8.2342049 1 18
26900 5.420428 1.0024996 3.4374201 7.1444636 1 16
27000 6.165624 1.0019174 3.8726016 8.6588275 1 20
27100 6.7131697 1.0006541 4.266264 8.7063389 1 24
27200 6.4855163 1.0016139 4.2029778 7.667611 1 29
27300 6.0525608 1.000478 3.9169723 7.4515279 1 25
27400 6.1426194 1.0014522 3.9176108 6.8689671 1 24
27500 6.5981349 1.0001143 4.0620686 8.6804552 1 27
27600 6.7827138 1.0016694 4.2764286 9.3912843 1 21
27700 6.6368902 1.0025149 4.1452128 9.1814523 1 24
27800 6.9791025 1.0019486 4.3989933 7.9446882 1 24
27900 6.617142 1.0015736 4.360571 9.3732108 1 26
28000 7.2818263 1.0014101 4.6041512 8.2398587 1 28
28100 7.2543709 1.0007625 4.5724787 7.7373488 1 22
28200 7.0631847 1.0023922 4.4021705 8.3290554 1 29
28300 7.2999952 1.0012593 4.4655563 8.612666 1 27
28400 7.4124538 1.0014043 4.5011335 8.379391 1 29
28500 7.0350937 1.0011392 4.3528091 7.8167375 1 24
28600 7.9659642 1.0031684 4.8732467 8.0661929 1 30
28700 7.2865919 1.0010958 4.6650146 8.0325989 1 32
28800 7.7039529 1.0027912 4.8299888 9.5471747 1 30
28900 8.3288847 1.0012438 5.0785288 8.8964877 1 31
29000 7.9348665 1.0021794 4.9393968 9.5531767 1 31
29100 8.2473389 1.0013795 4.9890359 9.7697184 1 29
29200 8.6383362 1.0018356 4.9856954 7.6402719 1 25
29300 8.2504592 1.0011048 4.9631793 7.9466724 1 24
29400 8.0502922 1.0010516 5.2521065 8.4515028 1 26
29500 7.9475896 1.0012951 4.8584644 9.1225463 1 19
29600 8.5641641 1.0016228 5.4361335 9.2045399 1 23
29700 8.9932021 1.0011848 5.5727205 8.6045729 1 23
29800 8.0320178 1.0019073 5.2837013 8.9335413 1 22
29900 8.2676522 1.0012734 5.2213798 8.8966896 1 24
30000 9.1848984 1.001747 5.9147628 12.096129 1 27
30100 10.184519 0.99977427 6.4260136 11.140491 1 27
30200 9.271472 1.0023983 6.0252189 9.6954338 1 30
30300 9.0751572 1.000851 5.6010295 9.734426 1 28
30400 9.4581261 1.0018449 5.6987258 9.70456 1 34
30500 9.1574751 0.99944001 5.582217 9.300318 1 27
30600 8.619312 1.001388 5.3503985 8.2759155 1 26
30700 7.9370031 1.0026674 5.0702831 8.5368014 1 28
30800 7.9221619 1.0019077 5.1278637 11.046922 1 26
30900 9.9722884 1.0025903 6.4055506 10.167311 1 25
31000 8.8648667 0.99962676 5.4777514 10.142102 1 21
31100 8.576344 1.000906 5.3216342 8.7984921 1 18
31200 7.8480974 1.0010341 4.9584917 9.0696437 1 16
31300 8.3536183 1.0005758 5.208516 9.7971514 1 15
31400 8.5301933 1.0007603 5.2241536 9.0257241 1 17
31500 8.5196226 1.0018215 5.0576064 8.8847294 1 19
31600 8.1470823 1.0023147 4.9182956 9.0205413 1 20
31700 8.1475888 1.0005764 5.1814113 9.0603162 1 16
31800 7.8629717 1.0014194 4.9221218 9.366291 1 16
31900 7.7206559 1.0021082 4.9167636 7.4136735 1 16
32000 7.5152809 1.0004752 4.6330638 8.830959 1 16
32100 8.2693974 1.0011751 4.9094804 9.427636 1 13
32200 8.3067661 0.9997006 4.9036865 9.0374633 1 17
32300 7.2068514 1.0007866 4.3580755 8.6445065 1 17
32400 6.885063 1.0011887 4.1528011 8.1199454 1 16
32500 6.9147014 1.0020825 4.160405 7.5398034 1 19
32600 6.8809668 1.000971 4.3312782 8.2157688 1 16
32700 6.4818892 1.0000885 3.9433899 7.309605 1 22
32800 6.6875555 1.0018674 4.1017504 7.2327183 1 22
32900 7.6118502 0.99975736 4.4498951 8.5072395 1 19
33000 7.7576909 1.0022061 4.7239551 9.2132467 1 22
33100 7.8616235 1.000482 5.0031322 9.349805 1 20
33200 8.2620563 1.0015059 5.2482188 10.286446 1 17
33300 8.0217099 1.0015466 5.1166876 9.1381844 1 20
33400 7.6565746 1.0024855 4.7594208 9.2646824 1 22
33500 7.9633887 1.0010334 4.6754116 9.1085184 1 23
33600 7.9566834 1.0024542 4.6712679 9.2046594 1 25
33700 8.2639384 1.0003021 5.1326892 8.0930215 1 24
33800 8.5648917 1.0000947 5.2099387 8.8127486 1 21
33900 8.3593557 1.0002488 5.1291354 8.5938391 1 25
34000 8.1922068 1.0030011 5.1441189 7.1529563 1 24
34100 8.4260308 1.0004639 5.5876122 9.0450303 1 28
34200 8.3014654 1.0002204 5.1964772 8.4920822 1 33
34300 7.4736545 1.0010306 4.7932244 7.8442244 1 30
34400 7.0023126 1.0024002 4.5665168 8.4702188 1 29
34500 7.3797703 1.000813 4.7224014 8.4098954 1 30
34600 7.7158761 0.99973161 4.7441628 8.5818592 1 29
34700 7.6135895 1.0015768 4.6612844 7.2195952 1 28
34800 7.0458078 0.99992638 4.2805357 7.4162305 1 32
34900 7.6190708 1.0007146 4.8064968 8.2709405 1 27
35000 7.4614294 1.0006051 4.7807207 7.7137359 1 28
35100 7.7008336 1.0008263 4.6823621 7.0208513 1 26
35200 8.1510766 1.000271 5.1781834 7.3231692 1 24
35300 7.5106275 1.0010438 4.6988185 8.9418343 1 25
35400 7.8116652 1.0009688 4.8622216 7.4624002 1 17
35500 7.2159785 1.0027484 4.543984 8.3177043 1 21
35600 7.6978875 1.0004834 4.7021203 8.3706905 1 20
35700 7.7827655 1.0019919 4.775879 8.6083292 1 15
35800 7.8433537 1.001844 4.7506574 7.3250009 1 15
35900 7.9456497 1.0004336 4.7925775 7.9824359 1 18
36000 8.1044513 1.0022261 5.1213755 9.211699 1 16
36100 7.6657532 1.0025661 4.751804 8.9770412 1 19
36200 7.909323 1.0035462 4.8435293 10.232493 1 21
36300 8.4188244 1.0016775 5.4337725 9.2060079 1 24
36400 8.7352689 1.0011274 5.6313351 8.6202832 1 24
36500 8.3459273 1.0005659 5.187336 6.9333716 1 21
36600 7.7118105 1.0018769 4.9293347 8.2789615 1 14
36700 7.8069879 1.0014021 4.7782709 8.4841233 1 15
36800 7.862085 1.0005342 4.8680692 8.1055023 1 16
36900 7.9469362 1.0027815 4.9339095 9.157722 1 16
37000 7.9085375 1.0024851 5.0921374 8.9374239 1 16
37100 8.9464869 1.0005734 5.6837772 8.806998 1 16
37200 8.1482632 1.0021175 5.1266453 8.5772094 1 18
37300 7.7958072 1.0026336 4.788431 8.3233372 1 19
37400 7.3647655 1.0015482 4.4786134 9.6606112 1 23
37500 7.3071882 1.0003912 4.681549 8.6319438 1 17
37600 7.8672509 1.0000478 4.7981944 8.3051478 1 14
37700 7.9306696 0.99923102 4.9316544 9.3672856 1 15
37800 7.7397949 0.99948557 5.1168552 8.5978047 1 17
37900 7.9121039 1.0020122 4.9866234 7.640888 1 14
38000 7.433451 1.0007901 4.6254894 8.0853539 1 14
38100 7.4636908 1.0021552 4.8472833 8.1975615 1 10
38200 7.4453077 1.0010305 4.6910943 7.8192603 1 13
38300 7.0488536 1.0012587 4.5490462 8.190036 1 16
38400 8.0686748 1.0016782 5.0747029 7.7242015 1 15
38500 7.9575875 1.0007137 4.8361776 8.05268 1 15
38600 7.6690498 1.0027522 4.8823286 9.1926516 1 20
38700 7.1567 1.002374 4.5600354 10.098089 1 19
38800 6.9100518 1.0008695 4.4101446 7.8832032 1 19
38900 6.8021882 1.0017647 4.1844125 8.1858761 1 21
39000 8.3996464 1.0010263 4.8183813 8.0997387 1 16
39100 8.4533834 1.0021643 5.074254 11.291904 1 19
39200 8.2406701 1.002062 5.0117425 8.778159 1 24
39300 8.3134114 1.0008218 5.0067136 7.9871787 1 22
39400 7.4307571 1.0014205 4.5858283 8.8596594 1 25
39500 7.1146821 1.0016367 4.5021057 7.4890018 1 22
39600 8.0048978 0.99992107 4.9235747 7.8770845 1 24
39700 8.070853 1.0029024 5.0842957 9.020664 1 21
39800 7.6939108 1.0012543 4.8986595 8.3306129 1 20
39900 7.2915444 1.00267 4.5038291 8.3844384 1 20
40000 7.3023994 1.0020441 4.4960911 8.1023709 1 18
40100 7.0221648 1.0033695 4.6374149 8.3756822 1 24
40200 7.4114756 1.0019246 4.6733475 7.6547258 1 23
40300 7.5323108 1.0005472 4.8284493 8.2820085 1 26
40400 7.3890772 1.0010491 4.6599273 8.9203575 1 19
40500 7.5786764 1.0016114 4.8166885 8.6760107 1 25
40600 8.165763 1.0006961 5.1488995 7.9321524 1 22
40700 8.1277597 0.99933464 5.0441567 10.069551 1 16
40800 8.1050904 1.0024705 5.4408599 8.3244459 1 21
40900 7.805318 1.0022992 4.9965408 9.7193723 1 21
41000 9.0130932 1.0006842 5.7931112 6.1646073 1 20
41100 8.0387975 1.0017359 5.3355655 9.6123191 1 21
41200 8.4484723 1.0014151 5.4461007 8.5146504 1 27
41300 8.6181909 1.0007562 5.2963876 9.1122306 1 30
41400 9.6762899 1.0010931 5.950456 9.2851025 1 25
41500 9.9414226 1.0016186 6.1433384 10.741453 1 24
41600 9.3348435 1.0003483 5.9291766 11.460717 1 20
41700 9.6125587 1.0013661 5.8530052 9.2105722 1 19
41800 11.383056 1.0032034 7.1988684 10.312945 1 22
41900 10.884524 1.0034888 6.9126707 10.775457 1 20
42000 11.071218 1.0026753 7.0004189 10.740627 1 20
42100 11.054304 1.0008347 6.9602414 8.9885498 1 22
42200 22.478691 1.0020466 14.997099 12.72513 1 19
42300 18.303508 1.0027626 11.336523 12.638769 1 18
42400 15.998712 1.0030312 9.4092725 11.070501 1 24
42500 15.034488 1.0024472 9.3543751 11.48052 1 28
42600 14.538257 1.0033153 9.2523745 10.909576 1 27
42700 13.986613 1.001458 8.5544184 10.765136 1 29
42800 13.240256 1.0027899 8.2014429 10.506497 1 32
42900 12.784336 1.0001406 8.0823431 12.258209 1 33
43000 13.374145 1.0012996 8.4207155 10.32817 1 31
43100 13.142334 1.0022503 8.5908808 10.152205 1 32
43200 12.669284 1.0018944 7.8511966 10.580104 1 32
43300 13.155032 1.001144 8.0337768 10.6652 1 39
43400 12.155928 1.0019472 7.5886584 11.234772 1 35
43500 12.385603 1.0007639 7.8865245 9.3868914 1 32
43600 12.236179 1.0027456 7.7521353 10.456701 1 42
43700 11.49535 1.0008758 7.3633144 8.8490079 1 40
43800 11.469157 1.0015845 7.0035577 10.594522 1 41
43900 11.228266 1.0013014 7.0137223 8.0653711 1 38
44000 10.56742 1.0016631 6.6908938 8.1094154 1 35
44100 9.8964699 1.0008351 6.3550438 8.6578181 1 36
44200 9.041539 1.0019541 5.6721401 8.6518043 1 38
44300 9.0767434 1.0034191 5.7446596 8.3838528 1 38
44400 9.2299608 1.0019526 5.7117964 8.3106491 1 37
44500 9.458981 1.0030409 5.7612138 7.7679755 1 37
44600 8.9611997 1.0014848 5.6490756 6.9224078 1 37
44700 8.0853184 1.0018894 5.2288749 8.0910912 1 32
44800 7.9999755 1.0015853 4.8088312 7.1854304 1 30
44900 7.6598023 1.0009751 4.6690664 7.1999858 1 28
45000 7.4939315 1.0010307 4.8119666 7.9615769 1 26
45100 7.4690079 0.99913423 4.9704428 7.6026835 1 32
45200 7.7001199 1.001626 4.9315953 7.4926686 1 25
45300 7.8794405 1.0011648 4.8624857 8.0804457 1 26
45400 7.493909 1.0016257 4.7631808 8.0330626 1 26
45500 7.5963141 1.0005825 4.7220659 7.0971298 1 23
45600 7.9028612 1.0017008 4.9561022 8.440428 1 23
45700 7.2285584 1.0006033 4.5521456 9.385579 1 23
45800 7.5687284 1.0024318 4.8557498 8.3052658 1 23
45900 7.8938604 1.0013937 5.1393944 5.5323667 1 26
46000 8.318466 1.0020803 5.4761811 8.2227801 1 25
46100 7.9169512 1.0024598 5.0406355 8.64365 1 27
46200 7.5535458 1.0016318 4.8010133 9.370726 1 26
46300 7.8926896 1.0001525 5.18463 7.9830196 1 27
46400 7.487145 1.002671 4.7718312 8.300134 1 29
46500 7.3564658 1.0006114 4.6762189 7.34947 1 26
46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27
46700 7.2943203 1.0020164 4.3335327 7.7296507 1 25
46800 8.5849411 1.0014634 5.4501531 9.0933014 1 25
46900 10.176752 1.0023799 6.0456779 9.4050423 1 16
47000 9.1913098 1.0029076 5.7577256 9.1826215 1 22
47100 9.5479771 1.0022102 6.1100973 8.9440056 1 28
47200 9.9944172 1.0004924 6.3649417 9.1507264 1 25
47300 9.3543283 1.0013246 6.0873147 10.41657 1 24
47400 8.594101 1.0020068 5.6864295 9.2388304 1 24
47500 9.3191964 1.002411 6.0537511 9.3506828 1 23
47600 8.1615734 1.001364 5.3757905 10.303962 1 30
47700 8.3615046 1.0003075 5.2727936 9.3162209 1 32
47800 8.3566467 1.0026031 5.4379524 7.7644422 1 33
47900 8.4062556 1.0006471 5.3098736 8.0181121 1 33
48000 8.2233307 1.0012304 4.9650027 9.2644288 1 34
48100 8.4495256 1.000088 4.9940422 10.01023 1 27
48200 8.8068097 1.0014275 5.4732649 8.410093 1 31
48300 8.0008187 1.0017459 4.7732764 9.25726 1 27
48400 7.7242529 1.0026909 4.9084505 8.7147295 1 30
48500 8.3752816 1.001333 5.1071228 8.2267308 1 32
48600 9.0777805 1.0019328 5.7331841 9.6679383 1 29
48700 9.3623061 1.0001767 5.7117062 8.396895 1 25
48800 8.1186637 1.0013185 5.2697427 8.6058372 1 27
48900 7.3685497 1.0007173 4.6097553 7.8047228 1 24
49000 7.1661421 1.0023152 4.5389038 8.8759552 1 22
49100 6.9857144 1.0016394 4.6489319 8.2022359 1 24
49200 6.7160336 1.0018413 4.2488082 8.3393245 1 25
49300 7.9703755 1.0010628 5.2328567 7.968278 1 28
49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27
49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30
49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28
49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25
49800 7.336335 1.0020055 4.6365173 8.7210022 1 30
49900 7.432996 1.0016415 4.7090587 8.7033033 1 29
50000 7.4937053 1.001014 4.7212573 9.0890363 1 29
Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39
Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33
Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60
Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00
Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58
Other | | 1.023 | | | 0.10
Nlocal: 2033.88 ave 2657 max 1198 min
Histogram: 2 0 0 0 0 2 1 0 1 2
Nghost: 1628.12 ave 1719 max 1569 min
Histogram: 2 0 1 1 2 1 0 0 0 1
Neighs: 13566 ave 18212 max 8488 min
Histogram: 1 0 0 1 2 1 2 0 0 1
Total # of neighbors = 108528
Ave neighs/atom = 6.6700264
Neighbor list builds = 2447
Dangerous builds = 2
Total wall time: 0:19:22

243
examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8
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@ -1,243 +0,0 @@
LAMMPS (1 Feb 2014)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big
read_data data.tri.srd
orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
create_atoms 2 region box
Created 91125 atoms
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
125 rigid bodies with 1500 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 67 67 67
SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
SRD per actual grid cell = 0.0647662
SRD viscosity = -1.09837
big/SRD mass density ratio = 24.668
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.9708 35.1504
ave/max big velocity = 0 0
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
Memory usage per processor = 116.135 Mbytes
Step 1 tsmall 2[9] Temp Press
0 0 1.4405441 0 0 -0.15917996
1000 1.0535509 1.1241378 1.1224038 0 0.15526438
2000 2.4635987 1.0240667 0.94231519 0 0.011069846
3000 3.1093028 1.0070585 1.0176028 0 0.34124888
4000 2.9524179 1.0101774 1.0311733 0 -0.22118101
5000 2.9175438 1.0109144 1.0284445 0 0.1839507
6000 3.3200928 0.99108983 0.95968219 0 1.0229339
7000 3.3020156 0.99661428 0.98000621 0 2.3333851
8000 4.1500999 0.99129645 0.99723707 0 4.3054414
9000 6.537028 1.0074533 1.0251098 0 18.782913
10000 16.233245 1.0145766 1.0219787 0 147.83787
Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms
Pair time (%) = 145.018 (63.4492)
Neigh time (%) = 32.6283 (14.2757)
Comm time (%) = 43.3283 (18.9572)
Outpt time (%) = 0.000848889 (0.00037141)
Other time (%) = 7.58254 (3.31755)
Nlocal: 2033.88 ave 2092 max 1902 min
Histogram: 1 0 0 0 1 1 0 1 1 3
Nghost: 2805 ave 2855 max 2751 min
Histogram: 1 0 2 1 0 0 0 2 1 1
Neighs: 30026.5 ave 38700 max 24367 min
Histogram: 1 0 2 1 3 0 0 0 0 1
Total # of neighbors = 240212
Ave neighs/atom = 14.7632
Neighbor list builds = 501
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 40 40 40
SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
SRD per actual grid cell = -1.93929
SRD viscosity = -0.36972
big/SRD mass density ratio = -0.836253
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.0639 40
ave/max big velocity = 2.05735 6.73052
Memory usage per processor = 65.2471 Mbytes
Step 1 tsmall 2[9] Temp Press
10000 16.233245 1.0144194 0 0 146.27032
11000 17.301043 1.0619209 1 0 84.226323
12000 13.481177 1.063945 1 0 80.42834
13000 12.616615 1.0536125 1 0 68.365053
14000 12.16592 1.0581344 1 0 59.709941
15000 10.811557 1.0650453 1 0 59.869798
16000 9.9303081 1.0641012 1 0 59.289126
17000 10.452639 1.0589904 1 0 52.680235
18000 9.2488947 1.0556713 1 0 51.044123
19000 8.7179788 1.0566791 1 0 50.927924
20000 7.8641299 1.0668891 1 0 53.961014
21000 8.4333975 1.0628003 1 0 54.677068
22000 8.554623 1.0591872 1 0 51.784737
23000 7.895462 1.0598512 1 0 53.26885
24000 7.7014869 1.055569 1 0 54.236941
25000 7.508138 1.0581539 1 0 53.297709
26000 8.0707381 1.0586451 1 0 51.411341
27000 8.224223 1.0585509 1 0 52.775784
28000 8.8720461 1.0648837 1 0 49.681447
29000 8.503895 1.0538278 1 0 52.478556
30000 8.2272425 1.0625583 1 0 52.795709
31000 8.4626161 1.0599557 1 0 52.905343
32000 7.7410527 1.0587681 1 0 57.464472
33000 7.2765481 1.0677531 1 0 59.46728
34000 7.036016 1.0640728 1 0 60.636828
35000 8.497203 1.0577458 1 0 55.257312
36000 8.9218761 1.0585038 1 0 55.668201
37000 8.0469115 1.0561193 1 0 58.711565
38000 8.6456966 1.0663818 1 0 53.691658
39000 8.566667 1.0616928 1 0 52.866468
40000 7.7081259 1.0577046 1 0 54.105829
41000 7.4051952 1.0570277 1 0 56.094997
42000 7.331432 1.0632261 1 0 55.661067
43000 7.5587053 1.0602077 1 0 54.30762
44000 7.4521497 1.0594391 1 0 52.993548
45000 7.6234559 1.0641992 1 0 53.352202
46000 8.0659693 1.0609367 1 0 50.302682
47000 7.5227882 1.0563543 1 0 50.43551
48000 8.0798684 1.0628968 1 0 48.419201
49000 7.130784 1.0594143 1 0 50.656081
50000 7.3219268 1.0608236 1 0 54.808358
Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms
Pair time (%) = 1232.76 (74.6296)
Neigh time (%) = 171.893 (10.4061)
Comm time (%) = 193.625 (11.7218)
Outpt time (%) = 0.00338289 (0.000204795)
Other time (%) = 53.5578 (3.24231)
Nlocal: 2033.88 ave 2229 max 1953 min
Histogram: 2 1 2 2 0 0 0 0 0 1
Nghost: 2757.88 ave 2810 max 2692 min
Histogram: 1 1 1 0 1 0 0 1 1 2
Neighs: 30098.6 ave 37369 max 25592 min
Histogram: 1 3 0 1 0 1 1 0 0 1
Total # of neighbors = 240789
Ave neighs/atom = 14.7987
Neighbor list builds = 2007
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

7
examples/COUPLE/plugin/CMakeLists.txt
View File

@ -1,9 +1,8 @@
##########################################
# CMake build system for coupling to the LAMMPS library
# -*- CMake -*- file for example programs that use the LAMMPS library
# where the library is loaded dynamically at runtime.
##########################################
cmake_minimum_required(VERSION 3.10)
cmake_minimum_required(VERSION 3.16)
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
@ -23,10 +22,8 @@ endif()
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()

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