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

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This commit is contained in:
Richard Berger
2021-05-25 17:15:23 -04:00
parent a3a2bdc8f6 92e995d3a2
commit 735c5c52dc
3535 changed files with 30221 additions and 26577 deletions
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1
.gitattributes vendored
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@ -2,3 +2,4 @@
.gitignore export-ignore
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore

16
.github/CODEOWNERS vendored
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@ -13,29 +13,37 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @akohlmey
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/USER-BROWNIAN/* @samueljmcameron
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
src/USER-FEP/* @agiliopadua
src/USER-HDNNP/* @singraber
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MDI/* @taylor-a-barnes
src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PACE/* @yury-lysogorskiy
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-REACTION/* @jrgissing
src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
@ -47,7 +55,6 @@ src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-REACTION/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
@ -122,6 +129,8 @@ tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/code_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/offline/* @rbberger
# tests
unittest/* @akohlmey @rbberger
@ -130,7 +139,7 @@ unittest/* @akohlmey @rbberger
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
cmake/presets/*.cmake @akohlmey
# python
python/* @rbberger
@ -142,6 +151,7 @@ fortran/* @akohlmey
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
examples/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

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

35
SECURITY.md Normal file
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@ -0,0 +1,35 @@
# Security Policy
LAMMPS is designed as a user-level application to conduct computer
simulations for research using classical mechanics. As such LAMMPS
depends to some degrees on users providing correctly formatted input and
LAMMPS needs to read and write files based on uncontrolled user input.
As a parallel application for use in high-performance computing
environments, performance critical steps are also done without checking
data.
LAMMPS also is interfaced to a number of external libraries, including
libraries with experimental research software, that are not validated
and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.

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

4
bench/README
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@ -2,7 +2,7 @@ LAMMPS benchmark problems
This directory contains 5 benchmark problems which are discussed in
the Benchmark section of the LAMMPS documentation, and on the
Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
This directory also has several sub-directories:
@ -11,7 +11,7 @@ KEPLER benchmark scripts for GPU cluster with Kepler GPUs
POTENTIALS benchmarks scripts for various potentials in LAMMPS
The results for all of these benchmarks are displayed and discussed on
the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
The remainder of this file refers to the 5 problems in the top-level
of this directory and how to run them on CPUs, either in serial or

17
cmake/CMakeLists.txt
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@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
if(POLICY CMP0074)
cmake_policy(SET CMP0074 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()
########################################
project(lammps CXX)
@ -104,6 +109,12 @@ endif()
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
# allow enabling clang-tidy for C++ files
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
@ -121,7 +132,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
@ -324,8 +335,8 @@ else()
set(CUDA_REQUEST_PIC)
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

10
cmake/Modules/CodingStandard.cmake
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@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

118
cmake/Modules/Packages/USER-MDI.cmake Normal file
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@ -0,0 +1,118 @@
find_package(mdi QUIET)
if(${mdi_FOUND})
set(DOWNLOAD_MDI_DEFAULT OFF)
else()
set(DOWNLOAD_MDI_DEFAULT ON)
endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)
# only ON/OFF are allowed for "mpi" flag when building MDI library
# so translate boolean value of BUILD_MPI
# always disable MPI when cross-compiling to Windows.
if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
set(MDI_USE_MPI ON)
else()
set(MDI_USE_MPI OFF)
endif()
# 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)
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if (PYTHONLIBS_FOUND)
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()
# download/ build MDI library
# always build static library with -fpic
# support cross-compilation and ninja-build
include(ExternalProject)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-Dlanguage=C
-Dlibtype=STATIC
-Dmpi=${MDI_USE_MPI}
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
set(MDI_DEP_LIBS "")
# 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}")
endif()
if(MDI_DEP_LIBS)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}")
endif()
target_link_libraries(lammps PRIVATE LAMMPS::MDI)
target_link_libraries(lmp PRIVATE LAMMPS::MDI)
else()
find_package(mdi)
if(NOT mdi_FOUND)
message(FATAL_ERROR "MDI library not found. Help CMake to find it "
"by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
"to download and compile it")
endif()
# Link the lammps library against MDI
target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
# Link the lammps executable against MDI
target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

3
cmake/Modules/Packages/USER-PACE.cmake
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@ -14,13 +14,12 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)

18
cmake/Modules/YAML.cmake
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@ -6,15 +6,27 @@ set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of li
mark_as_advanced(YAML_URL)
mark_as_advanced(YAML_MD5)
# support cross-compilation to windows
if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
set(YAML_CROSS_HOST --host=i686-mingw64)
elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(YAML_CROSS_HOST --host=x86_64-mingw64)
else()
message(FATAL_ERROR "Unsupported cross-compilation "
" for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
" on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
endif()
endif()
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")

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

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

14
cmake/presets/all_off.cmake
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@ -5,13 +5,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

14
cmake/presets/all_on.cmake
View File

@ -7,13 +7,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

10
cmake/presets/clang.cmake
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@ -4,10 +4,18 @@ set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

8
cmake/presets/download.cmake
View File

@ -1,7 +1,7 @@
# preset that turns on packages with automatic downloads of sources of potentials
# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@ -9,9 +9,11 @@ endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_LATTE 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)
set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)

12
cmake/presets/intel.cmake
View File

@ -3,10 +3,20 @@
set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

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

@ -1,11 +1,11 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-PACE USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-YAFF)

2
cmake/presets/nolib.cmake
View File

@ -4,7 +4,7 @@
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})

14
cmake/presets/oneapi.cmake
View File

@ -1,12 +1,22 @@
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

8
doc/Makefile
View File

@ -68,7 +68,6 @@ help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML pages in html dir"
@echo " pdf create Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@ -185,13 +184,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@rm -rf latex/PDF/.[sg]*
@echo "Build finished. Manual.pdf is in this directory."
fetch:
@rm -rf html_www Manual_www.pdf
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
anchor_check : $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\

13
doc/README
View File

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

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "8 April 2021" "2021-04-08"
.TH LAMMPS "14 May 2021" "2021-05-14"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

50
doc/src/Build_development.rst
View File

@ -28,6 +28,28 @@ variable VERBOSE set to 1:
----------
.. _clang-tidy:
Enable static code analysis with clang-tidy
-------------------------------------------
The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
static code analysis tool to diagnose (and potentially fix) typical
programming errors or coding style violations. It has a modular framework
of tests that can be adjusted to help identifying problems before they
become bugs and also assist in modernizing large code bases (like LAMMPS).
It can be enabled for all C++ code with the following CMake flag
.. code-block:: bash
-D ENABLE_CLANG_TIDY=value # value = no (default) or yes
With this flag enabled all source files will be processed twice, first to
be compiled and then to be analyzed. Please note that the analysis can be
significantly more time consuming than the compilation itself.
----------
.. _iwyu_processing:
Report missing and unneeded '#include' statements
@ -447,12 +469,24 @@ The following options are available.
.. code-block:: bash
make check-whitespace # generate coverage report in HTML format
make fix-whitespace # generate coverage report in XML format
make check-permissions # delete folder with HTML format coverage report
make fix-permissions # delete all collected coverage data and HTML output
make check-whitespace # search for files with whitespace issues
make fix-whitespace # correct whitespace issues in files
make check-homepage # search for files with old LAMMPS homepage URLs
make fix-homepage # correct LAMMPS homepage URLs in files
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
For the code in the ``unittest`` tree we are using the `clang-format`
tool (Clang version 8.0 or later is required). If available, the source
code files in the ``unittest`` tree can be updated to conform to the
formatting settings using ``make format-tests``.
For the code in the ``unittest`` and ``src`` trees we are transitioning
to use the `clang-format` tool to assist with having a consistent source
code style. The `clang-format` command bundled with Clang version 8.0
or later is required. The configuration is in files ``.clang-format``
in the respective folders. Since the modifications from `clang-format`
can be significant and - especially for "legacy style code" - also is
not always improving readability, a large number of files currently have
a ``// clang-format off`` at the top, which will disable the processing.
Over time, files will be refactored and updated to that `clang-format`
may be applied to them (at least in part).
If `clang-format` is available, the source code files in the ``unittest``
tree can be updated to conform to the formatting settings using
``make format-tests`` and the files in ``src`` with ``make format-src``.

30
doc/src/Build_extras.rst
View File

@ -49,6 +49,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
@ -1539,6 +1540,35 @@ TBB and MKL.
----------
.. _user-mdi:
USER-MDI package
-----------------------------
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes
.. tab:: Traditional make
Before building LAMMPS, you must build the MDI Library in
``lib/mdi``\ . You can do this by executing a command like one
of the following from the ``lib/mdi`` directory:
.. code-block:: bash
$ python Install.py -m gcc # build using gcc compiler
$ python Install.py -m icc # build using icc compiler
The build should produce two files: ``lib/mdi/includelink/mdi.h``
and ``lib/mdi/liblink/libmdi.so``\ .
----------
.. _user-mesont:
USER-MESONT package

31
doc/src/Build_manual.rst
View File

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

1
doc/src/Commands_all.rst
View File

@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`mdi/engine <mdi_engine>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min_modify <min_modify>`

1
doc/src/Commands_fix.rst
View File

@ -101,6 +101,7 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/engine <fix_mdi_engine>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`

6
doc/src/Errors_bugs.rst
View File

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

2
doc/src/Errors_common.rst
View File

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

2
doc/src/Errors_messages.rst
View File

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

6
doc/src/Examples.rst
View File

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

3
doc/src/Howto.rst
View File

@ -3,7 +3,7 @@ Howto discussions
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
`glossary <https://lammps.sandia.gov/glossary.html>`_ website page also lists MD
`glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples directory of the LAMMPS
distribution and highlighted on the :doc:`Examples <Examples>` doc page
@ -23,6 +23,7 @@ General howto
Howto_library
Howto_couple
Howto_client_server
Howto_mdi
Settings howto
==============

132
doc/src/Howto_mdi.rst Normal file
View File

@ -0,0 +1,132 @@
Using LAMMPS with the MDI library for code coupling
===================================================
.. note::
This Howto doc page will eventually replace the
:doc:`Howto client/server <Howto_client_server>` doc page.
Client/server coupling of two codes is where one code is the "client"
and sends request messages (data) to a "server" code. The server
responds to each request with a reply message. This enables the two
codes to work in tandem to perform a simulation. LAMMPS can act as
either a client or server code; it does this by using the `MolSSI
Driver Interface (MDI) library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
developed by the `Molecular Sciences Software Institute (MolSSI)
<https://molssi.org>`_.
Alternate methods for code coupling with LAMMPS are described on the
:doc:`Howto couple <Howto_couple>` doc page.
Some advantages of client/server coupling are that the two codes can run
as stand-alone executables; they need not be linked together. Thus
neither code needs to have a library interface. This also makes it easy
to run the two codes on different numbers of processors. If a message
protocol (format and content) is defined for a particular kind of
simulation, then in principle any code which implements the client-side
protocol can be used in tandem with any code which implements the
server-side protocol. Neither code needs to know what specific other
code it is working with.
In MDI nomenclature, a client code is the "driver", and a server code is
an "engine". One driver code can communicate with one or more instances
of one or more engine codes. Driver and engine codes can be written in
any language: C, C++, Fortran, Python, etc.
In addition to allowing driver and engine(s) running to run as
stand-alone executables, MDI also enables a server code to be a
"plugin" to the client code. In this scenario, server code(s) are
compiled as shared libraries, and one (or more) instances of the
server are instantiated by the driver code. If the driver code runs
in parallel, it can split its MPI communicator into multiple
sub-communicators, and launch each plugin engine instance on a
sub-communicator. Driver processors in that sub-communicator exchange
messages with that engine instance, and can also send MPI messages to
other processors in the driver. The driver code can also destroy
engine instances and re-instantiate them.
The way that a driver communicates with an engine is by making
MDI_Send() and MDI_Recv() calls, which are conceptually similar to
MPI_Send() and MPI_Recv() calls. Each send or receive has a string
which identifies the command name, and optionally some data, which can
be a single value or vector of values of any data type. Inside the
MDI library, data is exchanged between the driver and engine via MPI
calls or sockets. This a run-time choice by the user.
-------------
As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
suite of quantum DFT codes), can work together via the MDI library to
perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
simulation and sends a message each timestep to ``pw.x`` asking it to
compute quantum forces on the current configuration of atoms. Here is
how the 2 codes are launched to communicate by MPI:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
-in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
processors.
Here is how the 2 codes are launched to communicate by sockets:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
These commands could be issued in different windows on a desktop
machine. Or in the same window, if the first command is ended with
"&" so as to run in the background. If "localhost" is replaced by an
IP address, ``pw.x`` could be run on another machine on the same network, or
even on another machine across the country.
After both codes initialize themselves to model the same system, this is
what occurs each timestep:
* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
* LAMMPS receives the forces and time integrates to complete a single timestep
-------------
Examples scripts for using LAMMPS as an MDI engine are in the
examples/mdi directory. See the README file in that directory for
instructions on how to run the examples.
.. note::
Work is underway to add commands that allow LAMMPS to be used as an
MDI driver, e.g. for the AIMD example discussed above. Example
scripts for this usage mode will be added the same directory when
available.
If LAMMPS is used as a stand-alone engine it should set up the system
it will be modeling in its input script, then invoke the
:doc:`mdi/engine <mdi_engine>` command. This will put LAMMPS into
"engine mode" where it waits for messages and data from the driver.
When the driver sends an "EXIT" command, LAMMPS will exit engine mode
and the input script will continue.
If LAMMPS is used as a plugin engine it operates the same way, except
that the driver will pass LAMMPS an input script to initialize itself.
Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
input script will continue. After finishing execution of the input
script, the instance of LAMMPS will be destroyed.
LAMMPS supports the full set of MD-appropriate engine commands defined
by the MDI library. See the :doc:`mdi/engine <mdi_engine>` doc page for
a list of these.
If those commands are not sufficient for a user-developed driver to use
LAMMPS as an engine, then new commands can be easily added. See these
two files which implement the definition of MDI commands and the logic
for responding to them:
* src/MDI/mdi_engine.cpp
* src/MDI/fix_mdi_engine.cpp

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

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

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

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

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

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

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

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

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

27
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@ -15,7 +15,7 @@ the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the
code. It includes links to an on-line version of this manual, a
`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
`mailing list <https://www.lammps.org/mail.html>`_ where users can
post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
where all LAMMPS development is coordinated.
@ -30,11 +30,13 @@ please :ref:`see this note <webbrowser>`.
-----------
The manual is organized in two parts:
The manual is organized in three parts:
1) the :ref:`User Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
and use LAMMPS, 2) the :ref:`Programmer Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS.
programming languages and how to modify and extend LAMMPS, and 3) the
:ref:`Command Reference <command_reference>` which includes detailed
descriptions of all commands included in the LAMMPS code.
.. only:: html
@ -42,7 +44,7 @@ programming languages and how to modify and extend LAMMPS.
:doc:`this page <Commands_all>` since it gives quick access
the documentation for all LAMMPS commands.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
----------
@ -89,10 +91,15 @@ Programmer Guide
Modify
Developer
*****************
Command Reference
*****************
.. _command_reference:
.. toctree::
:caption: Index
:name: index
:hidden:
:name: reference
:maxdepth: 1
:caption: Command Reference
commands_list
fixes
@ -118,10 +125,10 @@ Indices and tables
.. admonition:: Web Browser Compatibility
The HTML version of the manual makes use of advanced features present
int "modern" web browsers. This can lead to incompatibilities with older
in "modern" web browsers. This can lead to incompatibilities with older
web browsers (released more than 4 years ago) and specific vendor browsers
(e.g. Internet Explorer on Windows; Microsoft Edge works well though)
where parts of the pages are not rendered as expected (e.g. the layout is
broken or mathematical expressions not typeset). In that case we
recommend to install/use a different/newer web browser or use
the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.
the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.

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

87
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@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS
===============================================
We encourage users to submit new features or modifications for LAMMPS to
`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
`the core developers <https://www.lammps.org/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage and
coordinate this is via the LAMMPS project on `GitHub
<https://github.com/lammps/lammps>`_. Please see the :doc:`GitHub
@ -10,15 +10,15 @@ Tutorial <Howto_github>` for a demonstration on how to do that. An
alternative is to contact the LAMMPS developers or the indicated
developer of a package or feature directly and send in your contribution
via e-mail, but that can add a significant delay on getting your
contribution included, depending on how busy the developer is you
contact, how complex a task it would be to integrate that code, and how
contribution included, depending on how busy the respective developer
is, how complex a task it would be to integrate that code, and how
many - if any - changes are required before the code can be included.
For any larger modifications or programming project, you are encouraged
to contact the LAMMPS developers ahead of time, in order to discuss
implementation strategies and coding guidelines, that will make it
easier to integrate your contribution and result in less work for
everybody involved. You are also encouraged to search through the list
to contact the LAMMPS developers ahead of time in order to discuss
implementation strategies and coding guidelines. That will make it
easier to integrate your contribution and results in less work for
everybody involved. You are also encouraged to search through the list
of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
and submit a new issue for a planned feature, so you would not duplicate
the work of others (and possibly get scooped by them) or have your work
@ -31,21 +31,22 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
you are working on. Only discussions related to LAMMPS development are
tolerated, so this is **NOT** for people that look for help with compiling,
installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
list <https://www.lammps.org/mail.html>`_ for those purposes instead.
How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how much it requires
changes to the core codebase, and of how much interest it is to the
larger LAMMPS community. Please see below for a checklist of typical
requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
Tutorial <Howto_github>` page for instructions on
how to submit your changes or new files through a GitHub pull
request. If you prefer to submit patches or full files, you should first
make certain, that your code works correctly with the latest patch-level
version of LAMMPS and contains all bug fixes from it. Then create a
gzipped tar file of all changed or added files or a corresponding patch
file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
use gzip compression, as this works well on all platforms.
much effort it will cause to integrate and test it, how many and what
kind of changes it requires to the core codebase, and of how much
interest it is to the larger LAMMPS community. Please see below for a
checklist of typical requirements. Once you have prepared everything,
see the :doc:`LAMMPS GitHub Tutorial <Howto_github>` page for
instructions on how to submit your changes or new files through a GitHub
pull request. If you prefer to submit patches or full files, you should
first make certain, that your code works correctly with the latest
patch-level version of LAMMPS and contains all bug fixes from it. Then
create a gzipped tar file of all changed or added files or a
corresponding patch file using 'diff -u' or 'diff -c' and compress it
with gzip. Please only use gzip compression, as this works well and is
available on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`. Else we will add them as a
@ -57,13 +58,16 @@ added to the LAMMPS distribution. All the standard and user packages
are listed and described on the :doc:`Packages details <Packages_details>` doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license
<Intro_opensource>` doc page for details.
them open-source, i.e. we can release them under the terms of the GPL
(version 2), used as a license for the rest of LAMMPS. And as part of
a LGPL (version 2.1) distribution that we make available to developers
on request only and with files that are authorized for that kind of
distribution removed (e.g. interface to FFTW). See the
:doc:`LAMMPS license <Intro_opensource>` doc page for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_
code and on the `Authors page <https://www.lammps.org/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
@ -77,13 +81,13 @@ unusual event).
If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
`developers <https://lammps.sandia.gov/authors.html>`_ with info about
`developers <https://www.lammps.org/authors.html>`_ with info about
your package and we will post it there.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
@ -92,7 +96,7 @@ LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you should `communicate with the
developers <https://lammps.sandia.gov/authors.html>`_, since we may or
developers <https://www.lammps.org/authors.html>`_, since we may or
may not want to include those changes for some reason. An example of a
trivial change is making a parent-class method "virtual" when you derive
a new child class from it.
@ -112,7 +116,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
your contribution(s) to be added to main LAMMPS code or one of its
standard packages, it needs to be written in a style compatible with
other LAMMPS source files. This means: 2-character indentation per
level, **no tabs**\ , no lines over 80 characters. I/O is done via
level, **no tabs**\ , no lines over 100 characters. I/O is done via
the C-style stdio library (mixing of stdio and iostreams is generally
discouraged), class header files should not import any system headers
outside of <cstdio>, STL containers should be avoided in headers,
@ -131,6 +135,31 @@ packages in the src directory for examples. If you are uncertain, please ask.
LAMMPS source files, including the use of the error class for error
and warning messages.
* To simplify reformatting contributed code in a way that is compatible
with the LAMMPS formatting styles, you can use clang-format (version 8
or later). The LAMMPS distribution includes a suitable ``.clang-format``
file which will be applied if you run ``clang-format -i some_file.cpp``
on your files inside the LAMMPS src tree. Please only reformat files
that you have contributed. For header files containing a
``SomeStyle(keyword, ClassName)`` macros it is required to have this
macro embedded with a pair of ``// clang-format off``, ``// clang-format on``
commends and the line must be terminated with a semi-colon (;).
Example:
.. code-block:: c++
#ifdef COMMAND_CLASS
// clang-format off
CommandStyle(run,Run);
// clang-format on
#else
#ifndef LMP_RUN_H
[...]
You may also use ``// clang-format on/off`` throughout your file
to protect sections of the file from being reformatted.
* If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a \*.cpp and \*.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line

87
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@ -82,6 +82,7 @@ page gives those details.
* :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MDI <PKG-USER-MDI>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`USER-MESODPD <PKG-USER-MESODPD>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
@ -132,8 +133,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE
* examples/ellipse
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#tri
* https://www.lammps.org/movies.html#line
* https://www.lammps.org/movies.html#tri
----------
@ -329,7 +330,7 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
* :doc:`package gpu <package>`
* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
for styles followed by (g)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -355,11 +356,11 @@ potentials.
* examples/granregion
* examples/pour
* bench/in.chute
* https://lammps.sandia.gov/pictures.html#jamming
* https://lammps.sandia.gov/movies.html#hopper
* https://lammps.sandia.gov/movies.html#dem
* https://lammps.sandia.gov/movies.html#brazil
* https://lammps.sandia.gov/movies.html#granregion
* https://www.lammps.org/pictures.html#jamming
* https://www.lammps.org/movies.html#hopper
* https://www.lammps.org/movies.html#dem
* https://www.lammps.org/movies.html#brazil
* https://www.lammps.org/movies.html#granregion
----------
@ -446,7 +447,7 @@ time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
You must have a C++14 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
@ -478,7 +479,7 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (k)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -602,7 +603,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>`
* https://lammps.sandia.gov/movies.html#gcmc
* https://www.lammps.org/movies.html#gcmc
----------
@ -659,8 +660,8 @@ listing, "ls src/MISC", to see the list of commands.
* :doc:`fix viscosity <fix_viscosity>`
* examples/KAPPA
* examples/VISCOSITY
* https://lammps.sandia.gov/pictures.html#ttm
* https://lammps.sandia.gov/movies.html#evaporation
* https://www.lammps.org/pictures.html#ttm
* https://www.lammps.org/movies.html#evaporation
----------
@ -815,7 +816,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* :doc:`OPT package <Speed_opt>`
* :doc:`Section 2.6 -sf opt <Run_options>`
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -846,7 +847,7 @@ Foster (UTSA).
* :doc:`compute damage/atom <compute_damage_atom>`
* :doc:`compute plasticity/atom <compute_plasticity_atom>`
* examples/peri
* https://lammps.sandia.gov/movies.html#peri
* https://www.lammps.org/movies.html#peri
----------
@ -1007,8 +1008,8 @@ Also several computes which calculate properties of rigid bodies.
* examples/ASPHERE
* examples/rigid
* bench/in.rhodo
* https://lammps.sandia.gov/movies.html#box
* https://lammps.sandia.gov/movies.html#star
* https://www.lammps.org/movies.html#box
* https://www.lammps.org/movies.html#star
----------
@ -1109,9 +1110,9 @@ colloidal particles.
* :doc:`fix wall/srd <fix_wall_srd>`
* examples/srd
* examples/ASPHERE
* https://lammps.sandia.gov/movies.html#tri
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#poly
* https://www.lammps.org/movies.html#tri
* https://www.lammps.org/movies.html#line
* https://www.lammps.org/movies.html#poly
----------
@ -1203,7 +1204,7 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
* src/USER-ATC/README
* :doc:`fix atc <fix_atc>`
* examples/USER/atc
* https://lammps.sandia.gov/pictures.html#atc
* https://www.lammps.org/pictures.html#atc
----------
@ -1336,7 +1337,7 @@ acids.
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/USER/cgsdk
* https://lammps.sandia.gov/pictures.html#cg
* https://www.lammps.org/pictures.html#cg
----------
@ -1573,7 +1574,7 @@ tools/eff; see its README file.
* examples/USER/eff
* tools/eff/README
* tools/eff
* https://lammps.sandia.gov/movies.html#eff
* https://www.lammps.org/movies.html#eff
----------
@ -1682,7 +1683,7 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
* src/USER-INTEL/TEST
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -1787,7 +1788,29 @@ Waltham, MA, USA)
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* examples/USER/manifold
* https://lammps.sandia.gov/movies.html#manifold
* https://www.lammps.org/movies.html#manifold
----------
.. _PKG-USER-MDI:
USER-MDI package
----------------
**Contents:**
A LAMMPS command and fix to allow client-server coupling of LAMMPS to
other atomic or molecular simulation codes via the `MolSSI Driver Interface
(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
**Supporting info:**
* src/USER-MDI/README
* :doc:`mdi/engine <mdi_engine>`
* :doc:`fix mdi/engine <fix_mdi_engine>`
* examples/USER/mdi
----------
@ -1843,10 +1866,10 @@ algorithm.
* :doc:`pair_style tdpd <pair_mesodpd>`
* :doc:`fix mvv/dpd <fix_mvv_dpd>`
* examples/USER/mesodpd
* https://lammps.sandia.gov/movies.html#mesodpd
* https://www.lammps.org/movies.html#mesodpd
* examples/USER/meso
* http://lammps.sandia.gov/movies.html#mesodpd
* http://www.lammps.org/movies.html#mesodpd
----------
@ -2062,7 +2085,7 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (o)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -2245,8 +2268,8 @@ molecules, and chiral-sensitive reactions.
* src/USER-REACTION/README
* :doc:`fix bond/react <fix_bond_react>`
* examples/USER/reaction
* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org
----------
@ -2373,7 +2396,7 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do
* src/USER-SMD/README
* doc/PDF/SMD_LAMMPS_userguide.pdf
* examples/USER/smd
* https://lammps.sandia.gov/movies.html#smd
* https://www.lammps.org/movies.html#smd
----------
@ -2430,7 +2453,7 @@ Dynamics, Ernst Mach Institute, Germany).
* src/USER-SPH/README
* doc/PDF/SPH_LAMMPS_userguide.pdf
* examples/USER/sph
* https://lammps.sandia.gov/movies.html#sph
* https://www.lammps.org/movies.html#sph
----------

6
doc/src/Packages_standard.rst
View File

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

6
doc/src/Packages_user.rst
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@ -59,12 +59,14 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
@ -81,7 +83,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

19
doc/src/Run_options.rst
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@ -10,6 +10,7 @@ letter abbreviation can be used:
* :ref:`-i or -in <file>`
* :ref:`-k or -kokkos <run-kokkos>`
* :ref:`-l or -log <log>`
* :ref:`-mdi <mdi>`
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
@ -196,9 +197,23 @@ Option -plog will override the name of the partition log files file.N.
----------
.. _mdi:
**-mdi 'multiple flags'**
This flag is only recognized and used when LAMMPS has support for the MolSSI
Driver Interface (MDI) included as part of the :ref:`USER-MDI <PKG-USER-MDI>`
package. This flag is specific to the MDI library and controls how LAMMPS
interacts with MDI. There are usually multiple flags that have to follow it
and those have to be placed in quotation marks. For more information about
how to launch LAMMPS in MDI client/server mode please refer to the
:doc:`MDI Howto <Howto_mdi>`.
----------
.. _mpicolor:
**-mpicolor** color
**-mpicolor color**
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
@ -223,7 +238,7 @@ links with from the lib/message directory. See the
.. _cite:
**-cite style or file name**
**-cite style** or **file name**
Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are

2
doc/src/Speed.rst
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@ -12,7 +12,7 @@ accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi co-processors.
The `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS
The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
web site gives performance results for the various accelerator
packages discussed on the :doc:`Speed packages <Speed_packages>` doc
page, for several of the standard LAMMPS benchmark problems, as a

8
doc/src/Speed_bench.rst
View File

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

2
doc/src/Speed_gpu.rst
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@ -152,7 +152,7 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is
usually resulting in inferior performance compared to using LAMMPS' native
threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the GPU package on various
hardware, including the Titan HPC platform at ORNL.

2
doc/src/Speed_kokkos.rst
View File

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

2
doc/src/Speed_packages.rst
View File

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

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

1
doc/src/angle_table.rst
View File

@ -69,7 +69,6 @@ parenthesized comments):
HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...

2
doc/src/atom_modify.rst
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@ -80,7 +80,7 @@ LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The *map* keyword thus
allows you to force the creation of a map. The *yes* value will
create either an *array* or *hash* style map, as explained in the next
paragraph. The *array* and *hash* values create an atom-style or
paragraph. The *array* and *hash* values create an array-style or
hash-style map respectively.
For an *array*\ -style map, each processor stores a lookup table of

30
doc/src/comm_modify.rst
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@ -34,7 +34,7 @@ Examples
comm_modify mode multi reduce/multi
comm_modify mode multi group solvent
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify vel yes
comm_modify mode single cutoff 5.0 vel yes
comm_modify cutoff/multi * 0.0
@ -75,8 +75,8 @@ communicated. in *multi/old*, a similar technique is used but atoms
are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
:doc:`neighbor multi/old <neighbor>` commands for
neighbor list construction options that may also be beneficial for
simulations of this kind. The *multi* communiction mode is only compatable
with the *multi* neighbor style. The *multi/old* communication mode is compatble
simulations of this kind. The *multi* communication mode is only compatible
with the *multi* neighbor style. The *multi/old* communication mode is comparable
with both the *multi* and *multi/old* neighbor styles.
The *cutoff* keyword allows you to extend the ghost cutoff distance
@ -97,18 +97,18 @@ warning is printed, if this bond based estimate is larger than the
communication cutoff used.
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
communication mode *multi* instead. Since the communication
cutoffs are determined per atom collections, a collection specifier is needed and
cutoff for one or multiple collections can be extended. Also ranges of collections
using the usual asterisk notation can be given.
Collections are indexed from 1 to N where N is the total number of collections.
communication mode *multi* instead. Since the communication cutoffs are
determined per atom collections, a collection specifier is needed and
cutoff for one or multiple collections can be extended. Also ranges of
collections using the usual asterisk notation can be given. Collections
are indexed from 1 to N where N is the total number of collections.
Note that the arguments for *cutoff/multi* are parsed right before each
simulation to account for potential changes in the number of collections.
Custom cutoffs are preserved between runs but if collections are redefined,
one may want to respecify communication cutoffs.
For granular pair styles,the default cutoff is set to the sum of the
current maximum atomic radii for each collection.
The *cutoff/multi/old* option is similar to *cutoff/multi* except it
simulation to account for potential changes in the number of
collections. Custom cutoffs are preserved between runs but if
collections are redefined, one may want to re-specify the communication
cutoffs. For granular pair styles,the default cutoff is set to the sum
of the current maximum atomic radii for each collection. The
*cutoff/multi/old* option is similar to *cutoff/multi* except it
operates on atom types as opposed to collections.
The *reduce/multi* option applies to *multi* and sets the communication
@ -147,7 +147,7 @@ ghost cutoff should be set.
In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
:doc:`pairwise potential <pair_style>` needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
performs (e.g. locate neighbors of ghost atoms in a manybody pair
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.

1
doc/src/commands_list.rst
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@ -59,6 +59,7 @@ Commands
lattice
log
mass
mdi_engine
message
min_modify
min_spin

1
doc/src/fix.rst
View File

@ -244,6 +244,7 @@ accelerated styles exist.
* :doc:`lb/viscous <fix_lb_viscous>` -
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
* :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

5
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@ -92,6 +92,11 @@ The :doc:`thermo_modify <thermo_modify>` *press* option is supported
by this fix to add the rescaled kinetic pressure as part of
:doc:`thermodynamic output <thermo_style>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the effective
temperature :math:`T_{eff}`. The scalar value calculated by this
fix is "intensive".
Restrictions
""""""""""""

59
doc/src/fix_mdi_engine.rst Normal file
View File

@ -0,0 +1,59 @@
.. index:: fix mdi/engine
fix mdi/engine command
======================
Syntax
""""""
.. parsed-literal::
fix ID group-ID mdi/engine
* ID, group-ID are documented in :doc:`fix <fix>` command
* mdi/engine = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all mdi/engine
Description
"""""""""""
This fix is used along with the :doc:`mdi/engine <mdi_engine>` command
to enable LAMMPS to use the `MDI Library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ to run as
an MDI engine. The fix provides hooks that enable MDI driver codes to
communicate with LAMMPS at various points within a LAMMPS timestep.
It is not generally necessary to add this fix to a LAMMPS input file,
even when using the :doc:`mdi/engine <mdi_engine>` command. If the
:doc:`mdi/engine <mdi_engine>` command is executed and this fix is not
present, it will automatically be added and applied as a new fix for
all atoms for the duration of the command. Thus it is only necessary
to add this fix to an input file when you want to modify the group-ID
or the ordering of this fix relative to other fixes in the input script.
For more information about running LAMMPS as an MDI engine, see the
:doc:`mdi/engine <mdi_engine>` command and the :doc:`Howto mdi
<Howto_mdi>` doc page.
Restrictions
""""""""""""
This command is part of the USER-MDI package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`mdi/engine <mdi_engine>`
Default
"""""""
none

2
doc/src/fix_wall_gran_region.rst
View File

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

88
doc/src/mdi_engine.rst Normal file
View File

@ -0,0 +1,88 @@
.. index:: mdi/engine
mdi_engine command
==================
Syntax
""""""
.. parsed-literal::
mdi_engine
Description
"""""""""""
This command is used to have LAMMPS act as a server with another
client code to effectively couple the two codes together in
client/server mode.
More specifically, this command causes LAMMPS to begin using the `MDI
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
to run as an MDI engine (server), responding to commands made by an
external MDI driver code (client). See the :doc:`Howto mdi
<Howto_mdi>` doc page for more information about how LAMMPS can work
as both an MDI driver or engine.
General information about launching codes that communicate using the
MDI Library can be found in the `corresponding page
<https://molssi-mdi.github.io/MDI_Library/html/library_page.html#library_launching_sec>`_
of the MDI Library's documentation.
----------
This command should typically be used in an input script after LAMMPS
has setup the system it is going to model in collaboration with the
driver code. Depending on how the driver code tells the LAMMPS engine
to exit, other commands can be executed after this command, but
typically it should be used at the end of the LAMMPS input script.
To act as a MD-based MDI engine, this is the list of MDI commands from
a driver code which LAMMPS currently recognizes. See more details
about these commands in the `MDI library documentation
<https://molssi-mdi.github.io/MDI_Library/html/mdi_standard.html>`_
.. NOTE: Taylor - is this the best link for this info? Can we flesh this
.. out with the full list of supported commands? Maybe the distinction
.. of what "node" the commands refer to is not needed in this table?
.. list-table::
:widths: 20 80
:header-rows: 1
* - Command name
- Action
* - >NATOMS
- Driver sends the number of atoms in the system
* - <NATOMS
- Driver requests the number of atoms in the system
* - <COORDS
- Driver requests 3*N double-precision atom coordinates
* - >FORCES
- Driver sends 3*N double-precision atom forces
* - <COORDS
- Driver requests 3*N double-precision atom forces
* - EXIT
- Driver tells the engine (LAMMPS) to exit engine mode
If these commands are not sufficient to support what a driver which
you write needs, additional commands can be defined by simply using a
new command name not in this list. Code to support the new command
needs to be added to the USER-MDI package within LAMMPS; see its
src/USER-MDI/mdi_engine.cpp and fix_mdi_engine.cpp files.
Restrictions
""""""""""""
This command is part of the USER-MDI package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`fix mdi/engine <fix_mdi_engine>`
Default
"""""""
None

17
doc/src/neigh_modify.rst
View File

@ -221,14 +221,15 @@ from 1 to n (inclusive). A trailing asterisk means all types from n to M
(inclusive). A middle asterisk means all types from m to n (inclusive).
Note that all atom types must be included in exactly one of the N collections.
The *collection/interval* option provides a similar capability.
This command allows a user to define collections by specifying a
series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals
based on their type-dependent cutoffs or their finite size.
You must first specify the number of collections N to be
defined followed by N values representing the upper cutoff of each interval.
This command is particularly useful for granular pairstyles where the interaction distance
of particles depends on their radius and may not depend on their atom type.
The *collection/interval* option provides a similar capability. This
command allows a user to define collections by specifying a series of
cutoff intervals. LAMMPS will automatically sort atoms into these
intervals based on their type-dependent cutoffs or their finite size.
You must first specify the number of collections N to be defined
followed by N values representing the upper cutoff of each interval.
This command is particularly useful for granular pair styles where the
interaction distance of particles depends on their radius and may not
depend on their atom type.
Restrictions
""""""""""""

16
doc/src/pair_lj_cut_tip4p.rst
View File

@ -145,6 +145,22 @@ specified since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff specified in
the pair_style command.
.. warning::
Because of how these pair styles implement the coulomb interactions
by implicitly defining a fourth site for the negative charge
of the TIP4P and similar water models, special care must be taken
when using these pair styles with other computations that also use
charges. Unless they are specially set up to also handle the implicit
definition of the 4th site, results are likely incorrect. Example:
:doc:`compute dipole/chunk <compute_dipole_chunk>`. For the same
reason, when using one of these pair styles with
:doc:`pair_style hybrid <pair_hybrid>`, **all** coulomb interactions
should be handled by a single sub-style with TIP4P support. All other
instances and styles will "see" the M point charges at the position
of the Oxygen atom and thus compute incorrect forces and energies.
LAMMPS will print a warning when it detects one of these issues.
----------
A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable

4
doc/utils/sphinx-config/_static/css/lammps.css
View File

@ -35,6 +35,10 @@ hr {
display: none;
}
#command-reference.section h2 {
display: none;
}
.ui.tabular.menu .item {
padding-right: 1em;
padding-left: 1em;

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

@ -253,7 +253,7 @@ html_show_sourcelink = False
# Output file base name for HTML help builder.
htmlhelp_basename = 'LAMMPSdoc'
html_add_permalinks = ''
html_permalinks = True
if 'epub' in sys.argv:
html_math_renderer = 'imgmath'

10
doc/utils/sphinx-config/false_positives.txt
View File

@ -47,6 +47,7 @@ Agnolin
Ai
Aidan
aij
aimd
airebo
Aj
ajs
@ -196,6 +197,7 @@ Ballenegger
Bammann
Banna
Barashev
barnes
barostat
Barostats
barostatted
@ -1207,6 +1209,7 @@ Halver
Hamaker
Hamel
Hammerschmidt
Hanley
haptic
Hara
Harpertown
@ -1269,6 +1272,7 @@ holonomic
Homebrew
hooke
Hookean
hostname
hotpink
Houlle
howto
@ -1728,6 +1732,7 @@ Lmpsdata
lmptype
LMT
ln
localhost
localTemp
localvectors
Loewen
@ -1858,6 +1863,8 @@ mc
McLachlan
md
mdf
MDI
mdi
mdpd
mDPD
meam
@ -2843,6 +2850,8 @@ Runge
runtime
Rutuparna
rx
rxnave
rxnsum
ry
rz
Ryckaert
@ -3143,6 +3152,7 @@ Tanmoy
Tartakovsky
taskset
taubi
taylor
tb
tchain
Tchain

4
examples/ASPHERE/README
View File

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

2
examples/ASPHERE/box/in.box
View File

@ -67,7 +67,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/box/in.box.mp
View File

@ -67,7 +67,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/dimer/in.dimer
View File

@ -61,7 +61,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/dimer/in.dimer.mp
View File

@ -61,7 +61,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/ellipsoid/in.ellipsoid
View File

@ -72,7 +72,7 @@ delete_atoms overlap 1.6 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/ellipsoid/in.ellipsoid.mp
View File

@ -72,7 +72,7 @@ delete_atoms overlap 1.6 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/line/in.line.srd
View File

@ -34,7 +34,7 @@ reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big

2
examples/ASPHERE/poly/in.poly
View File

@ -70,7 +70,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/poly/in.poly.mp
View File

@ -70,7 +70,7 @@ delete_atoms overlap 1.0 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/star/in.star
View File

@ -67,7 +67,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/star/in.star.mp
View File

@ -67,7 +67,7 @@ delete_atoms overlap 0.5 small big
reset_timestep 0
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes

2
examples/ASPHERE/tri/in.tri.srd
View File

@ -33,7 +33,7 @@ reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2
examples/README
View File

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

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

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

2
examples/USER/cgdna/util/generate.py
View File

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

3
examples/USER/cgsdk/sds-monolayer/in.sds-hybrid
View File

@ -37,10 +37,11 @@ atom_modify first charged
kspace_style pppm/cg 0.00001
kspace_modify order 3
comm_modify mode multi
neighbor 2.0 multi
neigh_modify delay 4 every 2 check yes
comm_modify mode multi
timestep 10.0
fix 1 all nvt temp 310.0 310.0 100.0

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